Starting phenix.real_space_refine on Mon Mar 18 10:07:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt4_26110/03_2024/7tt4_26110.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt4_26110/03_2024/7tt4_26110.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt4_26110/03_2024/7tt4_26110.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt4_26110/03_2024/7tt4_26110.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt4_26110/03_2024/7tt4_26110.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt4_26110/03_2024/7tt4_26110.pdb" } resolution = 4.2 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= 0.006 sd= 0.065 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 32 5.16 5 C 6637 2.51 5 N 1794 2.21 5 O 2063 1.98 5 H 10107 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 512": "OD1" <-> "OD2" Residue "A PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 585": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 608": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 648": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 663": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 675": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 686": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 729": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 754": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 757": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 760": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 1300": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20633 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 9595 Classifications: {'peptide': 621} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 596} Chain breaks: 3 Chain: "P" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 393 Classifications: {'peptide': 25} Modifications used: {'COO': 1} Link IDs: {'TRANS': 24} Chain breaks: 1 Chain: "D" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3390 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 10, 'TRANS': 202} Chain: "C" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 675 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 6, 'TRANS': 41} Chain: "E" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1381 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "B" Number of atoms: 5199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 5199 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 11, 'TRANS': 338} Chain breaks: 2 Time building chain proxies: 9.33, per 1000 atoms: 0.45 Number of scatterers: 20633 At special positions: 0 Unit cell: (108.456, 124.563, 138.523, 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 32 16.00 O 2063 8.00 N 1794 7.00 C 6637 6.00 H 10107 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS P1299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.19 Conformation dependent library (CDL) restraints added in 2.1 seconds 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2454 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 15 sheets defined 24.4% alpha, 31.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 189 through 195 Processing helix chain 'A' and resid 215 through 232 Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 280 through 288 Processing helix chain 'A' and resid 297 through 316 removed outlier: 3.564A pdb=" N LEU A 311 " --> pdb=" O ASP A 307 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 366 removed outlier: 3.758A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 removed outlier: 4.164A pdb=" N GLN A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS A 386 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 552 removed outlier: 3.817A pdb=" N TYR A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 726 through 730 Processing helix chain 'D' and resid 32 through 45 Processing helix chain 'D' and resid 47 through 62 Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 118 removed outlier: 3.544A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 removed outlier: 3.698A pdb=" N PHE D 128 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 135 removed outlier: 4.437A pdb=" N ASP D 134 " --> pdb=" O ASP D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 removed outlier: 3.691A pdb=" N ASP D 172 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR D 177 " --> pdb=" O ARG D 173 