Starting phenix.real_space_refine on Sat Dec 9 17:16:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wth_21896/12_2023/6wth_21896_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wth_21896/12_2023/6wth_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_21896/12_2023/6wth_21896.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wth_21896/12_2023/6wth_21896.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wth_21896/12_2023/6wth_21896_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wth_21896/12_2023/6wth_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-1.21rc1-5172/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: 7.00, per 1000 atoms: 0.60 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: 5.02 Conformation dependent library (CDL) restraints added in 2.0 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: 2.19 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: 3.33 Time building geometry restraints manager: 5.35 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: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 12.250 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 34.500 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.080 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.650 ------------------------------------------------------------------------------- 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 : 1.266 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 191 average time/residue: 0.2850 time to fit residues: 74.5797 Evaluate side-chains 101 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 1.165 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1175 time to fit residues: 2.3132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7521 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.128 11972 Z= 0.673 Angle : 0.827 9.483 16309 Z= 0.408 Chirality : 0.051 0.178 1884 Planarity : 0.005 0.051 2128 Dihedral : 6.087 57.387 1901 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.24 % Allowed : 8.48 % Favored : 89.28 % 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: -2.47 (0.21), residues: 1163 helix: -1.38 (0.27), residues: 276 sheet: -1.91 (0.25), residues: 306 loop : -1.49 (0.23), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 462 HIS 0.010 0.002 HIS B 473 PHE 0.019 0.003 PHE C 261 TYR 0.036 0.003 TYR C 425 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 109 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 85 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 12 residues processed: 106 average time/residue: 0.2155 time to fit residues: 34.8709 Evaluate side-chains 85 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 73 time to evaluate : 1.232 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 12 outliers final: 1 residues processed: 12 average time/residue: 0.1239 time to fit residues: 4.2033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 chunk 96 optimal weight: 0.8980 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: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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: 0.7456 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11972 Z= 0.236 Angle : 0.522 9.754 16309 Z= 0.259 Chirality : 0.039 0.140 1884 Planarity : 0.003 0.047 2128 Dihedral : 5.073 50.955 1901 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.58 % Allowed : 8.57 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.23), residues: 1163 helix: -0.37 (0.30), residues: 282 sheet: -1.69 (0.25), residues: 314 loop : -1.15 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 229 HIS 0.003 0.001 HIS A 255 PHE 0.012 0.001 PHE C 219 TYR 0.026 0.001 TYR C 425 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 103 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 98 average time/residue: 0.2093 time to fit residues: 32.2324 Evaluate side-chains 88 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 1.493 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 7 average time/residue: 0.1253 time to fit residues: 3.4386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 73 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 67 optimal weight: 0.1980 chunk 95 optimal weight: 5.9990 chunk 142 optimal weight: 7.9990 chunk 150 optimal weight: 20.0000 chunk 74 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 417 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 11972 Z= 0.491 Angle : 0.675 7.630 16309 Z= 0.331 Chirality : 0.044 0.156 1884 Planarity : 0.004 0.052 2128 Dihedral : 5.356 48.303 1901 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.52 % Allowed : 9.23 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.23), residues: 1163 helix: -0.30 (0.30), residues: 289 sheet: -1.66 (0.25), residues: 309 loop : -1.15 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 229 HIS 0.006 0.001 HIS B 110 PHE 0.015 0.002 PHE C 261 TYR 0.029 0.002 TYR C 425 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 108 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 81 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 17 residues processed: 102 average time/residue: 0.2192 time to fit residues: 34.4107 Evaluate side-chains 92 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 75 time to evaluate : 1.359 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 2 residues processed: 17 average time/residue: 0.1221 time to fit residues: 5.3493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 2 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 128 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 135 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11972 Z= 0.259 Angle : 0.523 6.442 16309 Z= 0.260 Chirality : 0.039 0.163 1884 Planarity : 0.003 0.050 2128 Dihedral : 4.735 38.484 1901 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.93 % Allowed : 11.74 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.23), residues: 1163 helix: 0.33 (0.31), residues: 279 sheet: -1.39 (0.26), residues: 315 loop : -0.95 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 229 HIS 0.003 0.001 HIS A 296 PHE 0.011 0.001 PHE C 219 TYR 0.029 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 91 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 91 average time/residue: 0.2146 time to fit residues: 30.1827 Evaluate side-chains 81 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 1.264 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 5 average time/residue: 0.1062 time to fit residues: 2.6538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 29 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 150 optimal weight: 20.0000 chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 79 optimal weight: 7.