Starting phenix.real_space_refine on Mon Aug 25 14:52:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6giy_0008/08_2025/6giy_0008.cif Found real_map, /net/cci-nas-00/data/ceres_data/6giy_0008/08_2025/6giy_0008.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/cci-nas-00/data/ceres_data/6giy_0008/08_2025/6giy_0008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6giy_0008/08_2025/6giy_0008.map" model { file = "/net/cci-nas-00/data/ceres_data/6giy_0008/08_2025/6giy_0008.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6giy_0008/08_2025/6giy_0008.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 4 Type Number sf(0) Gaussians S 137 5.16 5 C 18375 2.51 5 N 5211 2.21 5 O 5246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28969 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4655 Classifications: {'peptide': 584} Link IDs: {'PTRANS': 36, 'TRANS': 547} Chain: "B" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4651 Classifications: {'peptide': 583} Link IDs: {'CIS': 2, 'PTRANS': 36, 'TRANS': 544} Chain: "C" Number of atoms: 2737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2737 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 2, 'PTRANS': 27, 'TRANS': 320} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2473 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 289} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 2479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2479 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 289} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 2482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2482 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 289} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 3509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3509 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 29, 'TRANS': 414} Chain: "H" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3498 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 29, 'TRANS': 414} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 2485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2485 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 21, 'TRANS': 289} Time building chain proxies: 7.07, per 1000 atoms: 0.24 Number of scatterers: 28969 At special positions: 0 Unit cell: (151.8, 160.6, 207.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 137 16.00 O 5246 8.00 N 5211 7.00 C 18375 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.55 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 7262 Ramachandran restraints generated. 3631 Oldfield, 0 Emsley, 3631 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6926 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 37 sheets defined 31.1% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 5 through 21 removed outlier: 3.893A pdb=" N ALA A 11 " --> pdb=" O ARG A 7 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU A 12 " --> pdb=" O TYR A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 51 removed outlier: 3.720A pdb=" N PHE A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 66 removed outlier: 3.752A pdb=" N LEU A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 77 removed outlier: 3.687A pdb=" N GLU A 73 " --> pdb=" O PRO A 69 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 173 removed outlier: 3.744A pdb=" N GLN A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 171 " --> pdb=" O ASP A 167 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 173 " --> pdb=" O SER A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 195 removed outlier: 4.410A pdb=" N THR A 189 " --> pdb=" O PRO A 185 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 190 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 195 " --> pdb=" O HIS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 removed outlier: 4.115A pdb=" N GLY A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 358 removed outlier: 3.527A pdb=" N SER A 357 " --> pdb=" O PRO A 354 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE A 358 " --> pdb=" O PHE A 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 354 through 358' Processing helix chain 'A' and resid 430 through 435 removed outlier: 3.925A pdb=" N GLU A 433 " --> pdb=" O ASP A 430 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN A 434 " --> pdb=" O ARG A 431 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL A 435 " --> pdb=" O CYS A 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 430 through 435' Processing helix chain 'A' and resid 461 through 466 Processing helix chain 'A' and resid 466 through 471 removed outlier: 4.780A pdb=" N THR A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 485 Processing helix chain 'A' and resid 494 through 500 Processing helix chain 'A' and resid 538 through 553 removed outlier: 4.009A pdb=" N PHE A 544 " --> pdb=" O ASP A 540 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASN A 549 " --> pdb=" O GLY A 545 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 27 removed outlier: 3.640A pdb=" N PHE B 9 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU B 12 " --> pdb=" O TYR B 8 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG B 17 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN B 25 " --> pdb=" O LYS B 21 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ALA B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 46 through 68 removed outlier: 3.718A pdb=" N MET B 57 " --> pdb=" O PHE B 53 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 60 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG B 61 " --> pdb=" O MET B 57 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLN B 62 " --> pdb=" O GLY B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 79 removed outlier: 3.833A pdb=" N VAL B 76 " --> pdb=" O GLU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 86 removed outlier: 3.502A pdb=" N THR B 86 " --> pdb=" O TYR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 171 removed outlier: 3.761A pdb=" N VAL B 171 " --> pdb=" O TRP B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 196 removed outlier: 3.551A pdb=" N MET B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 199 No H-bonds generated for 'chain 'B' and resid 197 through 199' Processing helix chain 'B' and resid 222 through 226 removed outlier: 4.161A pdb=" N GLU B 225 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 236 removed outlier: 3.716A pdb=" N GLY B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 280 Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 329 through 334 removed outlier: 3.963A pdb=" N GLU B 334 " --> pdb=" O ASP B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 361 removed outlier: 4.566A pdb=" N ARG B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 Processing helix chain 'B' and resid 459 through 464 Processing helix chain 'B' and resid 464 through 469 removed outlier: 3.755A pdb=" N LEU B 468 " --> pdb=" O VAL B 464 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY B 469 " --> pdb=" O MET B 465 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 464 through 469' Processing helix chain 'B' and resid 477 through 483 removed outlier: 3.773A pdb=" N ARG B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 490 removed outlier: 3.640A pdb=" N TYR B 489 " --> pdb=" O LEU B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 502 removed outlier: 3.650A pdb=" N ARG B 499 " --> pdb=" O GLU B 495 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP B 502 " --> pdb=" O HIS B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 551 removed outlier: 3.989A pdb=" N LEU B 543 " --> pdb=" O GLY B 539 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY B 545 " --> pdb=" O ILE B 541 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU B 546 " --> pdb=" O HIS B 542 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET B 547 " --> pdb=" O LEU B 543 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 548 " --> pdb=" O PHE B 544 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN B 549 " --> pdb=" O GLY B 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 15 Processing helix chain 'C' and resid 22 through 26 removed outlier: 3.936A pdb=" N ILE C 26 " --> pdb=" O LEU C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 39 removed outlier: 3.910A pdb=" N GLN C 33 " --> pdb=" O TYR C 29 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU C 36 " --> pdb=" O CYS C 32 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN C 39 " --> pdb=" O LEU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 51 removed outlier: 3.691A pdb=" N TRP C 49 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLN C 50 " --> pdb=" O SER C 47 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA C 51 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 109 Processing helix chain 'C' and resid 112 through 117 Processing helix chain 'C' and resid 118 through 123 Processing helix chain 'C' and resid 123 through 139 removed outlier: 3.804A pdb=" N ARG C 128 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU C 129 " --> pdb=" O PHE C 125 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 130 " --> pdb=" O SER C 126 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR C 131 " --> pdb=" O HIS C 127 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLN C 132 " --> pdb=" O ARG C 128 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TRP C 137 " --> pdb=" O TYR C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 160 removed outlier: 3.647A pdb=" N LEU C 158 " --> pdb=" O THR C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 187 Proline residue: C 185 - end of helix Processing helix chain 'C' and resid 195 through 205 removed outlier: 3.899A pdb=" N SER C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL C 201 " --> pdb=" O LEU C 197 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 269 removed outlier: 3.617A pdb=" N GLN C 266 " --> pdb=" O GLY C 262 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY C 267 " --> pdb=" O SER C 263 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU C 269 " --> pdb=" O VAL C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 283 removed outlier: 3.565A pdb=" N ASP C 277 " --> pdb=" O HIS C 273 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU C 279 " --> pdb=" O TYR C 275 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU C 282 " --> pdb=" O LEU C 278 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N HIS C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 35 removed outlier: 4.015A pdb=" N PHE D 19 " --> pdb=" O MET D 15 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN D 21 " --> pdb=" O GLN D 17 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TRP D 25 " --> pdb=" O GLN D 21 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP D 26 " --> pdb=" O GLN D 22 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL D 27 " --> pdb=" O ALA D 23 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS D 28 " --> pdb=" O ALA D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 218 removed outlier: 3.571A pdb=" N MET D 198 " --> pdb=" O SER D 194 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU D 203 " --> pdb=" O THR D 199 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA D 210 " --> pdb=" O HIS D 206 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG D 211 " --> pdb=" O HIS D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 230 Processing helix chain 'D' and resid 235 through 245 removed outlier: 3.818A pdb=" N ALA D 242 " --> pdb=" O TRP D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 254 removed outlier: 3.830A pdb=" N LEU D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU D 252 " --> pdb=" O PRO D 248 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU D 254 " --> pdb=" O LEU D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 275 removed outlier: 4.250A pdb=" N LEU D 264 " --> pdb=" O HIS D 260 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU D 267 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG D 270 " --> pdb=" O ARG D 266 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY D 273 " --> pdb=" O ALA D 269 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER D 274 " --> pdb=" O ARG D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 297 Processing helix chain 'D' and resid 298 through 311 removed outlier: 3.518A pdb=" N SER D 304 " --> pdb=" O PRO D 300 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG D 308 " --> pdb=" O SER D 304 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU D 311 " --> pdb=" O ASN D 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 32 removed outlier: 4.178A pdb=" N PHE E 19 " --> pdb=" O MET E 15 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN E 21 " --> pdb=" O GLN E 17 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN E 22 " --> pdb=" O GLN E 18 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP E 26 " --> pdb=" O GLN E 22 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL E 27 " --> pdb=" O ALA E 23 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA E 30 " --> pdb=" O ASP E 26 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP E 31 " --> pdb=" O VAL E 27 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER E 32 " --> pdb=" O HIS E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 193 Processing helix chain 'E' and resid 194 through 218 removed outlier: 4.077A pdb=" N MET E 198 " --> pdb=" O SER E 194 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU E 200 " --> pdb=" O SER E 196 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU E 202 " --> pdb=" O MET E 198 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN E 213 " --> pdb=" O GLN E 209 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 222 Processing helix chain 'E' and resid 232 through 242 removed outlier: 4.018A pdb=" N PHE E 237 " --> pdb=" O ASP E 233 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TRP E 238 " --> pdb=" O VAL E 234 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU E 239 " --> pdb=" O SER E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 252 removed outlier: 3.603A pdb=" N GLU E 252 " --> pdb=" O PRO E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 277 removed outlier: 4.040A pdb=" N ARG E 266 " --> pdb=" O GLU E 262 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU E 267 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ARG E 270 " --> pdb=" O ARG E 266 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU E 271 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N THR E 277 " --> pdb=" O GLY E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 297 Processing helix chain 'E' and resid 298 through 310 removed outlier: 3.604A pdb=" N ASN E 307 " --> pdb=" O LEU E 303 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG E 308 " --> pdb=" O SER E 304 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU E 310 " --> pdb=" O LEU E 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 33 removed outlier: 4.156A pdb=" N PHE F 19 " --> pdb=" O MET F 15 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN F 20 " --> pdb=" O PRO F 16 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP F 26 " --> pdb=" O GLN F 22 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL F 27 " --> pdb=" O ALA F 23 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N HIS F 28 " --> pdb=" O ALA F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 57 Processing helix chain 'F' and resid 194 through 222 removed outlier: 4.212A pdb=" N MET F 198 " --> pdb=" O SER F 194 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU F 200 " --> pdb=" O SER F 196 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU F 204 " --> pdb=" O GLU F 200 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU F 205 " --> pdb=" O LEU F 201 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA F 210 " --> pdb=" O HIS F 206 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG F 211 " --> pdb=" O HIS F 207 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU F 215 " --> pdb=" O ARG F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 245 removed outlier: 3.861A pdb=" N SER F 245 " --> pdb=" O ASN F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 253 removed outlier: 3.801A pdb=" N LEU F 250 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU F 252 " --> pdb=" O PRO F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 275 removed outlier: 4.299A pdb=" N LEU F 264 " --> pdb=" O HIS F 260 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU F 267 " --> pdb=" O LEU F 263 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG F 270 " --> pdb=" O ARG F 266 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU F 275 " --> pdb=" O LEU F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 280 removed outlier: 4.667A pdb=" N SER F 279 " --> pdb=" O LEU F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 297 Processing helix chain 'F' and resid 298 through 310 removed outlier: 3.536A pdb=" N LEU F 306 " --> pdb=" O LEU F 302 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN F 307 " --> pdb=" O LEU F 303 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG F 308 " --> pdb=" O SER F 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 36 removed outlier: 4.102A pdb=" N GLN G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP G 26 " --> pdb=" O GLN G 22 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL G 27 " --> pdb=" O ALA G 23 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA G 30 " --> pdb=" O ASP G 26 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP G 31 " --> pdb=" O VAL G 27 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N MET G 36 " --> pdb=" O SER G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 137 removed outlier: 4.123A pdb=" N ALA G 136 " --> pdb=" O GLN G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 218 removed outlier: 3.955A pdb=" N MET G 198 " --> pdb=" O SER G 194 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA G 210 " --> pdb=" O HIS G 206 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG G 214 " --> pdb=" O ALA G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 218 through 223 Processing helix chain 'G' and resid 230 through 245 removed outlier: 3.597A pdb=" N VAL G 234 " --> pdb=" O ALA G 230 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU G 236 " --> pdb=" O ALA G 232 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER G 245 " --> pdb=" O ASN G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 253 removed outlier: 3.759A pdb=" N GLU G 252 " --> pdb=" O PRO G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 273 removed outlier: 4.302A pdb=" N LEU G 264 " --> pdb=" O HIS G 260 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG G 266 " --> pdb=" O GLU G 262 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU G 267 " --> pdb=" O LEU G 263 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG G 270 " --> pdb=" O ARG G 266 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 297 Processing helix chain 'G' and resid 298 through 311 removed outlier: 3.655A pdb=" N ARG G 308 " --> pdb=" O SER G 304 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU G 310 " --> pdb=" O LEU G 306 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU G 311 " --> pdb=" O ASN G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 354 through 366 removed outlier: 4.196A pdb=" N THR G 360 " --> pdb=" O HIS G 356 " (cutoff:3.500A) Proline residue: G 363 - end of helix Processing helix chain 'G' and resid 411 through 419 removed outlier: 3.697A pdb=" N ALA G 415 " --> pdb=" O SER G 411 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG G 416 " --> pdb=" O THR G 412 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 35 removed outlier: 4.284A pdb=" N PHE H 19 " --> pdb=" O MET H 15 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP H 25 " --> pdb=" O GLN H 21 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP H 26 " --> pdb=" O GLN H 22 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL H 27 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA H 34 " --> pdb=" O ALA H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 57 removed outlier: 3.508A pdb=" N SER H 57 " --> pdb=" O LEU H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 220 removed outlier: 3.961A pdb=" N MET H 198 " --> pdb=" O SER H 194 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU H 205 " --> pdb=" O LEU H 201 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG H 211 " --> pdb=" O HIS H 207 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG H 212 " --> pdb=" O LEU H 208 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN H 213 " --> pdb=" O GLN H 209 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG H 214 " --> pdb=" O ALA H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 235 through 254 removed outlier: 3.553A pdb=" N ASN H 241 " --> pdb=" O PHE H 237 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER H 245 " --> pdb=" O ASN H 241 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA H 246 " --> pdb=" O ALA H 242 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU H 247 " --> pdb=" O LEU H 243 " (cutoff:3.500A) Proline residue: H 248 - end of helix removed outlier: 5.152A pdb=" N GLU H 252 " --> pdb=" O PRO H 248 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU H 253 " --> pdb=" O VAL H 249 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU H 254 " --> pdb=" O LEU H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 260 through 276 removed outlier: 4.046A pdb=" N LEU H 264 " --> pdb=" O HIS H 260 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU H 267 " --> pdb=" O LEU H 263 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU H 276 " --> pdb=" O ALA H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 283 through 287 removed outlier: 3.602A pdb=" N ALA H 286 " --> pdb=" O ASN H 283 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 