Starting phenix.real_space_refine on Thu Jun 27 21:44:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tvi_26141/06_2024/7tvi_26141.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tvi_26141/06_2024/7tvi_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tvi_26141/06_2024/7tvi_26141.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tvi_26141/06_2024/7tvi_26141.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tvi_26141/06_2024/7tvi_26141.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tvi_26141/06_2024/7tvi_26141.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 89 5.16 5 C 8965 2.51 5 N 2221 2.21 5 O 2471 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 121": "OD1" <-> "OD2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 115": "OD1" <-> "OD2" Residue "D TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 181": "OE1" <-> "OE2" Residue "D ASP 189": "OD1" <-> "OD2" Residue "D GLU 215": "OE1" <-> "OE2" Residue "D GLU 216": "OE1" <-> "OE2" Residue "D GLU 241": "OE1" <-> "OE2" Residue "D ASP 308": "OD1" <-> "OD2" Residue "D PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 147": "OE1" <-> "OE2" Residue "E GLU 238": "OE1" <-> "OE2" Residue "E TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 13746 Number of models: 1 Model: "" Number of chains: 10 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 24 Unusual residues: {'NAG': 1} Classifications: {'peptide': 2, 'undetermined': 1} Modifications used: {'COO': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 24 Unusual residues: {'NAG': 1} Classifications: {'peptide': 2, 'undetermined': 1} Modifications used: {'COO': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.38, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied 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: 4.70 Conformation dependent library (CDL) restraints added in 2.4 seconds 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3228 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 24 sheets defined 36.6% alpha, 39.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 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: 4.23 Time building geometry restraints manager: 5.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2307 1.32 - 1.45: 3822 1.45 - 1.57: 7813 1.57 - 1.69: 0 1.69 - 1.81: 147 Bond restraints: 14089 Sorted by residual: bond pdb=" N GLY B 501 " pdb=" CA GLY B 501 " ideal model delta sigma weight residual 1.451 1.501 -0.050 1.60e-02 3.91e+03 9.94e+00 bond pdb=" N GLY D 503 " pdb=" CA GLY D 503 " ideal model delta sigma weight residual 1.451 1.501 -0.050 1.60e-02 3.91e+03 9.89e+00 bond pdb=" N GLY A 501 " pdb=" CA GLY A 501 " ideal model delta sigma weight residual 1.451 1.501 -0.050 1.60e-02 3.91e+03 9.68e+00 bond pdb=" N GLY D 501 " pdb=" CA GLY D 501 " ideal model delta sigma weight residual 1.451 1.500 -0.049 1.60e-02 3.91e+03 9.49e+00 bond pdb=" C PRO E 299 " pdb=" O PRO E 299 " ideal model delta sigma weight residual 1.237 1.202 0.036 1.20e-02 6.94e+03 8.87e+00 ... (remaining 14084 not shown) Histogram of bond angle deviations from ideal: 98.07 - 105.33: 328 105.33 - 112.59: 7148 112.59 - 119.85: 4741 119.85 - 127.11: 6733 127.11 - 134.37: 169 Bond angle restraints: 19119 Sorted by residual: angle pdb=" C PRO E 299 " pdb=" CA PRO E 299 " pdb=" CB PRO E 299 " ideal model delta sigma weight residual 112.55 103.39 9.16 1.50e+00 4.44e-01 3.73e+01 angle pdb=" N PRO D 274 " pdb=" CA PRO D 274 " pdb=" C PRO D 274 " ideal model delta sigma weight residual 113.53 107.59 5.94 1.39e+00 5.18e-01 1.83e+01 angle pdb=" C SER E 294 " pdb=" N ALA E 295 " pdb=" CA ALA E 295 " ideal model delta sigma weight residual 122.79 115.87 6.92 1.63e+00 3.76e-01 1.80e+01 angle pdb=" C ARG E 297 " pdb=" CA ARG E 297 " pdb=" CB ARG E 297 " ideal model delta sigma weight residual 110.79 117.58 -6.79 1.66e+00 3.63e-01 1.67e+01 angle pdb=" CA SER E 294 " pdb=" C SER E 294 " pdb=" O SER E 294 " ideal model delta sigma weight residual 120.82 116.54 4.28 1.05e+00 9.07e-01 1.66e+01 ... (remaining 19114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 7639 17.98 - 35.95: 663 35.95 - 53.93: 114 53.93 - 71.91: 21 71.91 - 89.89: 12 Dihedral