Starting phenix.real_space_refine on Wed Apr 10 19:26:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt1_26107/04_2024/7tt1_26107.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt1_26107/04_2024/7tt1_26107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt1_26107/04_2024/7tt1_26107.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt1_26107/04_2024/7tt1_26107.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt1_26107/04_2024/7tt1_26107.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt1_26107/04_2024/7tt1_26107.pdb" } resolution = 4.3 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= 0.007 sd= 0.056 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 6558 2.51 5 N 1773 2.21 5 O 2030 1.98 5 H 10005 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 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 394": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 428": "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 ASP 512": "OD1" <-> "OD2" Residue "A TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 550": "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 652": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 663": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 674": "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 688": "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 PHE 791": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 76": "OD1" <-> "OD2" Residue "B PHE 204": "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 PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 367": "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 "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 127": "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 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 205": "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" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 20398 Number of models: 1 Model: "" Number of chains: 6 Chain: "P" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 287 Classifications: {'peptide': 18} Modifications used: {'COO': 1} Link IDs: {'TRANS': 17} Chain breaks: 1 Chain: "A" Number of atoms: 9476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 9476 Classifications: {'peptide': 612} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 587} Chain breaks: 4 Chain: "B" Number of atoms: 5187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 5187 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 11, 'TRANS': 337} Chain breaks: 2 Chain: "E" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1382 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} 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: 676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 676 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 6, 'TRANS': 41} Time building chain proxies: 9.05, per 1000 atoms: 0.44 Number of scatterers: 20398 At special positions: 0 Unit cell: (113.825, 122.415, 137.449, 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 2030 8.00 N 1773 7.00 C 6558 6.00 H 10005 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS P1299 " - pdb=" SG CYS A 425 " 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: 16.32 Conformation dependent library (CDL) restraints added in 2.0 seconds 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2422 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 15 sheets defined 23.8% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 189 through 195 Processing helix chain 'A' and resid 218 through 232 removed outlier: 4.134A pdb=" N ASP A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 252 Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 297 through 316 Processing helix chain 'A' and resid 361 through 367 removed outlier: 4.105A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 389 removed outlier: 3.823A pdb=" N VAL A 382 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 726 through 731 Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 51 through 60 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: 3.877A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 127 Processing helix chain 'D' and resid 131 through 135 removed outlier: 4.366A 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 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.782A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix removed outlier: 3.765A pdb=" N GLU D 219 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN D 220 " --> pdb=" O PRO