Starting phenix.real_space_refine on Mon Mar 11 06:16:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cmi_30407/03_2024/7cmi_30407_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cmi_30407/03_2024/7cmi_30407.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cmi_30407/03_2024/7cmi_30407.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cmi_30407/03_2024/7cmi_30407.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cmi_30407/03_2024/7cmi_30407_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cmi_30407/03_2024/7cmi_30407_updated.pdb" } resolution = 2.9 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= 0.003 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 27 5.16 5 C 4814 2.51 5 N 1176 2.21 5 O 1334 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 181": "NH1" <-> "NH2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A ASP 325": "OD1" <-> "OD2" Residue "A PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "A GLU 562": "OE1" <-> "OE2" Residue "A GLU 613": "OE1" <-> "OE2" Residue "A GLU 618": "OE1" <-> "OE2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B ARG 122": "NH1" <-> "NH2" Residue "B ARG 162": "NH1" <-> "NH2" Residue "B ASP 260": "OD1" <-> "OD2" Residue "B GLU 308": "OE1" <-> "OE2" Residue "B ARG 361": "NH1" <-> "NH2" Residue "B GLU 481": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7353 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3650 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 22, 'TRANS': 446} Chain: "B" Number of atoms: 3480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3480 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 25, 'TRANS': 432} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 60 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 111 Unusual residues: {'3PH': 2} Classifications: {'peptide': 1, 'undetermined': 2, 'water': 6} Modifications used: {'COO': 1} Link IDs: {None: 8} Time building chain proxies: 4.73, per 1000 atoms: 0.64 Number of scatterers: 7353 At special positions: 0 Unit cell: (82.612, 86.96, 125.005, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 2 15.00 O 1334 8.00 N 1176 7.00 C 4814 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS B 154 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN A 507 " " NAG D 1 " - " ASN A 366 " " NAG E 1 " - " ASN A 382 " " NAG F 1 " - " ASN A 425 " Time building additional restraints: 2.83 Conformation dependent library (CDL) restraints added in 1.3 seconds 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1700 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 5 sheets defined 48.7% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 168 through 174 removed outlier: 4.142A pdb=" N LYS A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 168 through 174' Processing helix chain 'A' and resid 179 through 182 No H-bonds generated for 'chain 'A' and resid 179 through 182' Processing helix chain 'A' and resid 184 through 207 removed outlier: 3.549A pdb=" N LEU A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.521A pdb=" N GLN A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 231 through 235' Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 244 through 254 removed outlier: 3.693A pdb=" N LEU A 249 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASP A 250 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 252 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER A 253 " --> pdb=" O ASP A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 300 removed outlier: 3.793A pdb=" N SER A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 300 " --> pdb=" O GLN A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 341 removed outlier: 3.564A pdb=" N ALA A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 371 removed outlier: 4.269A pdb=" N ALA A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 413 through 426 removed outlier: 3.822A pdb=" N TYR A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 458 removed outlier: 3.506A pdb=" N MET A 457 " --> pdb=" O LEU A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 515 removed outlier: 4.205A pdb=" N GLU A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 removed outlier: 4.514A pdb=" N GLN A 530 " --> pdb=" O ARG A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 538 No H-bonds generated for 'chain 'A' and resid 535 through 538' Processing helix chain 'B' and resid 42 through 53 removed outlier: 3.858A pdb=" N GLY B 47 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE B 48 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 69 removed outlier: 3.597A pdb=" N VAL B 65 " --> pdb=" O PRO B 62 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU B 66 " --> pdb=" O LYS B 63 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU B 67 " --> pdb=" O GLY B 64 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASN B 68 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 99 removed outlier: 3.565A pdb=" N ILE B 77 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE B 80 