Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 01:02:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tvi_26141/04_2023/7tvi_26141.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tvi_26141/04_2023/7tvi_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_26141/04_2023/7tvi_26141.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tvi_26141/04_2023/7tvi_26141.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tvi_26141/04_2023/7tvi_26141.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tvi_26141/04_2023/7tvi_26141.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-1.21rc1-4938/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 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 chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.54, per 1000 atoms: 0.55 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: 5.33 Conformation dependent library (CDL) restraints added in 1.9 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: 0.87 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: 4.34 Time building geometry restraints manager: 5.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2307 1.32 - 1.45: 3822 1.45 - 1.57: 7813 1.57 - 1.69: 0 1.69 - 1.81: 147 Bond restraints: 14089 Sorted by residual: bond pdb=" N GLY B 501 " pdb=" CA GLY B 501 " ideal model delta sigma weight residual 1.451 1.501 -0.050 1.60e-02 3.91e+03 9.94e+00 bond pdb=" N GLY D 503 " pdb=" CA GLY D 503 " ideal model delta sigma weight residual 1.451 1.501 -0.050 1.60e-02 3.91e+03 9.89e+00 bond pdb=" N GLY A 501 " pdb=" CA GLY A 501 " ideal model delta sigma weight residual 1.451 1.501 -0.050 1.60e-02 3.91e+03 9.68e+00 bond pdb=" N GLY D 501 " pdb=" CA GLY D 501 " ideal model delta sigma weight residual 1.451 1.500 -0.049 1.60e-02 3.91e+03 9.49e+00 bond pdb=" C PRO E 299 " pdb=" O PRO E 299 " ideal model delta sigma weight residual 1.237 1.202 0.036 1.20e-02 6.94e+03 8.87e+00 ... (remaining 14084 not shown) Histogram of bond angle deviations from ideal: 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: 7531 17.98 - 35.95: 653 35.95 - 53.93: 109 53.93 - 71.91: 18 71.91 - 89.89: 12 Dihedral angle restraints: 8323 sinusoidal: 3348 harmonic: 4975 Sorted by residual: dihedral pdb=" CA MET B 287 " pdb=" C MET B 287 " pdb=" N THR B 288 " pdb=" CA THR B 288 " ideal model delta harmonic sigma weight residual 180.00 154.51 25.49 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CB CYS E 182 " pdb=" SG CYS E 182 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual -86.00 -125.61 39.61 1 1.00e+01 1.00e-02 2.20e+01 dihedral pdb=" CA ALA E 327 " pdb=" C ALA E 327 " pdb=" N ILE E 328 " pdb=" CA ILE E 328 " ideal model delta harmonic sigma weight residual 180.00 158.15 21.85 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 8320 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1875 0.076 - 0.152: 264 0.152 - 0.227: 19 0.227 - 0.303: 4 0.303 - 0.379: 2 Chirality restraints: 2164 Sorted by residual: chirality pdb=" C1 NAG A 502 " pdb=" ND2 ASN A 62 " pdb=" C2 NAG A 502 " pdb=" O5 NAG A 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" C1 NAG E 602 " pdb=" ND2 ASN E 241 " pdb=" C2 NAG E 602 " pdb=" O5 NAG E 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CA ALA E 295 " pdb=" N ALA E 295 " pdb=" C ALA E 295 " pdb=" CB ALA E 295 " both_signs ideal model delta sigma weight residual False 2.48 2.23 0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 2161 not shown) Planarity restraints: 2390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 110 " -0.050 5.00e-02 4.00e+02 7.65e-02 9.36e+00 pdb=" N PRO A 111 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 111 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 111 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 169 " 0.039 5.00e-02 4.00e+02 5.84e-02 5.45e+00 pdb=" N PRO C 170 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO C 170 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 170 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 263 " 0.017 2.00e-02 2.50e+03 1.46e-02 5.30e+00 pdb=" CG TRP D 263 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP D 263 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP D 263 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 263 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 263 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 263 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 263 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 263 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP D 263 " 0.003 2.00e-02 2.50e+03 ... (remaining 2387 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2061 2.76 - 3.30: 12995 3.30 - 3.83: 21732 3.83 - 4.37: 25292 4.37 - 4.90: 43325 Nonbonded interactions: 105405 Sorted by model distance: nonbonded pdb=" OG1 THR E 206 " pdb=" OD1 ASP E 208 " model vdw 2.228 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: 2.120 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: 7.010 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 35.520 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.070 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.830 ------------------------------------------------------------------------------- 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 : 13.997 89.886 5089 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 0.07 % 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 *********************** 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 : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 415 average time/residue: 0.2531 time to fit residues: 152.0098 Evaluate side-chains 239 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 238 time to evaluate : 1.559 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1227 time to fit residues: 2.4918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 GLN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7400 moved from start: 0.5284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.087 14089 Z= 0.510 Angle : 0.905 12.367 19119 Z= 0.476 Chirality : 0.055 0.377 2164 Planarity : 0.006 0.055 2384 Dihedral : 6.203 82.061 1832 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 3.