Starting phenix.real_space_refine on Sat Apr 6 15:06:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9n_36111/04_2024/8j9n_36111.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9n_36111/04_2024/8j9n_36111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9n_36111/04_2024/8j9n_36111.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9n_36111/04_2024/8j9n_36111.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9n_36111/04_2024/8j9n_36111.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9n_36111/04_2024/8j9n_36111.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 5396 2.51 5 N 1461 2.21 5 O 1571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 15": "OE1" <-> "OE2" Residue "C ASP 32": "OD1" <-> "OD2" Residue "C GLU 230": "OE1" <-> "OE2" Residue "C GLU 314": "OE1" <-> "OE2" Residue "C TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 291": "OD1" <-> "OD2" Residue "N PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 132": "OD1" <-> "OD2" Residue "N TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8483 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2775 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 356, 2761 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 16, 'TRANS': 339} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 62 Conformer: "B" Number of residues, atoms: 356, 2761 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 16, 'TRANS': 339} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 62 bond proxies already assigned to first conformer: 2827 Chain: "C" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1884 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 2500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2500 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 64 Chain: "E" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 380 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "N" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 944 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 11 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATRP B 322 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP B 322 " occ=0.50 Time building chain proxies: 6.11, per 1000 atoms: 0.72 Number of scatterers: 8483 At special positions: 0 Unit cell: (76.32, 98.58, 150.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 1571 8.00 N 1461 7.00 C 5396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 276 " - pdb=" SG CYS B 296 " distance=2.03 Simple disulfide: pdb=" SG CYS B 300 " - pdb=" SG CYS B 381 " distance=2.03 Simple disulfide: pdb=" SG CYS B 402 " - pdb=" SG CYS B 477 " distance=2.03 Simple disulfide: pdb=" SG CYS N 45 " - pdb=" SG CYS N 119 " distance=2.04 Simple disulfide: pdb=" SG CYS N 122 " - pdb=" SG CYS N 130 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.24 Conformation dependent library (CDL) restraints added in 2.3 seconds 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2070 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 11 sheets defined 37.8% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'B' and resid 277 through 281 removed outlier: 3.603A pdb=" N LYS B 281 " --> pdb=" O ARG B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 344 removed outlier: 3.594A pdb=" N LEU B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE B 318 " --> pdb=" O GLU B 314 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THR B 321 " --> pdb=" O ARG B 317 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TRP B 326 " --> pdb=" O ATRP B 322 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP B 344 " --> pdb=" O THR B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 376 removed outlier: 4.368A pdb=" N ILE B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA B 364 " --> pdb=" O GLY B 360 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 365 " --> pdb=" O CYS B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 432 removed outlier: 3.838A pdb=" N ALA B 415 " --> pdb=" O PHE B 411 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B 417 " --> pdb=" O SER B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 466 removed outlier: 4.330A pdb=" N VAL B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 484 through 489 Processing helix chain 'B' and resid 491 through 524 Processing helix chain 'B' and resid 527 through 573 removed outlier: 3.540A pdb=" N TYR B 544 " --> pdb=" O PHE B 540 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL B 546 " --> pdb=" O VAL B 542 " (cutoff:3.500A) Proline residue: B 547 - end of helix removed outlier: 3.509A pdb=" N ILE B 550 " --> pdb=" O VAL B 546 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL B 551 " --> pdb=" O PRO B 547 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE B 552 " --> pdb=" O ALA B 548 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA B 553 " --> pdb=" O THR B 549 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASP B 563 " --> pdb=" O GLN B 559 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLN B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 