Starting phenix.real_space_refine on Tue Mar 19 18:52:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yry_34066/03_2024/7yry_34066_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yry_34066/03_2024/7yry_34066.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yry_34066/03_2024/7yry_34066.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yry_34066/03_2024/7yry_34066.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yry_34066/03_2024/7yry_34066_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yry_34066/03_2024/7yry_34066_updated.pdb" } resolution = 3.0 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= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 99 5.16 5 C 15741 2.51 5 N 4306 2.21 5 O 4894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 68": "OE1" <-> "OE2" Residue "A GLU 248": "OE1" <-> "OE2" Residue "A GLU 416": "OE1" <-> "OE2" Residue "A GLU 479": "OE1" <-> "OE2" Residue "B GLU 416": "OE1" <-> "OE2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "E GLU 235": "OE1" <-> "OE2" Residue "F GLU 19": "OE1" <-> "OE2" Residue "F GLU 389": "OE1" <-> "OE2" Residue "F GLU 390": "OE1" <-> "OE2" Residue "F GLU 413": "OE1" <-> "OE2" Residue "g GLU 6": "OE1" <-> "OE2" Residue "g PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 216": "OE1" <-> "OE2" Residue "g GLU 227": "OE1" <-> "OE2" Residue "g GLU 278": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25056 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3702 Classifications: {'peptide': 489} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 471} Chain: "B" Number of atoms: 3703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3703 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 471} Chain: "C" Number of atoms: 3703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3703 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 471} Chain: "D" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3525 Classifications: {'peptide': 463} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 440} Chain: "E" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3525 Classifications: {'peptide': 463} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 440} Chain: "F" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3525 Classifications: {'peptide': 463} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 440} Chain: "e" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1010 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "g" Number of atoms: 2234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2234 Classifications: {'peptide': 288} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 279} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.07, per 1000 atoms: 0.56 Number of scatterers: 25056 At special positions: 0 Unit cell: (154.512, 131.335, 133.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 99 16.00 P 12 15.00 Mg 4 11.99 O 4894 8.00 N 4306 7.00 C 15741 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 10.30 Conformation dependent library (CDL) restraints added in 4.6 seconds 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5970 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 128 helices and 25 sheets defined 41.0% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.04 Creating SS restraints... Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 152 through 157 removed outlier: 3.549A pdb=" N THR A 156 " --> pdb=" O LYS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 187 removed outlier: 3.854A pdb=" N GLN A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 removed outlier: 3.504A pdb=" N THR A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 221 removed outlier: 3.520A pdb=" N TYR A 221 " --> pdb=" O ALA A 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 218 through 221' Processing helix chain 'A' and resid 233 through 253 Proline residue: A 240 - end of helix removed outlier: 3.865A pdb=" N TYR A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N PHE A 250 " --> pdb=" O MET A 246 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG A 253 " --> pdb=" O TYR A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 277 removed outlier: 3.607A pdb=" N ALA A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 291 through 301 removed outlier: 3.857A pdb=" N HIS A 295 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ARG A 301 " --> pdb=" O ARG A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 314 Processing helix chain 'A' and resid 341 through 347 Processing helix chain 'A' and resid 358 through 362 Processing helix chain 'A' and resid 379 through 382 removed outlier: 3.502A pdb=" N ALA A 382 " --> pdb=" O GLY A 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 379 through 382' Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 394 through 407 Processing helix chain 'A' and resid 416 through 431 removed outlier: 3.546A pdb=" N ARG A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 453 Processing helix chain 'A' and resid 462 through 479 removed outlier: 3.595A pdb=" N ILE A 465 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N VAL A 466 " --> pdb=" O LYS A 463 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP A 467 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 479 " --> pdb=" O PHE A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 490 Processing helix chain 'A' and resid 495 through 511 Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 137 through 139 No H-bonds generated for 'chain 'B' and resid 137 through 139' Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 177 through 187 Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 218 through 221 Processing helix chain 'B' and resid 233 through 253 Proline residue: B 240 - end of helix removed outlier: 3.699A pdb=" N TYR B 249 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N PHE B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG B 253 " --> pdb=" O TYR B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 277 Processing helix chain 'B' and resid 284 through 286 No H-bonds generated for 'chain 'B' and resid 284 through 286' Processing helix chain 'B' and resid 291 through 301 removed outlier: 3.679A pdb=" N ARG B 297 " --> pdb=" O TYR B 293 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG B 301 " --> pdb=" O ARG B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 314 Processing helix chain 'B' and resid 341 through 347 Processing helix chain 'B' and resid 358 through 361 No H-bonds generated for 'chain 'B' and resid 358 through 361' Processing helix chain 'B' and resid 379 through 382 Processing helix chain 'B' and resid 385 through 403 removed outlier: 4.672A pdb=" N GLY B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLY B 393 " --> pdb=" O LYS B 389 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 431 Processing helix chain 'B' and resid 442 through 453 Processing helix chain 'B' and resid 462 through 479 removed outlier: 4.731A pdb=" N VAL B 466 " --> pdb=" O LYS B 463 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU B 479 " --> pdb=" O PHE B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 490 Processing helix chain 'B' and resid 495 through 511 removed outlier: 4.101A pdb=" N ALA B 510 " --> pdb=" O GLU B 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 139 No H-bonds generated for 'chain 'C' and resid 137 through 139' Processing helix chain 'C' and resid 152 through 157 Processing helix chain 'C' and resid 176 through 187 removed outlier: 3.932A pdb=" N GLN C 187 " --> pdb=" O ALA C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 215 Processing helix chain 'C' and resid 218 through 221 removed outlier: 3.932A pdb=" N TYR C 221 " --> pdb=" O ALA C 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 218 through 221' Processing helix chain 'C' and resid 233 through 253 Proline residue: C 240 - end of helix removed outlier: 4.348A pdb=" N PHE C 250 " --> pdb=" O MET C 246 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG C 251 " --> pdb=" O GLY C 247 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG C 253 " --> pdb=" O TYR C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 277 Processing helix chain 'C' and resid 284 through 286 No H-bonds generated for 'chain 'C' and resid 284 through 286' Processing helix chain 'C' and resid 291 through 301 removed outlier: 3.753A pdb=" N LEU C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ARG C 301 " --> pdb=" O ARG