angle restraints: 8449 sinusoidal: 3474 harmonic: 4975 Sorted by residual: dihedral pdb=" CA MET B 287 " pdb=" C MET B 287 " pdb=" N THR B 288 " pdb=" CA THR B 288 " ideal model delta harmonic sigma weight residual 180.00 154.51 25.49 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CB CYS E 182 " pdb=" SG CYS E 182 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual -86.00 -125.61 39.61 1 1.00e+01 1.00e-02 2.20e+01 dihedral pdb=" CA ALA E 327 " pdb=" C ALA E 327 " pdb=" N ILE E 328 " pdb=" CA ILE E 328 " ideal model delta harmonic sigma weight residual 180.00 158.15 21.85 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 8446 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1875 0.076 - 0.152: 264 0.152 - 0.227: 19 0.227 - 0.303: 4 0.303 - 0.379: 2 Chirality restraints: 2164 Sorted by residual: chirality pdb=" C1 NAG A 502 " pdb=" ND2 ASN A 62 " pdb=" C2 NAG A 502 " pdb=" O5 NAG A 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" C1 NAG E 602 " pdb=" ND2 ASN E 241 " pdb=" C2 NAG E 602 " pdb=" O5 NAG E 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CA ALA E 295 " pdb=" N ALA E 295 " pdb=" C ALA E 295 " pdb=" CB ALA E 295 " both_signs ideal model delta sigma weight residual False 2.48 2.23 0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 2161 not shown) Planarity restraints: 2390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 110 " -0.050 5.00e-02 4.00e+02 7.65e-02 9.36e+00 pdb=" N PRO A 111 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 111 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 111 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 169 " 0.039 5.00e-02 4.00e+02 5.84e-02 5.45e+00 pdb=" N PRO C 170 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO C 170 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 170 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 263 " 0.017 2.00e-02 2.50e+03 1.46e-02 5.30e+00 pdb=" CG TRP D 263 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP D 263 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP D 263 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 263 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 263 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 263 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 263 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 263 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP D 263 " 0.003 2.00e-02 2.50e+03 ... (remaining 2387 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2061 2.76 - 3.30: 12995 3.30 - 3.83: 21732 3.83 - 4.37: 25292 4.37 - 4.90: 43325 Nonbonded interactions: 105405 Sorted by model distance: nonbonded pdb=" OG1 THR E 206 " pdb=" OD1 ASP E 208 " model vdw 2.228 2.440 nonbonded pdb=" O LEU B 285 " pdb=" OG1 THR B 288 " model vdw 2.242 2.440 nonbonded pdb=" O ALA E 327 " pdb=" OH TYR E 489 " model vdw 2.305 2.440 nonbonded pdb=" O PRO C 60 " pdb=" O6 NAG C 501 " model vdw 2.320 2.440 nonbonded pdb=" NE2 HIS B 133 " pdb=" OG1 THR B 157 " model vdw 2.329 2.520 ... (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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 334 or resid 403 through 435 or resid 502)) selection = (chain 'B' and (resid 33 through 334 or resid 403 through 435 or resid 502)) selection = (chain 'C' and (resid 33 through 334 or resid 403 through 435 or resid 501)) selection = (chain 'D' and (resid 33 through 334 or resid 403 through 435 or resid 502)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 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: 6.120 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 36.570 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 14089 Z= 0.302 Angle : 0.822 10.013 19119 Z= 0.435 Chirality : 0.053 0.379 2164 Planarity : 0.006 0.076 2384 Dihedral : 14.018 89.886 5215 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.07 % Allowed : 0.33 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.19), residues: 1662 helix: 0.33 (0.23), residues: 458 sheet: 0.42 (0.27), residues: 380 loop : -1.56 (0.19), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 263 HIS 0.003 0.001 HIS A 133 PHE 0.029 0.002 PHE E 480 TYR 0.021 0.002 TYR A 82 