Starting phenix.real_space_refine on Fri Mar 15 13:21:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wth_21896/03_2024/6wth_21896_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wth_21896/03_2024/6wth_21896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wth_21896/03_2024/6wth_21896.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wth_21896/03_2024/6wth_21896.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wth_21896/03_2024/6wth_21896_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wth_21896/03_2024/6wth_21896_updated.pdb" } resolution = 3.06 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= 0.005 sd= 0.055 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 S 85 5.16 5 Na 1 4.78 5 C 7374 2.51 5 N 2015 2.21 5 O 2265 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 152": "NH1" <-> "NH2" Residue "A ARG 253": "NH1" <-> "NH2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 386": "NH1" <-> "NH2" Residue "A ARG 438": "NH1" <-> "NH2" Residue "A TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 259": "NH1" <-> "NH2" Residue "B ARG 317": "NH1" <-> "NH2" Residue "B ARG 324": "NH1" <-> "NH2" Residue "B ARG 353": "NH1" <-> "NH2" Residue "B PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 479": "NH1" <-> "NH2" Residue "B TYR 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 505": "NH1" <-> "NH2" Residue "C ARG 111": "NH1" <-> "NH2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11740 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3093 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 19, 'TRANS': 361} Chain breaks: 2 Chain: "B" Number of atoms: 3316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3316 Classifications: {'peptide': 413} Link IDs: {'PTRANS': 21, 'TRANS': 391} Chain breaks: 3 Chain: "C" Number of atoms: 3135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3135 Classifications: {'peptide': 389} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 370} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 525 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'TRANS': 104} Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 105 Planarities with less than four sites: {'UNK:plan-1': 105} Unresolved non-hydrogen planarities: 105 Chain: "E" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 590 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'TRANS': 117} Chain breaks: 1 Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 118 Planarities with less than four sites: {'UNK:plan-1': 118} Unresolved non-hydrogen planarities: 118 Chain: "F" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 575 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'TRANS': 114} Chain breaks: 1 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 345 Unresolved non-hydrogen dihedrals: 115 Planarities with less than four sites: {'UNK:plan-1': 115} Unresolved non-hydrogen planarities: 115 Chain: "G" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 365 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'TRANS': 72} Chain breaks: 3 Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 73 Planarities with less than four sites: {'UNK:plan-1': 73} Unresolved non-hydrogen planarities: 73 Chain: "H" 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: "I" 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: "J" 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: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' NA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.79, per 1000 atoms: 0.58 Number of scatterers: 11740 At special positions: 0 Unit cell: (101.26, 102.92, 162.68, 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 85 16.00 Na 1 11.00 O 2265 8.00 N 2015 7.00 C 7374 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=25, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 305 " distance=2.05 Simple disulfide: pdb=" SG CYS A 229 " - pdb=" SG CYS A 236 " distance=2.05 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 289 " distance=2.05 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 479 " distance=2.05 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 475 " distance=2.05 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 471 " distance=2.05 Simple disulfide: pdb=" SG CYS A 429 " - pdb=" SG CYS A 456 " distance=2.03 Simple disulfide: pdb=" SG CYS A 431 " - pdb=" SG CYS A 445 " distance=2.05 Simple disulfide: pdb=" SG CYS B 98 " - pdb=" SG CYS B 272 " distance=2.05 Simple