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU D 178 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG D 188 " --> pdb=" O TYR D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.749A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix removed outlier: 3.554A pdb=" N MET D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 241 removed outlier: 3.855A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 44 removed outlier: 3.811A pdb=" N ALA C 44 " --> pdb=" O TYR C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'E' and resid 23 through 27 removed outlier: 3.831A pdb=" N VAL E 26 " --> pdb=" O LEU E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'E' and resid 81 through 84 Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 183 removed outlier: 7.995A pdb=" N VAL A 256 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE A 180 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N VAL A 258 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ILE A 182 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE A 260 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER A 242 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 267 through 276 removed outlier: 6.224A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N SER A 269 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 12.422A pdb=" N VAL A 339 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 9.628A pdb=" N VAL A 271 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 11.726A pdb=" N VAL A 341 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 9.780A pdb=" N VAL A 273 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 348 through 355 removed outlier: 6.240A pdb=" N TYR A 348 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL A 414 " --> pdb=" O TYR A 348 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ARG A 350 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 12.759A pdb=" N TYR A 416 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 10.055A pdb=" N ILE A 352 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 12.338A pdb=" N VAL A 418 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 9.920A pdb=" N PHE A 354 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 11.940A pdb=" N GLU A 420 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LYS A 417 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL A 398 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LYS A 419 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 355 removed outlier: 6.240A pdb=" N TYR A 348 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL A 414 " --> pdb=" O TYR A 348 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ARG A 350 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 12.759A pdb=" N TYR A 416 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 10.055A pdb=" N ILE A 352 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 12.338A pdb=" N VAL A 418 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 9.920A pdb=" N PHE A 354 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 11.940A pdb=" N GLU A 420 " --> pdb=" O PHE A 354 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 802 through 805 removed outlier: 3.601A pdb=" N ALA A 770 " --> pdb=" O GLN A 789 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE A 791 " --> pdb=" O MET A 768 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 33 through 35 removed outlier: 3.926A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 33 through 35 removed outlier: 6.689A pdb=" N THR E 90 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASN E 106 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR E 92 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE E 104 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR E 94 " --> pdb=" O THR E 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 48 through 50 Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 68 removed outlier: 5.918A pdb=" N ASN B 85 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLU B 91 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 111 through 118 removed outlier: 6.307A pdb=" N GLY B 114 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TYR B 123 " --> pdb=" O GLY B 114 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR B 116 " --> pdb=" O HIS B 121 