ARG 0.006 0.001 ARG A 96 *********************** 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 fitting. rotamer outliers: 1 poor density : 415 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 PRO cc_start: 0.6032 (Cg_exo) cc_final: 0.5744 (Cg_endo) REVERT: A 179 GLN cc_start: 0.8283 (tt0) cc_final: 0.7915 (tp40) REVERT: A 181 GLU cc_start: 0.6269 (mp0) cc_final: 0.5937 (mp0) REVERT: A 235 GLU cc_start: 0.6392 (tt0) cc_final: 0.6185 (tt0) REVERT: A 419 PRO cc_start: 0.5881 (Cg_exo) cc_final: 0.5398 (Cg_endo) REVERT: D 114 LEU cc_start: 0.7925 (tt) cc_final: 0.7670 (tp) REVERT: D 210 GLN cc_start: 0.7981 (mp10) cc_final: 0.7327 (tt0) REVERT: D 300 LYS cc_start: 0.8979 (mmtp) cc_final: 0.8421 (mmtm) REVERT: D 311 MET cc_start: 0.7492 (tpt) cc_final: 0.7256 (mmt) REVERT: D 403 PHE cc_start: 0.6854 (m-10) cc_final: 0.6156 (m-80) REVERT: C 123 PHE cc_start: 0.6475 (t80) cc_final: 0.6238 (t80) REVERT: C 270 MET cc_start: 0.7820 (mpp) cc_final: 0.7401 (mtm) REVERT: B 176 CYS cc_start: 0.7634 (m) cc_final: 0.7342 (m) REVERT: B 235 GLU cc_start: 0.6223 (tt0) cc_final: 0.5923 (tt0) REVERT: E 473 TYR cc_start: 0.6523 (p90) cc_final: 0.6123 (p90) outliers start: 1 outliers final: 1 residues processed: 415 average time/residue: 0.2470 time to fit residues: 148.2821 Evaluate side-chains 240 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 239 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 261 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 GLN C 90 GLN C 131 ASN ** C 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 211 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 14089 Z= 0.508 Angle : 0.902 12.025 19119 Z= 0.470 Chirality : 0.054 0.342 2164 Planarity : 0.006 0.055 2384 Dihedral : 7.078 81.184 1960 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.03 % Allowed : 13.96 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.19), residues: 1662 helix: 0.70 (0.21), residues: 496 sheet: -0.50 (0.27), residues: 381 loop : -1.64 (0.19), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 118 HIS 0.010 0.002 HIS A 133 PHE 0.025 0.003 PHE A 238 TYR 0.032 0.003 TYR B 325 ARG 0.014 0.001 ARG E 195 *********************** 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 316 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 255 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 251 MET cc_start: 0.6889 (mtp) cc_final: 0.6660 (mtt) REVERT: D 300 LYS cc_start: 0.8987 (mmtp) cc_final: 0.8544 (mppt) REVERT: D 403 PHE cc_start: 0.6661 (m-10) cc_final: 0.5860 (m-80) REVERT: C 138 ASP cc_start: 0.6549 (t70) cc_final: 0.5920 (t0) REVERT: B 37 PHE cc_start: 0.8851 (t80) cc_final: 0.8089 (t80) REVERT: B 135 VAL cc_start: 0.7782 (p) cc_final: 0.7437 (m) REVERT: E 345 GLU cc_start: 0.7689 (pp20) cc_final: 0.7308 (pp20) outliers start: 61 outliers final: 34 residues processed: 293 average time/residue: 0.2153 time to fit residues: 96.0578 Evaluate side-chains 247 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 213 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASP 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 217 LYS Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain 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 228 THR 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 C residue 168 ASN Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain E residue 61 ASN 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 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 83 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 41 optimal weight: 0.0070 chunk 150 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 148 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 225 HIS D 149 ASN D 290 GLN C 290 GLN ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.5525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14089 Z= 0.190 Angle : 0.653 11.950 19119 Z= 0.329 Chirality : 0.046 0.302 2164 Planarity : 0.004 0.048 2384 Dihedral : 6.182 80.575 1958 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.44 % Allowed : 16.80 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.20), residues: 1662 helix: 1.13 (0.22), residues: 496 sheet: -0.26 (0.27), residues: 391 loop : -1.49 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 310 HIS 0.003 0.001 HIS A 133 PHE 0.019 0.001 PHE C 319 TYR 0.021 0.001 TYR B 325 ARG 0.005 0.000 ARG A 237 *********************** 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 293 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 241 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLN cc_start: 0.7495 (mm110) cc_final: 0.7243 (mm-40) REVERT: D 114 LEU cc_start: 0.8489 (tt) cc_final: 0.8279 (tp) REVERT: D 210 GLN cc_start: 0.8607 (mp10) cc_final: 0.7828 (tt0) REVERT: D 287 MET cc_start: 0.9031 (tpp) cc_final: 0.8675 (mmm) REVERT: D 289 THR cc_start: 0.8400 (m) cc_final: 0.8145 (p) REVERT: D 300 LYS cc_start: 0.8986 (mmtp) cc_final: 0.8365 (mmtm) REVERT: D 311 MET cc_start: 0.7728 (tpt) cc_final: 0.7488 (mmt) REVERT: D 403 PHE cc_start: 0.6327 (m-10) cc_final: 0.5535 (m-80) REVERT: C 105 ASP cc_start: 0.7987 (p0) cc_final: 0.7743 (p0) REVERT: B 37 PHE cc_start: 0.8972 (t80) cc_final: 0.8313 (t80) REVERT: B 135 VAL cc_start: 0.7516 (OUTLIER) cc_final: 0.7170 (m) REVERT: B 204 ASP cc_start: 0.7769 (p0) cc_final: 0.7470 (m-30) REVERT: B 210 GLN cc_start: 0.6910 (tp-100) cc_final: 0.6603 (tp-100) REVERT: E 102 ARG cc_start: 0.7236 (ttt-90) cc_final: 0.7028 (ttt-90) REVERT: E 352 MET cc_start: 0.7894 (ppp) cc_final: 0.6812 (mmt) outliers start: 52 outliers final: 36 residues processed: 277 average time/residue: 0.2076 time to fit residues: 88.0416 Evaluate side-chains 256 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 219 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 301 VAL 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 322 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 99 MET Chi-restraints excluded: chain E residue 167 ASN Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 329 ASP Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 477 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 150 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN E 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.6070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14089 Z= 0.214 Angle : 0.626 10.611 19119 Z= 0.317 Chirality : 0.045 0.297 2164 Planarity : 0.004 0.043 2384 Dihedral : 5.734 73.077 1958 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.23 % Allowed : 17.26 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.20), residues: 1662 helix: 1.34 (0.23), residues: 495 sheet: -0.08 (0.27), residues: 380 loop : -1.46 (0.20), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 310 HIS 0.004 0.001 HIS A 133 PHE 0.015 0.001 PHE E 163 TYR 0.018 0.001 TYR E 473 ARG 0.004 0.000 ARG E 262 *********************** 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 297 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 233 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 GLU cc_start: 0.7979 (tt0) cc_final: 0.7749 (tt0) REVERT: A 334 GLN cc_start: 0.7648 (mm110) cc_final: 0.7339 (mm-40) REVERT: D 114 LEU cc_start: 0.8751 (tt) cc_final: 0.8539 (tp) REVERT: D 289 THR cc_start: 0.8215 (m) cc_final: 0.7999 (p) REVERT: D 300 LYS cc_start: 0.8997 (mmtp) cc_final: 0.8372 (mmtm) REVERT: D 403 PHE cc_start: 0.6390 (m-10) cc_final: 0.5660 (m-80) REVERT: C 329 ASN cc_start: 0.9058 (OUTLIER) cc_final: 0.8780 (t0) REVERT: B 37 PHE cc_start: 0.9045 (t80) cc_final: 0.8251 (t80) REVERT: B 102 TYR cc_start: 0.6017 (m-10) cc_final: 0.5806 (m-10) REVERT: B 113 MET cc_start: 0.7781 (ppp) cc_final: 0.6625 (ppp) REVERT: B 135 VAL cc_start: 0.7505 (OUTLIER) cc_final: 0.7135 (m) REVERT: B 168 ASN cc_start: 0.8318 (OUTLIER) cc_final: 0.7721 (p0) REVERT: B 204 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7525 (m-30) REVERT: B 210 GLN cc_start: 0.6812 (tp-100) cc_final: 0.6520 (tp-100) REVERT: E 262 ARG cc_start: 0.6085 (ttt-90) cc_final: 0.5514 (tpt-90) REVERT: E 352 MET cc_start: 0.7923 (ppp) cc_final: 0.7710 (ppp) outliers start: 64 outliers final: 40 residues processed: 275 average time/residue: 0.2107 time to fit residues: 88.4418 Evaluate side-chains 268 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 224 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASP 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 212 ILE Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 283 THR 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 106 SER Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 229 GLN Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 329 ASP 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 132 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 chunk 110 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 290 GLN ** D 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.6464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14089 Z= 0.190 Angle : 0.604 8.764 19119 Z= 0.305 Chirality : 0.045 0.304 2164 Planarity : 0.004 0.039 2384 Dihedral : 5.526 62.648 1958 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.56 % Allowed : 18.58 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.20), residues: 1662 helix: 1.39 (0.23), residues: 498 sheet: 0.02 (0.27), residues: 383 loop : -1.44 (0.20), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 310 HIS 0.003 0.001 HIS A 133 PHE 0.028 0.001 PHE E 189 TYR 0.023 0.001 TYR D 325 ARG 0.003 0.000 ARG E 262 *********************** 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 292 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 223 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 GLU cc_start: 0.8087 (tt0) cc_final: 0.7703 (tt0) REVERT: A 257 LEU cc_start: 0.8927 (mp) cc_final: 0.8571 (tp) REVERT: A 334 GLN cc_start: 0.7736 (mm110) cc_final: 0.7374 (mm-40) REVERT: D 81 ASP cc_start: 0.7497 (p0) cc_final: 0.7178 (p0) REVERT: D 144 ILE cc_start: 0.8511 (pt) cc_final: 0.8311 (mt) REVERT: D 289 THR cc_start: 0.8321 (m) cc_final: 0.8069 (p) REVERT: D 300 LYS cc_start: 0.8938 (mmtp) cc_final: 0.8344 (mmtm) REVERT: D 403 PHE cc_start: 0.6386 (m-10) cc_final: 0.5662 (m-80) REVERT: C 329 ASN cc_start: 0.9040 (OUTLIER) cc_final: 0.8834 (t0) REVERT: B 113 MET cc_start: 0.7829 (ppp) cc_final: 0.6960 (ppp) REVERT: B 135 VAL cc_start: 0.7657 (OUTLIER) cc_final: 0.7330 (m) REVERT: B 168 ASN cc_start: 0.8355 (OUTLIER) cc_final: 0.7748 (p0) REVERT: B 204 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7566 (m-30) REVERT: B 210 GLN cc_start: 0.6963 (tp-100) cc_final: 0.6653 (tp-100) REVERT: E 352 MET cc_start: 0.7960 (ppp) cc_final: 0.7718 (ppp) outliers start: 69 outliers final: 45 residues processed: 272 average time/residue: 0.2149 time to fit residues: 89.4814 Evaluate side-chains 255 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 206 time to evaluate : 1.723 ------------------------------------------------------------------------------- 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 212 ILE Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 286 THR 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 168 ASN Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 167 ASN Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 329 ASP Chi-restraints excluded: chain E residue 337 LEU 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 53 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 13 optimal weight: 0.0970 chunk 52 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN C 139 ASN B 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.7024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14089 Z= 0.230 Angle : 0.620 9.506 19119 Z= 0.315 Chirality : 0.046 0.315 2164 Planarity : 0.004 0.040 2384 Dihedral : 5.455 55.395 1958 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 5.09 % Allowed : 18.25 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.20), residues: 1662 helix: 1.48 (0.23), residues: 498 sheet: -0.12 (0.27), residues: 389 loop : -1.43 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 310 HIS 0.006 0.001 HIS A 133 PHE 0.020 0.001 PHE E 189 TYR 0.019 0.001 TYR E 473 ARG 0.004 0.000 ARG B 333 *********************** 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 294 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 217 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 LEU cc_start: 0.8953 (mp) cc_final: 0.8650 (tp) REVERT: A 334 GLN cc_start: 0.7905 (mm110) cc_final: 0.7542 (mm-40) REVERT: D 300 LYS cc_start: 0.8939 (mmtp) cc_final: 