disulfide: pdb=" SG CYS B 184 " - pdb=" SG CYS B 189 " distance=2.05 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 203 " distance=2.05 Simple disulfide: pdb=" SG CYS B 249 " - pdb=" SG CYS B 256 " distance=2.05 Simple disulfide: pdb=" SG CYS B 361 " - pdb=" SG CYS B 448 " distance=2.05 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 444 " distance=2.05 Simple disulfide: pdb=" SG CYS B 390 " - pdb=" SG CYS B 440 " distance=2.04 Simple disulfide: pdb=" SG CYS B 399 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 401 " - pdb=" SG CYS B 415 " distance=2.05 Simple disulfide: pdb=" SG CYS C 100 " - pdb=" SG CYS C 283 " distance=2.05 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 214 " distance=2.05 Simple disulfide: pdb=" SG CYS C 260 " - pdb=" SG CYS C 267 " distance=2.05 Simple disulfide: pdb=" SG CYS C 372 " - pdb=" SG CYS C 457 " distance=2.05 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 453 " distance=2.05 Simple disulfide: pdb=" SG CYS C 398 " - pdb=" SG CYS C 449 " distance=2.05 Simple disulfide: pdb=" SG CYS C 407 " - pdb=" SG CYS C 434 " distance=2.05 Simple disulfide: pdb=" SG CYS C 409 " - pdb=" SG CYS C 423 " distance=2.05 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 H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 701 " - " ASN A 232 " " NAG A 702 " - " ASN A 397 " " NAG B 700 " - " ASN B 141 " " NAG B 705 " - " ASN B 449 " " NAG H 1 " - " ASN B 207 " " NAG I 1 " - " ASN B 260 " " NAG J 1 " - " ASN C 271 " Time building additional restraints: 4.31 Conformation dependent library (CDL) restraints added in 1.8 seconds 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3080 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 22 sheets defined 24.3% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 144 through 161 removed outlier: 3.536A pdb=" N GLU A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 260 Processing helix chain 'A' and resid 362 through 365 No H-bonds generated for 'chain 'A' and resid 362 through 365' Processing helix chain 'A' and resid 413 through 429 Processing helix chain 'A' and resid 454 through 465 Processing helix chain 'A' and resid 471 through 474 No H-bonds generated for 'chain 'A' and resid 471 through 474' Processing helix chain 'A' and resid 499 through 509 Processing helix chain 'B' and resid 105 through 107 No H-bonds generated for 'chain 'B' and resid 105 through 107' Processing helix chain 'B' and resid 113 through 126 removed outlier: 3.508A pdb=" N ALA B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 145 No H-bonds generated for 'chain 'B' and resid 142 through 145' Processing helix chain 'B' and resid 211 through 227 removed outlier: 3.760A pdb=" N THR B 216 " --> pdb=" O THR B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 237 removed outlier: 4.225A pdb=" N GLU B 237 " --> pdb=" O GLN B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 245 No H-bonds generated for 'chain 'B' and resid 242 through 245' Processing helix chain 'B' and resid 258 through 260 No H-bonds generated for 'chain 'B' and resid 258 through 260' Processing helix chain 'B' and resid 291 through 293 No H-bonds generated for 'chain 'B' and resid 291 through 293' Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 375 through 377 No H-bonds generated for 'chain 'B' and resid 375 through 377' Processing helix chain 'B' and resid 383 through 398 removed outlier: 3.550A pdb=" N PHE B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 431 removed outlier: 4.298A pdb=" N ALA B 424 " --> pdb=" O PRO B 421 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR B 427 " --> pdb=" O ALA B 424 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B 428 " --> pdb=" O HIS B 425 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN B 431 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 443 Processing helix chain 'B' and resid 468 through 480 Processing helix chain 'C' and resid 115 through 128 Processing helix chain 'C' and resid 222 through 240 removed outlier: 3.677A pdb=" N ASN C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA C 239 " --> pdb=" O MET C 235 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN C 240 " --> pdb=" O ASN C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 249 Processing helix chain 'C' and resid 253 through 256 No H-bonds generated for 'chain 'C' and resid 253 through 256' Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'C' and resid 314 through 316 No H-bonds