Starting phenix.real_space_refine on Fri Jul 3 11:29:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tvi_26141/07_2026/7tvi_26141.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tvi_26141/07_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_26141/07_2026/7tvi_26141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tvi_26141/07_2026/7tvi_26141.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7tvi_26141/07_2026/7tvi_26141.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tvi_26141/07_2026/7tvi_26141.cif" model { file = "/net/cci-nas-00/data/ceres_data/7tvi_26141/07_2026/7tvi_26141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tvi_26141/07_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-6108/lib/python3.11/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 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 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 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 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 chiralities: 2 Time building chain proxies: 2.95, per 1000 atoms: 0.21 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: 0.83 Conformation dependent library (CDL) restraints added in 567.8 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: 0.36 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: 2.05 Time building geometry restraints manager: 1.20 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: 7531 17.98 - 35.95: 653 35.95 - 53.93: 109 53.93 - 71.91: 18 71.91 - 89.89: 12 Dihedral angle restraints: 8323 sinusoidal: 3348 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 8320 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: 2.640 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 12.000 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 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 : 13.997 89.886 5089 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/Z covalent geometry : bond 0.00463 / 0.21 (14089) covalent geometry : angle 0.82172 / 0.44 (19119) SS BOND : bond 0.00026 / 0.02 ( 2) SS BOND : angle 1.06914 / 0.70 ( 4) hydrogen bonds : bond 0.29897 / 20.38 ( 554) hydrogen bonds : angle 7.57087 / 5.28 ( 1926) link_NAG-ASN : bond 0.01275 / 0.94 ( 6) link_NAG-ASN : angle 5.71329 / 3.65 ( 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 : 0.536 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: 0.1110 time to fit residues: 67.9322 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 : 0.406 ------------------------------------------------------------------------------- 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... 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 = 0.147396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.124149 restraints weight = 27322.576| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 3.18 r_work: 0.3797 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 14097 Z= 0.247 Angle : 0.806 12.446 19141 Z= 0.418 Chirality : 0.050 0.364 2164 Planarity : 0.005 0.057 2384 Dihedral : 5.480 57.592 1834 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.84 % Allowed : 12.50 % Favored : 84.66 % 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: -0.63 (0.19), residues: 1662 helix: 0.79 (0.22), residues: 498 sheet: 0.09 (0.27), residues: 395 loop : -1.52 (0.19), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 195 TYR 0.035 0.002 TYR B 325 PHE 0.021 0.002 PHE B 422 TRP 0.027 0.002 TRP A 118 HIS 0.006 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.25 (14089) covalent geometry : angle 0.78988 / 0.41 (19119) SS BOND : bond 0.00682 / 0.49 ( 2) SS BOND : angle 0.67394 / 0.48 ( 4) hydrogen bonds : bond 0.05942 / 3.90 ( 554) hydrogen bonds : angle 4.87217 / 3.37 ( 1926) link_NAG-ASN : bond 0.01506 / 0.96 ( 6) link_NAG-ASN : angle 5.37357 / 3.16 ( 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: 43 poor density : 269 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 114 LEU cc_start: 0.8225 (tt) cc_final: 0.7831 (tp) REVERT: D 210 GLN cc_start: 0.8415 (mp10) cc_final: 0.7560 (tt0) REVERT: D 251 MET cc_start: 0.6980 (mtp) cc_final: 0.6779 (mtt) REVERT: D 300 LYS cc_start: 0.9040 (mmtp) cc_final: 0.8703 (mppt) REVERT: D 325 TYR cc_start: 0.8932 (t80) cc_final: 0.8725 (t80) REVERT: D 403 PHE cc_start: 0.6700 (m-10) cc_final: 0.5867 (m-80) REVERT: B 37 PHE cc_start: 0.8852 (t80) cc_final: 0.8064 (t80) REVERT: B 113 MET cc_start: 0.7516 (ppp) cc_final: 0.6632 (ppp) REVERT: B 268 ILE cc_start: 0.6703 (mm) cc_final: 0.6432 (mm) REVERT: E 88 ILE cc_start: 0.8735 (pt) cc_final: 0.8319 (mm) REVERT: E 132 LYS cc_start: 0.8387 (tptp) cc_final: 0.8151 (tptp) REVERT: E 185 ASP cc_start: 0.8182 (p0) cc_final: 0.7875 (p0) REVERT: E 256 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6553 (mp0) REVERT: E 345 GLU cc_start: 0.7430 (pp20) cc_final: 0.7140 (pp20) outliers start: 43 outliers final: 24 residues processed: 293 average time/residue: 0.0885 time to fit residues: 40.1595 Evaluate side-chains 250 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 225 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 256 GLU Chi-restraints excluded: chain E residue 312 CYS Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 477 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 44 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 134 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 GLN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.143926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.120640 restraints weight = 27197.267| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 3.22 r_work: 0.3742 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14097 Z= 0.160 Angle : 0.674 13.327 19141 Z= 0.337 Chirality : 0.046 0.268 2164 Planarity : 0.004 0.050 2384 Dihedral : 4.951 38.788 1832 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.71 % Allowed : 16.34 % Favored : 80.95 % 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: -0.45 (0.20), residues: 1662 helix: 1.10 (0.22), residues: 501 sheet: 0.12 (0.27), residues: 380 loop : -1.47 (0.20), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 276 TYR 0.022 0.001 TYR B 325 PHE 0.022 0.001 PHE C 319 TRP 0.018 0.001 TRP A 118 HIS 0.004 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (14089) covalent geometry : angle 0.65523 / 0.33 (19119) SS BOND : bond 0.00661 / 0.47 ( 2) SS BOND : angle 0.25734 / 0.18 ( 4) hydrogen bonds : bond 0.05606 / 3.75 ( 554) hydrogen bonds : angle 4.40944 / 3.06 ( 1926) link_NAG-ASN : bond 0.01109 / 0.77 ( 6) link_NAG-ASN : angle 5.13429 / 3.14 ( 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 292 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 251 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 334 GLN cc_start: 0.7751 (mm110) cc_final: 0.7526 (mm-40) REVERT: D 210 GLN cc_start: 0.8456 (mp10) cc_final: 0.7878 (tt0) REVERT: D 287 MET cc_start: 0.9044 (tpp) cc_final: 0.8769 (mmm) REVERT: D 300 LYS cc_start: 0.9049 (mmtp) cc_final: 0.8588 (mmtm) REVERT: D 325 TYR cc_start: 0.8867 (t80) cc_final: 0.8600 (t80) REVERT: D 403 PHE cc_start: 0.6480 (m-10) cc_final: 0.5697 (m-80) REVERT: B 37 PHE cc_start: 0.8953 (t80) cc_final: 0.8157 (t80) REVERT: B 113 MET cc_start: 0.7622 (ppp) cc_final: 0.6561 (ppp) REVERT: B 135 VAL cc_start: 0.7506 (OUTLIER) cc_final: 0.7184 (m) REVERT: E 95 GLN cc_start: 0.8480 (pt0) cc_final: 0.7908 (pp30) REVERT: E 185 ASP cc_start: 0.8209 (p0) cc_final: 0.7906 (p0) REVERT: E 340 PHE cc_start: 0.7072 (OUTLIER) cc_final: 0.5850 (m-80) REVERT: E 473 TYR cc_start: 0.6519 (p90) cc_final: 0.6121 (p90) outliers start: 41 outliers final: 25 residues processed: 273 average time/residue: 0.0914 time to fit residues: 38.8974 Evaluate side-chains 251 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 224 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 301 VAL 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 144 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 418 PHE 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 B residue 416 VAL Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 