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY B 83 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR B 93 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 96 " --> pdb=" O CYS B 92 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 112 removed outlier: 3.679A pdb=" N VAL B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS B 111 " --> pdb=" O TYR B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 130 through 146 removed outlier: 3.671A pdb=" N ILE B 138 " --> pdb=" O ASN B 134 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 177 removed outlier: 3.636A pdb=" N ARG B 162 " --> pdb=" O GLU B 158 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 163 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 167 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TRP B 174 " --> pdb=" O LEU B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 removed outlier: 3.659A pdb=" N THR B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 209 removed outlier: 3.545A pdb=" N GLY B 193 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS B 194 " --> pdb=" O PHE B 190 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL B 207 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN B 208 " --> pdb=" O MET B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 241 removed outlier: 3.675A pdb=" N LEU B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN B 240 " --> pdb=" O LEU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 266 through 288 removed outlier: 3.765A pdb=" N PHE B 270 " --> pdb=" O PRO B 266 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE B 271 " --> pdb=" O ARG B 267 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE B 273 " --> pdb=" O ILE B 269 " (cutoff:3.500A) Proline residue: B 274 - end of helix removed outlier: 3.562A pdb=" N TYR B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL B 288 " --> pdb=" O ASN B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 296 No H-bonds generated for 'chain 'B' and resid 293 through 296' Processing helix chain 'B' and resid 302 through 308 Processing helix chain 'B' and resid 314 through 335 removed outlier: 3.656A pdb=" N MET B 318 " --> pdb=" O MET B 314 " (cutoff:3.500A) Proline residue: B 319 - end of helix removed outlier: 3.535A pdb=" N GLY B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 345 Processing helix chain 'B' and resid 365 through 377 removed outlier: 3.533A pdb=" N PHE B 370 " --> pdb=" O PRO B 366 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR B 371 " --> pdb=" O ALA B 367 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER B 374 " --> pdb=" O PHE B 370 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 411 removed outlier: 3.953A pdb=" N ILE B 394 " --> pdb=" O TYR B 390 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR B 396 " --> pdb=" O GLY B 392 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE B 398 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR B 402 " --> pdb=" O PHE B 398 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 403 " --> pdb=" O TYR B 399 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG B 410 " --> pdb=" O GLN B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 444 removed outlier: 3.798A pdb=" N ILE B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR B 430 " --> pdb=" O PHE B 426 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE B 440 " --> pdb=" O PHE B 436 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 466 removed outlier: 3.692A pdb=" N ILE B 451 " --> pdb=" O VAL B 447 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY B 452 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU B 453 " --> pdb=" O CYS B 449 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B 455 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET B 456 " --> pdb=" O GLY B 452 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL B 460 " --> pdb=" O MET B 456 " (cutoff:3.500A) Proline residue: B 461 - end of helix removed outlier: 3.729A pdb=" N PHE B 464 " --> pdb=" O VAL B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 490 removed outlier: 3.524A pdb=" N ASP B 478 " --> pdb=" O LYS B 474 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N PHE B 479 " --> pdb=" O CYS B 475 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE B 480 " --> pdb=" O PHE B 476 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU B 481 " --> pdb=" O SER B 477 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 225 through 227 Processing sheet with id= B, first strand: chain 'A' and resid 259 through 262 removed outlier: 7.232A pdb=" N ARG A 304 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LEU A 262 " --> pdb=" O ARG A 304 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE A 306 " --> pdb=" O LEU A 262 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 345 through 348 removed outlier: 6.263A pdb=" N LEU A 376 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N VAL A 348 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE A 378 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU A 400 " --> pdb=" O ALA A 379 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 541 through 545 removed outlier: 4.624A pdb=" N SER A 553 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ARG A 626 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LEU A 596 " --> pdb=" O ARG A 626 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 356 through 358 234 hydrogen bonds defined for protein. 