609 removed outlier: 3.891A pdb=" N PHE B 603 " --> pdb=" O ASP B 599 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 605 " --> pdb=" O THR B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 616 removed outlier: 3.972A pdb=" N ILE B 615 " --> pdb=" O LEU B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 621 removed outlier: 3.931A pdb=" N TRP B 620 " --> pdb=" O SER B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 636 removed outlier: 3.631A pdb=" N LEU B 627 " --> pdb=" O SER B 623 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR B 635 " --> pdb=" O ARG B 631 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 636 " --> pdb=" O LYS B 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 36 removed outlier: 3.673A pdb=" N ALA C 36 " --> pdb=" O ASP C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 238 removed outlier: 3.552A pdb=" N CYS C 237 " --> pdb=" O TRP C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 265 No H-bonds generated for 'chain 'C' and resid 253 through 265' Processing helix chain 'C' and resid 266 through 279 Processing helix chain 'C' and resid 280 through 283 removed outlier: 3.828A pdb=" N ARG C 283 " --> pdb=" O ARG C 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 280 through 283' Processing helix chain 'C' and resid 293 through 303 removed outlier: 3.752A pdb=" N GLU C 299 " --> pdb=" O ASP C 295 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 312 removed outlier: 4.220A pdb=" N TYR C 311 " --> pdb=" O LYS C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 316 removed outlier: 3.987A pdb=" N ALA C 316 " --> pdb=" O PRO C 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 313 through 316' Processing helix chain 'C' and resid 331 through 353 removed outlier: 3.537A pdb=" N THR C 335 " --> pdb=" O ASP C 331 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA C 337 " --> pdb=" O ARG C 333 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE C 348 " --> pdb=" O GLU C 344 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER C 349 " --> pdb=" O PHE C 345 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C 353 " --> pdb=" O SER C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 391 removed outlier: 3.640A pdb=" N TYR C 391 " --> pdb=" O ASN C 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 26 Processing helix chain 'D' and resid 29 through 35 removed outlier: 3.883A pdb=" N ILE D 33 " --> pdb=" O THR D 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 47 removed outlier: 3.950A pdb=" N ALA E 47 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 68 Processing helix chain 'N' and resid 110 through 114 removed outlier: 3.829A pdb=" N THR N 114 " --> pdb=" O PRO N 111 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 468 through 470 Processing sheet with id=AA2, first strand: chain 'C' and resid 207 through 214 removed outlier: 3.585A pdb=" N LEU C 43 " --> pdb=" O HIS C 220 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N VAL C 224 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU C 44 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N VAL C 247 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE C 244 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N PHE C 290 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE C 246 " --> pdb=" O PHE C 290 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ASN C 292 " --> pdb=" O PHE C 246 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL C 248 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL C 287 " --> pdb=" O TYR C 360 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N HIS C 362 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU C 289 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 47 through 52 removed outlier: 7.108A pdb=" N ILE D 338 " --> pdb=" O ARG D 48 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N THR D 50 " --> pdb=" O LEU D 336 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LEU D 336 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 58 through 63 removed outlier: 4.051A pdb=" N ALA D 60 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 70 " --> pdb=" O TRP D 82 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS D 91 " --> pdb=" O ILE D 81 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 100 through 105 removed outlier: 7.010A pdb=" N GLY D 115 " --> pdb=" O MET D 101 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N CYS D 103 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA D 113 " --> pdb=" O CYS D 103 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N TYR D 105 " --> pdb=" O TYR D 111 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N TYR D 111 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY D 116 " --> pdb=" O ILE D 120 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ILE D 120 " --> pdb=" O GLY D 116 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N CYS D 121 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU D 138 " --> pdb=" O CYS D 121 