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 477 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 133 optimal weight: 0.0070 chunk 156 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 163 optimal weight: 0.0570 chunk 6 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN E 194 GLN E 211 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.143248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.119915 restraints weight = 26991.647| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 3.21 r_work: 0.3738 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14097 Z= 0.126 Angle : 0.645 13.209 19141 Z= 0.318 Chirality : 0.045 0.277 2164 Planarity : 0.004 0.043 2384 Dihedral : 4.684 24.435 1832 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.44 % Allowed : 17.13 % Favored : 79.43 % 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: 1.23 (0.22), residues: 497 sheet: 0.26 (0.27), residues: 376 loop : -1.39 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 276 TYR 0.019 0.001 TYR B 325 PHE 0.014 0.001 PHE C 319 TRP 0.013 0.001 TRP A 118 HIS 0.002 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (14089) covalent geometry : angle 0.62739 / 0.31 (19119) SS BOND : bond 0.00410 / 0.29 ( 2) SS BOND : angle 0.11397 / 0.08 ( 4) hydrogen bonds : bond 0.04446 / 2.95 ( 554) hydrogen bonds : angle 4.12344 / 2.84 ( 1926) link_NAG-ASN : bond 0.01052 / 0.75 ( 6) link_NAG-ASN : angle 4.86526 / 3.03 ( 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 288 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 236 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLN cc_start: 0.7825 (mm110) cc_final: 0.7539 (mm-40) REVERT: D 210 GLN cc_start: 0.8550 (mp10) cc_final: 0.7932 (tt0) REVERT: D 251 MET cc_start: 0.7171 (mtp) cc_final: 0.6831 (mtt) REVERT: D 287 MET cc_start: 0.9031 (tpp) cc_final: 0.8765 (mmm) REVERT: D 300 LYS cc_start: 0.9044 (mmtp) cc_final: 0.8539 (mmtm) REVERT: D 403 PHE cc_start: 0.6404 (m-10) cc_final: 0.5654 (m-80) REVERT: B 37 PHE cc_start: 0.9039 (t80) cc_final: 0.8368 (t80) REVERT: B 113 MET cc_start: 0.7579 (ppp) cc_final: 0.6452 (ppp) REVERT: B 135 VAL cc_start: 0.7534 (OUTLIER) cc_final: 0.7175 (m) REVERT: B 334 GLN cc_start: 0.7595 (pm20) cc_final: 0.6870 (pm20) REVERT: E 95 GLN cc_start: 0.8521 (pt0) cc_final: 0.8015 (pp30) REVERT: E 102 ARG cc_start: 0.7303 (ttt-90) cc_final: 0.7096 (ttt-90) REVERT: E 185 ASP cc_start: 0.8144 (p0) cc_final: 0.7837 (p0) REVERT: E 261 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7680 (pp) REVERT: E 340 PHE cc_start: 0.6975 (OUTLIER) cc_final: 0.5748 (m-80) REVERT: E 352 MET cc_start: 0.8285 (ppp) cc_final: 0.7100 (mmt) REVERT: E 353 LEU cc_start: 0.8222 (pp) cc_final: 0.7592 (pp) outliers start: 52 outliers final: 28 residues processed: 268 average time/residue: 0.0991 time to fit residues: 41.1883 Evaluate side-chains 254 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 223 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 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 228 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 418 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 229 GLN Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 251 TYR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 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: 2.9990 chunk 161 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.0470 chunk 68 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.141647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.118673 restraints weight = 27062.382| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 3.26 r_work: 0.3711 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.5701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14097 Z= 0.124 Angle : 0.624 13.277 19141 Z= 0.308 Chirality : 0.045 0.277 2164 Planarity : 0.004 0.053 2384 Dihedral : 4.536 24.094 1832 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.24 % Allowed : 17.66 % Favored : 79.10 % 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: -0.19 (0.20), residues: 1662 helix: 1.26 (0.23), residues: 494 sheet: 0.34 (0.28), residues: 375 loop : -1.29 (0.20), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 262 TYR 0.024 0.001 TYR B 102 PHE 0.021 0.001 PHE E 189 TRP 0.018 0.001 TRP B 310 HIS 0.003 0.001 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (14089) covalent geometry : angle 0.60693 / 0.30 (19119) SS BOND : bond 0.00197 / 0.14 ( 2) SS BOND : angle 0.39063 / 0.22 ( 4) hydrogen bonds : bond 0.04217 / 2.80 ( 554) hydrogen bonds : angle 4.02032 / 2.78 ( 1926) link_NAG-ASN : bond 0.01029 / 0.74 ( 6) link_NAG-ASN : angle 4.76493 / 2.97 ( 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 289 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 240 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLN cc_start: 0.7872 (mm110) cc_final: 0.7613 (mm-40) REVERT: D 300 LYS cc_start: 0.9053 (mmtp) cc_final: 0.8555 (mmtm) REVERT: D 403 PHE cc_start: 0.6315 (m-10) cc_final: 0.5553 (m-80) REVERT: B 113 MET cc_start: 0.7706 (ppp) cc_final: 0.6787 (ppp) REVERT: B 135 VAL cc_start: 0.7397 (OUTLIER) cc_final: 0.7054 (m) REVERT: B 168 ASN cc_start: 0.8397 (OUTLIER) cc_final: 0.7927 (p0) REVERT: B 204 ASP cc_start: 0.8029 (p0) cc_final: 0.7459 (m-30) REVERT: B 269 ASN cc_start: 0.7858 (m-40) cc_final: 0.7503 (m-40) REVERT: B 287 MET cc_start: 0.9047 (ttp) cc_final: 0.8821 (ttp) REVERT: B 413 VAL cc_start: 0.6940 (t) cc_final: 0.6739 (p) REVERT: E 185 ASP cc_start: 0.8175 (p0) cc_final: 0.7887 (p0) REVERT: E 340 PHE cc_start: 0.6905 (OUTLIER) cc_final: 0.5615 (m-80) REVERT: E 352 MET cc_start: 0.8101 (ppp) cc_final: 0.7843 (ppp) outliers start: 49 outliers final: 32 residues processed: 268 average time/residue: 0.0935 time to fit residues: 39.2743 Evaluate side-chains 260 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 225 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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 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 A residue 316 LEU Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 192 PHE Chi-restraints excluded: chain D residue 279 LEU 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 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: 3.9990 chunk 144 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 145 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 139 ASN ** C 174 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 = 0.4117 r_free = 0.4117 target = 0.136018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.112382 restraints weight = 27000.885| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 3.33 r_work: 0.3610 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.6676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14097 Z= 0.170 Angle : 0.679 13.177 19141 Z= 0.343 Chirality : 0.047 0.291 2164 Planarity : 0.004 0.047 2384 Dihedral : 4.780 25.547 1832 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.44 % Allowed : 18.65 % Favored : 77.91 % 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: -0.24 (0.20), residues: 1662 helix: 1.29 (0.23), residues: 506 sheet: 0.20 (0.28), residues: 372 loop : -1.34 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 117 TYR 0.022 0.002 TYR E 473 PHE 0.019 0.002 PHE E 189 TRP 0.014 0.001 TRP A 310 HIS 0.007 0.001 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (14089) covalent geometry : angle 0.66322 / 0.34 (19119) SS BOND : bond 0.00821 / 0.59 ( 2) SS BOND : angle 0.55127 / 0.29 ( 4) hydrogen bonds : bond 0.04501 / 2.99 ( 554) hydrogen bonds : angle 4.13580 / 2.83 ( 1926) link_NAG-ASN : bond 0.00981 / 0.71 ( 6) link_NAG-ASN : angle 4.82760 / 2.99 ( 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 272 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 220 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 LEU cc_start: 0.8883 (mp) cc_final: 0.8617 (tp) REVERT: A 270 MET cc_start: 0.6870 (ptp) cc_final: 0.6626 (ptp) REVERT: A 334 GLN cc_start: 0.7828 (mm110) cc_final: 0.7433 (mm-40) REVERT: D 80 MET cc_start: 0.8544 (mmm) cc_final: 0.8336 (mmp) REVERT: D 210 GLN cc_start: 0.8554 (mp10) cc_final: 0.7923 (tt0) REVERT: D 300 LYS cc_start: 0.9015 (mmtp) cc_final: 0.8464 (mmtm) REVERT: D 403 PHE cc_start: 0.6500 (m-10) cc_final: 0.5679 (m-80) REVERT: C 75 ILE cc_start: 0.9122 (mp) cc_final: 0.8858 (mt) REVERT: B 37 PHE cc_start: 0.9017 (t80) cc_final: 0.7997 (t80) REVERT: B 102 TYR cc_start: 0.6016 (m-10) cc_final: 0.5807 (m-10) REVERT: B 113 MET cc_start: 0.7960 (ppp) cc_final: 0.7303 (ppp) REVERT: B 135 VAL cc_start: 0.7632 (OUTLIER) cc_final: 0.7307 (m) REVERT: B 168 ASN cc_start: 0.8691 (OUTLIER) cc_final: 0.8142 (p0) REVERT: B 204 ASP cc_start: 0.7846 (p0) cc_final: 0.7504 (m-30) REVERT: B 269 ASN cc_start: 0.7734 (m-40) cc_final: 0.7353 (m-40) REVERT: B 270 MET cc_start: 0.7483 (mmm) cc_final: 0.7183 (ptp) REVERT: E 135 LYS cc_start: 0.7417 (tptt) cc_final: 0.7152 (ttmt) REVERT: E 185 ASP cc_start: 0.8327 (p0) cc_final: 0.8078 (p0) REVERT: E 282 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8202 (mp) REVERT: E 340 PHE cc_start: 0.7049 (OUTLIER) cc_final: 0.5551 (m-80) outliers start: 52 outliers final: 32 residues processed: 256 average time/residue: 0.0866 time to fit residues: 34.8714 Evaluate side-chains 244 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 208 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 217 LYS Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 279 LEU 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 279 LEU Chi-restraints excluded: chain D residue 418 PHE Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain C residue 259 VAL 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 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 184 LEU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 282 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 9 optimal weight: 0.5980 chunk 140 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 161 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 160 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 157 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 GLN E 157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.137853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.113971 restraints weight = 27025.357| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 3.23 r_work: 0.3640 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.6871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14097 Z= 0.125 Angle : 0.624 13.297 19141 Z= 0.308 Chirality : 0.044 0.284 2164 Planarity : 0.004 0.043 2384 Dihedral : 4.577 23.758 1832 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.98 % Allowed : 19.58 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.19 (0.20), residues: 1662 helix: 1.35 (0.23), residues: 496 sheet: 0.28 (0.28), residues: 372 loop : -1.31 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 415 TYR 0.018 0.001 TYR E 473 PHE 0.019 0.001 PHE C 319 TRP 0.014 0.001 TRP A 310 HIS 0.004 0.001 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (14089) covalent geometry : angle 0.60668 / 0.30 (19119) SS BOND : bond 0.00405 / 0.29 ( 2) SS BOND : angle 0.37110 / 0.22 ( 4) hydrogen bonds : bond 0.04015 / 2.65 ( 554) hydrogen bonds : angle 3.95935 / 2.73 ( 1926) link_NAG-ASN : bond 0.01003 / 0.73 ( 6) link_NAG-ASN : angle 4.76799 / 2.98 ( 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 266 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 221 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 LEU cc_start: 0.8870 (mp) cc_final: 0.8649 (tp) REVERT: A 270 MET cc_start: 0.6991 (ptp) cc_final: 0.6731 (ptm) REVERT: A 334 GLN cc_start: 0.7969 (mm110) cc_final: 0.7578 (mm-40) REVERT: D 144 ILE cc_start: 0.8603 (pt) cc_final: 0.8367 (mt) REVERT: D 210 GLN cc_start: 0.8696 (mp10) cc_final: 0.8075 (tt0) REVERT: D 287 MET cc_start: 0.9198 (tpp) cc_final: 0.8948 (tpp) REVERT: D 300 LYS cc_start: 0.8991 (mmtp) cc_final: 0.8481 (mmtm) REVERT: D 403 PHE cc_start: 0.6472 (m-10) cc_final: 0.5644 (m-80) REVERT: C 75 ILE cc_start: 0.9070 (mp) cc_final: 0.8824 (mt) REVERT: B 37 PHE cc_start: 0.8979 (t80) cc_final: 0.8217 (t80) REVERT: B 113 MET cc_start: 0.7719 (ppp) cc_final: 0.7352 (ppp) REVERT: B 135 VAL cc_start: 0.7559 (OUTLIER) cc_final: 0.7267 (m) REVERT: B 168 ASN cc_start: 0.8645 (OUTLIER) cc_final: 0.8145 (p0) REVERT: B 204 ASP cc_start: 0.7756 (p0) cc_final: 0.7492 (m-30) REVERT: B 269 ASN cc_start: 0.7734 (m-40) cc_final: 0.7282 (m-40) REVERT: B 270 MET cc_start: 0.7500 (mmm) cc_final: 0.7272 (ptp) REVERT: B 409 ARG cc_start: 0.5076 (tmm160) cc_final: 0.4773 (tmm160) REVERT: E 185 ASP cc_start: 0.8298 (p0) cc_final: 0.8030 (p0) REVERT: E 223 ASP cc_start: 0.6331 (t0) cc_final: 0.5728 (t0) outliers start: 45 outliers final: 32 residues processed: 253 average time/residue: 0.0878 time to fit residues: 34.9808 Evaluate side-chains 246 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 212 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 122 LEU 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 279 LEU 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 315 LEU Chi-restraints excluded: chain D residue 319 PHE 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 310 TRP Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 421 VAL 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 278 LEU 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: 9.9990 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.133271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.108986 restraints weight = 27012.304| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 3.17 r_work: 0.3572 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.7413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14097 Z= 0.190 Angle : 0.707 13.337 19141 Z= 0.349 Chirality : 0.048 0.509 2164 Planarity : 0.004 0.054 2384 Dihedral : 4.862 25.058 1832 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.84 % Allowed : 20.44 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.28 (0.20), residues: 1662 helix: 1.23 (0.22), residues: 509 sheet: 0.16 (0.28), residues: 370 loop : -1.34 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 333 TYR 0.020 0.002 TYR B 325 PHE 0.028 0.002 PHE E 189 TRP 0.019 0.001 TRP A 310 HIS 0.008 0.001 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 (14089) covalent geometry : angle 0.69130 / 0.35 (19119) SS BOND : bond 0.00298 / 0.21 ( 2) SS BOND : angle 0.67236 / 0.36 ( 4) hydrogen bonds : bond 0.04488 / 2.96 ( 554) hydrogen bonds : angle 4.17069 / 2.87 ( 1926) link_NAG-ASN : bond 0.00957 / 0.70 ( 6) link_NAG-ASN : angle 4.91683 / 3.04 ( 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 252 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 209 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.6514 (mpp) cc_final: 0.5885 (mmt) REVERT: A 257 LEU cc_start: 0.8929 (mp) cc_final: 0.8712 (tp) REVERT: A 334 GLN cc_start: 0.8180 (mm110) cc_final: 0.7804 (mm110) REVERT: D 287 MET cc_start: 0.9157 (tpp) cc_final: 0.8742 (tpp) REVERT: D 300 LYS cc_start: 0.9010 (mmtp) cc_final: 0.8448 (mmtm) REVERT: D 403 PHE cc_start: 0.6601 (m-10) cc_final: 0.5787 (m-80) REVERT: B 37 PHE cc_start: 0.9106 (t80) cc_final: 0.8631 (t80) REVERT: B 135 VAL cc_start: 0.7726 (OUTLIER) cc_final: 0.7395 (m) REVERT: B 164 MET cc_start: 0.8508 (mmt) cc_final: 0.7956 (mmt) REVERT: B 168 ASN cc_start: 0.8679 (OUTLIER) cc_final: 0.8241 (p0) REVERT: B 204 ASP cc_start: 0.7765 (p0) cc_final: 0.7533 (m-30) REVERT: B 250 GLN cc_start: 0.8786 (tp-100) cc_final: 0.8531 (tp40) REVERT: B 266 PHE cc_start: 0.6971 (m-80) cc_final: 0.6672 (m-10) REVERT: B 269 ASN cc_start: 0.7724 (m-40) cc_final: 0.7346 (t0) REVERT: B 433 TYR cc_start: 0.7605 (m-80) cc_final: 0.7334 (m-80) REVERT: E 185 ASP cc_start: 0.8348 (p0) cc_final: 0.8120 (p0) REVERT: E 288 TRP cc_start: 0.8098 (m-90) cc_final: 0.7890 (m100) outliers start: 43 outliers final: 34 residues processed: 242 average time/residue: 0.0850 time to fit residues: 32.4542 Evaluate side-chains 238 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 202 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 