675 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: 1.85 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1834 1.33 - 1.45: 1445 1.45 - 1.57: 4199 1.57 - 1.69: 2 1.69 - 1.81: 41 Bond restraints: 7521 Sorted by residual: bond pdb=" C31 3PH B 602 " pdb=" O31 3PH B 602 " ideal model delta sigma weight residual 1.325 1.454 -0.129 2.00e-02 2.50e+03 4.14e+01 bond pdb=" C31 3PH B 603 " pdb=" O31 3PH B 603 " ideal model delta sigma weight residual 1.325 1.449 -0.124 2.00e-02 2.50e+03 3.83e+01 bond pdb=" C21 3PH B 603 " pdb=" O21 3PH B 603 " ideal model delta sigma weight residual 1.328 1.451 -0.123 2.00e-02 2.50e+03 3.77e+01 bond pdb=" C21 3PH B 602 " pdb=" O21 3PH B 602 " ideal model delta sigma weight residual 1.328 1.449 -0.121 2.00e-02 2.50e+03 3.67e+01 bond pdb=" O11 3PH B 603 " pdb=" P 3PH B 603 " ideal model delta sigma weight residual 1.703 1.607 0.096 2.00e-02 2.50e+03 2.31e+01 ... (remaining 7516 not shown) Histogram of bond angle deviations from ideal: 98.65 - 106.57: 233 106.57 - 114.50: 4450 114.50 - 122.42: 4551 122.42 - 130.34: 947 130.34 - 138.26: 44 Bond angle restraints: 10225 Sorted by residual: angle pdb=" C LEU B 265 " pdb=" N PRO B 266 " pdb=" CA PRO B 266 " ideal model delta sigma weight residual 119.64 114.12 5.52 1.01e+00 9.80e-01 2.98e+01 angle pdb=" N TYR B 385 " pdb=" CA TYR B 385 " pdb=" C TYR B 385 " ideal model delta sigma weight residual 113.50 107.10 6.40 1.23e+00 6.61e-01 2.70e+01 angle pdb=" N GLY B 115 " pdb=" CA GLY B 115 " pdb=" C GLY B 115 " ideal model delta sigma weight residual 112.49 118.69 -6.20 1.21e+00 6.83e-01 2.63e+01 angle pdb=" N THR B 386 " pdb=" CA THR B 386 " pdb=" C THR B 386 " ideal model delta sigma weight residual 112.23 105.86 6.37 1.26e+00 6.30e-01 2.55e+01 angle pdb=" N SER B 179 " pdb=" CA SER B 179 " pdb=" C SER B 179 " ideal model delta sigma weight residual 111.02 117.09 -6.07 1.25e+00 6.40e-01 2.36e+01 ... (remaining 10220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.27: 4152 22.27 - 44.54: 313 44.54 - 66.80: 54 66.80 - 89.07: 9 89.07 - 111.34: 8 Dihedral angle restraints: 4536 sinusoidal: 1884 harmonic: 2652 Sorted by residual: dihedral pdb=" CA SER B 178 " pdb=" C SER B 178 " pdb=" N SER B 179 " pdb=" CA SER B 179 " ideal model delta harmonic sigma weight residual 180.00 151.28 28.72 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA SER A 176 " pdb=" C SER A 176 " pdb=" N PRO A 177 " pdb=" CA PRO A 177 " ideal model delta harmonic sigma weight residual 180.00 154.21 25.79 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA PHE B 114 " pdb=" C PHE B 114 " pdb=" N GLY B 115 " pdb=" CA GLY B 115 " ideal model delta harmonic sigma weight residual -180.00 -156.10 -23.90 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 4533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 1178 0.134 - 0.269: 20 0.269 - 0.403: 2 0.403 - 0.538: 0 0.538 - 0.672: 1 Chirality restraints: 1201 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 366 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" CB VAL B 493 " pdb=" CA VAL B 493 " pdb=" CG1 VAL B 493 " pdb=" CG2 VAL B 493 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 425 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 1198 not shown) Planarity restraints: 1262 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 228 " -0.056 5.00e-02 4.00e+02 8.33e-02 1.11e+01 pdb=" N PRO B 229 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO B 229 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 229 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 618 " -0.041 5.00e-02 4.00e+02 6.23e-02 6.22e+00 pdb=" N PRO A 619 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 619 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 619 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 131 " -0.035 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO B 132 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 132 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 132 " -0.030 5.00e-02 4.00e+02 ... (remaining 1259 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 35 2.50 - 3.10: 4446 3.10 - 3.70: 10944 3.70 - 4.30: 15897 4.30 - 4.90: 25672 Nonbonded interactions: 56994 Sorted by model distance: nonbonded pdb=" O THR B 381 " pdb=" O SER B 382 " model vdw 1.904 3.040 nonbonded pdb=" OG1 THR B 381 " pdb=" N SER B 382 " model vdw 2.246 2.520 nonbonded pdb=" O PHE B 243 " pdb=" CB LEU B 601 " model vdw 2.248 3.440 nonbonded pdb=" O LEU B 379 " pdb=" N THR B 381 " model vdw 2.258 2.520 nonbonded pdb=" OH TYR B 396 " pdb=" O HOH B 701 " model vdw 2.262 