310 removed outlier: 3.827A pdb=" N LEU H 302 " --> pdb=" O VAL H 298 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG H 308 " --> pdb=" O SER H 304 " (cutoff:3.500A) Processing helix chain 'H' and resid 336 through 341 removed outlier: 3.705A pdb=" N ARG H 340 " --> pdb=" O ALA H 337 " (cutoff:3.500A) Processing helix chain 'H' and resid 355 through 359 removed outlier: 3.860A pdb=" N LEU H 358 " --> pdb=" O GLY H 355 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN H 359 " --> pdb=" O HIS H 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 355 through 359' Processing helix chain 'H' and resid 413 through 422 Processing helix chain 'H' and resid 428 through 433 removed outlier: 3.531A pdb=" N SER H 431 " --> pdb=" O THR H 428 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU H 432 " --> pdb=" O PRO H 429 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 24 removed outlier: 4.016A pdb=" N PHE I 19 " --> pdb=" O MET I 15 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN I 20 " --> pdb=" O PRO I 16 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN I 21 " --> pdb=" O GLN I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 25 through 35 removed outlier: 3.543A pdb=" N ASP I 31 " --> pdb=" O VAL I 27 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER I 32 " --> pdb=" O HIS I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 92 Processing helix chain 'I' and resid 194 through 220 removed outlier: 3.669A pdb=" N LEU I 202 " --> pdb=" O MET I 198 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU I 203 " --> pdb=" O THR I 199 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS I 207 " --> pdb=" O GLU I 203 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA I 210 " --> pdb=" O HIS I 206 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG I 211 " --> pdb=" O HIS I 207 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG I 212 " --> pdb=" O LEU I 208 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET I 218 " --> pdb=" O ARG I 214 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG I 219 " --> pdb=" O LEU I 215 " (cutoff:3.500A) Processing helix chain 'I' and resid 230 through 255 removed outlier: 4.042A pdb=" N SER I 235 " --> pdb=" O VAL I 231 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER I 245 " --> pdb=" O ASN I 241 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA I 246 " --> pdb=" O ALA I 242 " (cutoff:3.500A) Proline residue: I 248 - end of helix Processing helix chain 'I' and resid 260 through 276 removed outlier: 4.249A pdb=" N LEU I 264 " --> pdb=" O HIS I 260 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU I 267 " --> pdb=" O LEU I 263 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG I 270 " --> pdb=" O ARG I 266 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU I 271 " --> pdb=" O GLU I 267 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 287 removed outlier: 3.580A pdb=" N ALA I 286 " --> pdb=" O ASN I 283 " (cutoff:3.500A) Processing helix chain 'I' and resid 298 through 310 removed outlier: 3.571A pdb=" N LEU I 303 " --> pdb=" O PHE I 299 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG I 308 " --> pdb=" O SER I 304 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU I 309 " --> pdb=" O LEU I 305 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 300 through 302 removed outlier: 3.723A pdb=" N VAL A 301 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER A 91 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 305 through 307 removed outlier: 3.625A pdb=" N GLY A 414 " --> pdb=" O PHE A 305 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE A 412 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N SER A 409 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL A 341 " --> pdb=" O SER A 409 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG A 411 " --> pdb=" O ASP A 339 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 504 through 509 removed outlier: 4.845A pdb=" N LEU A 505 " --> pdb=" O THR A 529 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N THR A 529 " --> pdb=" O LEU A 505 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL A 526 " --> pdb=" O THR A 565 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE A 567 " --> pdb=" O VAL A 526 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N VAL A 528 " --> pdb=" O ILE A 567 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 512 through 514 Processing sheet with id=AA5, first strand: chain 'B' and resid 147 through 148 Processing sheet with id=AA6, first strand: chain 'B' and resid 203 through 204 Processing sheet with id=AA7, first strand: chain 'B' and resid 305 through 307 removed outlier: 7.578A pdb=" N ARG B 411 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N VAL B 341 " --> pdb=" O ARG B 411 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N THR B 413 " --> pdb=" O ASP B 339 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 374 through 376 Processing sheet with id=AA9, first strand: chain 'B' and resid 379 through 380 Processing sheet with id=AB1, first strand: chain 'B' and resid 508 through 510 removed outlier: 3.787A pdb=" N GLN B 508 " --> pdb=" O ASP B 525 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP B 525 " --> pdb=" O GLN B 508 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 565 through 566 Processing sheet with id=AB3, first strand: chain 'C' and resid 209 through 213 removed outlier: 3.603A pdb=" N ARG C 211 " --> pdb=" O GLN C 256 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N LEU C 294 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ALA C 336 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU C 296 " --> pdb=" O SER C 334 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 44 through 50 removed outlier: 4.415A pdb=" N ALA D 47 " --> pdb=" O ARG D 63 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ARG D 63 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N PHE D 49 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ALA D 61 " --> pdb=" O PHE D 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 151 through 153 removed outlier: 5.945A pdb=" N LEU D 101 " --> pdb=" O PRO D 166 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N LEU D 103 " --> pdb=" O THR D 164 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N THR D 164 " --> pdb=" O LEU D 103 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 124 through 133 removed outlier: 5.865A pdb=" N VAL D 143 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASN D 131 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N SER D 141 " --> pdb=" O ASN D 131 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 44 through 49 removed outlier: 5.242A pdb=" N VAL E 44 " --> pdb=" O ARG E 67 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ARG E 67 " --> pdb=" O VAL E 44 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 151 through 154 removed outlier: 3.762A pdb=" N THR E 151 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA E 102 " --> pdb=" O THR E 151 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 151 through 154 removed outlier: 3.762A pdb=" N THR E 151 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA E 102 " --> pdb=" O THR E 151 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL E 97 " --> pdb=" O ARG E 169 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ARG E 169 " --> pdb=" O VAL E 97 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE E 99 " --> pdb=" O VAL E 167 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 126 through 133 removed outlier: 3.553A pdb=" N GLU E 128 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER E 141 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 44 through 49 removed outlier: 7.055A pdb=" N VAL F 44 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL F 66 " --> pdb=" O VAL F 44 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA F 46 " --> pdb=" O LEU F 64 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU F 64 " --> pdb=" O ALA F 46 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU F 48 " --> pdb=" O THR F 62 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 128 through 132 removed outlier: 3.649A pdb=" N VAL F 130 " --> pdb=" O VAL F 143 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER F 141 " --> pdb=" O VAL F 132 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 170 through 172 Processing sheet with id=AC5, first strand: chain 'G' and resid 44 through 49 removed outlier: 4.973A pdb=" N VAL G 44 " --> pdb=" O ARG G 67 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ARG G 67 " --> pdb=" O VAL G 44 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 58 through 59 removed outlier: 3.941A pdb=" N LEU G 59 " --> pdb=" O CYS G 86 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 151 through 154 removed outlier: 3.584A pdb=" N THR G 151 " --> pdb=" O ALA G 102 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE G 99 " --> pdb=" O VAL G 167 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS G 165 " --> pdb=" O LEU G 101 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 125 through 131 removed outlier: 5.093A pdb=" N LYS G 126 " --> pdb=" O ARG G 147 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ARG G 147 " --> pdb=" O LYS G 126 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU G 128 " --> pdb=" O VAL G 145 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 318 through 321 removed outlier: 4.672A pdb=" N LEU G 439 " --> pdb=" O ILE G 321 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE G 345 " --> pdb=" O LEU G 408 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG G 388 " --> pdb=" O ALA G 407 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP G 409 " --> pdb=" O ILE G 386 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE G 386 " --> pdb=" O ASP G 409 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 325 through 326 removed outlier: 3.772A pdb=" N THR G 425 " --> pdb=" O GLY G 369 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 44 through 49 removed outlier: 6.807A pdb=" N ILE H 65 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA H 47 " --> pdb=" O ARG H 63 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ARG H 63 " --> pdb=" O ALA H 47 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N PHE H 49 " --> pdb=" O ALA H 61 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA H 61 " --> pdb=" O PHE H 49 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 151 through 154 removed outlier: 3.691A pdb=" N THR H 151 " --> pdb=" O ALA H 102 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU H 101 " --> pdb=" O PRO H 166 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 125 through 132 removed outlier: 3.701A pdb=" N VAL H 130 " --> pdb=" O VAL H 143 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER H 141 " --> pdb=" O VAL H 132 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 331 through 332 removed outlier: 3.614A pdb=" N GLY H 332 " --> pdb=" O CYS H 424 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N CYS H 424 " --> pdb=" O GLY H 332 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'H' and resid 389 through 390 removed outlier: 4.146A pdb=" N TYR H 405 " --> pdb=" O VAL H 390 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 44 through 50 removed outlier: 5.456A pdb=" N VAL I 44 " --> pdb=" O ARG I 67 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG I 67 " --> pdb=" O VAL I 44 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ASP I 50 " --> pdb=" O ALA I 61 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ALA I 61 " --> pdb=" O ASP I 50 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR I 72 " --> pdb=" O PHE I 68 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 44 through 50 removed outlier: 5.456A pdb=" N VAL I 44 " --> pdb=" O ARG I 67 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG I 67 " --> pdb=" O VAL I 44 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ASP I 50 " --> pdb=" O ALA I 61 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ALA I 61 " --> pdb=" O ASP I 50 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 151 through 153 removed outlier: 3.766A pdb=" N ALA I 102 " --> pdb=" O THR I 151 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG I 153 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL I 100 " --> pdb=" O ARG I 153 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL I 97 " --> pdb=" O ARG I 169 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG I 169 " --> pdb=" O VAL I 97 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ILE I 99 " --> pdb=" O VAL I 167 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 126 through 130 removed outlier: 3.575A pdb=" N VAL I 143 " --> pdb=" O VAL I 130 " (cutoff:3.500A) 677 hydrogen bonds defined for protein. 1851 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: 5.73 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9720 1.34 - 1.46: 6188 1.46 - 1.58: 13522 1.58 - 1.70: 0 1.70 - 1.82: 231 Bond restraints: 29661 Sorted by residual: bond pdb=" C SER C 316 " pdb=" N PRO C 317 " ideal model delta sigma weight residual 1.328 1.394 -0.066 1.25e-02 6.40e+03 2.83e+01 bond pdb=" C ASP H 255 " pdb=" N MET H 256 " ideal model delta sigma weight residual 1.327 1.279 0.048 1.39e-02 5.18e+03 1.20e+01 bond pdb=" CA TYR D 290 " pdb=" CB TYR D 290 " ideal model delta sigma weight residual 1.525 1.481 0.044 1.29e-02 6.01e+03 1.16e+01 bond pdb=" C MET H 15 " pdb=" N PRO H 16 " ideal model delta sigma weight residual 1.335 1.372 -0.038 1.19e-02 7.06e+03 1.00e+01 bond pdb=" C ASN E 81 " pdb=" N LEU E 82 " ideal model delta sigma weight residual 1.329 1.275 0.054 1.86e-02 2.89e+03 8.31e+00 ... (remaining 29656 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 39236 3.05 - 6.11: 997 6.11 - 9.16: 133 9.16 - 12.21: 14 12.21 - 15.26: 3 Bond angle restraints: 40383 Sorted by residual: angle pdb=" C ARG C 345 " pdb=" N TYR C 346 " pdb=" CA TYR C 346 " ideal model delta sigma weight residual 121.54 136.80 -15.26 1.91e+00 2.74e-01 6.39e+01 angle pdb=" N ILE C 220 " pdb=" CA ILE C 220 " pdb=" C ILE C 220 " ideal model delta sigma weight residual 108.88 123.61 -14.73 2.16e+00 2.14e-01 4.65e+01 angle pdb=" C ARG C 219 " pdb=" N ILE C 220 " pdb=" CA ILE C 220 " ideal model delta sigma weight residual 122.13 134.24 -12.11 1.85e+00 2.92e-01 4.29e+01 angle pdb=" N THR B 248 " pdb=" CA THR B 248 " pdb=" C THR B 248 " ideal model delta sigma weight residual 114.75 106.64 8.11 1.26e+00 6.30e-01 4.14e+01 angle pdb=" N VAL F 45 " pdb=" CA VAL F 45 " pdb=" C VAL F 45 " ideal model delta sigma weight residual 111.62 106.74 4.88 7.90e-01 1.60e+00 3.81e+01 ... (remaining 40378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.01: 16826 15.01 - 30.02: 929 30.02 - 45.03: 200 45.03 - 60.03: 22 60.03 - 75.04: 9 Dihedral angle restraints: 17986 sinusoidal: 7341 harmonic: 10645 Sorted by residual: dihedral pdb=" CA ILE C 220 " pdb=" C ILE C 220 " pdb=" N PRO C 221 " pdb=" CA PRO C 221 " ideal model delta harmonic sigma weight residual -180.00 -115.79 -64.21 0 5.00e+00 4.00e-02 1.65e+02 dihedral pdb=" CA ARG C 219 " pdb=" C ARG C 219 " pdb=" N ILE C 220 " pdb=" CA ILE C 220 " ideal model delta harmonic sigma weight residual -180.00 -117.54 -62.46 0 5.00e+00 4.00e-02 1.56e+02 dihedral pdb=" CA GLN C 347 " pdb=" C GLN C 347 " pdb=" N ARG C 348 " pdb=" CA ARG C 348 " ideal model delta harmonic sigma weight residual -180.00 -118.04 -61.96 0 5.00e+00 4.00e-02 1.54e+02 ... (remaining 17983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 4057 0.096 - 0.192: 441 0.192 - 0.288: 27 0.288 - 0.384: 1 0.384 - 0.481: 1 Chirality restraints: 4527 Sorted by residual: chirality pdb=" CA HIS G 40 " pdb=" N HIS G 40 " pdb=" C HIS G 40 " pdb=" CB HIS G 40 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.77e+00 chirality pdb=" CB ILE B 313 " pdb=" CA ILE B 313 " pdb=" CG1 ILE B 313 " pdb=" CG2 ILE B 313 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CB VAL G 234 " pdb=" CA VAL G 234 " pdb=" CG1 VAL G 234 " pdb=" CG2 VAL G 234 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 4524 not shown) Planarity restraints: 5284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 220 " -0.078 5.00e-02 4.00e+02 1.19e-01 2.27e+01 pdb=" N PRO C 221 " 0.206 5.00e-02 4.00e+02 pdb=" CA PRO C 221 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO C 221 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 453 " 0.069 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO A 454 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO A 454 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 454 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS G 40 " -0.062 5.00e-02 4.00e+02 9.46e-02 1.43e+01 pdb=" N PRO G 41 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO G 41 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO G 41 " -0.052 5.00e-02 4.00e+02 ... (remaining 5281 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 5032 2.77 - 3.30: 25080 3.30 - 3.83: 44086 3.83 - 4.37: 50788 4.37 - 4.90: 84052 Nonbonded interactions: 209038 Sorted by model distance: nonbonded pdb=" O VAL G 374 " pdb=" OH TYR G 427 " model vdw 2.232 3.040 nonbonded pdb=" O ALA A 184 " pdb=" OG SER A 188 " model vdw 2.266 3.040 nonbonded pdb=" OE1 GLU D 120 " pdb=" NH1 ARG D 121 " model vdw 2.278 3.120 nonbonded pdb=" OH TYR A 352 " pdb=" O THR A 407 " model vdw 2.280 3.040 nonbonded pdb=" ND1 HIS H 40 " pdb=" O PRO H 41 " model vdw 2.287 3.120 ... (remaining 209033 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 4 through 586) selection = chain 'B' } ncs_group { reference = (chain 'D' and (resid 1 through 158 or (resid 159 through 161 and (name N or nam \ e CA or name C or name O or name CB )) or resid 162 through 311)) selection = (chain 'E' and (resid 1 through 158 or (resid 159 through 161 and (name N or nam \ e CA or name C or name O or name CB )) or resid 162 through 221 or (resid 222 th \ rough 225 and (name N or name CA or name C or name O or name CB )) or resid 226 \ through 311)) selection = (chain 'F' and (resid 1 through 221 or (resid 222 through 225 and (name N or nam \ e CA or name C or name O or name CB )) or resid 226 through 311)) selection = (chain 'I' and (resid 1 through 158 or (resid 159 through 161 and (name N or nam \ e CA or name C or name O or name CB )) or resid 162 through 221 or (resid 222 th \ rough 225 and (name N or name CA or name C or name O or name CB )) or resid 226 \ through 311)) } ncs_group { reference = (chain 'G' and (resid 1 through 333 or (resid 334 through 335 and (name N or nam \ e CA or name C or name O or name CB )) or resid 336 through 346 or (resid 347 an \ d (name N or name CA or name C or name O or name CB )) or resid 348 through 444) \ ) selection = chain 'H' } 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: 7.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 27.430 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 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 : 0.007 0.073 29661 Z= 0.327 Angle : 1.178 15.263 40383 Z= 0.661 Chirality : 0.059 0.481 4527 Planarity : 0.009 0.119 5284 Dihedral : 10.186 75.042 11060 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.67 % Favored : 87.06 % Rotamer: Outliers : 0.29 % Allowed : 2.49 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 4.15 % Twisted General : 1.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.09 (0.11), residues: 3631 helix: -4.25 (0.08), residues: 971 sheet: -2.30 (0.22), residues: 470 loop : -3.36 (0.11), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 132 TYR 0.027 0.003 TYR G 4 PHE 0.035 0.003 PHE H 278 TRP 0.039 0.004 TRP E 125 HIS 0.014 0.003 HIS G 40 Details of bonding type rmsd covalent geometry : bond 0.00705 (29661) covalent geometry : angle 1.17822 (40383) hydrogen bonds : bond 0.32289 ( 671) hydrogen bonds : angle 10.35302 ( 1851) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7262 Ramachandran restraints generated. 3631 Oldfield, 0 Emsley, 3631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7262 Ramachandran restraints generated. 3631 Oldfield, 0 Emsley, 3631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 636 time to evaluate : 1.250 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: A 14 ARG cc_start: 0.8477 (ttt180) cc_final: 0.8242 (ptp-170) REVERT: A 15 TYR cc_start: 0.8692 (m-10) cc_final: 0.8321 (m-10) REVERT: A 27 HIS cc_start: 0.8156 (m-70) cc_final: 0.7888 (m-70) REVERT: A 55 PHE cc_start: 0.6884 (m-10) cc_final: 0.6679 (m-80) REVERT: A 61 ARG cc_start: 0.9094 (mtp85) cc_final: 0.8730 (mtp85) REVERT: A 62 GLN cc_start: 0.7377 (tt0) cc_final: 0.6831 (pp30) REVERT: A 214 ILE cc_start: 0.6948 (OUTLIER) cc_final: 0.6557 (pt) REVERT: A 217 TRP cc_start: 0.7859 (m-10) cc_final: 0.7307 (m-10) REVERT: A 263 ASN cc_start: 0.6832 (m-40) cc_final: 0.6436 (p0) REVERT: A 385 MET cc_start: 0.5932 (mtt) cc_final: 0.5164 (ttt) REVERT: A 467 HIS cc_start: 0.8006 (t70) cc_final: 0.7654 (t-90) REVERT: A 526 VAL cc_start: 0.9094 (p) cc_final: 0.8313 (m) REVERT: A 527 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7652 (mp0) REVERT: A 582 ASN cc_start: 0.7758 (m-40) cc_final: 0.7219 (p0) REVERT: B 17 ARG cc_start: 0.5974 (mtt180) cc_final: 0.4898 (mmp80) REVERT: B 23 PHE cc_start: 0.7806 (m-10) cc_final: 0.7578 (m-80) REVERT: B 66 ASP cc_start: 0.8373 (t0) cc_final: 0.7968 (p0) REVERT: B 156 LEU cc_start: 0.8335 (pt) cc_final: 0.8114 (pt) REVERT: B 230 TRP cc_start: 0.7671 (t-100) cc_final: 0.7442 (t-100) REVERT: B 237 PHE cc_start: 0.7720 (t80) cc_final: 0.7037 (t80) REVERT: B 375 HIS cc_start: 0.6598 (t70) cc_final: 0.6229 (t70) REVERT: B 377 ARG cc_start: 0.5107 (mtt180) cc_final: 0.4129 (tmm-80) REVERT: C 66 PHE cc_start: 0.4646 (m-10) cc_final: 0.3754 (m-80) REVERT: C 91 MET cc_start: 0.4619 (mmm) cc_final: 0.4301 (ptp) REVERT: C 116 GLU cc_start: 0.5657 (mt-10) cc_final: 0.5352 (mm-30) REVERT: C 299 GLU cc_start: 0.7830 (mt-10) cc_final: 0.6826 (pp20) REVERT: D 36 MET cc_start: 0.8076 (mtp) cc_final: 0.7611 (mtm) REVERT: D 114 ASP cc_start: 0.5559 (t0) cc_final: 0.4751 (t0) REVERT: D 240 LEU cc_start: 0.9142 (mt) cc_final: 0.8882 (mm) REVERT: D 251 LYS cc_start: 0.8763 (tttt) cc_final: 0.8383 (ttpt) REVERT: E 128 GLU cc_start: 0.8125 (tp30) cc_final: 0.7860 (mm-30) REVERT: E 218 MET cc_start: 0.9109 (mtm) cc_final: 0.8908 (mtt) REVERT: F 20 GLN cc_start: 0.8377 (mt0) cc_final: 0.7406 (mt0) REVERT: F 198 MET cc_start: 0.8743 (mmm) cc_final: 0.8467 (mmm) REVERT: F 290 TYR cc_start: 0.8936 (t80) cc_final: 0.8637 (t80) REVERT: G 125 TRP cc_start: 0.7812 (p-90) cc_final: 0.7407 (p-90) REVERT: G 320 PHE cc_start: 0.7707 (t80) cc_final: 0.7287 (t80) REVERT: G 356 HIS cc_start: 0.8031 (t70) cc_final: 0.7774 (t-90) REVERT: G 426 PHE cc_start: 0.8482 (m-10) cc_final: 0.8218 (m-10) REVERT: H 185 ILE cc_start: 0.9269 (pt) cc_final: 0.9004 (mp) REVERT: H 340 ARG cc_start: 0.8239 (ptt-90) cc_final: 0.7810 (mtt90) REVERT: H 426 PHE cc_start: 0.7964 (t80) cc_final: 0.7084 (t80) REVERT: I 15 MET cc_start: 0.7858 (mtm) cc_final: 0.7604 (mtm) REVERT: I 42 TRP cc_start: 0.6303 (m-10) cc_final: 0.6016 (m-10) REVERT: I 138 HIS cc_start: 0.7779 (p-80) cc_final: 0.7459 (p90) outliers start: 9 outliers final: 0 residues processed: 644 average time/residue: 0.2353 time to fit residues: 227.0073 Evaluate side-chains 356 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 355 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.0770 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 10.0000 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 GLN A 513 GLN A 542 HIS A 559 ASN ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 208 ASN B 360 HIS ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 HIS B 510 HIS C 111 GLN C 127 HIS C 132 GLN C 250 ASN C 318 GLN C 350 GLN C 352 HIS D 149 ASN ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN E 206 HIS E 222 ASN F 40 HIS F 209 GLN F 292 HIS G 157 GLN G 335 HIS G 392 HIS I 18 GLN I 28 HIS ** I 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 138 HIS I 241 ASN I 282 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.102020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.078402 restraints weight = 124057.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.079757 restraints weight = 81817.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.080640 restraints weight = 60541.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.081300 restraints weight = 49264.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.081650 restraints weight = 42897.145| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29661 Z= 0.148 Angle : 0.776 14.076 40383 Z= 0.401 Chirality : 0.046 0.220 4527 Planarity : 0.007 0.123 5284 Dihedral : 7.871 63.599 4026 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.63 % Favored : 89.26 % Rotamer: Outliers : 0.10 % Allowed : 2.65 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.07 % Twisted General : 0.62 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.10 (0.12), residues: 3631 helix: -2.67 (0.13), residues: 1000 sheet: -2.01 (0.22), residues: 488 loop : -3.05 (0.12), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 584 TYR 0.023 0.002 TYR C 346 PHE 0.021 0.002 PHE H 362 TRP 0.032 0.002 TRP B 283 HIS 0.009 0.001 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00321 (29661) covalent geometry : angle 0.77554 (40383) hydrogen bonds : bond 0.06026 ( 671) hydrogen bonds : angle 6.28753 ( 1851) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7262 Ramachandran restraints generated. 3631 Oldfield, 0 Emsley, 3631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7262 Ramachandran restraints generated. 3631 Oldfield, 0 Emsley, 3631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 484 time to evaluate : 1.167 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: A 15 TYR cc_start: 0.8723 (m-10) cc_final: 0.8321 (m-10) REVERT: A 33 MET cc_start: 0.5925 (tmm) cc_final: 0.5636 (tmm) REVERT: A 62 GLN cc_start: 0.7387 (tt0) cc_final: 0.7052 (pp30) REVERT: A 193 MET cc_start: 0.7611 (mmm) cc_final: 0.7207 (mmm) REVERT: A 194 MET cc_start: 0.7081 (mmm) cc_final: 0.6316 (mmm) REVERT: A 230 TRP cc_start: 0.6008 (m-10) cc_final: 0.5572 (m-10) REVERT: A 263 ASN cc_start: 0.6989 (m-40) cc_final: 0.6638 (p0) REVERT: A 364 MET cc_start: 0.7194 (tmm) cc_final: 0.6591 (tmm) REVERT: A 385 MET cc_start: 0.6423 (mtt) cc_final: 0.5967 (ttt) REVERT: A 425 GLN cc_start: 0.8325 (mt0) cc_final: 0.8075 (tm-30) REVERT: A 462 TRP cc_start: 0.6917 (m100) cc_final: 0.6489 (m100) REVERT: A 467 HIS cc_start: 0.8330 (t70) cc_final: 0.8043 (t-90) REVERT: A 526 VAL cc_start: 0.9162 (p) cc_final: 0.8548 (m) REVERT: A 527 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7716 (mp0) REVERT: B 17 ARG cc_start: 0.5842 (mtt180) cc_final: 0.4982 (mmp80) REVERT: B 23 PHE cc_start: 0.7746 (m-10) cc_final: 0.7535 (m-80) REVERT: B 55 PHE cc_start: 0.7733 (t80) cc_final: 0.7524 (t80) REVERT: B 80 TRP cc_start: 0.6558 (t-100) cc_final: 0.6018 (t60) REVERT: B 95 LEU cc_start: 0.7303 (mp) cc_final: 0.6572 (tp) REVERT: B 102 MET cc_start: 0.7192 (ppp) cc_final: 0.6350 (pmm) REVERT: B 237 PHE cc_start: 0.7974 (t80) cc_final: 0.7641 (t80) REVERT: B 274 ASP cc_start: 0.8046 (m-30) cc_final: 0.7688 (t70) REVERT: B 364 MET cc_start: 0.2558 (ttm) cc_final: 0.2330 (ttm) REVERT: B 377 ARG cc_start: 0.4906 (mtt180) cc_final: 0.4284 (tmm-80) REVERT: C 66 PHE cc_start: 0.3943 (m-10) cc_final: 0.3625 (m-80) REVERT: C 91 MET cc_start: 0.5064 (mmm) cc_final: 0.4818 (ptp) REVERT: C 138 ARG cc_start: 0.7426 (tmt-80) cc_final: 0.7123 (tmm-80) REVERT: D 202 LEU cc_start: 0.9365 (tp) cc_final: 0.9152 (tt) REVERT: D 251 LYS cc_start: 0.8576 (tttt) cc_final: 0.8376 (ttpt) REVERT: E 81 ASN cc_start: 0.7652 (m-40) cc_final: 0.7341 (m110) REVERT: F 290 TYR cc_start: 0.8758 (t80) cc_final: 0.8430 (t80) REVERT: G 125 TRP cc_start: 0.7558 (p-90) cc_final: 0.7098 (p-90) REVERT: G 126 LYS cc_start: 0.8884 (tmtt) cc_final: 0.8608 (tptp) REVERT: G 283 ASN cc_start: 0.7293 (m-40) cc_final: 0.6832 (t0) REVERT: G 320 PHE cc_start: 0.7704 (t80) cc_final: 0.7504 (t80) REVERT: G 356 HIS cc_start: 0.7716 (t70) cc_final: 0.7516 (t-90) REVERT: H 340 ARG cc_start: 0.8391 (ptt-90) cc_final: 0.7926 (mtt90) REVERT: I 42 TRP cc_start: 0.6545 (m-10) cc_final: 0.6220 (m-10) outliers start: 3 outliers final: 1 residues processed: 486 average time/residue: 0.2261 time to fit residues: 167.1404 Evaluate side-chains 336 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 335 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 34 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 289 optimal weight: 5.9990 chunk 240 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 320 optimal weight: 0.9990 chunk 218 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 355 optimal weight: 7.9990 chunk 145 optimal weight: 6.9990 chunk 167 optimal weight: 1.9990 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 123 ASN ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 HIS ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 HIS A 513 GLN B 27 HIS ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 HIS B 581 HIS D 149 ASN ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 GLN ** I 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 HIS I 159 ASN I 177 GLN I 241 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.096446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.072400 restraints weight = 116103.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.074104 restraints weight = 69641.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.075233 restraints weight = 48410.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.075947 restraints weight = 37522.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.076452 restraints weight = 31654.021| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 29661 Z= 0.215 Angle : 0.819 14.080 40383 Z= 0.415 Chirality : 0.048 0.242 4527 Planarity : 0.007 0.128 5284 Dihedral : 7.629 61.121 4026 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.28 % Favored : 87.58 % Rotamer: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 1.66 % Twisted General : 0.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.59 (0.13), residues: 3631 helix: -1.68 (0.15), residues: 1011 sheet: -2.04 (0.21), residues: 509 loop : -2.96 (0.12), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 317 TYR 0.023 0.002 TYR C 346 PHE 0.029 0.002 PHE B 50 TRP 0.027 0.002 TRP B 283 HIS 0.010 0.002 HIS D 156 Details of bonding type rmsd covalent geometry : bond 0.00492 (29661) covalent geometry : angle 0.81933 (40383) hydrogen bonds : bond 0.05150 ( 671) hydrogen bonds : angle 5.88211 ( 1851) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7262 Ramachandran restraints generated. 3631 Oldfield, 0 Emsley, 3631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7262 Ramachandran restraints generated. 3631 Oldfield, 0 Emsley, 3631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 409 time to evaluate : 1.169 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: A 14 ARG cc_start: 0.8574 (ttt180) cc_final: 0.8328 (ptt180) REVERT: A 15 TYR cc_start: 0.8537 (m-10) cc_final: 0.8193 (m-10) REVERT: A 33 MET cc_start: 0.6330 (tmm) cc_final: 0.5988 (tmm) REVERT: A 48 ARG cc_start: 0.6075 (mtt180) cc_final: 0.5304 (mtt90) REVERT: A 61 ARG cc_start: 0.9129 (mtp85) cc_final: 0.8516 (ttm110) REVERT: A 62 GLN cc_start: 0.7329 (tt0) cc_final: 0.6939 (pp30) REVERT: A 258 LEU cc_start: 0.7664 (tt) cc_final: 0.7327 (tt) REVERT: A 263 ASN cc_start: 0.6866 (m-40) cc_final: 0.6452 (p0) REVERT: A 462 TRP cc_start: 0.6894 (m100) cc_final: 0.6610 (m100) REVERT: A 467 HIS cc_start: 0.8288 (t70) cc_final: 0.8047 (t-90) REVERT: A 525 ASP cc_start: 0.7723 (m-30) cc_final: 0.6567 (m-30) REVERT: A 526 VAL cc_start: 0.9114 (p) cc_final: 0.8859 (m) REVERT: B 13 MET cc_start: 0.6642 (mmm) cc_final: 0.6297 (mmm) REVERT: B 17 ARG cc_start: 0.6180 (mtt180) cc_final: 0.5030 (mmp80) REVERT: B 99 LEU cc_start: 0.6778 (pt) cc_final: 0.6370 (pt) REVERT: B 375 HIS cc_start: 0.6711 (t70) cc_final: 0.6356 (t70) REVERT: B 377 ARG cc_start: 0.5004 (mtt180) cc_final: 0.4194 (tmm-80) REVERT: C 137 TRP cc_start: 0.8205 (t60) cc_final: 0.7802 (t60) REVERT: D 251 LYS cc_start: 0.8745 (tttt) cc_final: 0.8456 (ttpt) REVERT: E 15 MET cc_start: 0.8134 (mpp) cc_final: 0.7899 (mpp) REVERT: E 265 TYR cc_start: 0.6406 (m-10) cc_final: 0.6169 (m-80) REVERT: H 185 ILE cc_start: 0.9252 (pt) cc_final: 0.8782 (mp) REVERT: H 340 ARG cc_start: 0.8202 (ptt-90) cc_final: 0.7772 (mtt90) REVERT: H 426 PHE cc_start: 0.8035 (t80) cc_final: 0.7825 (t80) REVERT: I 42 TRP cc_start: 0.6666 (m-10) cc_final: 0.6312 (m-10) REVERT: I 113 LEU cc_start: 0.5704 (tp) cc_final: 0.5360 (tp) outliers start: 0 outliers final: 0 residues processed: 409 average time/residue: 0.2140 time to fit residues: 135.7253 Evaluate side-chains 300 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 261 optimal weight: 5.9990 chunk 345 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 chunk 196 optimal weight: 0.7980 chunk 222 optimal weight: 1.9990 chunk 314 optimal weight: 0.8980 chunk 184 optimal weight: 0.6980 chunk 148 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 107 optimal weight: 0.0870 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 GLN D 149 ASN ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN G 207 HIS G 222 ASN H 282 HIS ** H 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 GLN ** I 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 241 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.099138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.074994 restraints weight = 112484.