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N HIS B 121 " --> pdb=" O THR B 116 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASN B 135 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL B 141 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 158 removed outlier: 6.625A pdb=" N LEU B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR B 184 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA B 173 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 201 through 203 removed outlier: 6.833A pdb=" N VAL B 216 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLN B 229 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA B 218 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 252 through 254 removed outlier: 6.701A pdb=" N LEU B 267 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS B 280 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA B 269 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 290 through 292 removed outlier: 6.735A pdb=" N VAL B 305 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR B 318 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ALA B 307 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 331 through 333 removed outlier: 6.870A pdb=" N LEU B 346 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLN B 359 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TRP B 348 " --> pdb=" O VAL B 357 " (cutoff:3.500A) 471 hydrogen bonds defined for protein. 1281 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: 7.40 Time building geometry restraints manager: 14.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10107 1.03 - 1.23: 15 1.23 - 1.42: 4663 1.42 - 1.62: 6018 1.62 - 1.81: 60 Bond restraints: 20863 Sorted by residual: bond pdb=" CB TRP A 376 " pdb=" CG TRP A 376 " ideal model delta sigma weight residual 1.498 1.458 0.040 3.10e-02 1.04e+03 1.67e+00 bond pdb=" CB PHE A 354 " pdb=" CG PHE A 354 " ideal model delta sigma weight residual 1.502 1.475 0.027 2.30e-02 1.89e+03 1.34e+00 bond pdb=" CB ARG D 197 " pdb=" CG ARG D 197 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.17e+00 bond pdb=" CB PHE A 738 " pdb=" CG PHE A 738 " ideal model delta sigma weight residual 1.502 1.478 0.024 2.30e-02 1.89e+03 1.08e+00 bond pdb=" CA TYR A 348 " pdb=" CB TYR A 348 " ideal model delta sigma weight residual 1.534 1.510 0.024 2.33e-02 1.84e+03 1.06e+00 ... (remaining 20858 not shown) Histogram of bond angle deviations from ideal: 99.73 - 106.59: 317 106.59 - 113.45: 23833 113.45 - 120.30: 7195 120.30 - 127.16: 6020 127.16 - 134.02: 120 Bond angle restraints: 37485 Sorted by residual: angle pdb=" C TYR D 185 " pdb=" N THR D 186 " pdb=" CA THR D 186 " ideal model delta sigma weight residual 120.72 115.65 5.07 1.67e+00 3.59e-01 9.22e+00 angle pdb=" N ASP D 204 " pdb=" CA ASP D 204 " pdb=" C ASP D 204 " ideal model delta sigma weight residual 112.90 116.87 -3.97 1.31e+00 5.83e-01 9.18e+00 angle pdb=" N ASN E 103 " pdb=" CA ASN E 103 " pdb=" C ASN E 103 " ideal model delta sigma weight residual 108.99 113.65 -4.66 1.57e+00 4.06e-01 8.82e+00 angle pdb=" C ARG P1297 " pdb=" N TYR P1298 " pdb=" CA TYR P1298 " ideal model delta sigma weight residual 122.81 127.32 -4.51 1.57e+00 4.06e-01 8.25e+00 angle pdb=" N LEU B 192 " pdb=" CA LEU B 192 " pdb=" C LEU B 192 " ideal model delta sigma weight residual 110.80 116.74 -5.94 2.13e+00 2.20e-01 7.78e+00 ... (remaining 37480 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 9324 16.89 - 33.78: 341 33.78 - 50.67: 161 50.67 - 67.57: 78 67.57 - 84.46: 10 Dihedral angle restraints: 9914 sinusoidal: 5319 harmonic: 4595 Sorted by residual: dihedral pdb=" CA ASN A 422 " pdb=" C ASN A 422 " pdb=" N THR A 423 " pdb=" CA THR A 423 " ideal model delta harmonic sigma weight residual -180.00 -158.91 -21.09 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA LEU B 298 " pdb=" C LEU B 298 " pdb=" N VAL B 299 " pdb=" CA VAL B 299 " ideal model delta harmonic sigma weight residual 180.00 161.07 18.93 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA LEU B 192 " pdb=" C LEU B 192 " pdb=" N SER B 193 " pdb=" CA SER B 193 " ideal model delta harmonic sigma weight residual 180.00 -161.54 -18.46 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 9911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1033 0.038 - 0.075: 372 0.075 - 0.113: 134 0.113 - 0.150: 40 0.150 - 0.188: 4 