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE D 123 " --> pdb=" O SER D 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 146 through 153 removed outlier: 6.783A pdb=" N SER D 160 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N CYS D 149 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL D 158 " --> pdb=" O CYS D 149 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N PHE D 151 " --> pdb=" O GLN D 156 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N GLN D 156 " --> pdb=" O PHE D 151 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N THR D 165 " --> pdb=" O SER D 161 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR D 178 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 187 through 192 removed outlier: 3.845A pdb=" N PHE D 199 " --> pdb=" O TRP D 211 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA D 203 " --> pdb=" O SER D 207 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N SER D 207 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ASP D 212 " --> pdb=" O CYS D 218 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N CYS D 218 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 229 through 233 removed outlier: 3.658A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 273 through 277 removed outlier: 6.686A pdb=" N GLY D 288 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL D 276 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU D 286 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N CYS D 294 " --> pdb=" O LEU D 308 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU D 308 " --> pdb=" O CYS D 294 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY D 306 " --> pdb=" O VAL D 296 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 26 through 29 removed outlier: 3.552A pdb=" N ASP N 96 " --> pdb=" O THR N 101 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 68 through 69 357 hydrogen bonds defined for protein. 1030 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 3.53 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: 2768 1.34 - 1.46: 2069 1.46 - 1.58: 3763 1.58 - 1.70: 0 1.70 - 1.82: 76 Bond restraints: 8676 Sorted by residual: bond pdb=" N PRO B 598 " pdb=" CD PRO B 598 " ideal model delta sigma weight residual 1.473 1.537 -0.064 1.40e-02 5.10e+03 2.08e+01 bond pdb=" C ALA B 493 " pdb=" N PRO B 494 " ideal model delta sigma weight residual 1.334 1.373 -0.039 2.34e-02 1.83e+03 2.77e+00 bond pdb=" N THR D 196 " pdb=" CA THR D 196 " ideal model delta sigma weight residual 1.457 1.478 -0.020 1.29e-02 6.01e+03 2.47e+00 bond pdb=" CB GLU B 301 " pdb=" CG GLU B 301 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.41e+00 bond pdb=" CB GLN D 17 " pdb=" CG GLN D 17 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.40e+00 ... (remaining 8671 not shown) Histogram of bond angle deviations from ideal: 98.67 - 107.04: 215 107.04 - 115.41: 5195 115.41 - 123.77: 6095 123.77 - 132.14: 266 132.14 - 140.51: 26 Bond angle restraints: 11797 Sorted by residual: angle pdb=" CA LEU B 608 " pdb=" CB LEU B 608 " pdb=" CG LEU B 608 " ideal model delta sigma weight residual 116.30 140.51 -24.21 3.50e+00 8.16e-02 4.78e+01 angle pdb=" CB MET B 609 " pdb=" CG MET B 609 " pdb=" SD MET B 609 " ideal model delta sigma weight residual 112.70 130.78 -18.08 3.00e+00 1.11e-01 3.63e+01 angle pdb=" N PRO B 598 " pdb=" CA PRO B 598 " pdb=" C PRO B 598 " ideal model delta sigma weight residual 111.77 102.54 9.23 1.67e+00 3.59e-01 3.06e+01 angle pdb=" CA LEU B 291 " pdb=" CB LEU B 291 " pdb=" CG LEU B 291 " ideal model delta sigma weight residual 116.30 130.42 -14.12 3.50e+00 8.16e-02 1.63e+01 angle pdb=" C LYS B 294 " pdb=" N ASP B 295 " pdb=" CA ASP B 295 " ideal model delta sigma weight residual 121.54 128.85 -7.31 1.91e+00 2.74e-01 1.47e+01 ... (remaining 11792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.61: 4581 16.61 - 33.22: 394 33.22 - 49.82: 99 49.82 - 66.43: 19 66.43 - 83.04: 7 Dihedral angle restraints: 5100 sinusoidal: 1889 harmonic: 3211 Sorted by residual: dihedral pdb=" CA LEU B 608 " pdb=" C LEU B 608 " pdb=" N MET B 609 " pdb=" CA MET B 609 " ideal model delta harmonic sigma weight residual 180.00 -144.88 -35.12 0 5.00e+00 4.00e-02 4.93e+01 dihedral pdb=" CB CYS B 402 " pdb=" SG CYS B 402 " pdb=" SG CYS B 477 " pdb=" CB CYS B 477 " ideal model delta sinusoidal sigma weight residual -86.00 -140.88 54.88 1 1.00e+01 1.00e-02 4.08e+01 dihedral pdb=" CB CYS B 276 " pdb=" SG CYS B 276 " pdb=" SG CYS B 296 " pdb=" CB CYS B 296 " ideal model delta sinusoidal sigma weight residual -86.00 -139.85 53.85 1 1.00e+01 1.00e-02 3.94e+01 ... (remaining 5097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 958 0.049 - 0.098: 286 0.098 - 0.147: 74 0.147 - 0.197: 9 0.197 - 0.246: 3 Chirality restraints: 1330 Sorted by residual: chirality pdb=" CB ILE D 43 " pdb=" CA ILE D 43 " pdb=" CG1 ILE D 43 " pdb=" CG2 ILE D 43 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CB ILE B 579 " pdb=" CA ILE B 579 " pdb=" CG1 ILE B 579 " pdb=" CG2 ILE B 579 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB ILE B 440 " pdb=" CA ILE B 440 " pdb=" CG1 ILE B 440 " pdb=" CG2 ILE B 440 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1327 not shown) Planarity restraints: 1509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 597 " -0.082 5.00e-02 4.00e+02 1.22e-01 2.39e+01 pdb=" N PRO B 598 " 0.211 5.00e-02 4.00e+02 pdb=" CA PRO B 598 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO B 598 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER B 597 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.33e+00 pdb=" C SER B 597 " -0.053 2.00e-02 2.50e+03 pdb=" O SER B 597 " 0.020 2.00e-02 2.50e+03 pdb=" N PRO B 598 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 331 " 0.044 5.00e-02 4.00e+02 6.72e-02 7.22e+00 pdb=" N PRO C 332 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 332 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 332 " 0.037 5.00e-02 4.00e+02 ... (remaining 1506 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1733 2.78 - 3.31: 7916 3.31 - 3.84: 13951 3.84 - 4.37: 15682 4.37 - 4.90: 27304 Nonbonded interactions: 66586 Sorted by model distance: nonbonded pdb=" OH TYR C 318 " pdb=" OD2 ASP C 343 " model vdw 2.245 2.440 nonbonded pdb=" OG SER B 327 " pdb=" O ALA B 366 " model vdw 2.252 2.440 nonbonded pdb=" OH TYR B 410 " pdb=" NZ LYS B 458 " model vdw 2.256 2.520 nonbonded pdb=" OG SER D 331 " pdb=" OD1 ASP D 333 " model vdw 2.273 2.440 nonbonded pdb=" O GLU B 441 " pdb=" OG SER B 444 " model vdw 2.290 2.440 ... (remaining 66581 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.350 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 28.150 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 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 : 0.004 0.064 8676 Z= 0.249 Angle : 0.869 24.207 11797 Z= 0.431 Chirality : 0.050 0.246 1330 Planarity : 0.006 0.122 1509 Dihedral : 13.711 83.038 3015 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.50 (0.25), residues: 1096 helix: 0.20 (0.26), residues: 387 sheet: -0.79 (0.35), residues: 226 loop : -2.10 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 63 HIS 0.005 0.001 HIS C 220 PHE 0.035 0.002 PHE B 600 TYR 0.035 0.002 TYR B 498 ARG 0.012 0.001 ARG D 251 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 441 GLU cc_start: 0.6560 (mm-30) cc_final: 0.6338 (mm-30) REVERT: B 500 PHE cc_start: 0.6938 (t80) cc_final: 0.6717 (t80) REVERT: B 558 GLU cc_start: 0.6386 (mm-30) cc_final: 0.6002 (mm-30) REVERT: C 274 LYS cc_start: 0.7902 (ttmt) cc_final: 0.7644 (ttpt) REVERT: C 295 ASP cc_start: 0.7412 (m-30) cc_final: 0.7000 (m-30) REVERT: C 300 LYS cc_start: 0.7912 (tttm) cc_final: 0.7569 (tttp) REVERT: C 382 THR cc_start: 0.8087 (m) cc_final: 0.7876 (m) REVERT: D 148 CYS cc_start: 0.7766 (t) cc_final: 0.7388 (t) REVERT: D 163 ASP cc_start: 0.6613 (p0) cc_final: 0.6225 (p0) REVERT: D 188 MET cc_start: 0.7132 (mmm) cc_final: 0.6564 (mmm) REVERT: D 204 CYS cc_start: 0.7468 (m) cc_final: 0.7172 (m) REVERT: D 280 LYS cc_start: 0.8090 (mtpp) cc_final: 0.7882 (mtpp) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.2603 time to fit residues: 81.0463 Evaluate side-chains 223 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 0.4980 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 HIS N 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8676 Z= 0.216 Angle : 0.632 18.642 11797 Z= 0.318 Chirality : 0.043 0.192 1330 Planarity : 0.005 0.069 1509 Dihedral : 4.607 24.480 1201 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.26 % Allowed : 10.55 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.09 (0.26), residues: 1096 helix: 0.99 (0.28), residues: 384 sheet: -1.03 (0.34), residues: 243 loop : -2.02 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 420 HIS 0.003 0.001 HIS D 183 PHE 0.032 0.002 PHE C 212 TYR 0.024 0.002 TYR B 498 ARG 0.003 0.000 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 234 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 500 PHE cc_start: 0.6993 (t80) cc_final: 0.6775 (t80) REVERT: B 558 GLU cc_start: 0.6479 (mm-30) cc_final: 0.6055 (mm-30) REVERT: C 212 PHE cc_start: 0.6913 (p90) cc_final: 0.6660 (p90) REVERT: C 221 MET cc_start: 0.7258 (ttm) cc_final: 0.7028 (ttm) REVERT: C 274 LYS cc_start: 0.7683 (ttmt) cc_final: 0.7432 (ttpt) REVERT: C 295 ASP cc_start: 0.7444 (m-30) cc_final: 0.7023 (m-30) REVERT: C 341 ILE cc_start: 0.7362 (mm) cc_final: 0.7148 (mt) REVERT: C 382 THR cc_start: 0.8153 (m) cc_final: 0.7935 (m) REVERT: D 111 TYR cc_start: 0.8192 (m-80) cc_final: 0.7863 (m-80) REVERT: D 121 CYS cc_start: 0.7589 (t) cc_final: 0.7186 (t) REVERT: D 148 CYS cc_start: 0.7888 (t) cc_final: 0.7509 (t) REVERT: D 188 MET cc_start: 0.7114 (mmm) cc_final: 0.6672 (mmm) REVERT: D 204 CYS cc_start: 0.7554 (m) cc_final: 0.7268 (m) REVERT: D 284 LEU cc_start: 0.7907 (tp) cc_final: 0.7696 (tt) outliers start: 11 outliers final: 6 residues processed: 237 average time/residue: 0.2768 time to fit residues: 85.0563 Evaluate side-chains 233 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 227 