C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 314 Processing helix chain 'C' and resid 341 through 349 removed outlier: 3.923A pdb=" N ASN C 345 " --> pdb=" O PHE C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 362 Processing helix chain 'C' and resid 379 through 382 removed outlier: 3.500A pdb=" N ALA C 382 " --> pdb=" O GLY C 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 379 through 382' Processing helix chain 'C' and resid 385 through 404 removed outlier: 4.708A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N GLY C 393 " --> pdb=" O LYS C 389 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU C 404 " --> pdb=" O GLN C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 409 removed outlier: 4.213A pdb=" N GLN C 409 " --> pdb=" O ALA C 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 406 through 409' Processing helix chain 'C' and resid 416 through 431 Processing helix chain 'C' and resid 442 through 453 Processing helix chain 'C' and resid 465 through 479 Processing helix chain 'C' and resid 481 through 489 Processing helix chain 'C' and resid 495 through 509 Processing helix chain 'D' and resid 80 through 82 No H-bonds generated for 'chain 'D' and resid 80 through 82' Processing helix chain 'D' and resid 130 through 135 Processing helix chain 'D' and resid 154 through 165 Processing helix chain 'D' and resid 182 through 194 Processing helix chain 'D' and resid 198 through 200 No H-bonds generated for 'chain 'D' and resid 198 through 200' Processing helix chain 'D' and resid 212 through 230 removed outlier: 3.661A pdb=" N ARG D 217 " --> pdb=" O GLY D 213 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ALA D 219 " --> pdb=" O ARG D 215 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N LEU D 220 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR D 221 " --> pdb=" O ARG D 217 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY D 222 " --> pdb=" O VAL D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 259 removed outlier: 3.627A pdb=" N VAL D 259 " --> pdb=" O GLY D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 263 No H-bonds generated for 'chain 'D' and resid 261 through 263' Processing helix chain 'D' and resid 276 through 284 removed outlier: 3.850A pdb=" N LEU D 283 " --> pdb=" O GLU D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 306 No H-bonds generated for 'chain 'D' and resid 304 through 306' Processing helix chain 'D' and resid 311 through 319 removed outlier: 4.485A pdb=" N ALA D 318 " --> pdb=" O ALA D 314 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N HIS D 319 " --> pdb=" O THR D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 333 removed outlier: 3.573A pdb=" N SER D 333 " --> pdb=" O ASP D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 354 No H-bonds generated for 'chain 'D' and resid 351 through 354' Processing helix chain 'D' and resid 356 through 381 removed outlier: 4.765A pdb=" N ASP D 377 " --> pdb=" O LYS D 373 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ILE D 378 " --> pdb=" O GLU D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 404 Processing helix chain 'D' and resid 413 through 416 No H-bonds generated for 'chain 'D' and resid 413 through 416' Processing helix chain 'D' and resid 425 through 437 Processing helix chain 'D' and resid 445 through 448 removed outlier: 3.635A pdb=" N PHE D 448 " --> pdb=" O GLU D 445 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 445 through 448' Processing helix chain 'D' and resid 454 through 463 Processing helix chain 'E' and resid 80 through 82 No H-bonds generated for 'chain 'E' and resid 80 through 82' Processing helix chain 'E' and resid 130 through 134 Processing helix chain 'E' and resid 154 through 168 Processing helix chain 'E' and resid 182 through 195 Processing helix chain 'E' and resid 197 through 200 removed outlier: 3.563A pdb=" N LYS E 200 " --> pdb=" O VAL E 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 197 through 200' Processing helix chain 'E' and resid 212 through 230 removed outlier: 4.896A pdb=" N ALA E 219 " --> pdb=" O ARG E 215 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU E 220 " --> pdb=" O LEU E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 262 Processing helix chain 'E' and resid 276 through 286 removed outlier: 4.145A pdb=" N ARG E 286 " --> pdb=" O VAL E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 306 No H-bonds generated for 'chain 'E' and resid 304 through 306' Processing helix chain 'E' and resid 311 through 317 removed outlier: 3.925A pdb=" N THR E 316 " --> pdb=" O SER E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 332 Processing helix chain 'E' and resid 351 through 354 No H-bonds generated for 'chain 'E' and resid 351 through 354' Processing helix chain 'E' and resid 356 through 381 removed outlier: 3.912A pdb=" N LYS E 376 " --> pdb=" O TYR E 372 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASP E 377 " --> pdb=" O LYS E 373 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE E 378 " --> pdb=" O GLU E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 405 removed outlier: 3.563A pdb=" N PHE E 405 " --> pdb=" O ILE E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 437 Processing helix chain 'E' and resid 445 through 448 Processing helix chain 'E' and resid 454 through 463 Processing helix chain 'F' and resid 80 through 82 No H-bonds generated for 'chain 'F' and resid 80 through 82' Processing helix chain 'F' and resid 115 through 117 No H-bonds generated for 'chain 'F' and resid 115 through 117' Processing helix chain 'F' and resid 130 through 135 Processing helix chain 'F' and resid 155 through 167 Processing helix chain 'F' and resid 182 through 194 Processing helix chain 'F' and resid 198 through 200 No H-bonds generated for 'chain 'F' and resid 198 through 200' Processing helix chain 'F' and resid 212 through 216 Processing helix chain 'F' and resid 219 through 231 Processing helix chain 'F' and resid 235 through 237 No H-bonds generated for 'chain 'F' and resid 235 through 237' Processing helix chain 'F' and resid 249 through 263 Processing helix chain 'F' and resid 276 through 284 Processing helix chain 'F' and resid 304 through 306 No H-bonds generated for 'chain 'F' and resid 304 through 306' Processing helix chain 'F' and resid 311 through 317 Processing helix chain 'F' and resid 328 through 333 removed outlier: 3.563A pdb=" N SER F 333 " --> pdb=" O ASP F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 354 No H-bonds generated for 'chain 'F' and resid 351 through 354' Processing helix chain 'F' and resid 356 through 382 removed outlier: 4.116A pdb=" N ASP F 377 " --> pdb=" O LYS F 373 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE F 378 " --> pdb=" O GLU F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 405 Processing helix chain 'F' and resid 413 through 416 No H-bonds generated for 'chain 'F' and resid 413 through 416' Processing helix chain 'F' and resid 425 through 437 removed outlier: 3.522A pdb=" N ILE F 429 " --> pdb=" O LEU F 425 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 448 Processing helix chain 'F' and resid 454 through 463 Processing helix chain 'e' and resid 92 through 124 removed outlier: 4.574A pdb=" N ALA e 97 " --> pdb=" O ALA e 93 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG e 98 " --> pdb=" O ILE e 94 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA e 119 " --> pdb=" O ALA e 115 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA e 120 " --> pdb=" O ALA e 116 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA e 122 " --> pdb=" O LEU e 118 " (cutoff:3.500A) Processing helix chain 'e' and resid 129 through 134 removed outlier: 4.290A pdb=" N ILE e 134 " --> pdb=" O THR e 130 " (cutoff:3.500A) Processing helix chain 'g' and resid 4 through 38 removed outlier: 3.967A pdb=" N ARG g 38 " --> pdb=" O ARG g 34 " (cutoff:3.500A) Processing helix chain 'g' and resid 43 through 59 Processing helix chain 'g' and resid 66 through 68 No H-bonds generated for 'chain 'g' and resid 66 through 68' Processing helix chain 'g' and resid 91 through 109 removed outlier: 3.692A pdb=" N GLU g 108 " --> pdb=" O LYS g 104 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLN g 109 " --> pdb=" O ALA g 105 " (cutoff:3.500A) Processing helix chain 'g' and resid 120 through 127 Processing helix chain 'g' and resid 151 through 160 Processing helix chain 'g' and resid 