Chirality restraints: 1583 Sorted by residual: chirality pdb=" CA TYR D 185 " pdb=" N TYR D 185 " pdb=" C TYR D 185 " pdb=" CB TYR D 185 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.83e-01 chirality pdb=" CA ARG A 366 " pdb=" N ARG A 366 " pdb=" C ARG A 366 " pdb=" CB ARG A 366 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CA ARG D 141 " pdb=" N ARG D 141 " pdb=" C ARG D 141 " pdb=" CB ARG D 141 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.15e-01 ... (remaining 1580 not shown) Planarity restraints: 3203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 282 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.17e+00 pdb=" C ALA A 282 " -0.052 2.00e-02 2.50e+03 pdb=" O ALA A 282 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU A 283 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 86 " 0.013 2.00e-02 2.50e+03 2.51e-02 6.30e+00 pdb=" C PRO D 86 " -0.043 2.00e-02 2.50e+03 pdb=" O PRO D 86 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU D 87 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 136 " -0.041 5.00e-02 4.00e+02 6.20e-02 6.14e+00 pdb=" N PRO D 137 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO D 137 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 137 " -0.034 5.00e-02 4.00e+02 ... (remaining 3200 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 661 2.15 - 2.76: 38966 2.76 - 3.38: 53372 3.38 - 3.99: 69854 3.99 - 4.60: 109055 Nonbonded interactions: 271908 Sorted by model distance: nonbonded pdb=" HZ3 LYS A 310 " pdb=" OD1 ASP A 380 " model vdw 1.541 1.850 nonbonded pdb=" HG SER A 360 " pdb=" OE2 GLU A 420 " model vdw 1.550 1.850 nonbonded pdb=" OD1 ASP D 134 " pdb=" HG SER D 180 " model vdw 1.558 1.850 nonbonded pdb=" H ILE A 352 " pdb=" OE2 GLU A 373 " model vdw 1.562 1.850 nonbonded pdb=" H ASP A 568 " pdb=" OD2 ASP A 605 " model vdw 1.569 1.850 ... (remaining 271903 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 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: 0.290 Extract box with map and model: 3.840 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 61.660 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 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 : 0.005 0.040 10756 Z= 0.295 Angle : 0.774 5.942 14613 Z= 0.465 Chirality : 0.046 0.188 1583 Planarity : 0.005 0.062 1925 Dihedral : 10.614 84.456 3877 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: 0.72 (0.22), residues: 1322 helix: 0.34 (0.28), residues: 278 sheet: 0.95 (0.24), residues: 430 loop : 0.35 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 576 HIS 0.007 0.001 HIS B 165 PHE 0.010 0.002 PHE A 586 TYR 0.021 0.002 TYR D 177 ARG 0.029 0.001 ARG A 734 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 410 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7438 (mt-10) REVERT: A 768 MET cc_start: 0.8555 (mtt) cc_final: 0.8221 (mtm) REVERT: D 56 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8359 (tm-30) REVERT: D 60 ASN cc_start: 0.8802 (m-40) cc_final: 0.8442 (m110) REVERT: D 82 ASN cc_start: 0.7879 (t0) cc_final: 0.7526 (t0) REVERT: C 41 TYR cc_start: 0.8158 (p90) cc_final: 0.7938 (p90) REVERT: C 42 LEU cc_start: 0.8907 (mt) cc_final: 0.8183 (tp) REVERT: E 31 ASP cc_start: 0.8453 (m-30) cc_final: 0.8006 (p0) REVERT: E 93 LEU cc_start: 0.9333 (mt) cc_final: 0.9116 (mt) REVERT: E 101 LEU cc_start: 0.8035 (tp) cc_final: 0.7756 (tp) REVERT: B 157 VAL cc_start: 0.8624 (t) cc_final: 0.7833 (t) REVERT: B 343 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7634 (mp0) outliers start: 0 outliers final: 0 residues processed: 410 average time/residue: 0.5445 time to fit residues: 307.6934 Evaluate side-chains 267 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 67 optimal weight: 10.0000 chunk 53 optimal weight: 0.0570 chunk 103 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 overall best weight: 2.