D 216 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 241 removed outlier: 3.772A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 44 removed outlier: 3.538A pdb=" N ALA C 44 " --> pdb=" O TYR C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 Processing sheet with id=AA1, first strand: chain 'P' and resid 1272 through 1276 removed outlier: 3.784A pdb=" N ARG P1273 " --> pdb=" O ARG P1297 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY P1275 " --> pdb=" O ASN P1295 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN P1295 " --> pdb=" O GLY P1275 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 445 " --> pdb=" O CYS A 425 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE A 440 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASN A 523 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 532 " --> pdb=" O ASP A 569 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP A 569 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A 600 " --> pdb=" O TYR A 608 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 710 " --> pdb=" O TRP A 745 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 179 through 183 removed outlier: 4.061A pdb=" N GLN A 179 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER A 242 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 276 removed outlier: 6.525A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N SER A 269 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 12.975A pdb=" N VAL A 339 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 10.287A pdb=" N VAL A 271 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 12.056A pdb=" N VAL A 341 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 9.800A pdb=" N VAL A 273 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 355 removed outlier: 6.267A pdb=" N TYR A 348 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL A 414 " --> pdb=" O TYR A 348 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ARG A 350 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 12.940A pdb=" N TYR A 416 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 10.073A pdb=" N ILE A 352 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 12.554A pdb=" N VAL A 418 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 9.980A pdb=" N PHE A 354 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 11.845A pdb=" N GLU A 420 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 415 " --> pdb=" O ASP A 401 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS A 419 " --> pdb=" O THR A 397 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 671 through 674 removed outlier: 4.923A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TYR A 674 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N SER A 702 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.026A pdb=" N GLY B 385 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE B 380 " --> pdb=" O TYR B 388 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 68 removed outlier: 5.707A pdb=" N ASN B 85 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLU B 91 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 111 through 118 removed outlier: 6.268A pdb=" N GLY B 114 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLY B 125 " --> pdb=" O GLY B 114 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLN B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL B 131 " --> pdb=" O GLN B 144 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN B 144 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ALA B 133 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 156 through 157 removed outlier: 3.646A pdb=" N VAL B 156 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N THR B 184 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ALA B 173 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 201 through 203 removed outlier: 3.732A pdb=" N THR B 201 " --> pdb=" O VAL B 208 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TRP B 228 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU B 220 " --> pdb=" O MET B 226 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N MET B 226 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 252 through 254 removed outlier: 3.566A pdb=" N ASN B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TRP B 279 " --> pdb=" O ALA B 269 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 290 through 292 removed outlier: 3.860A pdb=" N ILE B 290 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET B 306 