214 through 243 removed outlier: 3.785A pdb=" N SER g 243 " --> pdb=" O ALA g 239 " (cutoff:3.500A) Processing helix chain 'g' and resid 245 through 287 Processing sheet with id= A, first strand: chain 'A' and resid 29 through 31 removed outlier: 6.548A pdb=" N GLY A 73 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET A 34 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N HIS A 43 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE A 32 " --> pdb=" O HIS A 43 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 97 through 100 removed outlier: 3.628A pdb=" N VAL A 100 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU A 126 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 353 through 356 removed outlier: 8.271A pdb=" N ILE A 354 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU A 167 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N LEU A 356 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE A 169 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N GLU A 166 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ALA A 327 " --> pdb=" O GLU A 166 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE A 168 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N GLY A 170 " --> pdb=" O PRO A 329 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE A 331 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 257 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LYS A 193 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ILE A 260 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL A 195 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ASP A 262 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL A 197 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.537A pdb=" N GLY B 73 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET B 34 " --> pdb=" O ARG B 41 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N HIS B 43 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE B 32 " --> pdb=" O HIS B 43 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 97 through 100 removed outlier: 4.565A pdb=" N LEU B 126 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 353 through 355 removed outlier: 6.628A pdb=" N LEU B 167 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 257 through 261 removed outlier: 6.577A pdb=" N LYS B 193 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N ILE B 260 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL B 195 " --> pdb=" O ILE B 260 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 29 through 31 removed outlier: 6.750A pdb=" N GLY C 73 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU C 67 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N SER C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET C 34 " --> pdb=" O ARG C 41 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N HIS C 43 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ILE C 32 " --> pdb=" O HIS C 43 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 97 through 100 removed outlier: 4.110A pdb=" N LEU C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 107 through 109 removed outlier: 4.148A pdb=" N ARG C 107 " --> pdb=" O THR C 222 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N CYS C 194 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N VAL C 225 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TYR C 196 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ALA C 227 " --> pdb=" O TYR C 196 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA C 198 " --> pdb=" O ALA C 227 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N SER C 324 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N ILE C 259 " --> pdb=" O SER C 324 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N THR C 326 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N TYR C 261 " --> pdb=" O THR C 326 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU C 328 " --> pdb=" O TYR C 261 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 352 through 356 Processing sheet with id= L, first strand: chain 'D' and resid 3 through 5 removed outlier: 6.628A pdb=" N ARG D 51 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLN D 44 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL D 49 " --> pdb=" O GLN D 44 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN D 8 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLU D 17 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ILE D 6 " --> pdb=" O GLU D 17 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 75 through 77 Processing sheet with id= N, first strand: chain 'D' and resid 322 through 325 removed outlier: 8.131A pdb=" N VAL D 144 " --> pdb=" O ILE D 295 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N SER D 297 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N LEU D 146 " --> pdb=" O SER D 297 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLN D 299 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLY D 148 " --> pdb=" O GLN D 299 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL D 301 " --> pdb=" O GLY D 148 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL D 242 " --> pdb=" O THR D 296 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N ILE D 298 " --> pdb=" O VAL D 242 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU D 244 " --> pdb=" O ILE D 298 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ALA D 300 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N VAL D 246 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N TYR D 302 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU D 172 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N PHE D 245 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL D 174 " --> pdb=" O PHE D 245 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ASP D 247 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ALA D 176 " --> pdb=" O ASP D 247 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 3 through 5 removed outlier: 6.714A pdb=" N ARG E 51 " --> pdb=" O GLN E 42 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLN E 44 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL E 49 " --> pdb=" O GLN E 44 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN E 8 " --> pdb=" O ASP E 15 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLU E 17 " --> pdb=" O ILE E 6 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ILE E 6 " --> pdb=" O GLU E 17 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 75 through 77 Processing sheet with id= Q, first strand: chain 'E' and resid 297 through 301 removed outlier: 6.271A pdb=" N ALA E 322 " --> pdb=" O GLY E 145 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N PHE E 147 " --> pdb=" O ALA E 322 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N VAL E 324 " --> pdb=" O PHE E 147 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 244 through 246 removed outlier: 6.939A pdb=" N VAL E 174 " --> pdb=" O PHE E 245 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 5 through 10 removed outlier: 6.732A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL F 13 " --> pdb=" O ILE F 9 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE F 53 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N VAL F 41 " --> pdb=" O ILE F 53 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N MET F 55 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU F 39 " --> pdb=" O MET F 55 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 75 through 77 Processing sheet with id= U, first strand: chain 'F' and resid 322 through 324 removed outlier: 3.640A pdb=" N ALA F 322 " --> pdb=" O LYS F 143 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N VAL F 144 " --> pdb=" O ILE F 295 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER F 297 " --> pdb=" O VAL F 144 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LEU F 146 " --> pdb=" O SER F 297 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLN F 299 " --> pdb=" O LEU F 146 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA F 300 " --> pdb=" O VAL F 246 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU F 172 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N PHE F 245 " --> pdb=" O LEU F 172 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL F 174 " --> pdb=" O PHE F 245 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ALA F 202 " --> pdb=" O PHE F 175 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N GLY F 177 " --> pdb=" O