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN A 651 ASN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 GLN ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 HIS ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.123 10756 Z= 0.310 Angle : 0.617 17.731 14613 Z= 0.346 Chirality : 0.045 0.343 1583 Planarity : 0.004 0.056 1925 Dihedral : 4.852 40.610 1475 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.09 % Allowed : 0.71 % Favored : 99.20 % 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: 0.99 (0.22), residues: 1322 helix: 1.35 (0.30), residues: 286 sheet: 0.78 (0.24), residues: 424 loop : 0.37 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 576 HIS 0.004 0.001 HIS C 51 PHE 0.019 0.002 PHE A 426 TYR 0.015 0.002 TYR B 123 ARG 0.003 0.000 ARG D 141 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 299 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ILE cc_start: 0.9440 (mt) cc_final: 0.9183 (tt) REVERT: A 287 LEU cc_start: 0.8453 (mt) cc_final: 0.8179 (mt) REVERT: A 420 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7404 (mt-10) REVERT: A 545 MET cc_start: 0.8465 (mtm) cc_final: 0.8190 (mtm) REVERT: A 765 ASN cc_start: 0.8518 (m-40) cc_final: 0.8183 (m-40) REVERT: D 82 ASN cc_start: 0.7903 (t0) cc_final: 0.7612 (t0) REVERT: E 31 ASP cc_start: 0.8457 (m-30) cc_final: 0.8158 (p0) REVERT: B 76 ASP cc_start: 0.8034 (t0) cc_final: 0.7776 (t0) REVERT: B 82 LYS cc_start: 0.7719 (mtmt) cc_final: 0.7473 (mtmt) REVERT: B 150 GLU cc_start: 0.8517 (mp0) cc_final: 0.7866 (mp0) REVERT: B 300 ASP cc_start: 0.8182 (t0) cc_final: 0.7873 (t0) REVERT: B 343 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7644 (mp0) outliers start: 1 outliers final: 0 residues processed: 300 average time/residue: 0.5122 time to fit residues: 211.2146 Evaluate side-chains 237 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 99 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS A 276 ASN A 534 ASN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 10756 Z= 0.271 Angle : 0.574 14.719 14613 Z= 0.317 Chirality : 0.044 0.294 1583 Planarity : 0.004 0.046 1925 Dihedral : 4.765 40.926 1475 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.18 % Allowed : 0.98 % Favored : 98.84 % 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: 0.75 (0.23), residues: 1322 helix: 1.33 (0.30), residues: 285 sheet: 0.37 (0.23), residues: 426 loop : 0.34 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 576 HIS 0.004 0.001 HIS B 165 PHE 0.012 0.002 PHE A 426 TYR 0.026 0.002 TYR D 79 ARG 0.003 0.000 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 275 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ILE cc_start: 0.9438 (mt) cc_final: 0.9204 (tt) REVERT: A 420 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7449 (mt-10) REVERT: A 741 MET cc_start: 0.7339 (ptm) cc_final: 0.7102 (ptt) REVERT: A 765 ASN cc_start: 0.8470 (m-40) cc_final: 0.7926 (m-40) REVERT: A 787 TYR cc_start: 0.6440 (t80) cc_final: 0.5993 (t80) REVERT: D 82 ASN cc_start: 0.8029 (t0) cc_final: 0.7595 (t0) REVERT: E 31 ASP cc_start: 0.8488 (m-30) cc_final: 0.8241 (p0) REVERT: B 76 ASP cc_start: 0.7875 (t0) cc_final: 0.7592 (t0) REVERT: B 82 LYS cc_start: 0.7834 (mttt) cc_final: 0.7500 (mtmt) REVERT: B 300 ASP cc_start: 0.8266 (t0) cc_final: 0.7846 (t0) REVERT: B 303 ASP cc_start: 0.8053 (m-30) cc_final: 0.6895 (m-30) REVERT: B 327 LEU cc_start: 0.8276 (mt) cc_final: 0.7788 (mt) outliers start: 2 outliers final: 0 residues processed: 277 average time/residue: 0.5204 time to fit residues: 201.6010 Evaluate side-chains 240 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 127 optimal weight: 9.9990 chunk 114 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN A 198 GLN ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN A 651 ASN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 HIS ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 10756 Z= 0.336 Angle : 0.589 13.021 14613 Z= 0.327 Chirality : 0.044 0.247 1583 Planarity : 0.004 0.056 1925 Dihedral : 4.826 42.934 1475 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.18 % Allowed : 1.25 % Favored : 98.57 % 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: 0.32 (0.23), residues: 1322 helix: 0.97 (0.30), residues: 285 sheet: 0.20 (0.23), residues: 425 loop : 0.00 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 317 HIS 0.004 0.001 HIS B 165 PHE 0.011 0.002 PHE A 426 TYR 0.018 0.002 TYR D 79 ARG 0.027 0.001 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 262 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ILE cc_start: 0.9446 (mt) cc_final: 0.9202 (tt) REVERT: A 420 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7040 (mt-10) REVERT: A 741 MET cc_start: 0.7393 (ptm) cc_final: 0.7173 (ptt) REVERT: A 787 TYR cc_start: 0.6555 (t80) cc_final: 0.6122 (t80) REVERT: D 40 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8239 (tp40) REVERT: D 56 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8112 (tm-30) REVERT: D 82 ASN cc_start: 0.7977 (t0) cc_final: 0.7746 (t0) REVERT: B 76 ASP cc_start: 0.7620 (t0) cc_final: 0.7370 (t0) REVERT: B 82 LYS cc_start: 0.7915 (mttt) cc_final: 0.7598 (mtmt) REVERT: B 127 GLU cc_start: 0.8540 (mp0) cc_final: 0.8331 (mp0) REVERT: B 161 LEU cc_start: 0.8584 (mm) cc_final: 0.8325 (mm) REVERT: B 189 MET cc_start: 0.8644 (pmm) cc_final: 0.7601 (pmm) outliers start: 2 outliers final: 0 residues processed: 264 average time/residue: 0.4974 time to fit residues: 182.5042 Evaluate side-chains 229 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 114 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN A 276 ASN A 651 ASN A 765 ASN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 10756 Z= 0.178 Angle : 0.517 12.578 14613 Z= 0.280 Chirality : 0.043 0.222 1583 Planarity : 0.003 0.035 1925 Dihedral : 4.592 41.351 1475 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.09 % Allowed : 1.25 % Favored : 98.66 % 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: 0.52 (0.23), residues: 1322 helix: 1.24 (0.30), residues: 285 sheet: 0.33 (0.24), residues: 412 loop : 0.05 (0.26), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 576 HIS 0.010 0.001 HIS B 165 PHE 0.031 0.001 PHE A 238 TYR 0.013 0.001 TYR C 41 ARG 0.003 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 265 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ILE cc_start: 0.9437 (mt) cc_final: 0.9188 (tt) REVERT: A 311 LEU cc_start: 0.8742 (tp) cc_final: 0.8523 (tt) REVERT: A 420 GLU cc_start: 0.7668 (mt-10) cc_final: 0.6974 (mt-10) REVERT: A 741 MET cc_start: 0.7405 (ptm) cc_final: 0.7174 (ptt) REVERT: A 787 TYR cc_start: 0.6552 (t80) cc_final: 0.6145 (t80) REVERT: D 56 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8089 (tm-30) REVERT: D 82 ASN cc_start: 0.8023 (t0) cc_final: 0.7755 (t0) REVERT: B 76 ASP cc_start: 0.7646 (t0) cc_final: 0.7356 (t0) REVERT: B 82 LYS cc_start: 0.7909 (mttt) cc_final: 0.7571 (mtmt) REVERT: B 127 GLU cc_start: 0.8555 (mp0) cc_final: 0.8311 (mp0) REVERT: B 161 LEU cc_start: 0.8642 (mm) cc_final: 0.8351 (mm) REVERT: B 189 MET cc_start: 0.8569 (pmm) cc_final: 0.7650 (pmm) REVERT: B 303 ASP cc_start: 0.7774 (m-30) cc_final: 0.6587 (m-30) REVERT: B 327 LEU cc_start: 0.8261 (mt) cc_final: 0.7892 (mt) outliers start: 1 outliers final: 0 residues processed: 266 average time/residue: 0.4982 time to fit residues: 183.9575 Evaluate side-chains 231 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.0470 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 67 optimal weight: 8.9990 chunk 123 optimal weight: 10.0000 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10756 Z= 0.182 Angle : 0.501 11.137 14613 Z= 0.273 Chirality : 0.042 0.202 1583 Planarity : 0.003 0.036 1925 Dihedral : 4.423 39.627 1475 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.09 % Allowed : 0.71 % Favored : 99.20 % 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: 0.56 (0.23), residues: 1322 helix: 1.39 (0.30), residues: 285 sheet: 0.32 (0.24), residues: 422 loop : 0.05 (0.27), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 317 HIS 0.006 0.001 HIS B 165 PHE 0.016 0.001 PHE A 428 TYR 0.013 0.001 TYR D 107 ARG 0.003 0.000 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 257 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ILE cc_start: 0.9443 (mt) cc_final: 0.9177 (tt) REVERT: A 311 LEU cc_start: 0.8711 (tp) cc_final: 0.8510 (tt) REVERT: A 420 GLU cc_start: 0.7634 (mt-10) cc_final: 0.6982 (mt-10) REVERT: A 428 PHE cc_start: 0.8107 (t80) cc_final: 0.7814 (t80) REVERT: A 646 MET cc_start: 0.8252 (ttp) cc_final: 0.7897 (ttp) REVERT: A 741 MET cc_start: 0.7429 (ptm) cc_final: 0.7216 (ptt) REVERT: A 765 ASN cc_start: 0.8300 (m110) cc_final: 0.8031 (m-40) REVERT: A 787 TYR cc_start: 0.6438 (t80) cc_final: 0.6074 (t80) REVERT: D 56 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8093 (tm-30) REVERT: D 82 ASN cc_start: 0.8010 (t0) cc_final: 0.7731 (t0) REVERT: D 109 MET cc_start: 0.8792 (mtp) cc_final: 0.8468 (mtt) REVERT: C 82 ILE cc_start: 0.8966 (pt) cc_final: 0.8649 (pt) REVERT: B 76 ASP cc_start: 0.7688 (t0) cc_final: 0.7397 (t0) REVERT: B 82 LYS cc_start: 0.7901 (mttt) cc_final: 