186 THR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 418 PHE Chi-restraints excluded: chain C residue 121 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 B residue 135 VAL Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 310 TRP Chi-restraints excluded: chain B residue 415 ARG Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 421 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 60 optimal weight: 3.9990 chunk 164 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 148 optimal weight: 0.0470 chunk 102 optimal weight: 0.9980 chunk 144 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 101 optimal weight: 0.0470 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 179 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 = 0.4115 r_free = 0.4115 target = 0.136037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.111928 restraints weight = 26769.959| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 3.18 r_work: 0.3614 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.7510 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= 0.121 Angle : 0.664 13.428 19141 Z= 0.322 Chirality : 0.046 0.427 2164 Planarity : 0.004 0.056 2384 Dihedral : 4.601 23.003 1832 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.05 % Allowed : 21.76 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.18 (0.20), residues: 1662 helix: 1.31 (0.23), residues: 502 sheet: 0.32 (0.28), residues: 376 loop : -1.32 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 333 TYR 0.020 0.001 TYR B 325 PHE 0.021 0.001 PHE B 266 TRP 0.014 0.001 TRP D 267 HIS 0.002 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (14089) covalent geometry : angle 0.64798 / 0.32 (19119) SS BOND : bond 0.00217 / 0.15 ( 2) SS BOND : angle 0.35142 / 0.23 ( 4) hydrogen bonds : bond 0.03959 / 2.63 ( 554) hydrogen bonds : angle 3.95072 / 2.72 ( 1926) link_NAG-ASN : bond 0.01017 / 0.74 ( 6) link_NAG-ASN : angle 4.80188 / 2.99 ( 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 234 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 203 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 LEU cc_start: 0.8936 (mp) cc_final: 0.8704 (tp) REVERT: A 334 GLN cc_start: 0.8127 (mm110) cc_final: 0.7813 (mm110) REVERT: D 210 GLN cc_start: 0.8689 (mp10) cc_final: 0.7986 (tt0) REVERT: D 300 LYS cc_start: 0.8950 (mmtp) cc_final: 0.8419 (mmtm) REVERT: D 403 PHE cc_start: 0.6364 (m-10) cc_final: 0.5554 (m-80) REVERT: B 113 MET cc_start: 0.7909 (ppp) cc_final: 0.7315 (ppp) REVERT: B 135 VAL cc_start: 0.7517 (OUTLIER) cc_final: 0.7241 (m) REVERT: B 250 GLN cc_start: 0.8791 (tp-100) cc_final: 0.8545 (tp40) REVERT: B 269 ASN cc_start: 0.7642 (m-40) cc_final: 0.7416 (t0) REVERT: B 271 ASP cc_start: 0.8170 (p0) cc_final: 0.7810 (p0) REVERT: E 185 ASP cc_start: 0.8344 (p0) cc_final: 0.8141 (p0) REVERT: E 223 ASP cc_start: 0.6265 (t0) cc_final: 0.5625 (t0) REVERT: E 270 MET cc_start: 0.8445 (tmm) cc_final: 0.7606 (mmt) outliers start: 31 outliers final: 24 residues processed: 228 average time/residue: 0.0885 time to fit residues: 31.7535 Evaluate side-chains 225 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 186 THR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 288 THR 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 319 PHE 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 307 ILE Chi-restraints excluded: chain B residue 310 TRP Chi-restraints excluded: chain B residue 415 ARG Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 261 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: 9.9990 chunk 53 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 63 optimal weight: 0.0980 chunk 88 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 162 optimal weight: 0.9980 chunk 35 optimal weight: 0.1980 chunk 57 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.136108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.112125 restraints weight = 26823.602| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 3.16 r_work: 0.3621 