ALA F 202 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL F 204 " --> pdb=" O GLY F 177 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'e' and resid 17 through 20 removed outlier: 6.595A pdb=" N VAL e 76 " --> pdb=" O ASP e 7 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N VAL e 9 " --> pdb=" O VAL e 76 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL e 78 " --> pdb=" O VAL e 9 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'e' and resid 31 through 34 removed outlier: 4.150A pdb=" N LEU e 23 " --> pdb=" O ILE e 34 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG e 51 " --> pdb=" O ILE e 24 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LYS e 26 " --> pdb=" O PRO e 49 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL e 52 " --> pdb=" O GLU e 60 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'g' and resid 76 through 81 removed outlier: 3.528A pdb=" N ALA g 116 " --> pdb=" O TYR g 78 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE g 80 " --> pdb=" O ALA g 116 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'g' and resid 169 through 174 removed outlier: 3.770A pdb=" N GLU g 186 " --> pdb=" O LEU g 170 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER g 172 " --> pdb=" O LYS g 184 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS g 184 " --> pdb=" O SER g 172 " (cutoff:3.500A) 964 hydrogen bonds defined for protein. 2745 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: 8.77 Time building geometry restraints manager: 11.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8453 1.34 - 1.46: 4816 1.46 - 1.58: 11968 1.58 - 1.70: 15 1.70 - 1.82: 184 Bond restraints: 25436 Sorted by residual: bond pdb=" C VAL g 176 " pdb=" N ASN g 177 " ideal model delta sigma weight residual 1.332 1.264 0.068 1.40e-02 5.10e+03 2.35e+01 bond pdb=" O3 PO4 E 601 " pdb=" P PO4 E 601 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 8.94e+00 bond pdb=" O4 PO4 E 601 " pdb=" P PO4 E 601 " ideal model delta sigma weight residual 1.568 1.510 0.058 2.00e-02 2.50e+03 8.40e+00 bond pdb=" O2 PO4 E 601 " pdb=" P PO4 E 601 " ideal model delta sigma weight residual 1.567 1.510 0.057 2.00e-02 2.50e+03 8.17e+00 bond pdb=" O1 PO4 E 601 " pdb=" P PO4 E 601 " ideal model delta sigma weight residual 1.565 1.510 0.055 2.00e-02 2.50e+03 7.58e+00 ... (remaining 25431 not shown) Histogram of bond angle deviations from ideal: 98.03 - 106.39: 649 106.39 - 114.76: 15268 114.76 - 123.13: 17341 123.13 - 131.50: 1199 131.50 - 139.87: 17 Bond angle restraints: 34474 Sorted by residual: angle pdb=" CB MET E 55 " pdb=" CG MET E 55 " pdb=" SD MET E 55 " ideal model delta sigma weight residual 112.70 125.39 -12.69 3.00e+00 1.11e-01 1.79e+01 angle pdb=" C GLU F 389 " pdb=" CA GLU F 389 " pdb=" CB GLU F 389 " ideal model delta sigma weight residual 110.42 118.14 -7.72 1.99e+00 2.53e-01 1.51e+01 angle pdb=" CA ILE g 226 " pdb=" CB ILE g 226 " pdb=" CG1 ILE g 226 " ideal model delta sigma weight residual 110.40 116.71 -6.31 1.70e+00 3.46e-01 1.38e+01 angle pdb=" N ILE e 94 " pdb=" CA ILE e 94 " pdb=" C ILE e 94 " ideal model delta sigma weight residual 111.81 108.72 3.09 8.60e-01 1.35e+00 1.29e+01 angle pdb=" CA GLU F 389 " pdb=" CB GLU F 389 " pdb=" CG GLU F 389 " ideal model delta sigma weight residual 114.10 120.71 -6.61 2.00e+00 2.50e-01 1.09e+01 ... (remaining 34469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 14879 35.87 - 71.74: 582 71.74 - 107.61: 51 107.61 - 143.49: 1 143.49 - 179.36: 1 Dihedral angle restraints: 15514 sinusoidal: 6145 harmonic: 9369 Sorted by residual: dihedral pdb=" C5' ADP D 502 " pdb=" O5' ADP D 502 " pdb=" PA ADP D 502 " pdb=" O2A ADP D 502 " ideal model delta sinusoidal sigma weight residual -60.00 119.36 -179.36 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP D 502 " pdb=" O3A ADP D 502 " pdb=" PB ADP D 502 " pdb=" PA ADP D 502 " ideal model delta sinusoidal sigma weight residual -60.00 61.57 -121.57 1 2.00e+01 2.50e-03 3.66e+01 dihedral pdb=" CA MET F 203 " pdb=" C MET F 203 " pdb=" N VAL F 204 " pdb=" CA VAL F 204 " ideal model delta harmonic sigma weight residual 180.00 157.71 22.29 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 15511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2867 0.040 - 0.080: 775 0.080 - 0.120: 295 0.120 - 0.161: 40 0.161 - 0.201: 2 Chirality restraints: 3979 Sorted by residual: chirality pdb=" CB ILE e 24 " pdb=" CA ILE e 24 " pdb=" CG1 ILE e 24 " pdb=" CG2 ILE e 24 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA GLU F 389 " pdb=" N GLU F 389 " pdb=" C GLU F 389 " pdb=" CB GLU F 389 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.46e-01 chirality pdb=" CB ILE g 226 " pdb=" CA ILE g 226 " pdb=" CG1 ILE g 226 " pdb=" CG2 ILE g 226 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 3976 not shown) Planarity restraints: 4494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL g 176 " 0.017 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C VAL g 176 " -0.057 2.00e-02 2.50e+03 pdb=" O VAL g 176 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN g 177 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN g 177 " -0.014 2.00e-02 2.50e+03 2.70e-02 7.30e+00 pdb=" C ASN g 177 " 0.047 2.00e-02 2.50e+03 pdb=" O ASN g 177 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA g 178 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP F 310 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO F 311 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO F 311 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 311 " 0.025 5.00e-02 4.00e+02 ... (remaining 4491 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 212 2.61 - 3.18: 21290 3.18 - 3.76: 37521 3.76 - 4.33: 51169 4.33 - 4.90: 86156 Nonbonded interactions: 196348 Sorted by model distance: nonbonded pdb=" O2G ATP B 601 " pdb="MG MG B 602 " model vdw 2.041 2.170 nonbonded pdb="MG MG C 601 " pdb=" O2B ATP C 602 " model vdw 2.051 2.170 nonbonded pdb=" OG1 THR A 177 " pdb="MG MG A 602 " model vdw 2.066 2.170 nonbonded pdb=" N GLU D 104 " pdb=" OE1 GLU D 104 " model vdw 2.167 2.520 nonbonded pdb="MG MG D 501 " pdb=" O3B ADP D 502 " model vdw 2.171 2.170 ... (remaining 196343 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 26 through 514) selection = (chain 'B' and (resid 26 through 513 or (resid 514 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )))) selection = (chain 'C' and (resid 26 through 513 or (resid 514 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )))) } ncs_group { reference = (chain 'D' and resid 2 through 464) selection = (chain 'E' and resid 2 through 464) selection = chain 'F' } 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: 4.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 10.140 Check model and map are aligned: 0.350 Set scattering table: 0.240 Process input model: 68.930 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 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 : 0.002 0.068 25436 Z= 0.164 Angle : 0.544 12.692 34474 Z= 0.280 Chirality : 0.043 0.201 3979 Planarity : 0.003 0.045 4494 Dihedral : 17.926 179.358 9544 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.35 % Allowed : 26.64 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.38 (0.15), residues: 3266 helix: 1.60 (0.15), residues: 1310 sheet: 0.20 (0.24), residues: 491 loop : -0.98 (0.15), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP g 206 HIS 0.002 0.000 HIS D 190 PHE 0.011 0.001 PHE F 415 TYR 0.023 0.001 TYR g 63 ARG 0.007 0.000 ARG F 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 213 time to evaluate : 3.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 266 MET cc_start: 0.7148 (mpt) cc_final: 0.6892 (mpp) REVERT: E 404 PHE cc_start: 0.5689 (OUTLIER) cc_final: 0.5429 (t80) REVERT: e 22 MET cc_start: 0.3467 (tmm) cc_final: 0.3228 (tpp) REVERT: g 6 GLU cc_start: 0.6541 (tm-30) cc_final: 0.6334 (tp30) REVERT: g 39 MET cc_start: 0.7600 (mmp) cc_final: 0.6803 (tpp) REVERT: g 115 PHE cc_start: 0.8722 (p90) cc_final: 0.8262 (p90) REVERT: g 229 MET cc_start: 0.7984 (mmt) cc_final: 0.7758 (mmm) outliers start: 88 outliers final: 74 residues processed: 296 average time/residue: 1.1941 time to fit residues: 417.5569 Evaluate side-chains 268 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 193 time to evaluate : 3.