generated for 'chain 'C' and resid 314 through 316' Processing helix chain 'C' and resid 340 through 343 No H-bonds generated for 'chain 'C' and resid 340 through 343' Processing helix chain 'C' and resid 391 through 406 Processing helix chain 'C' and resid 432 through 443 removed outlier: 3.531A pdb=" N TYR C 436 " --> pdb=" O MET C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 487 removed outlier: 3.721A pdb=" N LEU C 480 " --> pdb=" O GLU C 477 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LEU C 481 " --> pdb=" O LYS C 478 " (cutoff:3.500A) Proline residue: C 482 - end of helix removed outlier: 3.935A pdb=" N THR C 485 " --> pdb=" O PRO C 482 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP C 487 " --> pdb=" O LEU C 484 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 115 through 121 removed outlier: 3.537A pdb=" N ASN A 121 " --> pdb=" O TYR A 533 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TYR A 533 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS A 534 " --> pdb=" O LYS A 381 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 294 through 298 removed outlier: 4.615A pdb=" N ASN A 304 " --> pdb=" O THR A 134 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA A 349 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 224 through 228 removed outlier: 3.615A pdb=" N PHE A 226 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 374 through 379 removed outlier: 7.168A pdb=" N LYS A 523 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ILE A 377 " --> pdb=" O LYS A 523 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ASN A 525 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N MET A 379 " --> pdb=" O ASN A 525 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N PHE A 527 " --> pdb=" O MET A 379 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA A 281 " --> pdb=" O MET A 331 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 79 through 86 removed outlier: 3.501A pdb=" N TYR B 504 " --> pdb=" O GLY B 86 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL B 348 " --> pdb=" O ARG B 505 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ILE B 507 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LYS B 350 " --> pdb=" O ILE B 507 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N GLU B 509 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLN B 352 " --> pdb=" O GLU B 509 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N ALA B 511 " --> pdb=" O GLN B 352 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 316 through 321 removed outlier: 4.508A pdb=" N ASN B 99 " --> pdb=" O ASN B 271 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASN B 271 " --> pdb=" O ASN B 99 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 162 through 165 Processing sheet with id= H, first strand: chain 'B' and resid 456 through 458 removed outlier: 8.741A pdb=" N THR B 342 " --> pdb=" O ILE B 492 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LYS B 494 " --> pdb=" O THR B 342 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE B 344 " --> pdb=" O LYS B 494 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASN B 496 " --> pdb=" O ILE B 344 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL B 346 " --> pdb=" O ASN B 496 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N TYR B 498 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASP B 300 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ILE B 246 " --> pdb=" O ASP B 300 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 81 through 89 removed outlier: 4.629A pdb=" N LEU C 359 " --> pdb=" O ASN C 512 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 161 through 163 removed outlier: 3.895A pdb=" N VAL C 201 " --> pdb=" O PHE C 163 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 273 through 277 Processing sheet with id= L, first strand: chain 'C' and resid 306 through 311 removed outlier: 6.312A pdb=" N THR C 353 " --> pdb=" O LEU C 505 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N PHE C 507 " --> pdb=" O THR C 353 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE C 355 " --> pdb=" O PHE C 507 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 326 through 329 Processing sheet with id= N, first strand: chain 'D' and resid 20 through 25 Processing sheet with id= O, first strand: chain 'D' and resid 86 through 91 removed outlier: 5.913A pdb=" N UNK D 38 " --> pdb=" O UNK D 47 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N