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain N residue 54 ASN Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 92 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 106 optimal weight: 0.9980 chunk 87 optimal weight: 0.0770 chunk 97 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8676 Z= 0.183 Angle : 0.592 19.089 11797 Z= 0.299 Chirality : 0.042 0.191 1330 Planarity : 0.004 0.057 1509 Dihedral : 4.407 23.024 1201 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.72 % Allowed : 15.14 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.26), residues: 1096 helix: 1.23 (0.28), residues: 388 sheet: -1.00 (0.34), residues: 238 loop : -1.92 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 420 HIS 0.003 0.001 HIS D 183 PHE 0.025 0.001 PHE C 212 TYR 0.023 0.001 TYR B 498 ARG 0.003 0.000 ARG D 251 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 227 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 407 MET cc_start: 0.6660 (mmt) cc_final: 0.6191 (mmt) REVERT: B 500 PHE cc_start: 0.6968 (t80) cc_final: 0.6766 (t80) REVERT: B 558 GLU cc_start: 0.6432 (mm-30) cc_final: 0.5995 (mm-30) REVERT: C 212 PHE cc_start: 0.6912 (p90) cc_final: 0.6616 (p90) REVERT: C 221 MET cc_start: 0.7287 (ttm) cc_final: 0.6905 (ttm) REVERT: C 274 LYS cc_start: 0.7660 (ttmt) cc_final: 0.7428 (ttpt) REVERT: C 295 ASP cc_start: 0.7405 (m-30) cc_final: 0.6980 (m-30) REVERT: C 382 THR cc_start: 0.8147 (m) cc_final: 0.7930 (m) REVERT: D 17 GLN cc_start: 0.8491 (tm-30) cc_final: 0.8237 (tm-30) REVERT: D 65 THR cc_start: 0.8419 (p) cc_final: 0.8163 (p) REVERT: D 121 CYS cc_start: 0.7631 (t) cc_final: 0.7225 (t) REVERT: D 148 CYS cc_start: 0.7876 (t) cc_final: 0.7483 (t) REVERT: D 188 MET cc_start: 0.7076 (mmm) cc_final: 0.6635 (mmm) REVERT: D 204 CYS cc_start: 0.7597 (m) cc_final: 0.7264 (m) REVERT: D 284 LEU cc_start: 0.7942 (tp) cc_final: 0.7569 (tp) outliers start: 15 outliers final: 11 residues processed: 228 average time/residue: 0.2611 time to fit residues: 76.9368 Evaluate side-chains 237 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 226 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain N residue 54 ASN Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 97 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.0030 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 237 ASN ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8676 Z= 0.255 Angle : 0.611 20.407 11797 Z= 0.311 Chirality : 0.043 0.186 1330 Planarity : 0.004 0.055 1509 Dihedral : 4.431 22.291 1201 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.21 % Allowed : 15.25 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.26), residues: 1096 helix: 1.32 (0.28), residues: 388 sheet: -0.93 (0.35), residues: 233 loop : -1.95 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 420 HIS 0.005 0.001 HIS D 183 PHE 0.026 0.002 PHE B 540 TYR 0.019 0.002 TYR B 498 ARG 0.003 0.000 ARG N 141 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 231 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 407 MET cc_start: 0.6547 (mmt) cc_final: 0.6036 (mmt) REVERT: B 558 GLU cc_start: 0.6544 (mm-30) cc_final: 0.6065 (mm-30) REVERT: C 15 GLU cc_start: 0.6783 (tp30) cc_final: 0.6464 (tp30) REVERT: C 30 ARG cc_start: 0.7802 (tpp80) cc_final: 0.7277 (tpp80) REVERT: C 212 PHE cc_start: 0.6935 (p90) cc_final: 0.6713 (p90) REVERT: C 274 LYS cc_start: 0.7689 (ttmt) cc_final: 0.7457 (ttpt) REVERT: C 295 ASP cc_start: 0.7405 (m-30) cc_final: 0.6980 (m-30) REVERT: C 382 THR cc_start: 0.8175 (m) cc_final: 0.7962 (m) REVERT: D 65 THR cc_start: 0.8507 (p) cc_final: 0.8272 (p) REVERT: D 121 CYS cc_start: 0.7607 (t) cc_final: 0.7271 (t) REVERT: D 148 CYS cc_start: 0.7886 (t) cc_final: 0.7490 (t) REVERT: D 186 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.6757 (p0) REVERT: D 188 MET cc_start: 0.7089 (mmm) cc_final: 0.6662 (mmm) REVERT: D 204 CYS cc_start: 0.7682 (m) cc_final: 0.7072 (m) REVERT: D 284 LEU cc_start: 0.7942 (tp) cc_final: 0.7539 (tp) REVERT: N 106 MET cc_start: 0.6497 (mmm) cc_final: 0.6125 (tpp) outliers start: 28 outliers final: 21 residues processed: 241 average time/residue: 0.2517 time to fit residues: 78.6657 Evaluate side-chains 253 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 231 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 259 GLN Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain N residue 54 ASN Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 97 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.5980 chunk 59 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 237 ASN ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8676 Z= 0.237 Angle : 0.606 19.826 11797 Z= 0.306 Chirality : 0.043 0.183 1330 Planarity : 0.004 0.054 1509 Dihedral : 4.408 21.253 1201 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.10 % Allowed : 16.06 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.26), residues: 1096 helix: 1.36 (0.28), residues: 386 sheet: -0.93 (0.35), residues: 236 loop : -1.88 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 420 HIS 0.005 