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 404 PHE Chi-restraints excluded: chain E residue 409 PHE Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 44 LEU Chi-restraints excluded: chain e residue 77 THR Chi-restraints excluded: chain e residue 114 SER Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain g residue 16 SER Chi-restraints excluded: chain g residue 18 GLN Chi-restraints excluded: chain g residue 60 ASN Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 129 TYR Chi-restraints excluded: chain g residue 166 ASP Chi-restraints excluded: chain g residue 198 ASP Chi-restraints excluded: chain g residue 206 TRP Chi-restraints excluded: chain g residue 228 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 272 optimal weight: 8.9990 chunk 244 optimal weight: 8.9990 chunk 135 optimal weight: 0.2980 chunk 83 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 253 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 188 optimal weight: 0.7980 chunk 293 optimal weight: 20.0000 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 148 GLN E 190 HIS F 248 ASN ** e 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.0607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25436 Z= 0.264 Angle : 0.541 10.400 34474 Z= 0.282 Chirality : 0.044 0.209 3979 Planarity : 0.004 0.044 4494 Dihedral : 8.666 156.858 3796 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.76 % Allowed : 25.19 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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 (0.15), residues: 3266 helix: 1.46 (0.15), residues: 1324 sheet: 0.19 (0.23), residues: 521 loop : -1.03 (0.15), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 139 HIS 0.003 0.001 HIS D 190 PHE 0.014 0.001 PHE g 175 TYR 0.024 0.001 TYR E 396 ARG 0.005 0.000 ARG F 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 202 time to evaluate : 3.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8262 (tt0) REVERT: A 476 PHE cc_start: 0.8990 (OUTLIER) cc_final: 0.7792 (t80) REVERT: B 53 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8274 (mmm) REVERT: B 297 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8212 (ptt180) REVERT: C 427 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7276 (mpt-90) REVERT: E 158 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7385 (mpm) REVERT: E 192 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8203 (mtp) REVERT: E 266 MET cc_start: 0.7050 (mpt) cc_final: 0.6758 (mpp) REVERT: E 404 PHE cc_start: 0.5641 (OUTLIER) cc_final: 0.5374 (t80) REVERT: F 203 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8222 (mpp) REVERT: F 249 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8240 (pp) REVERT: g 8 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.6629 (mpp80) REVERT: g 68 MET cc_start: 0.8708 (pmm) cc_final: 0.8488 (pmm) REVERT: g 129 TYR cc_start: 0.7270 (OUTLIER) cc_final: 0.6887 (p90) REVERT: g 229 MET cc_start: 0.8160 (mmt) cc_final: 0.7951 (mmm) outliers start: 125 outliers final: 55 residues processed: 305 average time/residue: 1.2868 time to fit residues: 456.4850 Evaluate side-chains 259 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 192 time to evaluate : 3.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 427 ARG Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 404 PHE Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 203 MET Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 329 ASP Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 450 MET Chi-restraints excluded: chain e residue 81 ASP Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain g residue 8 ARG Chi-restraints excluded: chain g residue 18 GLN Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 129 TYR Chi-restraints excluded: chain g residue 166 ASP Chi-restraints excluded: chain g residue 210 TYR Chi-restraints excluded: chain g residue 238 VAL Chi-restraints excluded: chain g residue 279 ILE Chi-restraints excluded: chain g residue 281 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 163 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 244 optimal weight: 6.9990 chunk 199 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 293 optimal weight: 9.9990 chunk 317 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 291 optimal weight: 9.9990 chunk 100 optimal weight: 0.6980 chunk 235 optimal weight: 0.7980 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 190 HIS F 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 25436 Z= 0.365 Angle : 0.587 9.948 34474 Z= 0.308 Chirality : 0.046 0.208 3979 Planarity : 0.004 0.047 4494 Dihedral : 7.865 128.975 3729 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 5.83 % Allowed : 24.92 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.08 (0.15), residues: 3266 helix: 1.29 (0.15), residues: 1313 sheet: 0.10 (0.23), residues: 495 loop : -1.11 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP g 206 HIS 0.004 0.001 HIS D 190 PHE 0.016 0.001 PHE g 175 TYR 0.013 0.001 TYR C 237 ARG 0.005 0.000 ARG F 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 199 time to evaluate : 2.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8298 (tt0) REVERT: A 476 PHE cc_start: 0.9017 (OUTLIER) cc_final: 0.7958 (t80) REVERT: B 110 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.8117 (m-30) REVERT: B 297 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8214 (ptt180) REVERT: C 435 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8630 (mtpt) REVERT: E 158 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7468 (mpm) REVERT: E 192 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8140 (mmm) REVERT: E 266 MET cc_start: 0.7069 (mpt) cc_final: 0.6780 (mpp) REVERT: E 404 PHE cc_start: 0.5709 (OUTLIER) cc_final: 0.5506 (t80) REVERT: F 39 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7689 (mt) REVERT: F 249 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8247 (pp) REVERT: g 8 ARG cc_start: 0.6995 (OUTLIER) cc_final: 0.6711 (mpt-90) outliers start: 153 outliers final: 80 residues processed: 327 average time/residue: 1.1927 time to fit residues: 456.9440 Evaluate side-chains 277 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 186 time to evaluate : 2.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 299 GLN Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 382 LEU Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 404 PHE Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 451 VAL Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 329 ASP Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain e residue 81 ASP Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain g residue 8 ARG Chi-restraints excluded: chain g residue 32 MET Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 129 TYR Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain g residue 142 ASP Chi-restraints excluded: chain g residue 166 ASP Chi-restraints excluded: chain g residue 210 TYR Chi-restraints excluded: chain g residue 253 THR Chi-restraints excluded: chain g residue 262 ASP Chi-restraints excluded: chain g residue 279 ILE Chi-restraints excluded: chain g residue 281 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 290 optimal weight: 7.9990 chunk 220 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 294 optimal weight: 9.9990 chunk 312 optimal weight: 10.0000 chunk 154 optimal weight: 1.9990 chunk 279 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 190 HIS E 196 ASN F 248 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 25436 Z= 0.374 Angle : 0.593 10.882 34474 Z= 0.311 Chirality : 0.046 0.224 3979 Planarity : 0.004 0.049 4494 Dihedral : 7.706 103.243 3724 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 6.21 % Allowed : 25.04 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -0.05 (0.14), residues: 3266 helix: 1.20 (0.15), residues: 1313 sheet: 0.03 (0.23), residues: 491 loop : -1.19 (0.15), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP g 206 HIS 0.005 0.001 HIS g 65 PHE 0.017 0.002 PHE g 175 TYR 0.025 0.002 TYR E 396 ARG 0.006 0.000 ARG F 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 204 time to evaluate : 3.