UNK D 47 " --> pdb=" O UNK D 38 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.712A pdb=" N UNK E 36 " --> pdb=" O UNK E 48 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N UNK E 50 " --> pdb=" O UNK E 34 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N UNK E 34 " --> pdb=" O UNK E 50 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N UNK E 111 " --> pdb=" O UNK E 98 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 68 through 72 removed outlier: 5.735A pdb=" N UNK E 16 " --> pdb=" O UNK E 85 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.601A pdb=" N UNK F 18 " --> pdb=" O UNK F 83 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 37 through 40 removed outlier: 3.584A pdb=" N UNK F 92 " --> pdb=" O UNK F 114 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N UNK F 112 " --> pdb=" O UNK F 94 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 49 through 52 removed outlier: 3.527A pdb=" N UNK F 57 " --> pdb=" O UNK F 52 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 4 through 6 Processing sheet with id= V, first strand: chain 'G' and resid 40 through 42 removed outlier: 3.834A pdb=" N UNK G 40 " --> pdb=" O UNK G 53 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N UNK G 53 " --> pdb=" O UNK G 40 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N UNK G 42 " --> pdb=" O UNK G 51 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N UNK G 51 " --> pdb=" O UNK G 42 " (cutoff:3.500A) No H-bonds generated for sheet with id= V 372 hydrogen bonds defined for protein. 1017 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: 3.53 Time building geometry restraints manager: 4.74 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: 3911 1.34 - 1.46: 2375 1.46 - 1.58: 5566 1.58 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 11972 Sorted by residual: bond pdb=" C1 NAG B 700 " pdb=" O5 NAG B 700 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.18e+00 bond pdb=" C3 NAG I 2 " pdb=" O3 NAG I 2 " ideal model delta sigma weight residual 1.403 1.432 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" C1 NAG B 705 " pdb=" O5 NAG B 705 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.92e+00 bond pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.84e+00 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.83e+00 ... (remaining 11967 not shown) Histogram of bond angle deviations from ideal: 100.46 - 107.17: 346 107.17 - 113.87: 6659 113.87 - 120.57: 4431 120.57 - 127.27: 4758 127.27 - 133.98: 115 Bond angle restraints: 16309 Sorted by residual: angle pdb=" C UNK G 70 " pdb=" N UNK G 71 " pdb=" CA UNK G 71 " ideal model delta sigma weight residual 121.70 128.76 -7.06 1.80e+00 3.09e-01 1.54e+01 angle pdb=" N ILE B 108 " pdb=" CA ILE B 108 " pdb=" C ILE B 108 " ideal model delta sigma weight residual 113.20 109.49 3.71 9.60e-01 1.09e+00 1.49e+01 angle pdb=" C GLY A 520 " pdb=" N VAL A 521 " pdb=" CA VAL A 521 " ideal model delta sigma weight residual 120.49 123.67 -3.18 1.38e+00 5.25e-01 5.31e+00 angle pdb=" C GLU C 367 " pdb=" CA GLU C 367 " pdb=" CB GLU C 367 " ideal model delta sigma weight residual 113.57 110.32 3.25 1.57e+00 4.06e-01 4.28e+00 angle pdb=" C GLU C 374 " pdb=" N ASP C 375 " pdb=" CA ASP C 375 " ideal model delta sigma weight residual 121.54 125.26 -3.72 1.91e+00 2.74e-01 3.79e+00 ... (remaining 16304 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.34: 6945 11.34 - 22.68: 286 22.68 - 34.02: 88 34.02 - 45.36: 23 45.36 - 56.70: 9 Dihedral angle restraints: 7351 sinusoidal: 2628 harmonic: 4723 Sorted by residual: dihedral pdb=" CA SER C 366 " pdb=" C SER C 366 " pdb=" N GLU C 367 " pdb=" CA GLU C 367 " ideal model delta harmonic sigma weight residual -180.00 -164.08 -15.92 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" N ASN A 397 " pdb=" CA ASN A 397 " pdb=" CB ASN A 397 " pdb=" CG ASN A 397 " ideal model delta sinusoidal sigma weight residual -60.00 -116.70 56.70 3 1.50e+01 4.44e-03 9.41e+00 dihedral pdb=" CB CYS A 229 " pdb=" SG CYS A 229 " pdb=" SG CYS A 236 " pdb=" CB CYS A 236 " ideal model delta sinusoidal sigma weight residual 93.00 117.12 -24.12 1 1.00e+01 1.00e-02 8.38e+00 ... (remaining 7348 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.226: 1883 0.226 - 0.453: 0 0.453 - 0.679: 0 0.679 - 0.905: 0 0.905 - 1.132: 1 Chirality restraints: 1884 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.27 -1.13 2.00e-02 2.50e+03 3.20e+03 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-02 