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL B 305 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR B 318 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA B 307 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 331 through 333 removed outlier: 6.738A pdb=" N LEU B 346 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLN B 359 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TRP B 348 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.893A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 32 through 35 removed outlier: 6.825A pdb=" N THR E 90 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASN E 106 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR E 92 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE E 104 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR E 94 " --> pdb=" O THR E 102 " (cutoff:3.500A) 473 hydrogen bonds defined for protein. 1299 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: 7.43 Time building geometry restraints manager: 16.85 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: 10005 1.03 - 1.23: 361 1.23 - 1.43: 4284 1.43 - 1.63: 5916 1.63 - 1.83: 60 Bond restraints: 20626 Sorted by residual: bond pdb=" CA PRO C 84 " pdb=" C PRO C 84 " ideal model delta sigma weight residual 1.514 1.522 -0.007 5.50e-03 3.31e+04 1.82e+00 bond pdb=" C THR B 43 " pdb=" O THR B 43 " ideal model delta sigma weight residual 1.235 1.229 0.006 4.70e-03 4.53e+04 1.58e+00 bond pdb=" CA TYR A 348 " pdb=" CB TYR A 348 " ideal model delta sigma weight residual 1.534 1.508 0.026 2.33e-02 1.84e+03 1.25e+00 bond pdb=" CB LEU E 63 " pdb=" CG LEU E 63 " ideal model delta sigma weight residual 1.530 1.509 0.021 2.00e-02 2.50e+03 1.15e+00 bond pdb=" C LEU A 365 " pdb=" N ARG A 366 " ideal model delta sigma weight residual 1.335 1.320 0.015 1.38e-02 5.25e+03 1.13e+00 ... (remaining 20621 not shown) Histogram of bond angle deviations from ideal: 98.95 - 105.97: 246 105.97 - 113.00: 23355 113.00 - 120.03: 6312 120.03 - 127.05: 7014 127.05 - 134.08: 123 Bond angle restraints: 37050 Sorted by residual: angle pdb=" N MET D 225 " pdb=" CA MET D 225 " pdb=" C MET D 225 " ideal model delta sigma weight residual 109.76 103.34 6.42 1.64e+00 3.72e-01 1.53e+01 angle pdb=" N PHE A 738 " pdb=" CA PHE A 738 " pdb=" C PHE A 738 " ideal model delta sigma weight residual 109.07 114.32 -5.25 1.52e+00 4.33e-01 1.19e+01 angle pdb=" N PHE A 737 " pdb=" CA PHE A 737 " pdb=" C PHE A 737 " ideal model delta sigma weight residual 109.76 104.31 5.45 1.64e+00 3.72e-01 1.10e+01 angle pdb=" N ASP A 746 " pdb=" CA ASP A 746 " pdb=" C ASP A 746 " ideal model delta sigma weight residual 108.73 114.09 -5.36 1.63e+00 3.76e-01 1.08e+01 angle pdb=" N GLN D 224 " pdb=" CA GLN D 224 " pdb=" C GLN D 224 " ideal model delta sigma weight residual 111.82 108.01 3.81 1.16e+00 7.43e-01 1.08e+01 ... (remaining 37045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 9275 17.86 - 35.73: 303 35.73 - 53.59: 167 53.59 - 71.46: 49 71.46 - 89.32: 14 Dihedral angle restraints: 9808 sinusoidal: 5268 harmonic: 4540 Sorted by residual: dihedral pdb=" CA GLY A 482 " pdb=" C GLY A 482 " pdb=" N VAL A 483 " pdb=" CA VAL A 483 " ideal model delta harmonic sigma weight residual 180.00 159.04 20.96 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA ILE A 519 " pdb=" C ILE A 519 " pdb=" N ASN A 520 " pdb=" CA ASN A 520 " ideal model delta harmonic sigma weight residual 180.00 159.45 20.55 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CB CYS A 690 " pdb=" SG CYS A 690 " pdb=" SG CYS A 700 " pdb=" CB CYS A 700 " ideal model delta sinusoidal sigma weight residual -86.00 -118.74 32.74 1 1.00e+01 1.00e-02 1.53e+01 ... (remaining 9805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 921 0.032 - 0.063: 374 0.063 - 0.095: 162 0.095 - 0.127: 86 0.127 - 0.158: 21 Chirality restraints: 1564 Sorted by residual: chirality pdb=" CA TYR A 585 " pdb=" N TYR A 585 " pdb=" C TYR A 585 " pdb=" CB TYR A 585 " 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 ILE A 240 " pdb=" N ILE A 240 " pdb=" C ILE A 240 " pdb=" CB ILE A 240 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CA ILE A 806 " pdb=" N ILE A 806 " pdb=" C ILE A 806 " pdb=" CB ILE A 806 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.68e-01 ... (remaining 1561 not shown) Planarity restraints: 3157 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO D 86 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.22e+00 pdb=" C PRO D 86 " -0.053 2.00e-02 2.50e+03 pdb=" O PRO D 