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8285 (tt0) REVERT: A 123 ASP cc_start: 0.7449 (p0) cc_final: 0.7044 (p0) REVERT: A 476 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8011 (t80) REVERT: B 110 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8129 (m-30) REVERT: B 297 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8219 (ptt180) REVERT: B 463 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7814 (tptp) REVERT: C 427 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7223 (mpt-90) REVERT: C 435 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8631 (mtpt) REVERT: D 326 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9094 (mt) REVERT: E 180 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6678 (pm20) REVERT: E 192 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8186 (mmm) REVERT: E 404 PHE cc_start: 0.5702 (OUTLIER) cc_final: 0.5460 (t80) REVERT: F 39 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7720 (mt) REVERT: F 165 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8782 (tp) REVERT: F 249 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8229 (pp) REVERT: F 430 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8666 (ttp-110) REVERT: g 8 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.6687 (mpt-90) REVERT: g 68 MET cc_start: 0.8718 (pmm) cc_final: 0.8443 (pmm) REVERT: g 224 ARG cc_start: 0.8909 (mmt180) cc_final: 0.8662 (mmt180) outliers start: 163 outliers final: 85 residues processed: 341 average time/residue: 1.2461 time to fit residues: 495.6264 Evaluate side-chains 293 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 192 time to evaluate : 2.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 427 ARG Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 299 GLN Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 382 LEU Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 404 PHE Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 233 LYS Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 329 ASP Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 430 ARG Chi-restraints excluded: chain e residue 64 VAL Chi-restraints excluded: chain e residue 75 VAL Chi-restraints excluded: chain e residue 81 ASP Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain g residue 8 ARG Chi-restraints excluded: chain g residue 32 MET Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 129 TYR Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain g residue 166 ASP Chi-restraints excluded: chain g residue 210 TYR Chi-restraints excluded: chain g residue 219 ASN Chi-restraints excluded: chain g residue 262 ASP Chi-restraints excluded: chain g residue 279 ILE Chi-restraints excluded: chain g residue 281 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 260 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 232 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 266 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 159 optimal weight: 0.8980 chunk 280 optimal weight: 10.0000 chunk 78 optimal weight: 0.7980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 190 HIS F 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25436 Z= 0.219 Angle : 0.534 11.036 34474 Z= 0.276 Chirality : 0.044 0.218 3979 Planarity : 0.004 0.046 4494 Dihedral : 7.424 88.020 3723 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.80 % Allowed : 26.30 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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 (0.15), residues: 3266 helix: 1.39 (0.15), residues: 1314 sheet: 0.15 (0.23), residues: 515 loop : -1.10 (0.15), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP g 206 HIS 0.003 0.001 HIS D 190 PHE 0.016 0.001 PHE g 175 TYR 0.010 0.001 TYR A 237 ARG 0.005 0.000 ARG F 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 205 time to evaluate : 2.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7488 (p0) cc_final: 0.6986 (p0) REVERT: A 476 PHE cc_start: 0.8956 (OUTLIER) cc_final: 0.7994 (t80) REVERT: B 110 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.8070 (m-30) REVERT: B 297 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8201 (ptt180) REVERT: B 463 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7870 (tptp) REVERT: C 427 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7222 (mpt-90) REVERT: C 435 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8629 (mtpt) REVERT: E 25 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8634 (mtmm) REVERT: E 180 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6524 (pm20) REVERT: E 192 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8132 (mmm) REVERT: E 404 PHE cc_start: 0.5628 (OUTLIER) cc_final: 0.5368 (t80) REVERT: F 39 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7721 (mt) REVERT: F 165 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8709 (tp) REVERT: F 249 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8197 (pp) REVERT: F 430 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8685 (ttp-170) REVERT: g 8 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.6653 (mpt-90) REVERT: g 39 MET cc_start: 0.7589 (mmp) cc_final: 0.6796 (tpp) outliers start: 126 outliers final: 63 residues processed: 311 average time/residue: 1.2619 time to fit residues: 457.1103 Evaluate side-chains 270 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 192 time to evaluate : 3.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 427 ARG Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 299 GLN Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 382 LEU Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 404 PHE Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 451 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 233 LYS Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 329 ASP Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 430 ARG Chi-restraints excluded: chain e residue 75 VAL Chi-restraints excluded: chain e residue 81 ASP Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain g residue 8 ARG Chi-restraints excluded: chain g residue 32 MET Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 166 ASP Chi-restraints excluded: chain g residue 210 TYR Chi-restraints excluded: chain g residue 219 ASN Chi-restraints excluded: chain g residue 262 ASP Chi-restraints excluded: chain g residue 281 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 105 optimal weight: 0.0470 chunk 281 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 312 optimal weight: 0.8980 chunk 259 optimal weight: 9.9990 chunk 144 optimal weight: 0.0670 chunk 25 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 overall best weight: 1.0020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 190 HIS F 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.0816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25436 Z= 0.165 Angle : 0.518 10.436 34474 Z= 0.265 Chirality : 0.043 0.184 3979 Planarity : 0.003 0.042 4494 Dihedral : 7.080 87.274 3718 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.08 % Allowed : 27.02 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.15), residues: 3266 helix: 1.52 (0.15), residues: 1319 sheet: 0.29 (0.23), residues: 525 loop : -1.00 (0.15), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP g 206 HIS 0.003 0.000 HIS g 65 PHE 0.015 0.001 PHE g 175 TYR 0.031 0.001 TYR E 396 ARG 0.006 0.000 ARG F 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 210 time to evaluate : 3.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7596 (p0) cc_final: 0.7040 (p0) REVERT: A 476 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.7931 (t80) REVERT: B 53 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8150 (mmm) REVERT: B 110 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.8091 (m-30) REVERT: B 297 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8226 (ptt180) REVERT: B 463 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7812 (tptp) REVERT: C 427 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7206 (mpt-90) REVERT: E 180 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6475 (pm20) REVERT: E 192 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8294 (mmm) REVERT: E 266 MET cc_start: 0.7091 (mpt) cc_final: 0.6816 (mpp) REVERT: E 404 PHE cc_start: 0.5647 (OUTLIER) cc_final: 0.5396 (t80) REVERT: F 39 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7723 (mt) REVERT: F 165 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8689 (tp) REVERT: F 249 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8135 (pp) REVERT: F 430 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8719 (ttp-170) REVERT: g 8 ARG cc_start: 0.6980 (OUTLIER) cc_final: 0.6768 (mpt-90) REVERT: g 39 MET cc_start: 0.7578 (mmp) cc_final: 0.6798 (tpp) REVERT: g 129 TYR cc_start: 0.7285 (OUTLIER) cc_final: 0.6931 (p90) outliers start: 107 outliers final: 54 residues processed: 298 average time/residue: 1.3328 time to fit residues: 466.5034 Evaluate side-chains 265 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 196 time to evaluate : 2.