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.7674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14097 Z= 0.119 Angle : 0.661 13.355 19141 Z= 0.318 Chirality : 0.045 0.409 2164 Planarity : 0.004 0.059 2384 Dihedral : 4.507 22.729 1832 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.65 % Allowed : 22.35 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.40 (0.23), residues: 492 sheet: 0.34 (0.27), residues: 375 loop : -1.30 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 102 TYR 0.024 0.001 TYR E 473 PHE 0.021 0.001 PHE E 189 TRP 0.022 0.001 TRP E 288 HIS 0.002 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (14089) covalent geometry : angle 0.64532 / 0.31 (19119) SS BOND : bond 0.00256 / 0.18 ( 2) SS BOND : angle 0.29202 / 0.19 ( 4) hydrogen bonds : bond 0.03752 / 2.48 ( 554) hydrogen bonds : angle 3.84470 / 2.65 ( 1926) link_NAG-ASN : bond 0.01033 / 0.75 ( 6) link_NAG-ASN : angle 4.73941 / 2.96 ( 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 235 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 210 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 LEU cc_start: 0.8919 (mp) cc_final: 0.8706 (tp) REVERT: D 105 ASP cc_start: 0.7905 (p0) cc_final: 0.7657 (p0) REVERT: D 210 GLN cc_start: 0.8703 (mp10) cc_final: 0.8094 (tt0) REVERT: D 300 LYS cc_start: 0.8993 (mmtp) cc_final: 0.8453 (mmtm) REVERT: D 403 PHE cc_start: 0.6354 (m-10) cc_final: 0.5548 (m-80) REVERT: B 135 VAL cc_start: 0.7495 (OUTLIER) cc_final: 0.7234 (m) REVERT: B 250 GLN cc_start: 0.8797 (tp-100) cc_final: 0.8532 (tp40) REVERT: B 269 ASN cc_start: 0.7608 (m-40) cc_final: 0.7221 (p0) REVERT: B 271 ASP cc_start: 0.8157 (p0) cc_final: 0.7898 (t0) REVERT: B 330 PHE cc_start: 0.6769 (t80) cc_final: 0.6532 (t80) REVERT: E 223 ASP cc_start: 0.6328 (t0) cc_final: 0.5663 (t0) REVERT: E 270 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.7640 (mmt) outliers start: 25 outliers final: 21 residues processed: 229 average time/residue: 0.0922 time to fit residues: 33.0859 Evaluate side-chains 224 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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 258 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain D residue 279 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 157 THR Chi-restraints excluded: chain B residue 415 ARG Chi-restraints excluded: chain B residue 421 VAL 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=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: 0.5980 chunk 125 optimal weight: 0.0870 chunk 111 optimal weight: 4.9990 chunk 1 optimal weight: 0.2980 chunk 154 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 63 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 89 optimal weight: 0.2980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.137443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.113488 restraints weight = 26824.468| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 3.17 r_work: 0.3641 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.7755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14097 Z= 0.113 Angle : 0.653 13.362 19141 Z= 0.316 Chirality : 0.045 0.400 2164 Planarity : 0.004 0.058 2384 Dihedral : 4.388 21.830 1832 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.65 % Allowed : 22.35 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.35 (0.23), residues: 497 sheet: 0.46 (0.27), residues: 381 loop : -1.25 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 415 TYR 0.017 0.001 TYR B 325 PHE 0.015 0.001 PHE E 189 TRP 0.016 0.001 TRP E 288 HIS 0.003 0.001 HIS B 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (14089) covalent geometry : angle 0.63723 / 0.31 (19119) SS BOND : bond 0.00228 / 0.16 ( 2) SS BOND : angle 0.32643 / 0.24 ( 4) hydrogen bonds : bond 0.03590 / 2.39 ( 554) hydrogen bonds : angle 3.75191 / 2.60 ( 1926) link_NAG-ASN : bond 0.01047 / 0.76 ( 6) link_NAG-ASN : angle 4.67629 / 2.92 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2701.06 seconds wall clock time: 47 minutes 10.18 seconds (2830.18 seconds total)