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 11972 Z= 0.439 Angle : 0.626 6.652 16309 Z= 0.308 Chirality : 0.043 0.155 1884 Planarity : 0.004 0.048 2128 Dihedral : 5.021 35.279 1901 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.77 % Allowed : 11.93 % Favored : 86.30 % 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: -1.33 (0.23), residues: 1163 helix: 0.13 (0.30), residues: 298 sheet: -1.42 (0.26), residues: 309 loop : -1.01 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 229 HIS 0.005 0.001 HIS B 110 PHE 0.012 0.001 PHE C 261 TYR 0.031 0.002 TYR C 425 ARG 0.008 0.001 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 93 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 74 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 86 average time/residue: 0.2121 time to fit residues: 28.7123 Evaluate side-chains 85 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 1.350 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 11 average time/residue: 0.1189 time to fit residues: 4.1831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 127 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 150 optimal weight: 20.0000 chunk 94 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 69 optimal weight: 0.0050 chunk 93 optimal weight: 0.8980 overall best weight: 0.7794 ------------------------------------------------------------------------------- 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 418 HIS A 532 ASN C 103 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11972 Z= 0.186 Angle : 0.486 6.515 16309 Z= 0.242 Chirality : 0.038 0.160 1884 Planarity : 0.003 0.043 2128 Dihedral : 4.384 31.807 1901 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.84 % Allowed : 12.40 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.24), residues: 1163 helix: 0.47 (0.31), residues: 299 sheet: -1.16 (0.26), residues: 322 loop : -0.83 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 470 HIS 0.003 0.001 HIS C 276 PHE 0.010 0.001 PHE C 219 TYR 0.019 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 90 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 89 average time/residue: 0.2059 time to fit residues: 28.7003 Evaluate side-chains 80 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 1.356 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 5 average time/residue: 0.1198 time to fit residues: 2.7949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 45 optimal weight: 0.2980 chunk 29 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 chunk 144 optimal weight: 10.0000 overall best weight: 2.8588 ------------------------------------------------------------------------------- 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 ** C 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 11972 Z= 0.538 Angle : 0.685 7.415 16309 Z= 0.337 Chirality : 0.045 0.159 1884 Planarity : 0.004 0.047 2128 Dihedral : 5.098 34.007 1901 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.49 % Allowed : 12.67 % 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: -1.23 (0.23), residues: 1163 helix: 0.24 (0.30), residues: 295 sheet: -1.30 (0.26), residues: 309 loop : -1.00 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 462 HIS 0.007 0.001 HIS B 110 PHE 0.013 0.002 PHE C 261 TYR 0.033 0.002 TYR C 425 ARG 0.009 0.001 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 92 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 76 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 87 average time/residue: 0.2183 time to fit residues: 29.7183 Evaluate side-chains 85 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 75 time to evaluate : 1.403 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 10 average time/residue: 0.1233 time to fit residues: 3.9180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 110 optimal weight: 0.0870 chunk 42 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 139 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 overall best weight: 1.3162 ------------------------------------------------------------------------------- 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 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11972 Z= 0.272 Angle : 0.544 7.400 16309 Z= 0.269 Chirality : 0.040 0.165 1884 Planarity : 0.003 0.049 2128 Dihedral : 4.704 34.215 1901 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.37 % Allowed : 13.42 % Favored : 86.21 % 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 (0.24), residues: 1163 helix: 0.39 (0.31), residues: 298 sheet: -1.18 (0.26), residues: 315 loop : -0.90 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 470 HIS 0.004 0.001 HIS B 110 PHE 0.010 0.001 PHE C 219 TYR 0.049 0.001 TYR C 425 ARG 0.009 0.000 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 80 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 80 average time/residue: 0.2122 time to fit residues: 26.7107 Evaluate side-chains 78 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 76 time to evaluate : 1.207 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.1066 time to fit residues: 1.9788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 7.9990 chunk 90 optimal weight: 0.7980 chunk 70 optimal weight: 0.2980 chunk 102 optimal weight: 6.9990 chunk 155 optimal weight: 20.0000 chunk 143 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 C 277 HIS ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11972 Z= 0.286 Angle : 0.541 7.400 16309 Z= 0.268 Chirality : 0.040 0.165 1884 Planarity : 0.003 0.048 2128 Dihedral : 4.575 31.370 1901 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.28 % Allowed : 13.98 % 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: -0.94 (0.24), residues: 1163 helix: 0.58 (0.31), residues: 286 sheet: -1.11 (0.26), residues: 322 loop : -0.86 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 229 HIS 0.005 0.001 HIS B 110 PHE 0.010 0.001 PHE C 219 TYR 0.042 0.001 TYR C 425 ARG 0.009 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 79 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 79 average time/residue: 0.2139 time to fit residues: 26.3990 Evaluate side-chains 78 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 76 time to evaluate : 1.191 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.1064 time to fit residues: 1.9631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 114 optimal weight: 0.5980 chunk 18 optimal weight: 0.2980 chunk 34 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 127 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.113427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.094829 restraints weight = 19637.041| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.48 r_work: 0.3194 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11972 Z= 0.182 Angle : 0.482 7.333 16309 Z= 0.240 Chirality : 0.038 0.163 1884 Planarity : 0.003 0.047 2128 Dihedral : 4.229 25.956 1901 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.56 % Allowed : 13.89 % Favored : 85.55 % 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: -0.75 (0.24), residues: 1163 helix: 0.76 (0.32), residues: 286 sheet: -1.01 (0.26), residues: 322 loop : -0.75 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 229 HIS 0.004 0.001 HIS B 110 PHE 0.009 0.001 PHE C 219 TYR 0.030 0.001 TYR C 425 ARG 0.010 0.000 ARG B 410 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2291.04 seconds wall clock time: 42 minutes 23.44 seconds (2543.44 seconds total)