2.440 ... (remaining 56989 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 'C' selection = chain 'D' selection = chain 'E' 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: 1.340 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: 3.930 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 23.740 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 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 : 0.006 0.129 7521 Z= 0.411 Angle : 1.012 13.260 10225 Z= 0.549 Chirality : 0.055 0.672 1201 Planarity : 0.006 0.083 1258 Dihedral : 16.611 111.339 2833 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 1.41 % Allowed : 7.15 % Favored : 91.44 % Rotamer: Outliers : 1.44 % Allowed : 6.95 % Favored : 91.61 % 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: -5.99 (0.17), residues: 923 helix: -4.51 (0.10), residues: 471 sheet: -1.07 (0.58), residues: 72 loop : -3.68 (0.22), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 124 HIS 0.006 0.001 HIS B 358 PHE 0.023 0.002 PHE B 335 TYR 0.016 0.002 TYR A 313 ARG 0.003 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 253 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 500 ILE cc_start: 0.6211 (mt) cc_final: 0.5999 (mt) REVERT: B 99 THR cc_start: 0.6872 (m) cc_final: 0.6403 (m) outliers start: 11 outliers final: 4 residues processed: 258 average time/residue: 0.6868 time to fit residues: 192.9905 Evaluate side-chains 148 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 144 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 601 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 0.6980 chunk 68 optimal weight: 0.2980 chunk 38 optimal weight: 0.3980 chunk 23 optimal weight: 3.9990 chunk 46 optimal weight: 0.0020 chunk 36 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 27 optimal weight: 0.0010 chunk 43 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 overall best weight: 0.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 268 ASN A 296 GLN A 317 ASN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN A 561 ASN B 134 ASN B 264 ASN ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7521 Z= 0.204 Angle : 0.763 10.230 10225 Z= 0.372 Chirality : 0.045 0.317 1201 Planarity : 0.005 0.069 1258 Dihedral : 13.533 94.724 1249 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.39 % Favored : 93.50 % Rotamer: Outliers : 4.33 % Allowed : 20.84 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -4.08 (0.22), residues: 923 helix: -2.67 (0.18), residues: 461 sheet: -0.33 (0.63), residues: 67 loop : -3.09 (0.24), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 124 HIS 0.002 0.001 HIS B 349 PHE 0.030 0.002 PHE B 250 TYR 0.011 0.002 TYR B 93 ARG 0.005 0.001 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 156 time to evaluate : 0.805 Fit side-chains outliers start: 33 outliers final: 9 residues processed: 178 average time/residue: 0.7000 time to fit residues: 137.2982 Evaluate side-chains 135 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 126 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 465 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 89 optimal weight: 0.0770 chunk 73 optimal weight: 0.9980 chunk 28 optimal weight: 0.0270 chunk 66 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7521 Z= 0.206 Angle : 0.697 8.870 10225 Z= 0.338 Chirality : 0.045 0.315 1201 Planarity : 0.005 0.070 1258 Dihedral : 11.295 76.376 1242 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.93 % Favored : 92.96 % Rotamer: Outliers : 5.50 % Allowed : 22.80 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.65 (0.24), residues: 923 helix: -1.25 (0.22), residues: 469 sheet: 0.21 (0.62), residues: 59 loop : -2.69 (0.26), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 124 HIS 0.003 0.001 HIS A 557 PHE 0.042 0.002 PHE A 337 TYR 0.031 0.002 TYR A 554 ARG 0.006 0.001 ARG B 162 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 153 time to evaluate : 0.853 Fit side-chains REVERT: B 426 PHE cc_start: 0.7495 (OUTLIER) cc_final: 0.7096 (t80) outliers start: 42 outliers final: 11 residues processed: 173 average time/residue: 0.7429 time to fit residues: 139.8252 Evaluate side-chains 131 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain B residue 426 PHE Chi-restraints excluded: chain B residue 465 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 0.0970 chunk 43 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 GLN A 580 GLN B 134 ASN B 148 GLN B 406 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.6073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7521 Z= 0.224 Angle : 0.706 8.500 10225 Z= 0.338 Chirality : 0.046 0.316 1201 Planarity : 0.004 0.070 1258 Dihedral : 10.069 60.241 1242 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.18 % Favored : 93.61 % Rotamer: Outliers : 6.03 % Allowed : 24.25 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.86 (0.26), residues: 923 helix: -0.59 (0.23), residues: 474 sheet: 1.16 (0.66), residues: 52 loop : -2.37 (0.28), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 