0.8327 (mmtm) REVERT: D 403 PHE cc_start: 0.6414 (m-10) cc_final: 0.5654 (m-80) REVERT: C 75 ILE cc_start: 0.9133 (mp) cc_final: 0.8856 (mt) REVERT: C 329 ASN cc_start: 0.9014 (OUTLIER) cc_final: 0.8804 (t0) REVERT: B 113 MET cc_start: 0.7910 (ppp) cc_final: 0.7490 (ppp) REVERT: B 135 VAL cc_start: 0.7780 (OUTLIER) cc_final: 0.7442 (m) REVERT: B 164 MET cc_start: 0.8169 (mmt) cc_final: 0.7729 (mmt) REVERT: B 168 ASN cc_start: 0.8478 (OUTLIER) cc_final: 0.7937 (p0) REVERT: B 210 GLN cc_start: 0.6929 (tp-100) cc_final: 0.6628 (tp-100) REVERT: B 433 TYR cc_start: 0.7455 (m-80) cc_final: 0.7154 (m-80) REVERT: E 61 ASN cc_start: 0.7950 (OUTLIER) cc_final: 0.7544 (m110) REVERT: E 135 LYS cc_start: 0.7604 (tptt) cc_final: 0.7395 (ttmt) outliers start: 77 outliers final: 50 residues processed: 270 average time/residue: 0.2111 time to fit residues: 87.2185 Evaluate side-chains 261 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 207 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 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 271 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 286 THR 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 168 ASN Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 319 PHE Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 167 ASN Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 312 CYS Chi-restraints excluded: chain E residue 329 ASP Chi-restraints excluded: chain E residue 337 LEU 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 153 optimal weight: 5.9990 chunk 17 optimal weight: 0.0570 chunk 90 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 89 optimal weight: 0.0170 chunk 159 optimal weight: 0.9990 chunk 99 optimal weight: 0.0970 chunk 96 optimal weight: 8.9990 chunk 73 optimal weight: 0.0060 chunk 98 optimal weight: 0.9990 overall best weight: 0.2150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 290 GLN ** D 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.7091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14089 Z= 0.148 Angle : 0.604 9.400 19119 Z= 0.297 Chirality : 0.045 0.301 2164 Planarity : 0.004 0.038 2384 Dihedral : 5.171 54.561 1958 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.11 % Allowed : 20.57 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.20), residues: 1662 helix: 1.48 (0.23), residues: 498 sheet: 0.22 (0.28), residues: 373 loop : -1.38 (0.20), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 288 HIS 0.001 0.000 HIS B 225 PHE 0.020 0.001 PHE E 189 TYR 0.021 0.001 TYR E 473 ARG 0.003 0.000 ARG B 333 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 215 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 LEU cc_start: 0.8941 (mp) cc_final: 0.8617 (tp) REVERT: A 334 GLN cc_start: 0.7963 (mm110) cc_final: 0.7597 (mm-40) REVERT: D 300 LYS cc_start: 0.8940 (mmtp) cc_final: 0.8352 (mmtm) REVERT: D 403 PHE cc_start: 0.6545 (m-10) cc_final: 0.5772 (m-80) REVERT: C 75 ILE cc_start: 0.9056 (mp) cc_final: 0.8817 (mt) REVERT: C 80 MET cc_start: 0.7164 (tpt) cc_final: 0.6915 (tpp) REVERT: B 135 VAL cc_start: 0.7555 (OUTLIER) cc_final: 0.7259 (m) REVERT: B 168 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.7859 (p0) REVERT: B 210 GLN cc_start: 0.6959 (tp-100) cc_final: 0.6643 (tp-100) REVERT: B 268 ILE cc_start: 0.7196 (OUTLIER) cc_final: 0.6766 (mt) REVERT: B 269 ASN cc_start: 0.7822 (OUTLIER) cc_final: 0.7168 (p0) REVERT: E 135 LYS cc_start: 0.7642 (tptt) cc_final: 0.7361 (ttmt) REVERT: E 352 MET cc_start: 0.7977 (ppp) cc_final: 0.7776 (ppp) outliers start: 47 outliers final: 35 residues processed: 247 average time/residue: 0.2145 time to fit residues: 80.2755 Evaluate side-chains 243 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 204 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 319 PHE Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 312 CYS Chi-restraints excluded: chain E residue 329 ASP 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 63 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 0.0000 chunk 31 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 125 optimal weight: 0.5980 chunk 144 optimal weight: 0.8980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 