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 427 ARG Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 299 GLN Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 404 PHE Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 329 ASP Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 430 ARG Chi-restraints excluded: chain F residue 450 MET Chi-restraints excluded: chain e residue 75 VAL Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain g residue 8 ARG Chi-restraints excluded: chain g residue 32 MET Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 129 TYR Chi-restraints excluded: chain g residue 166 ASP Chi-restraints excluded: chain g residue 210 TYR Chi-restraints excluded: chain g residue 219 ASN Chi-restraints excluded: chain g residue 281 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 301 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 178 optimal weight: 0.3980 chunk 228 optimal weight: 10.0000 chunk 176 optimal weight: 4.9990 chunk 263 optimal weight: 0.9990 chunk 174 optimal weight: 4.9990 chunk 311 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 190 HIS E 284 GLN F 248 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25436 Z= 0.234 Angle : 0.546 11.748 34474 Z= 0.280 Chirality : 0.044 0.183 3979 Planarity : 0.004 0.042 4494 Dihedral : 7.028 88.494 3713 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.12 % Allowed : 27.10 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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 (0.15), residues: 3266 helix: 1.49 (0.15), residues: 1320 sheet: 0.26 (0.23), residues: 519 loop : -1.01 (0.15), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP g 206 HIS 0.003 0.001 HIS D 190 PHE 0.015 0.001 PHE g 175 TYR 0.013 0.001 TYR g 63 ARG 0.006 0.000 ARG F 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 201 time to evaluate : 3.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7659 (p0) cc_final: 0.7042 (p0) REVERT: A 476 PHE cc_start: 0.8883 (OUTLIER) cc_final: 0.7940 (t80) REVERT: B 110 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.8077 (m-30) REVERT: B 297 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8218 (ptt180) REVERT: B 463 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7843 (tptp) REVERT: C 427 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7191 (mpt-90) REVERT: C 435 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8622 (mtpt) REVERT: E 25 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8610 (mtmm) REVERT: E 158 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7329 (mpm) REVERT: E 180 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6526 (pm20) REVERT: E 192 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8305 (mmm) REVERT: E 266 MET cc_start: 0.7050 (mpt) cc_final: 0.6767 (mpp) REVERT: E 404 PHE cc_start: 0.5630 (OUTLIER) cc_final: 0.5383 (t80) REVERT: F 39 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7712 (mt) REVERT: F 165 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8727 (tp) REVERT: F 249 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8140 (pp) REVERT: F 430 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8694 (ttp-110) REVERT: g 8 ARG cc_start: 0.6976 (OUTLIER) cc_final: 0.6651 (mpp80) REVERT: g 39 MET cc_start: 0.7630 (mmp) cc_final: 0.6847 (tpp) REVERT: g 129 TYR cc_start: 0.7313 (OUTLIER) cc_final: 0.6899 (p90) REVERT: g 224 ARG cc_start: 0.8916 (mmt180) cc_final: 0.8662 (mmt180) outliers start: 108 outliers final: 64 residues processed: 294 average time/residue: 1.3028 time to fit residues: 445.8830 Evaluate side-chains 283 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 202 time to evaluate : 3.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 427 ARG Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 299 GLN Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 382 LEU Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 404 PHE Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 233 LYS Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 329 ASP Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 430 ARG Chi-restraints excluded: chain F residue 450 MET Chi-restraints excluded: chain e residue 75 VAL Chi-restraints excluded: chain e residue 81 ASP Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain g residue 8 ARG Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 129 TYR Chi-restraints excluded: chain g residue 166 ASP Chi-restraints excluded: chain g residue 210 TYR Chi-restraints excluded: chain g residue 219 ASN Chi-restraints excluded: chain g residue 279 ILE Chi-restraints excluded: chain g residue 281 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 192 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 185 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 197 optimal weight: 0.8980 chunk 212 optimal weight: 4.9990 chunk 153 optimal weight: 0.3980 chunk 29 optimal weight: 8.9990 chunk 244 optimal weight: 5.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 190 HIS E 236 ASN F 248 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25436 Z= 0.231 Angle : 0.552 12.213 34474 Z= 0.282 Chirality : 0.044 0.194 3979 Planarity : 0.003 0.042 4494 Dihedral : 6.982 87.361 3711 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.04 % Allowed : 27.36 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.32 (0.15), residues: 3266 helix: 1.49 (0.15), residues: 1321 sheet: 0.27 (0.23), residues: 519 loop : -1.02 (0.15), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP g 206 HIS 0.003 0.001 HIS D 190 PHE 0.016 0.001 PHE g 175 TYR 0.031 0.001 TYR E 396 ARG 0.007 0.000 ARG e 51 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 207 time to evaluate : 3.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7658 (p0) cc_final: 0.6972 (p0) REVERT: A 476 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.7981 (t80) REVERT: B 110 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.8079 (m-30) REVERT: B 297 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8215 (ptt180) REVERT: B 463 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7855 (tptp) REVERT: C 427 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7180 (mpt-90) REVERT: E 25 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8603 (mtmm) REVERT: E 158 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7320 (mpm) REVERT: E 180 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6461 (pm20) REVERT: E 192 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8303 (mmm) REVERT: E 266 MET cc_start: 0.7066 (mpt) cc_final: 0.6795 (mpp) REVERT: E 404 PHE cc_start: 0.5623 (OUTLIER) cc_final: 0.5301 (t80) REVERT: F 39 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7711 (mt) REVERT: F 159 MET cc_start: 0.8462 (mmt) cc_final: 0.8256 (mmp) REVERT: F 165 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8732 (tp) REVERT: F 249 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8153 (pp) REVERT: F 310 ASP cc_start: 0.8832 (OUTLIER) cc_final: 0.8373 (t70) REVERT: F 430 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8695 (ttp-110) REVERT: g 8 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6692 (mpp80) REVERT: g 39 MET cc_start: 0.7627 (mmp) cc_final: 0.6897 (tpp) REVERT: g 129 TYR cc_start: 0.7366 (OUTLIER) cc_final: 0.6934 (p90) REVERT: g 229 MET cc_start: 0.8048 (mmm) cc_final: 0.7829 (mmm) outliers start: 106 outliers final: 71 residues processed: 297 average time/residue: 1.2626 time to fit residues: 439.7823 Evaluate side-chains 284 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 196 time to evaluate : 3.