124 HIS 0.002 0.001 HIS A 266 PHE 0.022 0.001 PHE B 250 TYR 0.026 0.002 TYR B 253 ARG 0.005 0.001 ARG A 626 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 118 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: B 426 PHE cc_start: 0.7501 (OUTLIER) cc_final: 0.7015 (t80) outliers start: 46 outliers final: 14 residues processed: 145 average time/residue: 0.7822 time to fit residues: 122.6679 Evaluate side-chains 123 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 316 TRP Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 426 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 GLN B 331 ASN B 406 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.6880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 7521 Z= 0.213 Angle : 0.685 9.141 10225 Z= 0.322 Chirality : 0.044 0.316 1201 Planarity : 0.004 0.067 1258 Dihedral : 9.286 59.561 1242 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.83 % Favored : 93.07 % Rotamer: Outliers : 5.90 % Allowed : 26.08 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.40 (0.27), residues: 923 helix: -0.10 (0.24), residues: 471 sheet: 1.18 (0.64), residues: 52 loop : -2.26 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 124 HIS 0.003 0.001 HIS A 557 PHE 0.021 0.001 PHE B 250 TYR 0.026 0.002 TYR B 253 ARG 0.003 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 116 time to evaluate : 0.825 Fit side-chains revert: symmetry clash REVERT: B 426 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.7403 (t80) outliers start: 45 outliers final: 19 residues processed: 144 average time/residue: 0.7448 time to fit residues: 116.6019 Evaluate side-chains 120 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 316 TRP Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 426 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 GLN B 488 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.8101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7521 Z= 0.283 Angle : 0.748 10.357 10225 Z= 0.357 Chirality : 0.047 0.325 1201 Planarity : 0.005 0.064 1258 Dihedral : 8.810 59.979 1242 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.58 % Favored : 92.31 % Rotamer: Outliers : 6.29 % Allowed : 25.82 % Favored : 67.89 % 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: -1.22 (0.27), residues: 923 helix: 0.01 (0.24), residues: 477 sheet: 1.20 (0.66), residues: 52 loop : -2.14 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 124 HIS 0.003 0.001 HIS A 539 PHE 0.015 0.002 PHE B 250 TYR 0.016 0.002 TYR B 253 ARG 0.004 0.001 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 112 time to evaluate : 0.817 Fit side-chains REVERT: B 426 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7776 (t80) outliers start: 48 outliers final: 24 residues processed: 145 average time/residue: 0.7224 time to fit residues: 114.5178 Evaluate side-chains 119 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 94 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 316 TRP Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 426 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 64 optimal weight: 0.0770 chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.8562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7521 Z= 0.198 Angle : 0.705 10.271 10225 Z= 0.333 Chirality : 0.044 0.292 1201 Planarity : 0.004 0.060 1258 Dihedral : 8.488 59.433 1242 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.26 % Favored : 92.63 % Rotamer: Outliers : 4.33 % Allowed : 28.44 % Favored : 67.23 % 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: -0.86 (0.27), residues: 923 helix: 0.42 (0.24), residues: 483 sheet: 1.01 (0.64), residues: 58 loop : -2.17 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 124 HIS 0.001 0.001 HIS B 358 PHE 0.015 0.001 PHE B 250 TYR 0.017 0.001 TYR B 253 ARG 0.008 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 103 time to evaluate : 0.782 Fit side-chains REVERT: B 426 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.7872 (t80) outliers start: 33 outliers final: 15 residues processed: 129 average time/residue: 0.8592 time to fit residues: 119.6141 Evaluate side-chains 110 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 316 TRP Chi-restraints excluded: chain B residue 426 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN B 406 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.8909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7521 Z= 0.204 Angle : 0.699 9.174 10225 Z= 0.334 Chirality : 0.044 0.308 1201 Planarity : 0.004 0.058 1258 Dihedral : 8.278 58.749 1242 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.26 % Favored : 92.63 % Rotamer: Outliers : 3.93 % Allowed : 28.83 % Favored : 67.23 % 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: -0.60 (0.28), residues: 923 helix: 0.63 (0.24), residues: 488 sheet: 1.01 (0.64), residues: 58 loop : -2.05 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 124 HIS 0.005 0.001 HIS B 358 PHE 0.014 0.001 PHE B 436 TYR 0.016 0.001 TYR B 253 ARG 0.008 