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.076746 restraints weight = 66545.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.077900 restraints weight = 46076.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.078687 restraints weight = 35666.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.079221 restraints weight = 29866.673| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29661 Z= 0.121 Angle : 0.707 14.401 40383 Z= 0.358 Chirality : 0.045 0.235 4527 Planarity : 0.006 0.122 5284 Dihedral : 6.996 61.722 4026 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.83 % Favored : 90.06 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 1.66 % Twisted General : 0.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.11 (0.13), residues: 3631 helix: -1.01 (0.16), residues: 985 sheet: -1.71 (0.22), residues: 477 loop : -2.80 (0.12), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 400 TYR 0.024 0.002 TYR G 265 PHE 0.025 0.002 PHE B 561 TRP 0.023 0.002 TRP E 162 HIS 0.013 0.001 HIS D 156 Details of bonding type rmsd covalent geometry : bond 0.00268 (29661) covalent geometry : angle 0.70727 (40383) hydrogen bonds : bond 0.03942 ( 671) hydrogen bonds : angle 5.36511 ( 1851) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7262 Ramachandran restraints generated. 3631 Oldfield, 0 Emsley, 3631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7262 Ramachandran restraints generated. 3631 Oldfield, 0 Emsley, 3631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 419 time to evaluate : 1.222 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: A 33 MET cc_start: 0.6213 (tmm) cc_final: 0.5814 (tmm) REVERT: A 48 ARG cc_start: 0.6000 (mtt180) cc_final: 0.5187 (mtt90) REVERT: A 61 ARG cc_start: 0.9062 (mtp85) cc_final: 0.8502 (ttm110) REVERT: A 62 GLN cc_start: 0.7153 (tt0) cc_final: 0.6783 (pp30) REVERT: A 214 ILE cc_start: 0.6912 (mp) cc_final: 0.6583 (pt) REVERT: A 263 ASN cc_start: 0.6921 (m-40) cc_final: 0.6513 (p0) REVERT: A 462 TRP cc_start: 0.7003 (m100) cc_final: 0.6304 (m100) REVERT: A 525 ASP cc_start: 0.7766 (m-30) cc_final: 0.7233 (m-30) REVERT: A 547 MET cc_start: 0.7875 (mmp) cc_final: 0.7540 (mmp) REVERT: B 13 MET cc_start: 0.6651 (mmm) cc_final: 0.6242 (mmm) REVERT: B 16 LEU cc_start: 0.7632 (mt) cc_final: 0.7320 (mt) REVERT: B 17 ARG cc_start: 0.6205 (mtt180) cc_final: 0.5007 (mmp80) REVERT: B 23 PHE cc_start: 0.7570 (m-10) cc_final: 0.7306 (m-80) REVERT: B 66 ASP cc_start: 0.8262 (t70) cc_final: 0.8015 (t70) REVERT: B 95 LEU cc_start: 0.7026 (mp) cc_final: 0.6307 (tp) REVERT: B 102 MET cc_start: 0.6802 (ppp) cc_final: 0.6031 (pmm) REVERT: B 104 MET cc_start: 0.4914 (mtm) cc_final: 0.4656 (mtm) REVERT: B 274 ASP cc_start: 0.7620 (m-30) cc_final: 0.7236 (p0) REVERT: B 375 HIS cc_start: 0.6433 (t70) cc_final: 0.6205 (t70) REVERT: B 377 ARG cc_start: 0.4980 (mtt180) cc_final: 0.4425 (tmm-80) REVERT: C 116 GLU cc_start: 0.5997 (mt-10) cc_final: 0.5243 (mm-30) REVERT: C 138 ARG cc_start: 0.7761 (tmt-80) cc_final: 0.6719 (tmm-80) REVERT: C 252 GLN cc_start: 0.6192 (tm-30) cc_final: 0.5949 (tm-30) REVERT: C 299 GLU cc_start: 0.7380 (mt-10) cc_final: 0.6441 (pp20) REVERT: D 256 MET cc_start: 0.8025 (mmm) cc_final: 0.7684 (mmt) REVERT: E 15 MET cc_start: 0.8206 (mpp) cc_final: 0.7929 (mpp) REVERT: F 198 MET cc_start: 0.8791 (mmm) cc_final: 0.8541 (mmm) REVERT: F 290 TYR cc_start: 0.8679 (t80) cc_final: 0.8262 (t80) REVERT: G 233 ASP cc_start: 0.7470 (m-30) cc_final: 0.6861 (t0) REVERT: G 283 ASN cc_start: 0.7237 (m-40) cc_final: 0.6713 (t0) REVERT: H 1 MET cc_start: 0.7957 (mmm) cc_final: 0.7749 (mmp) REVERT: H 138 HIS cc_start: 0.6628 (t-90) cc_final: 0.6399 (t-90) REVERT: H 185 ILE cc_start: 0.9296 (pt) cc_final: 0.9057 (mp) REVERT: H 340 ARG cc_start: 0.8168 (ptt-90) cc_final: 0.7753 (mtt90) REVERT: I 42 TRP cc_start: 0.6783 (m-10) cc_final: 0.6370 (m-10) REVERT: I 113 LEU cc_start: 0.5504 (tp) cc_final: 0.5217 (tp) REVERT: I 277 THR cc_start: 0.7603 (p) cc_final: 0.7299 (m) outliers start: 0 outliers final: 0 residues processed: 419 average time/residue: 0.2066 time to fit residues: 136.1935 Evaluate side-chains 320 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 327 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 302 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 205 optimal weight: 0.5980 chunk 125 optimal weight: 0.0170 chunk 168 optimal weight: 4.9990 chunk 284 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 354 optimal weight: 9.9990 overall best weight: 2.5224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 HIS ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 HIS ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 ASN I 18 GLN ** I 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 241 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.109461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.085232 restraints weight = 112597.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.087053 restraints weight = 64754.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.088255 restraints weight = 44078.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.089111 restraints weight = 33625.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.089670 restraints weight = 27735.987| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 29661 Z= 0.176 Angle : 0.742 13.380 40383 Z= 0.374 Chirality : 0.046 0.318 4527 Planarity : 0.006 0.117 5284 Dihedral : 6.967 61.051 4026 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.81 % Favored : 88.07 % Rotamer: Outliers : 0.03 % Allowed : 2.40 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 1.66 % Twisted General : 0.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.93 (0.13), residues: 3631 helix: -0.74 (0.17), residues: 992 sheet: -1.69 (0.22), residues: 488 loop : -2.73 (0.13), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 179 TYR 0.020 0.002 TYR C 346 PHE 0.022 0.002 PHE B 561 TRP 0.029 0.002 TRP A 283 HIS 0.011 0.001 HIS D 156 Details of bonding type rmsd covalent geometry : bond 0.00403 (29661) covalent geometry : angle 0.74166 (40383) hydrogen bonds : bond 0.04011 ( 671) hydrogen bonds : angle 5.34718 ( 1851) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7262 Ramachandran restraints generated. 3631 Oldfield, 0 Emsley, 3631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7262 Ramachandran restraints generated. 3631 Oldfield, 0 Emsley, 3631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 382 time to evaluate : 1.238 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: A 14 ARG cc_start: 0.8511 (ttt180) cc_final: 0.8165 (ptt-90) REVERT: A 33 MET cc_start: 0.6293 (tmm) cc_final: 0.5860 (tmm) REVERT: A 48 ARG cc_start: 0.5948 (mtt180) cc_final: 0.5130 (mtt90) REVERT: A 62 GLN cc_start: 0.7147 (tt0) cc_final: 0.6169 (pp30) REVERT: A 214 ILE cc_start: 0.6911 (mp) cc_final: 0.6559 (pt) REVERT: A 263 ASN cc_start: 0.6864 (m-40) cc_final: 0.6462 (p0) REVERT: A 434 GLN cc_start: 0.6186 (mm-40) cc_final: 0.5743 (pm20) REVERT: A 462 TRP cc_start: 0.7054 (m100) cc_final: 0.6225 (m100) REVERT: A 547 MET cc_start: 0.7866 (mmp) cc_final: 0.7554 (mmp) REVERT: B 13 MET cc_start: 0.6673 (mmm) cc_final: 0.6315 (mmm) REVERT: B 16 LEU cc_start: 0.7461 (mt) cc_final: 0.7070 (mt) REVERT: B 17 ARG cc_start: 0.6298 (mtt180) cc_final: 0.5027 (mmp80) REVERT: B 23 PHE cc_start: 0.7624 (m-10) cc_final: 0.7377 (m-80) REVERT: B 66 ASP cc_start: 0.8334 (t70) cc_final: 0.8075 (t70) REVERT: B 95 LEU cc_start: 0.6961 (mp) cc_final: 0.6349 (tp) REVERT: B 274 ASP cc_start: 0.7607 (m-30) cc_final: 0.6930 (p0) REVERT: B 375 HIS cc_start: 0.6507 (t70) cc_final: 0.6176 (t70) REVERT: C 299 GLU cc_start: 0.7368 (mt-10) cc_final: 0.6434 (pp20) REVERT: D 237 PHE cc_start: 0.8189 (p90) cc_final: 0.7546 (p90) REVERT: D 238 TRP cc_start: 0.5927 (m100) cc_final: 0.5717 (m100) REVERT: D 256 MET cc_start: 0.7985 (mmm) cc_final: 0.7739 (mmt) REVERT: G 42 TRP cc_start: 0.6575 (m-10) cc_final: 0.6320 (m-10) REVERT: G 118 GLU cc_start: 0.4844 (tp30) cc_final: 0.4486 (tp30) REVERT: G 233 ASP cc_start: 0.7786 (m-30) cc_final: 0.7106 (t0) REVERT: H 1 MET cc_start: 0.7982 (mmm) cc_final: 0.7725 (mmp) REVERT: H 112 ASN cc_start: 0.7475 (OUTLIER) cc_final: 0.6896 (t0) REVERT: H 185 ILE cc_start: 0.9275 (pt) cc_final: 0.9010 (mp) REVERT: H 340 ARG cc_start: 0.8094 (ptt-90) cc_final: 0.7668 (mtt90) REVERT: I 42 TRP cc_start: 0.6907 (m-10) cc_final: 0.6601 (m-10) REVERT: I 113 LEU cc_start: 0.5599 (tp) cc_final: 0.5305 (tp) outliers start: 1 outliers final: 0 residues processed: 383 average time/residue: 0.2015 time to fit residues: 122.8966 Evaluate side-chains 303 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 302 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 283 optimal weight: 0.8980 chunk 131 optimal weight: 0.5980 chunk 81 optimal weight: 0.0030 chunk 352 optimal weight: 4.9990 chunk 351 optimal weight: 4.9990 chunk 314 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 254 optimal weight: 5.9990 chunk 315 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 327 optimal weight: 0.0870 overall best weight: 1.1170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 241 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.098359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.074259 restraints weight = 112222.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.076079 restraints weight = 64972.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.077279 restraints weight = 44243.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.078098 restraints weight = 33851.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.078638 restraints weight = 28147.260| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29661 Z= 0.122 Angle : 0.705 13.584 40383 Z= 0.352 Chirality : 0.045 0.491 4527 Planarity : 0.005 0.106 5284 Dihedral : 6.629 59.846 4026 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.41 % Favored : 89.53 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 1.24 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.75 (0.13), residues: 3631 helix: -0.52 (0.17), residues: 979 sheet: -1.54 (0.23), residues: 470 loop : -2.66 (0.13), residues: 2182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 138 TYR 0.021 0.001 TYR G 265 PHE 0.030 0.002 PHE H 278 TRP 0.027 0.002 TRP I 238 HIS 0.010 0.001 HIS D 156 Details of bonding type rmsd covalent geometry : bond 0.00276 (29661) covalent geometry : angle 0.70521 (40383) hydrogen bonds : bond 0.03583 ( 671) hydrogen bonds : angle 5.06383 ( 1851) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7262 Ramachandran restraints generated. 