86 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU D 87 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 33 " 0.014 2.00e-02 2.50e+03 2.72e-02 7.38e+00 pdb=" C ASN D 33 " -0.047 2.00e-02 2.50e+03 pdb=" O ASN D 33 " 0.017 2.00e-02 2.50e+03 pdb=" N GLU D 34 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 544 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.36e+00 pdb=" C ALA A 544 " 0.036 2.00e-02 2.50e+03 pdb=" O ALA A 544 " -0.014 2.00e-02 2.50e+03 pdb=" N MET A 545 " -0.012 2.00e-02 2.50e+03 ... (remaining 3154 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.09: 441 2.09 - 2.72: 34873 2.72 - 3.35: 54979 3.35 - 3.97: 71350 3.97 - 4.60: 111354 Nonbonded interactions: 272997 Sorted by model distance: nonbonded pdb=" OD2 ASP A 624 " pdb=" HZ2 LYS A 626 " model vdw 1.466 1.850 nonbonded pdb=" OD1 ASP A 569 " pdb=" H ASP A 605 " model vdw 1.493 1.850 nonbonded pdb=" H ASN B 85 " pdb=" O LYS B 90 " model vdw 1.497 1.850 nonbonded pdb=" HG SER B 285 " pdb=" O VAL B 299 " model vdw 1.501 1.850 nonbonded pdb=" H ASN B 350 " pdb=" O ARG B 355 " model vdw 1.527 1.850 ... (remaining 272992 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: 1.230 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: 0.310 Extract box with map and model: 4.040 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 64.010 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 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:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10621 Z= 0.237 Angle : 0.817 6.619 14427 Z= 0.507 Chirality : 0.047 0.158 1564 Planarity : 0.004 0.037 1896 Dihedral : 10.413 89.321 3826 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: 0.92 (0.22), residues: 1303 helix: 0.36 (0.28), residues: 284 sheet: 1.13 (0.25), residues: 384 loop : 0.56 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP D 191 HIS 0.009 0.002 HIS B 165 PHE 0.026 0.002 PHE A 586 TYR 0.016 0.003 TYR A 432 ARG 0.030 0.003 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 387 time to evaluate : 1.830 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: A 186 HIS cc_start: 0.8289 (m-70) cc_final: 0.8029 (p90) REVERT: A 227 ARG cc_start: 0.8908 (mtp180) cc_final: 0.8527 (mtp85) REVERT: A 232 ASP cc_start: 0.8983 (m-30) cc_final: 0.8769 (m-30) REVERT: A 574 TYR cc_start: 0.8655 (p90) cc_final: 0.8411 (p90) REVERT: A 719 ILE cc_start: 0.8267 (mt) cc_final: 0.7832 (mt) REVERT: B 164 ILE cc_start: 0.9347 (mm) cc_final: 0.9141 (mp) REVERT: B 296 ILE cc_start: 0.9062 (mt) cc_final: 0.8764 (mt) REVERT: E 111 SER cc_start: 0.7751 (m) cc_final: 0.7516 (p) REVERT: D 58 LEU cc_start: 0.8090 (mt) cc_final: 0.7842 (mt) REVERT: D 60 ASN cc_start: 0.8521 (m-40) cc_final: 0.8157 (m110) REVERT: D 171 LYS cc_start: 0.8567 (mtpt) cc_final: 0.8360 (ttmm) REVERT: D 180 SER cc_start: 0.8788 (m) cc_final: 0.8407 (t) REVERT: D 198 VAL cc_start: 0.9434 (t) cc_final: 0.9081 (t) outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 0.5851 time to fit residues: 307.0497 Evaluate side-chains 231 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 101 optimal weight: 0.0980 chunk 39 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 GLN B 170 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10621 Z= 0.298 Angle : 0.621 6.110 14427 Z= 0.356 Chirality : 0.044 0.170 1564 Planarity : 0.004 0.040 1896 Dihedral : 5.224 86.728 1455 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.22), residues: 1303 helix: 1.22 (0.29), residues: 284 sheet: 0.61 (0.24), residues: 411 loop : 0.29 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 376 HIS 0.008 0.002 HIS A 533 PHE 0.022 0.002 PHE A 738 TYR 0.020 0.002 TYR D 205 ARG 0.012 0.001 ARG B 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.650 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: A 196 HIS cc_start: 0.8880 (m90) cc_final: 0.8632 (m90) REVERT: A 232 ASP cc_start: 0.8920 (m-30) cc_final: 0.8697 (m-30) REVERT: A 408 SER cc_start: 0.8880 (t) cc_final: 0.8419 (m) REVERT: E 101 LEU cc_start: 0.7961 (tp) cc_final: 0.7476 (tt) REVERT: D 58 LEU cc_start: 0.8122 (mt) cc_final: 0.7856 (mt) REVERT: D 60 ASN cc_start: 0.8561 (m-40) cc_final: 0.8128 (m110) REVERT: D 79 TYR cc_start: 0.8706 (m-80) cc_final: 0.8382 (m-10) REVERT: D 180 SER cc_start: 0.8914 (m) cc_final: 0.8612 (t) REVERT: D 198 VAL cc_start: 0.9320 (t) cc_final: 0.9045 (t) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.5320 time to fit residues: 196.9767 Evaluate side-chains 208 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 