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 101 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: B 340 LEU cc_start: 0.8766 (tt) cc_final: 0.8523 (tp) REVERT: B 426 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7916 (t80) outliers start: 30 outliers final: 15 residues processed: 123 average time/residue: 0.8346 time to fit residues: 111.1447 Evaluate side-chains 103 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 87 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 316 TRP Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 426 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 0.0010 chunk 49 optimal weight: 0.7980 chunk 35 optimal weight: 0.2980 chunk 64 optimal weight: 0.0970 chunk 25 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 0.0970 chunk 86 optimal weight: 0.0970 chunk 52 optimal weight: 0.9990 overall best weight: 0.1180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN B 208 GLN B 349 HIS B 406 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.9022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7521 Z= 0.167 Angle : 0.708 11.470 10225 Z= 0.335 Chirality : 0.045 0.389 1201 Planarity : 0.004 0.059 1258 Dihedral : 8.053 57.467 1242 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.72 % Favored : 93.17 % Rotamer: Outliers : 3.01 % Allowed : 30.80 % Favored : 66.19 % 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: -0.43 (0.28), residues: 923 helix: 0.88 (0.25), residues: 477 sheet: 1.07 (0.65), residues: 58 loop : -2.06 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 469 HIS 0.003 0.000 HIS B 471 PHE 0.012 0.001 PHE B 250 TYR 0.009 0.001 TYR A 313 ARG 0.008 0.000 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 93 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: B 340 LEU cc_start: 0.8691 (tt) cc_final: 0.8431 (tp) REVERT: B 426 PHE cc_start: 0.8155 (OUTLIER) cc_final: 0.7797 (t80) REVERT: B 469 TRP cc_start: 0.7692 (OUTLIER) cc_final: 0.7354 (t60) outliers start: 23 outliers final: 13 residues processed: 108 average time/residue: 0.8577 time to fit residues: 99.8708 Evaluate side-chains 104 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 89 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 316 TRP Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 426 PHE Chi-restraints excluded: chain B residue 469 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 83 optimal weight: 0.0050 chunk 72 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS B 406 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.9492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7521 Z= 0.281 Angle : 0.770 11.505 10225 Z= 0.371 Chirality : 0.048 0.392 1201 Planarity : 0.005 0.057 1258 Dihedral : 8.178 58.491 1242 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.37 % Favored : 92.42 % Rotamer: Outliers : 3.01 % Allowed : 30.93 % Favored : 66.06 % 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: -0.48 (0.28), residues: 923 helix: 0.75 (0.24), residues: 483 sheet: 0.96 (0.66), residues: 58 loop : -1.98 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 319 HIS 0.004 0.001 HIS B 349 PHE 0.014 0.002 PHE B 436 TYR 0.028 0.002 TYR A 629 ARG 0.007 0.001 ARG B 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 93 time to evaluate : 0.819 Fit side-chains REVERT: A 511 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7793 (tptp) REVERT: B 426 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7963 (t80) outliers start: 23 outliers final: 12 residues processed: 108 average time/residue: 0.9172 time to fit residues: 106.4266 Evaluate side-chains 100 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 511 LYS Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 316 TRP Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 426 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 63 optimal weight: 0.0670 chunk 4 optimal weight: 0.6980 chunk 52 optimal weight: 0.3980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN B 406 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.105040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.081081 restraints weight = 12987.803| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 3.22 r_work: 0.2935 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.9603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7521 Z= 0.195 Angle : 0.746 11.430 10225 Z= 0.353 Chirality : 0.044 0.308 1201 Planarity : 0.004 0.057 1258 Dihedral : 8.192 57.594 1242 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.26 % Favored : 92.63 % Rotamer: Outliers : 1.83 % Allowed : 32.63 % Favored : 65.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.28), residues: 923 helix: 0.97 (0.25), residues: 481 sheet: 1.06 (0.69), residues: 52 loop : -1.96 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 124 HIS 0.002 0.000 HIS B 358 PHE 0.014 0.001 PHE B 327 TYR 0.011 0.001 TYR A 313 ARG 0.012 0.001 ARG B 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2790.15 seconds wall clock time: 50 minutes 20.73 seconds (3020.73 seconds total)