3631 Oldfield, 0 Emsley, 3631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7262 Ramachandran restraints generated. 3631 Oldfield, 0 Emsley, 3631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 396 time to evaluate : 1.478 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: A 33 MET cc_start: 0.6037 (tmm) cc_final: 0.5760 (tmm) REVERT: A 48 ARG cc_start: 0.5947 (mtt180) cc_final: 0.5125 (mtt90) REVERT: A 57 MET cc_start: 0.7858 (mmt) cc_final: 0.7653 (mmt) REVERT: A 194 MET cc_start: 0.8058 (mmp) cc_final: 0.7753 (mmm) REVERT: A 214 ILE cc_start: 0.7011 (mp) cc_final: 0.6793 (pt) REVERT: A 263 ASN cc_start: 0.6896 (m-40) cc_final: 0.6483 (p0) REVERT: A 320 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8145 (mp0) REVERT: A 434 GLN cc_start: 0.6094 (mm-40) cc_final: 0.5708 (pm20) REVERT: A 462 TRP cc_start: 0.6542 (m100) cc_final: 0.5998 (m100) REVERT: A 525 ASP cc_start: 0.8095 (t0) cc_final: 0.7838 (m-30) REVERT: B 13 MET cc_start: 0.6661 (mmm) cc_final: 0.5929 (mmm) REVERT: B 16 LEU cc_start: 0.7709 (mt) cc_final: 0.6979 (mt) REVERT: B 17 ARG cc_start: 0.6106 (mtt180) cc_final: 0.4847 (mmp80) REVERT: B 23 PHE cc_start: 0.7583 (m-10) cc_final: 0.7356 (m-80) REVERT: B 66 ASP cc_start: 0.8299 (t70) cc_final: 0.8029 (t70) REVERT: B 80 TRP cc_start: 0.6897 (t-100) cc_final: 0.6658 (t-100) REVERT: B 95 LEU cc_start: 0.6867 (mp) cc_final: 0.6296 (tp) REVERT: B 375 HIS cc_start: 0.6403 (t70) cc_final: 0.6022 (t70) REVERT: B 547 MET cc_start: 0.6643 (ptt) cc_final: 0.6420 (ptt) REVERT: C 250 ASN cc_start: 0.6802 (m-40) cc_final: 0.6567 (t0) REVERT: D 198 MET cc_start: 0.8260 (mmm) cc_final: 0.8038 (mmm) REVERT: D 237 PHE cc_start: 0.7997 (p90) cc_final: 0.7276 (p90) REVERT: D 256 MET cc_start: 0.7808 (mmm) cc_final: 0.7506 (mmt) REVERT: G 233 ASP cc_start: 0.7992 (m-30) cc_final: 0.7059 (t0) REVERT: G 283 ASN cc_start: 0.6977 (m-40) cc_final: 0.6595 (t0) REVERT: H 1 MET cc_start: 0.7937 (mmm) cc_final: 0.7646 (mmp) REVERT: H 185 ILE cc_start: 0.9312 (pt) cc_final: 0.9051 (mp) REVERT: H 340 ARG cc_start: 0.8197 (ptt-90) cc_final: 0.7783 (mtt90) REVERT: I 31 ASP cc_start: 0.8309 (p0) cc_final: 0.7980 (t70) REVERT: I 42 TRP cc_start: 0.6780 (m-10) cc_final: 0.6513 (m-10) REVERT: I 113 LEU cc_start: 0.5489 (tp) cc_final: 0.5278 (tp) REVERT: I 190 THR cc_start: 0.9410 (t) cc_final: 0.9188 (m) outliers start: 0 outliers final: 0 residues processed: 396 average time/residue: 0.2074 time to fit residues: 130.6000 Evaluate side-chains 315 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 136 optimal weight: 7.9990 chunk 154 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 167 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 58 optimal weight: 0.0270 chunk 176 optimal weight: 0.2980 chunk 356 optimal weight: 4.9990 chunk 180 optimal weight: 0.9980 chunk 190 optimal weight: 0.0000 chunk 249 optimal weight: 9.9990 overall best weight: 1.2644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 HIS ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 ASN B 580 ASN C 318 GLN D 149 ASN ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 HIS ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 HIS I 241 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.098809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.074868 restraints weight = 112625.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.076657 restraints weight = 65400.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.077853 restraints weight = 44737.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.078659 restraints weight = 34310.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.079163 restraints weight = 28481.335| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29661 Z= 0.126 Angle : 0.699 16.787 40383 Z= 0.349 Chirality : 0.045 0.277 4527 Planarity : 0.006 0.098 5284 Dihedral : 6.467 59.082 4026 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.80 % Favored : 89.12 % Rotamer: Outliers : 0.03 % Allowed : 1.25 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 1.24 % Twisted General : 0.35 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.58 (0.14), residues: 3631 helix: -0.31 (0.17), residues: 977 sheet: -1.40 (0.23), residues: 461 loop : -2.58 (0.13), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 550 TYR 0.018 0.001 TYR C 346 PHE 0.026 0.002 PHE B 55 TRP 0.039 0.002 TRP D 238 HIS 0.010 0.001 HIS D 156 Details of bonding type rmsd covalent geometry : bond 0.00288 (29661) covalent geometry : angle 0.69883 (40383) hydrogen bonds : bond 0.03462 ( 671) hydrogen bonds : angle 4.91151 ( 1851) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7262 Ramachandran restraints generated. 3631 Oldfield, 0 Emsley, 3631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7262 Ramachandran restraints generated. 3631 Oldfield, 0 Emsley, 3631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 395 time to evaluate : 1.200 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: A 33 MET cc_start: 0.6163 (tmm) cc_final: 0.5837 (tmm) REVERT: A 48 ARG cc_start: 0.5908 (mtt180) cc_final: 0.5111 (mtt90) REVERT: A 57 MET cc_start: 0.7834 (mmt) cc_final: 0.7565 (mmt) REVERT: A 194 MET cc_start: 0.8021 (mmp) cc_final: 0.7742 (mmm) REVERT: A 214 ILE cc_start: 0.7006 (mp) cc_final: 0.6786 (pt) REVERT: A 263 ASN cc_start: 0.6859 (m-40) cc_final: 0.6468 (p0) REVERT: A 320 GLU cc_start: 0.8429 (mt-10) cc_final: 0.7906 (mp0) REVERT: A 434 GLN cc_start: 0.6077 (mm-40) cc_final: 0.5771 (pm20) REVERT: A 462 TRP cc_start: 0.6528 (m100) cc_final: 0.6013 (m100) REVERT: A 511 ARG cc_start: 0.7840 (mmm-85) cc_final: 0.7393 (mmt90) REVERT: B 13 MET cc_start: 0.6415 (mmm) cc_final: 0.6097 (mmm) REVERT: B 17 ARG cc_start: 0.6088 (mtt180) cc_final: 0.4842 (mmp80) REVERT: B 23 PHE cc_start: 0.7583 (m-10) cc_final: 0.7345 (m-80) REVERT: B 66 ASP cc_start: 0.8278 (t70) cc_final: 0.8027 (t70) REVERT: B 95 LEU cc_start: 0.6850 (mp) cc_final: 0.6269 (tp) REVERT: B 102 MET cc_start: 0.6916 (ppp) cc_final: 0.6221 (pmm) REVERT: B 274 ASP cc_start: 0.7765 (m-30) cc_final: 0.6973 (p0) REVERT: B 321 TYR cc_start: 0.7019 (p90) cc_final: 0.6416 (p90) REVERT: B 375 HIS cc_start: 0.6474 (t70) cc_final: 0.6131 (t70) REVERT: B 390 LEU cc_start: 0.9036 (pt) cc_final: 0.8406 (tp) REVERT: C 299 GLU cc_start: 0.6786 (mt-10) cc_final: 0.6541 (pm20) REVERT: D 237 PHE cc_start: 0.7994 (p90) cc_final: 0.7316 (p90) REVERT: G 233 ASP cc_start: 0.7704 (m-30) cc_final: 0.6982 (t0) REVERT: G 234 VAL cc_start: 0.8640 (p) cc_final: 0.8408 (p) REVERT: G 283 ASN cc_start: 0.7029 (m-40) cc_final: 0.6616 (t0) REVERT: H 1 MET cc_start: 0.7912 (mmm) cc_final: 0.7599 (mmp) REVERT: H 185 ILE cc_start: 0.9321 (pt) cc_final: 0.9070 (mp) REVERT: H 340 ARG cc_start: 0.8114 (ptt-90) cc_final: 0.7892 (mtt90) REVERT: H 426 PHE cc_start: 0.8073 (t80) cc_final: 0.7739 (t80) REVERT: I 31 ASP cc_start: 0.8277 (p0) cc_final: 0.8014 (t70) REVERT: I 42 TRP cc_start: 0.6760 (m-10) cc_final: 0.6514 (m-10) outliers start: 1 outliers final: 0 residues processed: 395 average time/residue: 0.2044 time to fit residues: 128.1008 Evaluate side-chains 302 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 168 optimal weight: 3.9990 chunk 345 optimal weight: 0.8980 chunk 199 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 133 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 chunk 241 optimal weight: 4.9990 chunk 152 optimal weight: 0.7980 chunk 146 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS D 149 ASN ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 241 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.098663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.074722 restraints weight = 112351.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.076454 restraints weight = 66989.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.077623 restraints weight = 46356.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.078386 restraints weight = 35775.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.078863 restraints weight = 30013.116| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29661 Z= 0.124 Angle : 0.700 12.483 40383 Z= 0.349 Chirality : 0.045 0.252 4527 Planarity : 0.005 0.092 5284 Dihedral : 6.350 58.571 4026 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.66 % Favored : 89.31 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 1.24 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.47 (0.14), residues: 3631 helix: -0.21 (0.17), residues: 984 sheet: -1.38 (0.24), residues: 448 loop : -2.51 (0.13), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 550 TYR 0.020 0.001 TYR G 265 PHE 0.020 0.001 PHE B 358 TRP 0.069 0.002 TRP D 238 HIS 0.009 0.001 HIS D 156 Details of bonding type rmsd covalent geometry : bond 0.00287 (29661) covalent geometry : angle 0.70010 (40383) hydrogen bonds : bond 0.03323 ( 671) hydrogen bonds : angle 4.81229 ( 1851) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7262 Ramachandran restraints generated. 3631 Oldfield, 0 Emsley, 3631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7262 Ramachandran restraints generated. 3631 Oldfield, 0 Emsley, 3631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 391 time to evaluate : 1.313 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: A 14 ARG cc_start: 0.8623 (ttt180) cc_final: 0.8356 (ptt-90) REVERT: A 15 TYR cc_start: 0.8046 (m-80) cc_final: 0.7415 (m-80) REVERT: A 33 MET cc_start: 0.5873 (tmm) cc_final: 0.5496 (tmm) REVERT: A 48 ARG cc_start: 0.5954 (mtt180) cc_final: 0.5102 (mtt90) REVERT: A 194 MET cc_start: 0.7929 (mmp) cc_final: 0.7661 (mmm) REVERT: A 214 ILE cc_start: 0.6855 (mp) cc_final: 0.6653 (pt) REVERT: A 263 ASN cc_start: 0.6963 (m-40) cc_final: 0.6554 (p0) REVERT: A 320 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7930 (mp0) REVERT: A 434 GLN cc_start: 0.6018 (mm-40) cc_final: 0.5811 (pm20) REVERT: A 526 VAL cc_start: 0.8735 (m) cc_final: 0.8425 (m) REVERT: A 527 GLU cc_start: 0.5950 (pm20) cc_final: 0.5436 (pm20) REVERT: B 13 MET cc_start: 0.6270 (mmm) cc_final: 0.6068 (mmm) REVERT: B 16 LEU cc_start: 0.7194 (mt) cc_final: 0.6780 (mt) REVERT: B 17 ARG cc_start: 0.6091 (mtt180) cc_final: 0.4831 (mmp80) REVERT: B 23 PHE cc_start: 0.7550 (m-10) cc_final: 0.7335 (m-80) REVERT: B 95 LEU cc_start: 0.6795 (mp) cc_final: 0.6195 (tp) REVERT: B 321 TYR cc_start: 0.6961 (p90) cc_final: 0.6747 (p90) REVERT: B 375 HIS cc_start: 0.6538 (t70) cc_final: 0.6307 (t70) REVERT: B 377 ARG cc_start: 0.4893 (mtt180) cc_final: 0.4275 (tmm-80) REVERT: B 390 LEU cc_start: 0.8916 (pt) cc_final: 0.8252 (tp) REVERT: D 256 MET cc_start: 0.7794 (mpp) cc_final: 0.7548 (mmt) REVERT: E 189 LEU cc_start: 0.8522 (tp) cc_final: 0.8321 (tp) REVERT: G 233 ASP cc_start: 0.7501 (m-30) cc_final: 0.6844 (t0) REVERT: G 234 VAL cc_start: 0.8636 (p) cc_final: 0.8392 (p) REVERT: G 283 ASN cc_start: 0.7082 (m-40) cc_final: 0.6652 (t0) REVERT: H 185 ILE cc_start: 0.9329 (pt) cc_final: 0.9114 (mp) REVERT: H 426 PHE cc_start: 0.8045 (t80) cc_final: 0.7643 (t80) REVERT: I 31 ASP cc_start: 0.8255 (p0) cc_final: 0.8020 (t70) REVERT: I 42 TRP cc_start: 0.6737 (m-10) cc_final: 0.6497 (m-10) outliers start: 0 outliers final: 0 residues processed: 391 average time/residue: 0.2028 time to fit residues: 125.7082 Evaluate side-chains 313 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 292 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 289 optimal weight: 0.2980 chunk 325 optimal weight: 0.9990 chunk 250 optimal weight: 0.6980 chunk 50 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 chunk 163 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 170 optimal weight: 0.0870 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 ASN D 149 ASN ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 HIS ** I 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 241 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.099895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.075749 restraints weight = 113920.