0.001 HIS D 183 PHE 0.039 0.002 PHE B 540 TYR 0.021 0.002 TYR B 498 ARG 0.003 0.000 ARG N 141 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 234 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 407 MET cc_start: 0.6479 (mmt) cc_final: 0.6005 (mmt) REVERT: B 496 PHE cc_start: 0.7500 (t80) cc_final: 0.7229 (t80) REVERT: B 540 PHE cc_start: 0.7572 (t80) cc_final: 0.7320 (t80) REVERT: B 558 GLU cc_start: 0.6503 (mm-30) cc_final: 0.6042 (mm-30) REVERT: C 15 GLU cc_start: 0.6826 (tp30) cc_final: 0.6528 (tp30) REVERT: C 30 ARG cc_start: 0.7750 (tpp80) cc_final: 0.7263 (tpp80) REVERT: C 221 MET cc_start: 0.7330 (ttm) cc_final: 0.7093 (ttm) REVERT: C 274 LYS cc_start: 0.7696 (ttmt) cc_final: 0.7445 (ttpt) REVERT: C 382 THR cc_start: 0.8166 (m) cc_final: 0.7922 (m) REVERT: C 385 GLN cc_start: 0.8119 (tp40) cc_final: 0.7804 (mm-40) REVERT: D 65 THR cc_start: 0.8536 (p) cc_final: 0.8268 (p) REVERT: D 121 CYS cc_start: 0.7577 (t) cc_final: 0.7263 (t) REVERT: D 137 ARG cc_start: 0.7009 (tpp-160) cc_final: 0.6674 (tpp-160) REVERT: D 148 CYS cc_start: 0.7925 (t) cc_final: 0.7513 (t) REVERT: D 186 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.6820 (p0) REVERT: D 188 MET cc_start: 0.7034 (mmm) cc_final: 0.6653 (mmm) REVERT: D 204 CYS cc_start: 0.7593 (m) cc_final: 0.7002 (m) REVERT: D 234 PHE cc_start: 0.7842 (OUTLIER) cc_final: 0.7032 (t80) REVERT: D 284 LEU cc_start: 0.7933 (tp) cc_final: 0.7525 (tp) REVERT: N 106 MET cc_start: 0.6471 (mmm) cc_final: 0.6185 (tpp) outliers start: 27 outliers final: 19 residues processed: 243 average time/residue: 0.2595 time to fit residues: 82.5975 Evaluate side-chains 251 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 230 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 259 GLN Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain N residue 54 ASN Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 97 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 8 optimal weight: 0.0170 chunk 34 optimal weight: 5.9990 chunk 54 optimal weight: 0.0030 overall best weight: 0.5028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 237 ASN ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8676 Z= 0.195 Angle : 0.604 20.066 11797 Z= 0.303 Chirality : 0.042 0.168 1330 Planarity : 0.004 0.054 1509 Dihedral : 4.346 20.851 1201 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.33 % Allowed : 16.86 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.26), residues: 1096 helix: 1.45 (0.28), residues: 386 sheet: -0.89 (0.35), residues: 236 loop : -1.88 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP B 420 HIS 0.003 0.001 HIS D 183 PHE 0.036 0.001 PHE B 540 TYR 0.022 0.001 TYR B 498 ARG 0.002 0.000 ARG N 121 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 232 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 407 MET cc_start: 0.6529 (mmt) cc_final: 0.6084 (mmt) REVERT: B 496 PHE cc_start: 0.7493 (t80) cc_final: 0.7229 (t80) REVERT: B 540 PHE cc_start: 0.7546 (t80) cc_final: 0.7318 (t80) REVERT: C 221 MET cc_start: 0.7309 (ttm) cc_final: 0.7036 (ttp) REVERT: C 274 LYS cc_start: 0.7680 (ttmt) cc_final: 0.7437 (ttpt) REVERT: C 295 ASP cc_start: 0.7545 (m-30) cc_final: 0.7143 (m-30) REVERT: C 382 THR cc_start: 0.8154 (m) cc_final: 0.7936 (m) REVERT: D 65 THR cc_start: 0.8541 (p) cc_final: 0.8278 (p) REVERT: D 121 CYS cc_start: 0.7536 (t) cc_final: 0.7259 (t) REVERT: D 137 ARG cc_start: 0.7003 (tpp-160) cc_final: 0.6648 (tpp-160) REVERT: D 148 CYS cc_start: 0.7928 (t) cc_final: 0.7485 (t) REVERT: D 186 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.6785 (p0) REVERT: D 188 MET cc_start: 0.6983 (mmm) cc_final: 0.6591 (mmm) REVERT: D 204 CYS cc_start: 0.7469 (m) cc_final: 0.6870 (m) REVERT: D 234 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.6944 (t80) REVERT: D 301 LYS cc_start: 0.8195 (mtpt) cc_final: 0.7573 (mtmm) REVERT: N 106 MET cc_start: 0.6591 (mmm) cc_final: 0.6368 (tpp) REVERT: N 131 PHE cc_start: 0.4693 (m-80) cc_final: 0.4447 (m-80) outliers start: 29 outliers final: 22 residues processed: 240 average time/residue: 0.2633 time to fit residues: 81.3316 Evaluate side-chains 253 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 229 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 259 GLN Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain N residue 54 ASN Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 97 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 76 optimal weight: 0.4980 chunk 87 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8676 Z= 0.301 Angle : 0.655 19.984 11797 Z= 0.333 Chirality : 0.044 0.166 1330 Planarity : 0.005 0.052 1509 Dihedral : 4.544 21.135 1201 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.44 % Allowed : 17.66 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.74 (0.26), residues: 1096 helix: 1.39 (0.28), residues: 386 sheet: -0.79 (0.37), residues: 216 loop : -1.94 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 427 HIS 0.004 0.001 HIS D 183 PHE 0.023 0.002 PHE B 540 TYR 0.022 0.002 TYR D 59 ARG 0.004 0.000 