2.50e+03 1.02e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.29e+01 ... (remaining 1881 not shown) Planarity restraints: 2135 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 2 " 0.035 2.00e-02 2.50e+03 2.85e-02 1.02e+01 pdb=" C7 NAG I 2 " -0.010 2.00e-02 2.50e+03 pdb=" C8 NAG I 2 " 0.027 2.00e-02 2.50e+03 pdb=" N2 NAG I 2 " -0.045 2.00e-02 2.50e+03 pdb=" O7 NAG I 2 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 299 " -0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO A 300 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 300 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 300 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 368 " 0.016 5.00e-02 4.00e+02 2.49e-02 9.92e-01 pdb=" N PRO B 369 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO B 369 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 369 " 0.014 5.00e-02 4.00e+02 ... (remaining 2132 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1216 2.75 - 3.29: 11021 3.29 - 3.83: 18447 3.83 - 4.36: 21594 4.36 - 4.90: 38161 Nonbonded interactions: 90439 Sorted by model distance: nonbonded pdb=" OG SER A 295 " pdb=" OG1 THR A 307 " model vdw 2.217 2.440 nonbonded pdb=" O LEU C 365 " pdb=" OG SER C 370 " model vdw 2.246 2.440 nonbonded pdb=" OH TYR C 385 " pdb=" OE1 GLN C 414 " model vdw 2.255 2.440 nonbonded pdb=" OD1 ASP B 331 " pdb=" NH2 ARG B 388 " model vdw 2.274 2.520 nonbonded pdb=" O PHE A 254 " pdb=" ND2 ASN A 258 " model vdw 2.307 2.520 ... (remaining 90434 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 'D' selection = (chain 'E' and resid 16 through 122) selection = (chain 'F' and resid 11 through 116) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.620 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: 11.990 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 33.020 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11972 Z= 0.144 Angle : 0.562 7.064 16309 Z= 0.283 Chirality : 0.045 1.132 1884 Planarity : 0.002 0.029 2128 Dihedral : 7.452 56.696 4196 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.84 % Allowed : 2.80 % Favored : 96.37 % 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: -3.50 (0.20), residues: 1163 helix: -2.95 (0.19), residues: 292 sheet: -2.24 (0.25), residues: 307 loop : -1.87 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 462 HIS 0.002 0.000 HIS C 276 PHE 0.005 0.001 PHE A 297 TYR 0.008 0.001 TYR C 425 ARG 0.001 0.000 ARG B 388 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 183 time to evaluate : 1.186 Fit side-chains revert: symmetry clash REVERT: B 395 MET cc_start: 0.7966 (tpt) cc_final: 0.7256 (tpp) REVERT: C 231 LYS cc_start: 0.7828 (ttmt) cc_final: 0.7522 (ttpp) outliers start: 9 outliers final: 4 residues processed: 191 average time/residue: 0.2874 time to fit residues: 75.7047 Evaluate side-chains 102 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain C residue 425 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 8.9990 chunk 118 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 141 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 HIS A 336 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 HIS C 426 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.135 11972 Z= 0.648 Angle : 0.826 9.542 16309 Z= 0.407 Chirality : 0.050 0.185 1884 Planarity : 0.005 0.050 2128 Dihedral : 6.349 57.060 1907 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.52 % Allowed : 8.11 % Favored : 89.38 % 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: -2.53 (0.21), residues: 1163 helix: -1.56 (0.26), residues: 284 sheet: -1.92 (0.25), residues: 306 loop : -1.48 (0.24), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 462 HIS 0.010 0.002 HIS B 473 PHE 0.018 0.002 PHE C 131 TYR 0.021 0.002 TYR B 269 ARG 0.006 0.001 ARG B 324 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 86 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 LYS cc_start: 0.7449 (ttmm) cc_final: 0.7014 (tttt) REVERT: B 322 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7224 (mt-10) REVERT: B 510 SER cc_start: 0.8880 (m) cc_final: 0.8430 (p) REVERT: C 231 LYS cc_start: 0.7701 (ttmt) cc_final: 0.7414 (ttpp) outliers start: 27 outliers final: 14 residues processed: 110 average time/residue: 0.2105 time to fit residues: 34.9097 Evaluate side-chains 93 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 79 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 378 ASP Chi-restraints