290 GLN B 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.7278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14089 Z= 0.179 Angle : 0.605 11.050 19119 Z= 0.298 Chirality : 0.045 0.311 2164 Planarity : 0.004 0.037 2384 Dihedral : 5.106 54.337 1958 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.44 % Allowed : 21.16 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.20), residues: 1662 helix: 1.42 (0.23), residues: 500 sheet: 0.27 (0.28), residues: 379 loop : -1.32 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 263 HIS 0.003 0.001 HIS A 133 PHE 0.019 0.001 PHE E 189 TYR 0.020 0.001 TYR B 325 ARG 0.005 0.000 ARG E 102 *********************** 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 259 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 207 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 LEU cc_start: 0.8957 (mp) cc_final: 0.8678 (tp) REVERT: A 334 GLN cc_start: 0.7994 (mm110) cc_final: 0.7647 (mm-40) REVERT: D 210 GLN cc_start: 0.8516 (mp10) cc_final: 0.7886 (tt0) REVERT: D 300 LYS cc_start: 0.8985 (mmtp) cc_final: 0.8366 (mmtm) REVERT: D 403 PHE cc_start: 0.6539 (m-10) cc_final: 0.5776 (m-80) REVERT: C 75 ILE cc_start: 0.9056 (mp) cc_final: 0.8824 (mt) REVERT: C 80 MET cc_start: 0.7194 (tpt) cc_final: 0.6964 (tpp) REVERT: B 135 VAL cc_start: 0.7611 (OUTLIER) cc_final: 0.7306 (m) REVERT: B 168 ASN cc_start: 0.8439 (OUTLIER) cc_final: 0.7980 (p0) REVERT: B 210 GLN cc_start: 0.7001 (tp-100) cc_final: 0.6676 (tp-100) REVERT: B 268 ILE cc_start: 0.7197 (OUTLIER) cc_final: 0.6845 (mp) REVERT: B 269 ASN cc_start: 0.7809 (OUTLIER) cc_final: 0.7208 (p0) REVERT: B 271 ASP cc_start: 0.8262 (p0) cc_final: 0.7457 (p0) REVERT: B 415 ARG cc_start: 0.6419 (mtp180) cc_final: 0.6191 (mtp-110) REVERT: E 223 ASP cc_start: 0.6054 (t0) cc_final: 0.5390 (t0) outliers start: 52 outliers final: 41 residues processed: 245 average time/residue: 0.2149 time to fit residues: 80.6404 Evaluate side-chains 241 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 196 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 312 CYS Chi-restraints excluded: chain E residue 329 ASP 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 152 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 116 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 140 optimal weight: 0.1980 chunk 147 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 290 GLN B 179 GLN E 104 ASN E 153 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.7524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14089 Z= 0.215 Angle : 0.621 8.588 19119 Z= 0.310 Chirality : 0.045 0.312 2164 Planarity : 0.004 0.043 2384 Dihedral : 5.174 54.845 1958 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.70 % Allowed : 20.77 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.20), residues: 1662 helix: 1.51 (0.23), residues: 494 sheet: 0.22 (0.28), residues: 383 loop : -1.34 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 288 HIS 0.002 0.001 HIS A 133 PHE 0.019 0.001 PHE E 189 TYR 0.022 0.001 TYR E 473 ARG 0.003 0.000 ARG B 276 *********************** 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 260 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 204 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 LEU cc_start: 0.9018 (mp) cc_final: 0.8724 (tp) REVERT: A 334 GLN cc_start: 0.8009 (mm110) cc_final: 0.7768 (mm-40) REVERT: D 81 ASP cc_start: 0.7620 (p0) cc_final: 0.7318 (p0) REVERT: D 300 LYS cc_start: 0.8949 (mmtp) cc_final: 0.8328 (mmtm) REVERT: D 403 PHE cc_start: 0.6341 (m-10) cc_final: 0.5600 (m-80) REVERT: C 75 ILE cc_start: 0.9048 (mp) cc_final: 0.8832 (mt) REVERT: B 37 PHE cc_start: 0.8967 (t80) cc_final: 0.8298 (t80) REVERT: B 102 TYR cc_start: 0.6103 (m-10) cc_final: 0.5812 (m-10) REVERT: B 135 VAL cc_start: 0.7655 (OUTLIER) cc_final: 0.7362 (m) REVERT: B 164 MET cc_start: 0.8333 (mmt) cc_final: 0.7770 (mmt) REVERT: B 168 ASN cc_start: 0.8441 (OUTLIER) cc_final: 0.7943 (p0) REVERT: B 210 GLN cc_start: 0.7008 (tp-100) cc_final: 0.6701 (tp-100) REVERT: B 269 ASN cc_start: 0.7536 (OUTLIER) cc_final: 0.7223 (p0) REVERT: B 271 ASP cc_start: 0.8123 (p0) cc_final: 0.7744 (t0) outliers start: 56 outliers final: 49 residues processed: 245 average time/residue: 0.2109 time to fit residues: 79.5234 Evaluate side-chains 249 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 197 time to evaluate : 1.610 ------------------------------------------------------------------------------- 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 179 GLN 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 258 ILE Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 477 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 151 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 13 optimal weight: 0.0370 chunk 101 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN B 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.7545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.141 14089 Z= 0.272 Angle : 1.032 59.200 19119 Z= 0.610 Chirality : 0.049 0.521 2164 Planarity : 0.005 0.134 2384 Dihedral : 5.199 54.850 1958 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.24 % Allowed : 21.30 % Favored : 75.46 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.20), residues: 1662 helix: 1.49 (0.23), residues: 494 sheet: 0.21 (0.28), residues: 383 loop : -1.34 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 310 HIS 0.002 0.001 HIS A 133 PHE 0.017 0.001 PHE E 189 TYR 0.018 0.001 TYR D 325 ARG 0.006 0.000 ARG B 333 ********************** 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 246 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 197 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 LEU cc_start: 0.9016 (mp) cc_final: 0.8720 (tp) REVERT: A 334 GLN cc_start: 0.8009 (mm110) cc_final: 0.7765 (mm-40) REVERT: D 81 ASP cc_start: 0.7617 (p0) cc_final: 0.7316 (p0) REVERT: D 300 LYS cc_start: 0.8948 (mmtp) cc_final: 0.8327 (mmtm) REVERT: D 403 PHE cc_start: 0.6342 (m-10) cc_final: 0.5600 (m-80) REVERT: C 75 ILE cc_start: 0.9048 (mp) cc_final: 0.8831 (mt) REVERT: B 37 PHE cc_start: 0.8966 (t80) cc_final: 0.8296 (t80) REVERT: B 102 TYR cc_start: 0.6101 (m-10) cc_final: 0.5809 (m-10) REVERT: B 135 VAL cc_start: 0.7653 (OUTLIER) cc_final: 0.7358 (m) REVERT: B 164 MET cc_start: 0.8331 (mmt) cc_final: 0.7768 (mmt) REVERT: B 168 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.7940 (p0) REVERT: B 210 GLN cc_start: 0.7006 (tp-100) cc_final: 0.6700 (tp-100) REVERT: B 269 ASN cc_start: 0.7535 (OUTLIER) cc_final: 0.7223 (p0) REVERT: B 271 ASP cc_start: 0.8122 (p0) cc_final: 0.7743 (t0) outliers start: 49 outliers final: 45 residues processed: 234 average time/residue: 0.2100 time to fit residues: 76.6266 Evaluate side-chains 245 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 197 time to evaluate : 1.623 ------------------------------------------------------------------------------- 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 258 ILE Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 477 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 19 optimal weight: 0.3980 chunk 36 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 134 optimal weight: 0.0970 chunk 16 optimal weight: 0.0670 chunk 24 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN B 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.134496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.111819 restraints weight = 26800.981| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 3.20 r_work: 0.3601 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.7551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.141 14089 Z= 0.272 Angle : 1.032 59.200 19119 Z= 0.610 Chirality : 0.049 0.521 2164 Planarity : 0.005 0.134 2384 Dihedral : 5.199 54.850 1958 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.17 % Allowed : 21.49 % Favored : 75.33 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.20), residues: 1662 helix: 1.49 (0.23), residues: 494 sheet: 0.21 (0.28), residues: 383 loop : -1.34 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 310 HIS 0.002 0.001 HIS A 133 PHE 0.017 0.001 PHE E 189 TYR 0.018 0.001 TYR D 325 ARG 0.006 0.000 ARG B 333 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2974.89 seconds wall clock time: 53 minutes 39.72 seconds (3219.72 seconds total)