ARG E 51 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 233 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 407 MET cc_start: 0.6539 (mmt) cc_final: 0.6114 (mmt) REVERT: B 496 PHE cc_start: 0.7489 (t80) cc_final: 0.7252 (t80) REVERT: C 29 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7350 (tt) REVERT: C 30 ARG cc_start: 0.7682 (tpp80) cc_final: 0.7240 (tpp80) REVERT: C 221 MET cc_start: 0.7325 (ttm) cc_final: 0.7080 (ttp) REVERT: C 274 LYS cc_start: 0.7705 (ttmt) cc_final: 0.7465 (ttpt) REVERT: C 295 ASP cc_start: 0.7570 (m-30) cc_final: 0.6844 (m-30) REVERT: C 382 THR cc_start: 0.8171 (m) cc_final: 0.7948 (m) REVERT: D 65 THR cc_start: 0.8586 (p) cc_final: 0.8348 (p) REVERT: D 121 CYS cc_start: 0.7467 (t) cc_final: 0.7248 (t) REVERT: D 137 ARG cc_start: 0.7044 (tpp-160) cc_final: 0.6751 (tpp-160) REVERT: D 148 CYS cc_start: 0.7944 (t) cc_final: 0.7534 (t) REVERT: D 186 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.6793 (p0) REVERT: D 188 MET cc_start: 0.7027 (mmm) cc_final: 0.6697 (mmm) REVERT: D 204 CYS cc_start: 0.7580 (m) cc_final: 0.6934 (m) REVERT: D 228 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7499 (p0) REVERT: D 234 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.6769 (t80) REVERT: D 301 LYS cc_start: 0.8231 (mtpt) cc_final: 0.7665 (mtmm) REVERT: N 133 VAL cc_start: 0.8165 (t) cc_final: 0.7885 (p) outliers start: 30 outliers final: 24 residues processed: 243 average time/residue: 0.2478 time to fit residues: 78.8450 Evaluate side-chains 256 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 228 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 385 GLN Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 259 GLN Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain N residue 54 ASN Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 97 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 0.0870 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 51 optimal weight: 0.0370 chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8676 Z= 0.202 Angle : 0.636 19.945 11797 Z= 0.316 Chirality : 0.042 0.160 1330 Planarity : 0.004 0.054 1509 Dihedral : 4.439 21.281 1201 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.44 % Allowed : 18.81 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.26), residues: 1096 helix: 1.42 (0.28), residues: 385 sheet: -0.71 (0.37), residues: 220 loop : -1.88 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 420 HIS 0.003 0.001 HIS D 183 PHE 0.039 0.002 PHE B 540 TYR 0.025 0.001 TYR B 498 ARG 0.006 0.000 ARG E 51 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 233 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 407 MET cc_start: 0.6482 (mmt) cc_final: 0.6069 (mmt) REVERT: B 496 PHE cc_start: 0.7546 (t80) cc_final: 0.7296 (t80) REVERT: B 540 PHE cc_start: 0.7546 (t80) cc_final: 0.7305 (t80) REVERT: C 221 MET cc_start: 0.7287 (ttm) cc_final: 0.7034 (ttp) REVERT: C 274 LYS cc_start: 0.7672 (ttmt) cc_final: 0.7425 (ttpt) REVERT: C 295 ASP cc_start: 0.7465 (m-30) cc_final: 0.6807 (m-30) REVERT: D 65 THR cc_start: 0.8588 (p) cc_final: 0.8319 (p) REVERT: D 121 CYS cc_start: 0.7498 (t) cc_final: 0.7245 (t) REVERT: D 148 CYS cc_start: 0.7937 (t) cc_final: 0.7444 (t) REVERT: D 186 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.6801 (p0) REVERT: D 188 MET cc_start: 0.6945 (mmm) cc_final: 0.6595 (mmm) REVERT: D 204 CYS cc_start: 0.7405 (m) cc_final: 0.6670 (m) REVERT: D 234 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.6841 (t80) REVERT: D 301 LYS cc_start: 0.8217 (mtpt) cc_final: 0.7669 (mtmm) outliers start: 30 outliers final: 26 residues processed: 240 average time/residue: 0.2552 time to fit residues: 79.4964 Evaluate side-chains 258 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 230 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 385 GLN Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 259 GLN Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain N residue 54 ASN Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 97 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 3.9990 chunk 97 optimal weight: 0.1980 chunk 99 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 87 optimal weight: 0.2980 chunk 91 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 HIS ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN D 88 ASN D 237 ASN ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8676 Z= 0.211 Angle : 0.639 20.328 11797 Z= 0.319 Chirality : 0.042 0.159 1330 Planarity : 0.004 0.054 1509 Dihedral : 4.394 23.405 1201 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.67 % Allowed : 19.38 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.63 (0.26), residues: 1096 helix: 1.47 (0.28), residues: 385 sheet: -0.70 (0.36), residues: 228 loop : -1.90 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 620 HIS 0.003 0.001 HIS D 183 PHE 0.030 0.002 PHE B 540 TYR 0.025 0.001 TYR B 498 ARG 0.006 0.000 ARG E 51 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 229 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 