chunk 116 optimal weight: 0.0870 chunk 40 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10621 Z= 0.270 Angle : 0.564 5.056 14427 Z= 0.321 Chirality : 0.043 0.215 1564 Planarity : 0.004 0.040 1896 Dihedral : 5.150 86.805 1455 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % 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 (0.22), residues: 1303 helix: 1.17 (0.30), residues: 292 sheet: 0.38 (0.24), residues: 413 loop : 0.12 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 376 HIS 0.007 0.001 HIS A 533 PHE 0.018 0.002 PHE A 426 TYR 0.020 0.002 TYR B 123 ARG 0.004 0.001 ARG E 29 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 1.769 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: A 232 ASP cc_start: 0.8958 (m-30) cc_final: 0.8672 (m-30) REVERT: A 371 GLN cc_start: 0.8312 (tp40) cc_final: 0.7660 (tp-100) REVERT: A 648 PHE cc_start: 0.7940 (p90) cc_final: 0.7717 (p90) REVERT: B 306 MET cc_start: 0.8718 (mpp) cc_final: 0.8498 (mpp) REVERT: D 58 LEU cc_start: 0.8177 (mt) cc_final: 0.7951 (mt) REVERT: D 60 ASN cc_start: 0.8507 (m-40) cc_final: 0.8121 (m110) REVERT: D 166 ARG cc_start: 0.8196 (mtt90) cc_final: 0.7939 (mtt90) REVERT: D 180 SER cc_start: 0.8877 (m) cc_final: 0.8618 (t) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.5506 time to fit residues: 184.6837 Evaluate side-chains 196 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 chunk 12 optimal weight: 0.1980 chunk 56 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 33 optimal weight: 0.0970 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10621 Z= 0.234 Angle : 0.519 5.075 14427 Z= 0.293 Chirality : 0.042 0.156 1564 Planarity : 0.004 0.040 1896 Dihedral : 5.039 82.422 1455 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: 0.47 (0.23), residues: 1303 helix: 1.08 (0.30), residues: 296 sheet: 0.36 (0.24), residues: 423 loop : 0.01 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 546 HIS 0.005 0.001 HIS A 533 PHE 0.019 0.001 PHE A 738 TYR 0.012 0.002 TYR A 255 ARG 0.003 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 1.539 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: A 232 ASP cc_start: 0.8950 (m-30) cc_final: 0.8639 (m-30) REVERT: A 371 GLN cc_start: 0.8325 (tp40) cc_final: 0.7630 (tp-100) REVERT: A 372 MET cc_start: 0.8627 (mpp) cc_final: 0.7944 (mpp) REVERT: A 648 PHE cc_start: 0.8022 (p90) cc_final: 0.7743 (p90) REVERT: D 58 LEU cc_start: 0.8185 (mt) cc_final: 0.7964 (mt) REVERT: D 60 ASN cc_start: 0.8528 (m-40) cc_final: 0.8147 (m110) REVERT: D 79 TYR cc_start: 0.8810 (m-80) cc_final: 0.8250 (m-10) REVERT: D 116 ASN cc_start: 0.8642 (m-40) cc_final: 0.8223 (t0) REVERT: D 180 SER cc_start: 0.8816 (m) cc_final: 0.8529 (t) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.5257 time to fit residues: 169.3683 Evaluate side-chains 194 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 0.6980 chunk 111 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 overall best weight: 3.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN B 324 HIS B 347 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 10621 Z= 0.399 Angle : 0.598 5.935 14427 Z= 0.342 Chirality : 0.043 0.177 1564 Planarity : 0.005 0.045 1896 Dihedral : 5.251 78.923 1455 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % 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: -0.07 (0.23), residues: 1303 helix: 0.51 (0.29), residues: 295 sheet: 0.07 (0.24), residues: 420 loop : -0.28 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 376 HIS 0.005 0.001 HIS A 533 PHE 0.015 0.002 PHE E 77 TYR 0.036 0.002 TYR B 123 ARG 0.005 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 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: P 1293 ASN cc_start: 0.8234 (t0) cc_final: 0.7825 (t0) REVERT: A 284 ILE cc_start: 0.7677 (mm) cc_final: 0.6771 (tp) REVERT: A 648 PHE cc_start: 0.8124 (p90) cc_final: 0.7773 (p90) REVERT: D 79 TYR cc_start: 0.8863 (m-80) cc_final: 0.8336 (m-10) REVERT: D 116 ASN cc_start: 0.8755 (m-40) cc_final: 0.8381 (t0) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.5330 time to fit residues: 162.5156 Evaluate side-chains 181 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 120 optimal weight: 0.9980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10621 Z= 0.191 Angle : 0.502 4.565 14427 Z= 0.282 Chirality : 0.042 0.169 1564 Planarity : 0.004 0.046 1896 Dihedral : 5.023 77.767 1455 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: 0.11 (0.23), residues: 1303 helix: 0.87 (0.30), residues: 