0.7480 (mtmt) REVERT: B 127 GLU cc_start: 0.8584 (mp0) cc_final: 0.8299 (mp0) REVERT: B 161 LEU cc_start: 0.8618 (mm) cc_final: 0.8343 (mm) REVERT: B 189 MET cc_start: 0.8583 (pmm) cc_final: 0.7733 (pmm) REVERT: B 303 ASP cc_start: 0.7750 (m-30) cc_final: 0.6532 (m-30) REVERT: B 327 LEU cc_start: 0.8277 (mt) cc_final: 0.7895 (mt) outliers start: 1 outliers final: 0 residues processed: 258 average time/residue: 0.5179 time to fit residues: 185.8936 Evaluate side-chains 228 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 93 optimal weight: 0.0470 chunk 107 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 127 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN A 573 ASN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 10756 Z= 0.150 Angle : 0.485 9.780 14613 Z= 0.261 Chirality : 0.042 0.177 1583 Planarity : 0.003 0.064 1925 Dihedral : 4.287 37.093 1475 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.09 % Allowed : 0.54 % Favored : 99.38 % 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: 0.64 (0.23), residues: 1322 helix: 1.55 (0.31), residues: 285 sheet: 0.32 (0.24), residues: 422 loop : 0.09 (0.27), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 183 HIS 0.003 0.001 HIS B 165 PHE 0.017 0.001 PHE P1296 TYR 0.013 0.001 TYR A 794 ARG 0.009 0.000 ARG D 97 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 253 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ILE cc_start: 0.9438 (mt) cc_final: 0.9170 (tt) REVERT: A 311 LEU cc_start: 0.8700 (tp) cc_final: 0.8463 (tt) REVERT: A 420 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7169 (mt-10) REVERT: A 787 TYR cc_start: 0.6466 (t80) cc_final: 0.6056 (t80) REVERT: D 56 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8095 (tm-30) REVERT: D 82 ASN cc_start: 0.8026 (t0) cc_final: 0.7792 (t0) REVERT: D 109 MET cc_start: 0.8764 (mtp) cc_final: 0.8542 (mtt) REVERT: B 76 ASP cc_start: 0.7712 (t0) cc_final: 0.7435 (t0) REVERT: B 82 LYS cc_start: 0.7941 (mttt) cc_final: 0.7501 (mtmt) REVERT: B 127 GLU cc_start: 0.8617 (mp0) cc_final: 0.8387 (mp0) REVERT: B 161 LEU cc_start: 0.8612 (mm) cc_final: 0.8325 (mm) REVERT: B 189 MET cc_start: 0.8537 (pmm) cc_final: 0.7951 (pmm) outliers start: 1 outliers final: 0 residues processed: 254 average time/residue: 0.4723 time to fit residues: 167.1849 Evaluate side-chains 229 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 100 optimal weight: 0.5980 chunk 115 optimal weight: 9.9990 chunk 121 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10756 Z= 0.279 Angle : 0.537 9.321 14613 Z= 0.294 Chirality : 0.042 0.186 1583 Planarity : 0.004 0.057 1925 Dihedral : 4.418 38.787 1475 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % 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: 0.35 (0.23), residues: 1322 helix: 1.29 (0.30), residues: 285 sheet: 0.13 (0.24), residues: 425 loop : -0.07 (0.27), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 48 HIS 0.004 0.001 HIS B 165 PHE 0.012 0.002 PHE P1296 TYR 0.017 0.001 TYR A 348 ARG 0.009 0.001 ARG D 97 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ILE cc_start: 0.9455 (mt) cc_final: 0.9179 (tt) REVERT: A 231 LEU cc_start: 0.9232 (mt) cc_final: 0.9026 (mt) REVERT: A 311 LEU cc_start: 0.8726 (tp) cc_final: 0.8505 (tt) REVERT: A 420 GLU cc_start: 0.7636 (mt-10) cc_final: 0.6924 (mt-10) REVERT: A 787 TYR cc_start: 0.6535 (t80) cc_final: 0.6112 (t80) REVERT: D 56 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8108 (tm-30) REVERT: D 82 ASN cc_start: 0.8076 (t0) cc_final: 0.7780 (t0) REVERT: B 76 ASP cc_start: 0.7604 (t0) cc_final: 0.7369 (t0) REVERT: B 82 LYS cc_start: 0.7978 (mttt) cc_final: 0.7537 (mtmt) REVERT: B 161 LEU cc_start: 0.8584 (mm) cc_final: 0.8345 (mm) REVERT: B 189 MET cc_start: 0.8867 (pmm) cc_final: 0.7956 (pmm) REVERT: B 303 ASP cc_start: 0.7732 (m-30) cc_final: 0.7246 (m-30) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.4872 time to fit residues: 164.4118 Evaluate side-chains 225 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.4980 chunk 121 optimal weight: 4.9990 chunk 71 optimal weight: 0.1980 chunk 51 optimal weight: 6.9990 chunk 93 optimal weight: 0.3980 chunk 36 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 112 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 125 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.5252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 