407 MET cc_start: 0.6470 (mmt) cc_final: 0.6069 (mmt) REVERT: C 221 MET cc_start: 0.7278 (ttm) cc_final: 0.7027 (ttp) REVERT: C 274 LYS cc_start: 0.7675 (ttmt) cc_final: 0.7434 (ttpt) REVERT: C 295 ASP cc_start: 0.7492 (m-30) cc_final: 0.6784 (m-30) REVERT: D 65 THR cc_start: 0.8583 (p) cc_final: 0.8327 (p) REVERT: D 121 CYS cc_start: 0.7517 (t) cc_final: 0.7272 (t) REVERT: D 148 CYS cc_start: 0.7849 (t) cc_final: 0.7468 (t) REVERT: D 186 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.6877 (p0) REVERT: D 188 MET cc_start: 0.6923 (mmm) cc_final: 0.6590 (mmm) REVERT: D 204 CYS cc_start: 0.7513 (m) cc_final: 0.6898 (m) REVERT: D 228 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7450 (p0) REVERT: D 234 PHE cc_start: 0.7770 (OUTLIER) cc_final: 0.6783 (t80) outliers start: 32 outliers final: 25 residues processed: 238 average time/residue: 0.2501 time to fit residues: 77.5493 Evaluate side-chains 257 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 229 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 385 GLN Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 259 GLN Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain N residue 54 ASN Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 97 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 0.0570 chunk 71 optimal weight: 0.2980 chunk 107 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 HIS ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN D 237 ASN ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8676 Z= 0.201 Angle : 0.665 21.149 11797 Z= 0.325 Chirality : 0.042 0.156 1330 Planarity : 0.004 0.054 1509 Dihedral : 4.364 25.192 1201 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.56 % Allowed : 19.61 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.26), residues: 1096 helix: 1.54 (0.28), residues: 385 sheet: -0.72 (0.36), residues: 233 loop : -1.86 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP B 420 HIS 0.003 0.001 HIS D 183 PHE 0.027 0.001 PHE B 556 TYR 0.026 0.001 TYR B 498 ARG 0.006 0.000 ARG E 51 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 237 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 407 MET cc_start: 0.6492 (mmt) cc_final: 0.6120 (mmt) REVERT: B 496 PHE cc_start: 0.7543 (t80) cc_final: 0.7308 (t80) REVERT: B 608 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.7085 (mt) REVERT: C 221 MET cc_start: 0.7269 (ttm) cc_final: 0.7019 (ttp) REVERT: C 274 LYS cc_start: 0.7664 (ttmt) cc_final: 0.7419 (ttpt) REVERT: C 295 ASP cc_start: 0.7493 (m-30) cc_final: 0.6790 (m-30) REVERT: C 300 LYS cc_start: 0.7736 (tttm) cc_final: 0.7357 (tttp) REVERT: D 61 MET cc_start: 0.7387 (ppp) cc_final: 0.6964 (ppp) REVERT: D 65 THR cc_start: 0.8579 (p) cc_final: 0.8319 (p) REVERT: D 121 CYS cc_start: 0.7511 (t) cc_final: 0.7272 (t) REVERT: D 148 CYS cc_start: 0.7863 (t) cc_final: 0.7426 (t) REVERT: D 186 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.6876 (p0) REVERT: D 188 MET cc_start: 0.6874 (mmm) cc_final: 0.6565 (mmm) REVERT: D 204 CYS cc_start: 0.7406 (m) cc_final: 0.6663 (m) REVERT: D 228 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7196 (p0) REVERT: D 234 PHE cc_start: 0.7764 (OUTLIER) cc_final: 0.6768 (t80) REVERT: D 301 LYS cc_start: 0.8259 (mtpt) cc_final: 0.7639 (mtmm) outliers start: 31 outliers final: 24 residues processed: 244 average time/residue: 0.2494 time to fit residues: 79.1562 Evaluate side-chains 262 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 234 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 385 GLN Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 259 GLN Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain N residue 54 ASN Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 97 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 10.0000 chunk 26 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 HIS ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.144509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.123509 restraints weight = 13063.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.127478 restraints weight = 6556.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.130088 restraints weight = 4016.273| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3669 r_free = 0.3669 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3669 r_free = 0.3669 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8676 Z= 0.251 Angle : 0.680 21.611 11797 Z= 0.335 Chirality : 0.043 0.157 1330 Planarity : 0.004 0.052 1509 Dihedral : 4.440 27.418 1201 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.67 % Allowed : 19.72 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.26), residues: 1096 helix: 1.56 (0.28), residues: 385 sheet: -0.78 (0.37), residues: 225 loop : -1.86 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 620 HIS 0.004 0.001 HIS D 183 PHE 0.027 0.002 PHE B 556 TYR 0.029 0.002 TYR B 498 ARG 0.005 0.000 ARG E 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2330.20 seconds wall clock time: 43 minutes 9.29 seconds (2589.29 seconds total)