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.077601 restraints weight = 66000.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.078854 restraints weight = 44981.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.079662 restraints weight = 34301.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.080217 restraints weight = 28495.040| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 29661 Z= 0.111 Angle : 0.684 12.267 40383 Z= 0.340 Chirality : 0.044 0.243 4527 Planarity : 0.005 0.082 5284 Dihedral : 6.130 58.099 4026 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.67 % Favored : 90.31 % Rotamer: Outliers : 0.06 % Allowed : 0.54 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.83 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.32 (0.14), residues: 3631 helix: -0.04 (0.18), residues: 985 sheet: -1.27 (0.24), residues: 436 loop : -2.44 (0.13), residues: 2210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 61 TYR 0.020 0.001 TYR C 346 PHE 0.021 0.001 PHE B 472 TRP 0.059 0.002 TRP B 389 HIS 0.011 0.001 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00252 (29661) covalent geometry : angle 0.68400 (40383) hydrogen bonds : bond 0.03134 ( 671) hydrogen bonds : angle 4.66935 ( 1851) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7262 Ramachandran restraints generated. 3631 Oldfield, 0 Emsley, 3631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7262 Ramachandran restraints generated. 3631 Oldfield, 0 Emsley, 3631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 410 time to evaluate : 1.308 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: A 33 MET cc_start: 0.5764 (tmm) cc_final: 0.5350 (tmm) REVERT: A 48 ARG cc_start: 0.6047 (mtt180) cc_final: 0.5139 (mtt90) REVERT: A 61 ARG cc_start: 0.9233 (mtp85) cc_final: 0.8970 (mtp85) REVERT: A 194 MET cc_start: 0.7882 (mmp) cc_final: 0.7543 (mmm) REVERT: A 214 ILE cc_start: 0.6899 (mp) cc_final: 0.6695 (pt) REVERT: A 263 ASN cc_start: 0.6895 (m-40) cc_final: 0.6514 (p0) REVERT: A 320 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7893 (mp0) REVERT: A 511 ARG cc_start: 0.7795 (mmm-85) cc_final: 0.7333 (mmt90) REVERT: A 525 ASP cc_start: 0.8255 (t0) cc_final: 0.7713 (m-30) REVERT: B 13 MET cc_start: 0.6231 (mmm) cc_final: 0.5866 (mmm) REVERT: B 16 LEU cc_start: 0.7203 (mt) cc_final: 0.6910 (mt) REVERT: B 17 ARG cc_start: 0.6051 (mtt180) cc_final: 0.4808 (mmp80) REVERT: B 95 LEU cc_start: 0.6684 (mp) cc_final: 0.6057 (tp) REVERT: B 102 MET cc_start: 0.6945 (ppp) cc_final: 0.6283 (pmm) REVERT: B 274 ASP cc_start: 0.7682 (m-30) cc_final: 0.6936 (p0) REVERT: B 375 HIS cc_start: 0.6579 (t70) cc_final: 0.6361 (t70) REVERT: B 377 ARG cc_start: 0.4836 (mtt180) cc_final: 0.4286 (tmm-80) REVERT: B 390 LEU cc_start: 0.8797 (pt) cc_final: 0.8168 (tt) REVERT: B 562 ASN cc_start: 0.7570 (OUTLIER) cc_final: 0.7328 (p0) REVERT: C 28 PHE cc_start: 0.8560 (t80) cc_final: 0.8351 (t80) REVERT: C 347 GLN cc_start: 0.5292 (tp-100) cc_final: 0.4727 (tp40) REVERT: D 202 LEU cc_start: 0.9394 (tp) cc_final: 0.9185 (tt) REVERT: D 237 PHE cc_start: 0.8109 (p90) cc_final: 0.7564 (p90) REVERT: D 256 MET cc_start: 0.7644 (mpp) cc_final: 0.7420 (mmt) REVERT: E 189 LEU cc_start: 0.8534 (tp) cc_final: 0.8320 (tp) REVERT: G 125 TRP cc_start: 0.7652 (p-90) cc_final: 0.7254 (p-90) REVERT: G 126 LYS cc_start: 0.8850 (tmtt) cc_final: 0.8436 (tptp) REVERT: G 233 ASP cc_start: 0.7637 (m-30) cc_final: 0.6767 (t0) REVERT: G 234 VAL cc_start: 0.8535 (p) cc_final: 0.8292 (p) REVERT: G 283 ASN cc_start: 0.6962 (m-40) cc_final: 0.6585 (t0) REVERT: H 340 ARG cc_start: 0.7845 (ptp90) cc_final: 0.7218 (mtt90) REVERT: I 31 ASP cc_start: 0.8232 (p0) cc_final: 0.7923 (t0) REVERT: I 113 LEU cc_start: 0.5745 (tp) cc_final: 0.5515 (tp) outliers start: 2 outliers final: 0 residues processed: 411 average time/residue: 0.1982 time to fit residues: 129.7055 Evaluate side-chains 312 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 311 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 3 optimal weight: 9.9990 chunk 116 optimal weight: 0.0570 chunk 58 optimal weight: 9.9990 chunk 162 optimal weight: 9.9990 chunk 31 optimal weight: 0.0070 chunk 334 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 94 optimal weight: 0.0470 overall best weight: 1.2218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 241 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.099185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.075083 restraints weight = 113541.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.076796 restraints weight = 67579.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.077999 restraints weight = 47058.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.078767 restraints weight = 36313.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.079290 restraints weight = 30457.146| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 29661 Z= 0.122 Angle : 0.697 12.845 40383 Z= 0.346 Chirality : 0.045 0.266 4527 Planarity : 0.005 0.104 5284 Dihedral : 6.069 57.493 4026 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.33 % Favored : 89.64 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.83 % Twisted General : 0.35 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.25 (0.14), residues: 3631 helix: 0.02 (0.17), residues: 988 sheet: -1.15 (0.25), residues: 423 loop : -2.42 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 61 TYR 0.021 0.001 TYR C 140 PHE 0.018 0.001 PHE B 358 TRP 0.057 0.002 TRP B 389 HIS 0.009 0.001 HIS D 156 Details of bonding type rmsd covalent geometry : bond 0.00284 (29661) covalent geometry : angle 0.69711 (40383) hydrogen bonds : bond 0.03210 ( 671) hydrogen bonds : angle 4.69178 ( 1851) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7262 Ramachandran restraints generated. 3631 Oldfield, 0 Emsley, 3631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7262 Ramachandran restraints generated. 3631 Oldfield, 0 Emsley, 3631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 1.206 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: A 33 MET cc_start: 0.5674 (tmm) cc_final: 0.5342 (tmm) REVERT: A 61 ARG cc_start: 0.9186 (mtp85) cc_final: 0.8773 (ttm110) REVERT: A 194 MET cc_start: 0.7933 (mmp) cc_final: 0.7614 (mmm) REVERT: A 263 ASN cc_start: 0.6848 (m-40) cc_final: 0.6464 (p0) REVERT: A 320 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7896 (mp0) REVERT: A 511 ARG cc_start: 0.7738 (mmm-85) cc_final: 0.7438 (mmt90) REVERT: A 525 ASP cc_start: 0.8237 (t0) cc_final: 0.7654 (m-30) REVERT: B 17 ARG cc_start: 0.6049 (mtt180) cc_final: 0.5206 (tpp80) REVERT: B 95 LEU cc_start: 0.6654 (mp) cc_final: 0.6098 (tp) REVERT: B 102 MET cc_start: 0.6855 (ppp) cc_final: 0.6195 (pmm) REVERT: B 375 HIS cc_start: 0.6580 (t70) cc_final: 0.6373 (t70) REVERT: B 377 ARG cc_start: 0.4842 (mtt180) cc_final: 0.4305 (tmm-80) REVERT: B 390 LEU cc_start: 0.8795 (pt) cc_final: 0.8120 (tt) REVERT: C 347 GLN cc_start: 0.5363 (tp-100) cc_final: 0.4793 (tp40) REVERT: D 237 PHE cc_start: 0.7999 (p90) cc_final: 0.7028 (p90) REVERT: D 256 MET cc_start: 0.7693 (mpp) cc_final: 0.7457 (mmt) REVERT: E 202 LEU cc_start: 0.8743 (pp) cc_final: 0.8334 (tp) REVERT: G 233 ASP cc_start: 0.7590 (m-30) cc_final: 0.6776 (t0) REVERT: G 234 VAL cc_start: 0.8687 (p) cc_final: 0.8460 (p) REVERT: G 283 ASN cc_start: 0.7019 (m-40) cc_final: 0.6602 (t0) REVERT: H 340 ARG cc_start: 0.7903 (ptp90) cc_final: 0.7294 (mtt90) REVERT: I 31 ASP cc_start: 0.8351 (p0) cc_final: 0.8144 (t70) outliers start: 0 outliers final: 0 residues processed: 384 average time/residue: 0.1935 time to fit residues: 118.9163 Evaluate side-chains 298 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 0.0060 chunk 148 optimal weight: 0.0020 chunk 82 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 chunk 334 optimal weight: 5.9990 chunk 166 optimal weight: 0.0060 chunk 164 optimal weight: 0.0670 chunk 352 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 256 optimal weight: 7.9990 overall best weight: 0.4160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 HIS H 156 HIS ** I 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 241 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.100684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.076614 restraints weight = 112954.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.078417 restraints weight = 66540.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.079610 restraints weight = 45885.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.080423 restraints weight = 35305.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.080985 restraints weight = 29466.376| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 29661 Z= 0.111 Angle : 0.685 12.949 40383 Z= 0.337 Chirality : 0.044 0.260 4527 Planarity : 0.005 0.101 5284 Dihedral : 5.856 57.141 4026 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.23 % Favored : 90.75 % Rotamer: Outliers : 0.03 % Allowed : 0.35 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 1.24 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.14), residues: 3631 helix: 0.12 (0.18), residues: 991 sheet: -1.06 (0.25), residues: 418 loop : -2.35 (0.13), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 61 TYR 0.018 0.001 TYR C 346 PHE 0.024 0.001 PHE B 55 TRP 0.052 0.002 TRP B 389 HIS 0.009 0.001 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00250 (29661) covalent geometry : angle 0.68543 (40383) hydrogen bonds : bond 0.02918 ( 671) hydrogen bonds : angle 4.57019 ( 1851) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5628.55 seconds wall clock time: 97 minutes 55.18 seconds (5875.18 seconds total)