294 sheet: 0.14 (0.24), residues: 421 loop : -0.26 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 546 HIS 0.004 0.001 HIS A 533 PHE 0.022 0.001 PHE A 738 TYR 0.014 0.001 TYR B 123 ARG 0.005 0.000 ARG D 132 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.605 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: P 1293 ASN cc_start: 0.8500 (t0) cc_final: 0.7890 (t0) REVERT: A 232 ASP cc_start: 0.8849 (m-30) cc_final: 0.8611 (m-30) REVERT: A 284 ILE cc_start: 0.7625 (mm) cc_final: 0.6748 (tp) REVERT: A 371 GLN cc_start: 0.8134 (tp40) cc_final: 0.7791 (tp-100) REVERT: A 372 MET cc_start: 0.8726 (mpp) cc_final: 0.7956 (mpp) REVERT: A 648 PHE cc_start: 0.8039 (p90) cc_final: 0.7732 (p90) REVERT: D 60 ASN cc_start: 0.8564 (m-40) cc_final: 0.8190 (m110) REVERT: D 116 ASN cc_start: 0.8512 (m-40) cc_final: 0.8109 (t0) REVERT: D 218 MET cc_start: 0.7602 (mtp) cc_final: 0.7342 (mtt) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.5524 time to fit residues: 170.6297 Evaluate side-chains 188 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.5310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10621 Z= 0.337 Angle : 0.567 5.510 14427 Z= 0.321 Chirality : 0.042 0.163 1564 Planarity : 0.004 0.050 1896 Dihedral : 5.192 76.129 1455 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.09 % Allowed : 0.90 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.23), residues: 1303 helix: 0.34 (0.30), residues: 299 sheet: -0.06 (0.24), residues: 422 loop : -0.47 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 376 HIS 0.004 0.001 HIS B 347 PHE 0.018 0.002 PHE A 738 TYR 0.015 0.002 TYR A 348 ARG 0.005 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 219 time to evaluate : 1.498 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: P 1293 ASN cc_start: 0.8524 (t0) cc_final: 0.7971 (t0) REVERT: A 224 GLU cc_start: 0.8517 (mp0) cc_final: 0.8123 (mp0) REVERT: A 232 ASP cc_start: 0.8901 (m-30) cc_final: 0.8616 (m-30) REVERT: A 284 ILE cc_start: 0.7673 (mm) cc_final: 0.6859 (tp) REVERT: A 371 GLN cc_start: 0.8448 (tp40) cc_final: 0.7614 (tm-30) REVERT: A 372 MET cc_start: 0.8687 (mpp) cc_final: 0.8347 (mpp) REVERT: A 386 LYS cc_start: 0.8882 (tttp) cc_final: 0.8655 (tttp) REVERT: A 648 PHE cc_start: 0.8127 (p90) cc_final: 0.7680 (p90) REVERT: B 299 VAL cc_start: 0.8869 (t) cc_final: 0.8668 (t) REVERT: D 60 ASN cc_start: 0.8606 (m-40) cc_final: 0.8246 (m110) REVERT: D 116 ASN cc_start: 0.8594 (m-40) cc_final: 0.8221 (t0) outliers start: 1 outliers final: 1 residues processed: 220 average time/residue: 0.5146 time to fit residues: 157.0171 Evaluate side-chains 187 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 186 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 61 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN A 606 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.5400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10621 Z= 0.210 Angle : 0.507 4.957 14427 Z= 0.283 Chirality : 0.042 0.153 1564 Planarity : 0.004 0.050 1896 Dihedral : 5.029 75.350 1455 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.09 % Allowed : 0.63 % Favored : 99.28 % 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: -0.18 (0.23), residues: 1303 helix: 0.62 (0.30), residues: 298 sheet: -0.05 (0.24), residues: 424 loop : -0.42 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 546 HIS 0.003 0.001 HIS A 533 PHE 0.011 0.001 PHE A 238 TYR 0.028 0.002 TYR A 618 ARG 0.006 0.000 ARG B 215 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 222 time to evaluate : 1.837 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: P 1276 LEU cc_start: 0.7425 (tp) cc_final: 0.7213 (tt) REVERT: P 1293 ASN cc_start: 0.8632 (t0) cc_final: 0.7959 (t0) REVERT: A 232 ASP cc_start: 0.8865 (m-30) cc_final: 0.8607 (m-30) REVERT: A 284 ILE cc_start: 0.7654 (mm) cc_final: 0.6834 (tp) REVERT: A 305 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7786 (mt-10) REVERT: A 648 PHE cc_start: 0.8013 (p90) cc_final: 0.7722 (p90) REVERT: D 60 ASN cc_start: 0.8562 (m-40) cc_final: 0.8223 (m110) REVERT: D 116 ASN cc_start: 0.8456 (m-40) cc_final: 0.8150 (t0) outliers start: 1 outliers final: 1 residues processed: 223 average time/residue: 0.5518 time to fit residues: 171.2806 Evaluate side-chains 190 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 189 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 69 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 90 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 109 