excluded: chain C residue 425 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 117 optimal weight: 8.9990 chunk 96 optimal weight: 0.0770 chunk 39 optimal weight: 0.8980 chunk 141 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 113 optimal weight: 0.0970 overall best weight: 0.5936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 ASN ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 HIS ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11972 Z= 0.163 Angle : 0.490 6.885 16309 Z= 0.244 Chirality : 0.038 0.141 1884 Planarity : 0.003 0.045 2128 Dihedral : 5.168 50.240 1905 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.14 % Allowed : 8.29 % Favored : 89.56 % 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: -1.68 (0.22), residues: 1163 helix: -0.29 (0.30), residues: 281 sheet: -1.61 (0.25), residues: 312 loop : -1.13 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 229 HIS 0.003 0.001 HIS C 276 PHE 0.013 0.001 PHE C 219 TYR 0.011 0.001 TYR C 234 ARG 0.008 0.000 ARG B 410 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 91 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 322 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7212 (mt-10) REVERT: B 341 GLU cc_start: 0.7929 (tt0) cc_final: 0.7635 (tm-30) REVERT: B 395 MET cc_start: 0.7844 (tpp) cc_final: 0.7279 (tpp) REVERT: B 510 SER cc_start: 0.8873 (m) cc_final: 0.8422 (p) outliers start: 23 outliers final: 15 residues processed: 107 average time/residue: 0.2209 time to fit residues: 35.9612 Evaluate side-chains 97 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 378 ASP Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 425 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 chunk 142 optimal weight: 7.9990 chunk 150 optimal weight: 20.0000 chunk 74 optimal weight: 0.8980 chunk 134 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 11972 Z= 0.470 Angle : 0.648 6.995 16309 Z= 0.318 Chirality : 0.044 0.155 1884 Planarity : 0.004 0.053 2128 Dihedral : 5.392 48.163 1905 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.08 % Allowed : 8.95 % Favored : 87.98 % 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: -1.58 (0.23), residues: 1163 helix: -0.11 (0.30), residues: 283 sheet: -1.61 (0.25), residues: 306 loop : -1.09 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 462 HIS 0.005 0.001 HIS B 110 PHE 0.013 0.002 PHE C 261 TYR 0.014 0.002 TYR C 234 ARG 0.008 0.001 ARG B 410 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 76 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7918 (mp) REVERT: B 322 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7340 (mt-10) REVERT: B 323 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.7947 (mp10) REVERT: B 510 SER cc_start: 0.8852 (m) cc_final: 0.8400 (p) outliers start: 33 outliers final: 20 residues processed: 104 average time/residue: 0.2054 time to fit residues: 32.9496 Evaluate side-chains 95 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 73 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 378 ASP Chi-restraints excluded: chain C residue 407 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 62 optimal weight: 0.0040 chunk 128 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 135 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 532 ASN ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11972 Z= 0.198 Angle : 0.496 6.245 16309 Z= 0.246 Chirality : 0.038 0.159 1884 Planarity : 0.003 0.041 2128 Dihedral : 4.673 38.737 1903 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.80 % Allowed : 9.97 % Favored : 87.23 % 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: -1.21 (0.23), residues: 1163 helix: 0.32 (0.31), residues: 285 sheet: -1.41 (0.26), residues: 314 loop : -0.91 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 501 HIS 0.003 0.001 HIS C 276 PHE 0.011 0.001 PHE C 219 TYR 0.016 0.001 TYR C 425 ARG 0.008 0.000 ARG B 410 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 77 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 MET cc_start: 0.9132 (ptm) cc_final: 0.8854 (ptm) REVERT: B 322 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7333 (mt-10) REVERT: B 323 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.7992 (mp10) REVERT: B 510 SER cc_start: 0.8805 (m) cc_final: 0.8393 (p) REVERT: C 299 MET cc_start: 0.8881 (ttm) cc_final: 0.8407 (ttt) outliers start: 30 outliers final: 22 residues processed: 101 average time/residue: 0.2093 time to fit residues: 