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.19), residues: 1662 helix: 0.71 (0.21), residues: 497 sheet: -0.44 (0.27), residues: 381 loop : -1.64 (0.19), residues: 784 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 254 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 34 residues processed: 290 average time/residue: 0.2234 time to fit residues: 99.1680 Evaluate side-chains 243 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 209 time to evaluate : 2.609 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.1348 time to fit residues: 10.8642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 7.9990 chunk 46 optimal weight: 0.0870 chunk 124 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 133 optimal weight: 0.3980 chunk 148 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 GLN C 290 GLN B 210 GLN E 194 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.5639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 14089 Z= 0.193 Angle : 0.642 9.375 19119 Z= 0.327 Chirality : 0.046 0.277 2164 Planarity : 0.004 0.045 2384 Dihedral : 5.465 80.487 1832 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer Outliers : 2.18 % 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: -0.53 (0.20), residues: 1662 helix: 1.15 (0.22), residues: 499 sheet: -0.11 (0.27), residues: 386 loop : -1.50 (0.20), residues: 777 *********************** 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 273 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 240 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 21 residues processed: 262 average time/residue: 0.2281 time to fit residues: 90.6625 Evaluate side-chains 235 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 214 time to evaluate : 1.788 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 21 outliers final: 1 residues processed: 21 average time/residue: 0.1422 time to fit residues: 7.4718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 71 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 159 optimal weight: 0.0270 chunk 78 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.6034 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= 0.186 Angle : 0.612 7.951 19119 Z= 0.311 Chirality : 0.045 0.275 2164 Planarity : 0.004 0.041 2384 Dihedral : 5.105 73.428 1832 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 2.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.20), residues: 1662 helix: 1.30 (0.23), residues: 494 sheet: 0.08 (0.27), residues: 375 loop : -1.41 (0.20), residues: 793 *********************** 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 267 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 230 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 15 residues processed: 255 average time/residue: 0.2264 time to fit residues: 88.7963 Evaluate side-chains 228 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 213 time to evaluate : 1.687 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 15 outliers final: 1 residues processed: 15 average time/residue: 0.1560 time to fit residues: 6.5556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 118 optimal weight: 0.1980 chunk 65 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 143 optimal weight: 0.1980 chunk 40 optimal weight: 3.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 210 GLN C 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.6266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 14089 Z= 0.165 Angle : 0.602 10.115 19119 Z= 0.303 Chirality : 0.044 0.276 2164 Planarity : 0.004 0.037 2384 Dihedral : 4.887 63.939 1832 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.27 (0.20), residues: 1662 helix: 1.26 (0.23), residues: 499 sheet: 0.24 (0.28), residues: 375 loop : -1.36 (0.20), residues: 788 *********************** 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 243 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 220 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 233 average time/residue: 0.2306 time to fit residues: 82.5655 Evaluate side-chains 219 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 208 time to evaluate : 1.684 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.1279 time to fit residues: 4.9240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 31 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 13 optimal weight: 0.0980 chunk 52 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN C 131 ASN C 139 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.6884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 14089 Z= 0.274 Angle : 0.645 10.737 19119 Z= 0.327 Chirality : 0.046 0.317 2164 Planarity : 0.004 0.039 2384 Dihedral : 4.947 45.715 1832 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 2.