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.5550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10621 Z= 0.308 Angle : 0.550 4.936 14427 Z= 0.310 Chirality : 0.042 0.178 1564 Planarity : 0.004 0.051 1896 Dihedral : 5.156 74.591 1455 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.09 % Allowed : 0.09 % 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: -0.42 (0.23), residues: 1303 helix: 0.42 (0.30), residues: 299 sheet: -0.32 (0.23), residues: 427 loop : -0.48 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 376 HIS 0.004 0.001 HIS A 280 PHE 0.014 0.002 PHE A 238 TYR 0.027 0.002 TYR A 618 ARG 0.005 0.001 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 218 time to evaluate : 1.574 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: P 1276 LEU cc_start: 0.7438 (tp) cc_final: 0.7231 (tt) REVERT: P 1293 ASN cc_start: 0.8658 (t0) cc_final: 0.8016 (t0) REVERT: A 232 ASP cc_start: 0.8846 (m-30) cc_final: 0.8556 (m-30) REVERT: A 284 ILE cc_start: 0.7624 (mm) cc_final: 0.6628 (tp) REVERT: A 305 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7880 (mt-10) REVERT: A 648 PHE cc_start: 0.8095 (p90) cc_final: 0.7653 (p90) REVERT: A 732 SER cc_start: 0.8888 (m) cc_final: 0.8642 (p) REVERT: B 226 MET cc_start: 0.8626 (tpp) cc_final: 0.8193 (tmm) REVERT: D 53 THR cc_start: 0.8754 (m) cc_final: 0.8454 (p) REVERT: D 60 ASN cc_start: 0.8581 (m-40) cc_final: 0.8240 (m110) outliers start: 1 outliers final: 0 residues processed: 219 average time/residue: 0.5416 time to fit residues: 165.8041 Evaluate side-chains 192 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 79 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN A 803 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.5678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10621 Z= 0.191 Angle : 0.498 5.101 14427 Z= 0.277 Chirality : 0.042 0.162 1564 Planarity : 0.004 0.051 1896 Dihedral : 4.982 73.481 1455 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.09 % Allowed : 0.18 % 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: -0.13 (0.23), residues: 1303 helix: 0.89 (0.31), residues: 289 sheet: -0.15 (0.23), residues: 425 loop : -0.41 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 546 HIS 0.003 0.001 HIS A 196 PHE 0.011 0.001 PHE E 77 TYR 0.020 0.001 TYR A 618 ARG 0.004 0.000 ARG A 366 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 214 time to evaluate : 1.614 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: P 1276 LEU cc_start: 0.7409 (tp) cc_final: 0.7196 (tt) REVERT: P 1293 ASN cc_start: 0.8629 (t0) cc_final: 0.8000 (t0) REVERT: A 232 ASP cc_start: 0.8869 (m-30) cc_final: 0.8584 (m-30) REVERT: A 305 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7994 (mt-10) REVERT: A 648 PHE cc_start: 0.7997 (p90) cc_final: 0.7741 (p90) REVERT: A 732 SER cc_start: 0.8856 (m) cc_final: 0.8644 (p) REVERT: B 226 MET cc_start: 0.8718 (tpp) cc_final: 0.8284 (tmm) REVERT: D 60 ASN cc_start: 0.8525 (m-40) cc_final: 0.8268 (m110) REVERT: D 116 ASN cc_start: 0.8456 (m-40) cc_final: 0.8141 (t0) outliers start: 1 outliers final: 1 residues processed: 215 average time/residue: 0.5200 time to fit residues: 154.3244 Evaluate side-chains 187 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 186 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 89 optimal weight: 0.0970 chunk 5 optimal weight: 3.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN A 606 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.133933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.096148 restraints weight = 74264.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.098091 restraints weight = 41035.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.099457 restraints weight = 26187.470| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.5729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10621 Z= 0.149 Angle : 0.488 10.742 14427 Z= 0.266 Chirality : 0.042 0.158 1564 Planarity : 0.004 0.051 1896 Dihedral : 4.806 71.799 1455 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.09 % Allowed : 0.09 % 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: 0.04 (0.23), residues: 1303 helix: 1.15 (0.31), residues: 290 sheet: -0.14 (0.23), residues: 425 loop : -0.29 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 279 HIS 0.006 0.001 HIS A 280 PHE 0.012 0.001 PHE E 68 TYR 0.016 0.001 TYR A 618 ARG 0.004 0.000 ARG A 366 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4951.28 seconds wall clock time: 89 minutes 9.34 seconds (5349.34 seconds total)