32.7882 Evaluate side-chains 101 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 78 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 378 ASP Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 425 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 150 optimal weight: 20.0000 chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11972 Z= 0.237 Angle : 0.499 6.230 16309 Z= 0.247 Chirality : 0.039 0.159 1884 Planarity : 0.003 0.042 2128 Dihedral : 4.451 31.447 1903 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.80 % Allowed : 10.16 % Favored : 87.05 % 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: -0.93 (0.24), residues: 1163 helix: 0.69 (0.31), residues: 285 sheet: -1.25 (0.26), residues: 321 loop : -0.80 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 229 HIS 0.004 0.001 HIS C 280 PHE 0.009 0.001 PHE C 219 TYR 0.017 0.001 TYR C 425 ARG 0.009 0.000 ARG B 410 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 81 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 MET cc_start: 0.9134 (ptm) cc_final: 0.8836 (ptm) REVERT: B 322 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7371 (mt-10) REVERT: B 323 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8027 (mp10) REVERT: B 510 SER cc_start: 0.8815 (m) cc_final: 0.8374 (p) REVERT: C 299 MET cc_start: 0.8876 (ttm) cc_final: 0.8415 (ttt) outliers start: 30 outliers final: 25 residues processed: 105 average time/residue: 0.2061 time to fit residues: 33.5436 Evaluate side-chains 103 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 77 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 378 ASP Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 425 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 150 optimal weight: 20.0000 chunk 94 optimal weight: 0.0370 chunk 91 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 overall best weight: 1.3060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 532 ASN ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11972 Z= 0.261 Angle : 0.506 6.832 16309 Z= 0.251 Chirality : 0.039 0.158 1884 Planarity : 0.003 0.040 2128 Dihedral : 4.406 31.408 1903 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.08 % Allowed : 10.90 % Favored : 86.02 % 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 (0.24), residues: 1163 helix: 0.69 (0.31), residues: 291 sheet: -1.16 (0.26), residues: 324 loop : -0.80 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 229 HIS 0.004 0.001 HIS C 280 PHE 0.010 0.001 PHE C 219 TYR 0.018 0.001 TYR C 425 ARG 0.008 0.000 ARG B 410 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 80 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 323 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8045 (mp10) REVERT: B 510 SER cc_start: 0.8791 (m) cc_final: 0.8366 (p) REVERT: C 299 MET cc_start: 0.8880 (ttm) cc_final: 0.8429 (ttt) outliers start: 33 outliers final: 28 residues processed: 105 average time/residue: 0.1890 time to fit residues: 30.9933 Evaluate side-chains 109 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 80 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 378 ASP Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 425 TYR Chi-restraints excluded: chain C residue 463 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 136 optimal weight: 7.9990 chunk 144 optimal weight: 9.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 11972 Z= 0.374 Angle : 0.585 7.215 16309 Z= 0.289 Chirality : 0.041 0.154 1884 Planarity : 0.003 0.042 2128 Dihedral : 4.724 31.555 1903 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.26 % Allowed : 10.90 % Favored : 85.83 % 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: -0.98 (0.23), residues: 1163 helix: 0.53 (0.31), residues: 293 sheet: -1.17 (0.26), residues: 317 loop : -0.87 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 229 HIS 0.006 0.001 HIS C 280 PHE 0.011 0.001 PHE C 261 TYR 0.021 0.001 TYR C 425 ARG 0.008 0.000 ARG B 410 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 81 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 322 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7386 (mt-10) REVERT: B 323 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8018 (mp10) REVERT: B 329 ILE cc_start: 0.7838 (mm) cc_final: 0.7518 (mm) REVERT: B 510 SER cc_start: 0.8808 (m) cc_final: 0.8379 (p) REVERT: C 299 MET cc_start: 0.8879 (ttm) cc_final: 0.8429 (ttt) outliers start: 35 outliers final: 28 residues processed: 105 average