10756 Z= 0.132 Angle : 0.484 8.696 14613 Z= 0.258 Chirality : 0.042 0.159 1583 Planarity : 0.003 0.064 1925 Dihedral : 4.202 35.805 1475 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.24), residues: 1322 helix: 1.58 (0.31), residues: 285 sheet: 0.26 (0.25), residues: 403 loop : 0.02 (0.27), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 576 HIS 0.002 0.001 HIS C 51 PHE 0.018 0.001 PHE P1296 TYR 0.013 0.001 TYR C 41 ARG 0.011 0.000 ARG D 97 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ILE cc_start: 0.9448 (mt) cc_final: 0.9160 (tt) REVERT: A 231 LEU cc_start: 0.9197 (mt) cc_final: 0.8993 (mt) REVERT: A 287 LEU cc_start: 0.8418 (mt) cc_final: 0.8116 (mt) REVERT: A 420 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7202 (mt-10) REVERT: D 56 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8129 (tm-30) REVERT: D 82 ASN cc_start: 0.8073 (t0) cc_final: 0.7776 (t0) REVERT: B 76 ASP cc_start: 0.7760 (t0) cc_final: 0.7476 (t0) REVERT: B 82 LYS cc_start: 0.7980 (mttt) cc_final: 0.7532 (mtmt) REVERT: B 161 LEU cc_start: 0.8569 (mm) cc_final: 0.8328 (mm) REVERT: B 189 MET cc_start: 0.8787 (pmm) cc_final: 0.7741 (pmm) REVERT: B 303 ASP cc_start: 0.7697 (m-30) cc_final: 0.7255 (m-30) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.5263 time to fit residues: 190.2768 Evaluate side-chains 228 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 4.9990 chunk 87 optimal weight: 0.0670 chunk 131 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 64 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.5401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10756 Z= 0.244 Angle : 0.517 8.215 14613 Z= 0.280 Chirality : 0.042 0.159 1583 Planarity : 0.003 0.039 1925 Dihedral : 4.240 36.419 1475 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.23), residues: 1322 helix: 1.47 (0.31), residues: 285 sheet: 0.20 (0.24), residues: 414 loop : -0.07 (0.27), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 317 HIS 0.004 0.001 HIS B 165 PHE 0.017 0.001 PHE A 428 TYR 0.015 0.001 TYR A 348 ARG 0.005 0.000 ARG D 97 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ILE cc_start: 0.9464 (mt) cc_final: 0.9169 (tt) REVERT: A 231 LEU cc_start: 0.9220 (mt) cc_final: 0.9009 (mt) REVERT: A 382 VAL cc_start: 0.8347 (t) cc_final: 0.7519 (m) REVERT: A 420 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7384 (mt-10) REVERT: A 787 TYR cc_start: 0.6516 (t80) cc_final: 0.6087 (t80) REVERT: D 56 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8104 (tm-30) REVERT: D 82 ASN cc_start: 0.8118 (t0) cc_final: 0.7817 (t0) REVERT: B 76 ASP cc_start: 0.7645 (t0) cc_final: 0.7396 (t0) REVERT: B 82 LYS cc_start: 0.7943 (mttt) cc_final: 0.7503 (mtmt) REVERT: B 189 MET cc_start: 0.8816 (pmm) cc_final: 0.7817 (pmm) REVERT: B 303 ASP cc_start: 0.7760 (m-30) cc_final: 0.7336 (m-30) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.4865 time to fit residues: 169.4173 Evaluate side-chains 227 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 0.0980 chunk 104 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 13 optimal weight: 0.0970 chunk 19 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 765 ASN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** 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 = 0.3957 r_free = 0.3957 target = 0.157679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.107351 restraints weight = 54414.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.112789 restraints weight = 26311.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.116265 restraints weight = 17248.840| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.5464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 10756 Z= 0.137 Angle : 0.490 7.743 14613 Z= 0.259 Chirality : 0.042 0.156 1583 Planarity : 0.004 0.082 1925 Dihedral : 4.098 33.404 1475 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.24), residues: 1322 helix: 1.68 (0.31), residues: 285 sheet: 0.31 (0.25), residues: 397 loop : -0.05 (0.27), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 317 HIS 0.002 0.001 HIS C 51 PHE 0.015 0.001 PHE A 440 TYR 0.019 0.001 TYR A 230 ARG 0.009 0.001 ARG D 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5027.30 seconds wall clock time: 90 minutes 6.82 seconds (5406.82 seconds total)