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.20), residues: 1662 helix: 1.31 (0.23), residues: 502 sheet: -0.13 (0.27), residues: 387 loop : -1.41 (0.20), residues: 773 *********************** 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 245 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 208 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 21 residues processed: 228 average time/residue: 0.2423 time to fit residues: 85.4040 Evaluate side-chains 219 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 198 time to evaluate : 1.730 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 21 outliers final: 1 residues processed: 21 average time/residue: 0.1268 time to fit residues: 7.2291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 0.6980 chunk 17 optimal weight: 0.1980 chunk 90 optimal weight: 0.5980 chunk 116 optimal weight: 0.7980 chunk 134 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 159 optimal weight: 0.0670 chunk 99 optimal weight: 0.0040 chunk 96 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 overall best weight: 0.3130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 329 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.6967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 14089 Z= 0.154 Angle : 0.607 12.251 19119 Z= 0.302 Chirality : 0.044 0.279 2164 Planarity : 0.003 0.038 2384 Dihedral : 4.635 26.430 1832 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.20), residues: 1662 helix: 1.29 (0.23), residues: 497 sheet: 0.25 (0.28), residues: 373 loop : -1.40 (0.20), residues: 792 *********************** 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 221 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 209 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 218 average time/residue: 0.2251 time to fit residues: 75.7926 Evaluate side-chains 196 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 191 time to evaluate : 1.743 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.1232 time to fit residues: 3.4660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN E 104 ASN E 153 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.7829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.078 14089 Z= 0.442 Angle : 0.776 10.217 19119 Z= 0.399 Chirality : 0.051 0.458 2164 Planarity : 0.005 0.044 2384 Dihedral : 5.431 25.286 1832 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 1.65 % 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: -0.68 (0.20), residues: 1662 helix: 1.03 (0.23), residues: 510 sheet: -0.39 (0.27), residues: 396 loop : -1.52 (0.21), residues: 756 *********************** 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 221 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 196 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 16 residues processed: 210 average time/residue: 0.2248 time to fit residues: 73.0460 Evaluate side-chains 206 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 190 time to evaluate : 1.494 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 16 outliers final: 1 residues processed: 16 average time/residue: 0.1180 time to fit residues: 5.6082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 89 optimal weight: 0.0970 chunk 64 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 140 optimal weight: 0.8980 chunk 147 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.7908 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 : 0.657 11.355 19119 Z= 0.326 Chirality : 0.046 0.367 2164 Planarity : 0.004 0.041 2384 Dihedral : 4.931 21.708 1832 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.17 (0.23), residues: 505 sheet: 0.04 (0.27), residues: 385 loop : -1.45 (0.21), residues: 772 *********************** 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 205 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 195 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 200 average time/residue: 0.2297 time to fit residues: 71.1319 Evaluate side-chains 196 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 189 time to evaluate : 1.576 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.1351 time to fit residues: 3.8184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 103 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.8046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 14089 Z= 0.193 Angle : 0.630 10.596 19119 Z= 0.314 Chirality : 0.045 0.301 2164 Planarity : 0.004 0.042 2384 Dihedral : 4.700 21.374 1832 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer Outliers : 0.33 % 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: -0.34 (0.20), residues: 1662 helix: 1.25 (0.23), residues: 504 sheet: 0.16 (0.28), residues: 383 loop : -1.45 (0.21), residues: 775 ********************** 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 201 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 196 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 200 average time/residue: 0.2286 time to fit residues: 70.7752 Evaluate side-chains 194 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 191 time to evaluate : 1.696 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1269 time to fit residues: 2.9436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.0070 chunk 40 optimal weight: 0.5980 chunk 120 optimal weight: 3.9990 chunk 19 optimal weight: 0.0870 chunk 36 optimal weight: 3.9990 chunk 131 optimal weight: 0.5980 chunk 54 optimal weight: 0.0370 chunk 134 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 overall best weight: 0.2654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.135652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.112109 restraints weight = 26643.365| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 3.18 r_work: 0.3619 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.8091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 14089 Z= 0.158 Angle : 0.647 15.916 19119 Z= 0.315 Chirality : 0.045 0.289 2164 Planarity : 0.004 0.040 2384 Dihedral : 4.525 19.941 1832 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 0.26 % 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: -0.19 (0.20), residues: 1662 helix: 1.32 (0.23), residues: 501 sheet: 0.35 (0.27), residues: 388 loop : -1.39 (0.21), residues: 773 =============================================================================== Job complete usr+sys time: 2912.70 seconds wall clock time: 54 minutes 42.69 seconds (3282.69 seconds total)