time/residue: 0.1898 time to fit residues: 31.2808 Evaluate side-chains 110 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 81 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 378 ASP Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 425 TYR Chi-restraints excluded: chain C residue 463 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 8.9990 chunk 140 optimal weight: 8.9990 chunk 144 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 139 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 11972 Z= 0.416 Angle : 0.612 7.637 16309 Z= 0.302 Chirality : 0.042 0.159 1884 Planarity : 0.003 0.044 2128 Dihedral : 4.959 32.072 1903 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.98 % Allowed : 11.37 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.23), residues: 1163 helix: 0.38 (0.30), residues: 298 sheet: -1.17 (0.26), residues: 315 loop : -0.92 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 423 HIS 0.006 0.001 HIS C 280 PHE 0.011 0.001 PHE C 261 TYR 0.021 0.001 TYR C 425 ARG 0.008 0.001 ARG B 410 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 82 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 323 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.7988 (mp10) REVERT: B 329 ILE cc_start: 0.7859 (mm) cc_final: 0.7565 (mm) REVERT: B 510 SER cc_start: 0.8793 (m) cc_final: 0.8347 (p) REVERT: C 299 MET cc_start: 0.8884 (ttm) cc_final: 0.8419 (ttt) outliers start: 32 outliers final: 26 residues processed: 105 average time/residue: 0.1993 time to fit residues: 32.2926 Evaluate side-chains 107 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 80 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 378 ASP Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 425 TYR Chi-restraints excluded: chain C residue 463 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 102 optimal weight: 6.9990 chunk 155 optimal weight: 20.0000 chunk 143 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11972 Z= 0.346 Angle : 0.575 7.343 16309 Z= 0.284 Chirality : 0.041 0.166 1884 Planarity : 0.003 0.044 2128 Dihedral : 4.842 32.695 1903 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.61 % Allowed : 11.65 % Favored : 85.74 % 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: -1.02 (0.23), residues: 1163 helix: 0.37 (0.30), residues: 301 sheet: -1.14 (0.26), residues: 315 loop : -0.87 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 423 HIS 0.005 0.001 HIS C 280 PHE 0.011 0.001 PHE C 261 TYR 0.020 0.001 TYR C 425 ARG 0.008 0.000 ARG B 410 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 81 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 323 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8013 (mp10) REVERT: B 329 ILE cc_start: 0.7832 (mm) cc_final: 0.7542 (mm) REVERT: B 510 SER cc_start: 0.8723 (m) cc_final: 0.8289 (p) REVERT: C 299 MET cc_start: 0.8877 (ttm) cc_final: 0.8427 (ttt) outliers start: 28 outliers final: 25 residues processed: 100 average time/residue: 0.2036 time to fit residues: 31.9831 Evaluate side-chains 103 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 77 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 378 ASP Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 425 TYR Chi-restraints excluded: chain C residue 463 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 114 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 127 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 108 optimal weight: 0.1980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS A 532 ASN ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.113691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.094935 restraints weight = 19550.105| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.50 r_work: 0.3195 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11972 Z= 0.177 Angle : 0.481 6.924 16309 Z= 0.239 Chirality : 0.038 0.169 1884 Planarity : 0.003 0.041 2128 Dihedral : 4.325 31.255 1903 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.14 % Allowed : 12.21 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.24), residues: 1163 helix: 0.71 (0.31), residues: 292 sheet: -0.98 (0.26), residues: 322 loop : -0.73 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 470 HIS 0.003 0.001 HIS A 255 PHE 0.008 0.001 PHE C 219 TYR 0.014 0.001 TYR C 425 ARG 0.009 0.000 ARG B 410 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2247.18 seconds wall clock time: 41 minutes 17.28 seconds (2477.28 seconds total)