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 427 ARG Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 299 GLN Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 404 PHE Chi-restraints excluded: chain E residue 409 PHE Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 451 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 329 ASP Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 430 ARG Chi-restraints excluded: chain e residue 75 VAL Chi-restraints excluded: chain e residue 81 ASP Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain g residue 8 ARG Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 129 TYR Chi-restraints excluded: chain g residue 166 ASP Chi-restraints excluded: chain g residue 206 TRP Chi-restraints excluded: chain g residue 210 TYR Chi-restraints excluded: chain g residue 219 ASN Chi-restraints excluded: chain g residue 281 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 283 optimal weight: 4.9990 chunk 298 optimal weight: 5.9990 chunk 272 optimal weight: 3.9990 chunk 290 optimal weight: 6.9990 chunk 174 optimal weight: 0.0570 chunk 126 optimal weight: 0.9980 chunk 227 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 chunk 262 optimal weight: 0.0980 chunk 274 optimal weight: 9.9990 chunk 289 optimal weight: 2.9990 overall best weight: 1.0300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 190 HIS F 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25436 Z= 0.174 Angle : 0.531 12.495 34474 Z= 0.269 Chirality : 0.043 0.194 3979 Planarity : 0.003 0.043 4494 Dihedral : 6.742 89.775 3711 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.28 % Allowed : 28.16 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.45 (0.15), residues: 3266 helix: 1.56 (0.15), residues: 1323 sheet: 0.36 (0.23), residues: 521 loop : -0.94 (0.15), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP g 206 HIS 0.002 0.000 HIS D 190 PHE 0.014 0.001 PHE g 175 TYR 0.009 0.001 TYR C 456 ARG 0.012 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 199 time to evaluate : 2.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7686 (p0) cc_final: 0.6996 (p0) REVERT: A 476 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.7838 (t80) REVERT: B 110 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.8092 (m-30) REVERT: B 297 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8220 (ptt180) REVERT: B 463 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7907 (tptp) REVERT: C 427 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7274 (mpt-90) REVERT: E 180 GLU cc_start: 0.6658 (OUTLIER) cc_final: 0.6323 (pm20) REVERT: E 192 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8194 (mtp) REVERT: E 266 MET cc_start: 0.7042 (mpt) cc_final: 0.6778 (mpp) REVERT: F 39 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7684 (mt) REVERT: F 165 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8701 (tp) REVERT: F 249 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8090 (pp) REVERT: F 310 ASP cc_start: 0.8809 (OUTLIER) cc_final: 0.8298 (t0) REVERT: F 430 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8727 (ttp-110) REVERT: g 8 ARG cc_start: 0.6964 (OUTLIER) cc_final: 0.6693 (mpp80) REVERT: g 39 MET cc_start: 0.7657 (mmp) cc_final: 0.6932 (tpp) REVERT: g 129 TYR cc_start: 0.7258 (OUTLIER) cc_final: 0.6829 (p90) outliers start: 86 outliers final: 57 residues processed: 273 average time/residue: 1.2643 time to fit residues: 401.8936 Evaluate side-chains 264 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 193 time to evaluate : 2.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 427 ARG Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 299 GLN Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 409 PHE Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 329 ASP Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 430 ARG Chi-restraints excluded: chain F residue 450 MET Chi-restraints excluded: chain e residue 75 VAL Chi-restraints excluded: chain g residue 8 ARG Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 129 TYR Chi-restraints excluded: chain g residue 206 TRP Chi-restraints excluded: chain g residue 210 TYR Chi-restraints excluded: chain g residue 219 ASN Chi-restraints excluded: chain g residue 279 ILE Chi-restraints excluded: chain g residue 281 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 190 optimal weight: 4.9990 chunk 306 optimal weight: 4.9990 chunk 187 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 213 optimal weight: 10.0000 chunk 321 optimal weight: 1.9990 chunk 296 optimal weight: 4.9990 chunk 256 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 197 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 190 HIS F 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25436 Z= 0.243 Angle : 0.562 13.149 34474 Z= 0.286 Chirality : 0.044 0.197 3979 Planarity : 0.004 0.043 4494 Dihedral : 6.685 88.867 3706 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.16 % Allowed : 28.35 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.38 (0.15), residues: 3266 helix: 1.53 (0.15), residues: 1322 sheet: 0.32 (0.23), residues: 519 loop : -1.00 (0.15), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP g 206 HIS 0.011 0.001 HIS E 410 PHE 0.023 0.001 PHE E 409 TYR 0.031 0.001 TYR E 396 ARG 0.008 0.000 ARG A 90 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 196 time to evaluate : 2.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7690 (p0) cc_final: 0.7015 (p0) REVERT: A 476 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.7930 (t80) REVERT: B 110 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.8156 (m-30) REVERT: B 297 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8212 (ptt180) REVERT: B 463 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7902 (tptp) REVERT: C 427 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7211 (mpt-90) REVERT: E 180 GLU cc_start: 0.6634 (OUTLIER) cc_final: 0.6294 (pm20) REVERT: E 192 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8177 (mmm) REVERT: E 266 MET cc_start: 0.7051 (mpt) cc_final: 0.6781 (mpp) REVERT: E 404 PHE cc_start: 0.5666 (OUTLIER) cc_final: 0.5258 (t80) REVERT: F 39 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7707 (mt) REVERT: F 165 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8734 (tp) REVERT: F 249 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8125 (pp) REVERT: F 310 ASP cc_start: 0.8837 (OUTLIER) cc_final: 0.8324 (t0) REVERT: F 430 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8737 (ttp-110) REVERT: g 8 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.6513 (mpt-90) REVERT: g 39 MET cc_start: 0.7586 (mmp) cc_final: 0.6846 (tpp) REVERT: g 129 TYR cc_start: 0.7288 (OUTLIER) cc_final: 0.6874 (p90) outliers start: 83 outliers final: 59 residues processed: 268 average time/residue: 1.3719 time to fit residues: 427.0035 Evaluate side-chains 269 residues out of total 2627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 195 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 427 ARG Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 299 GLN Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 404 PHE Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 329 ASP Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 426 LYS Chi-restraints excluded: chain F residue 430 ARG Chi-restraints excluded: chain F residue 450 MET Chi-restraints excluded: chain e residue 64 VAL Chi-restraints excluded: chain e residue 75 VAL Chi-restraints excluded: chain e residue 108 GLN Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain g residue 8 ARG Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 129 TYR Chi-restraints excluded: chain g residue 206 TRP Chi-restraints excluded: chain g residue 210 TYR Chi-restraints excluded: chain g residue 219 ASN Chi-restraints excluded: chain g residue 279 ILE Chi-restraints excluded: chain g residue 281 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 203 optimal weight: 0.6980 chunk 272 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 236 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 256 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 263 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 190 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.113900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.079900 restraints weight = 48703.414| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.34 r_work: 0.2964 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 25436 Z= 0.178 Angle : 0.543 13.098 34474 Z= 0.275 Chirality : 0.043 0.190 3979 Planarity : 0.003 0.042 4494 Dihedral : 6.571 89.627 3706 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.01 % Allowed : 28.51 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.45 (0.15), residues: 3266 helix: 1.57 (0.15), residues: 1324 sheet: 0.37 (0.23), residues: 520 loop : -0.94 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP g 206 HIS 0.002 0.000 HIS D 190 PHE 0.015 0.001 PHE g 175 TYR 0.016 0.001 TYR g 267 ARG 0.008 0.000 ARG A 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8050.25 seconds wall clock time: 143 minutes 8.57 seconds (8588.57 seconds total)