Starting phenix.real_space_refine on Tue Jun 24 21:10:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6giy_0008/06_2025/6giy_0008.cif Found real_map, /net/cci-nas-00/data/ceres_data/6giy_0008/06_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_0008/06_2025/6giy_0008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6giy_0008/06_2025/6giy_0008.map" model { file = "/net/cci-nas-00/data/ceres_data/6giy_0008/06_2025/6giy_0008.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6giy_0008/06_2025/6giy_0008.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.40, per 1000 atoms: 0.57 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: 6.39 Conformation dependent library (CDL) restraints added in 3.6 seconds 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: 2.75 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: 8.26 Time building geometry restraints manager: 7.71 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: 6.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.070 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 58.480 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.450 ------------------------------------------------------------------------------- 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 : 6.19 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.039 0.004 TRP E 125 HIS 0.014 0.003 HIS G 40 PHE 0.035 0.003 PHE H 278 TYR 0.027 0.003 TYR G 4 ARG 0.018 0.001 ARG A 132 Details of bonding type rmsd hydrogen bonds : bond 0.32289 ( 671) hydrogen bonds : angle 10.35302 ( 1851) covalent geometry : bond 0.00705 (29661) covalent geometry : angle 1.17822 (40383) *********************** 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 : 3.139 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: 0.8219 (ptp-170) REVERT: A 15 TYR cc_start: 0.8692 (m-10) cc_final: 0.8294 (m-10) REVERT: A 27 HIS cc_start: 0.8156 (m-70) cc_final: 0.7887 (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: 0.8727 (mtp85) REVERT: A 62 GLN cc_start: 0.7377 (tt0) cc_final: 0.6912 (pp30) REVERT: A 214 ILE cc_start: 0.6948 (OUTLIER) cc_final: 0.6555 (pt) REVERT: A 217 TRP cc_start: 0.7859 (m-10) cc_final: 0.7306 (m-10) REVERT: A 263 ASN cc_start: 0.6832 (m-40) cc_final: 0.6435 (p0) REVERT: A 385 MET cc_start: 0.5932 (mtt) cc_final: 0.5165 (ttt) REVERT: A 467 HIS cc_start: 0.8006 (t70) cc_final: 0.7653 (t-90) REVERT: A 526 VAL cc_start: 0.9094 (p) cc_final: 0.8312 (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: 0.4899 (mmp80) REVERT: B 23 PHE cc_start: 0.7806 (m-10) cc_final: 0.7579 (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: 0.8113 (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: 0.7038 (t80) REVERT: B 375 HIS cc_start: 0.6598 (t70) cc_final: 0.6225 (t70) REVERT: B 377 ARG cc_start: 0.5107 (mtt180) cc_final: 0.4176 (tmm160) REVERT: C 66 PHE cc_start: 0.4646 (m-10) cc_final: 0.3757 (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: 0.5349 (mm-30) REVERT: C 299 GLU cc_start: 0.7830 (mt-10) cc_final: 0.6827 (pp20) REVERT: D 36 MET cc_start: 0.8076 (mtp) cc_final: 0.7612 (mtm) REVERT: D 114 ASP cc_start: 0.5559 (t0) cc_final: 0.4750 (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: 0.7407 (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: 0.9007 (mp) REVERT: H 340 ARG cc_start: 0.8239 (ptt-90) cc_final: 0.7811 (mtt90) REVERT: H 426 PHE cc_start: 0.7964 (t80) cc_final: 0.7086 (t80) REVERT: I 15 MET cc_start: 0.7858 (mtm) cc_final: 0.7603 (mtm) REVERT: I 42 TRP cc_start: 0.6303 (m-10) cc_final: 0.6017 (m-10) REVERT: I 138 HIS cc_start: 0.7779 (p-80) cc_final: 0.7458 (p90) outliers start: 9 outliers final: 0 residues processed: 644 average time/residue: 0.4676 time to fit residues: 451.0041 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 : 4.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 306 optimal weight: 0.5980 chunk 275 optimal weight: 0.8980 chunk 152 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 284 optimal weight: 6.9990 chunk 110 optimal weight: 0.0070 chunk 173 optimal weight: 9.9990 chunk 211 optimal weight: 0.6980 chunk 329 optimal weight: 1.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN C 127 HIS C 132 GLN C 250 ASN C 318 GLN C 350 GLN C 352 HIS ** 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 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: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.103051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.079711 restraints weight = 122562.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.081265 restraints weight = 86473.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.081842 restraints weight = 57203.168| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29661 Z= 0.137 Angle : 0.758 14.219 40383 Z= 0.391 Chirality : 0.045 0.215 4527 Planarity : 0.007 0.121 5284 Dihedral : 7.754 63.791 4026 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.08 % Favored : 89.81 % Rotamer: Outliers : 0.10 % Allowed : 2.59 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.07 % Twisted General : 0.59 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.10 (0.12), residues: 3631 helix: -2.68 (0.13), residues: 996 sheet: -1.95 (0.22), residues: 487 loop : -3.06 (0.12), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 283 HIS 0.008 0.001 HIS E 206 PHE 0.022 0.002 PHE A 50 TYR 0.023 0.002 TYR C 346 ARG 0.020 0.001 ARG A 499 Details of bonding type rmsd hydrogen bonds : bond 0.05952 ( 671) hydrogen bonds : angle 6.23360 ( 1851) covalent geometry : bond 0.00285 (29661) covalent geometry : angle 0.75753 (40383) *********************** 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 512 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 509 time to evaluate : 3.142 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: A 15 TYR cc_start: 0.8660 (m-10) cc_final: 0.8293 (m-10) REVERT: A 33 MET cc_start: 0.6131 (tmm) cc_final: 0.5797 (tmm) REVERT: A 62 GLN cc_start: 0.7265 (tt0) cc_final: 0.6919 (pp30) REVERT: A 193 MET cc_start: 0.7567 (mmm) cc_final: 0.7250 (mmm) REVERT: A 194 MET cc_start: 0.7011 (mmm) cc_final: 0.6293 (mmm) REVERT: A 214 ILE cc_start: 0.6959 (mp) cc_final: 0.6545 (pt) REVERT: A 230 TRP cc_start: 0.5973 (m-10) cc_final: 0.5526 (m-10) REVERT: A 263 ASN cc_start: 0.7046 (m-40) cc_final: 0.6691 (p0) REVERT: A 367 HIS cc_start: 0.7475 (m90) cc_final: 0.7138 (p90) REVERT: A 385 MET cc_start: 0.6373 (mtt) cc_final: 0.5987 (ttt) REVERT: A 425 GLN cc_start: 0.8325 (mt0) cc_final: 0.8103 (tm-30) REVERT: A 462 TRP cc_start: 0.6918 (m100) cc_final: 0.6620 (m100) REVERT: A 467 HIS cc_start: 0.8321 (t70) cc_final: 0.8059 (t-90) REVERT: A 526 VAL cc_start: 0.9181 (p) cc_final: 0.8667 (m) REVERT: A 527 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7751 (mp0) REVERT: B 16 LEU cc_start: 0.7563 (mt) cc_final: 0.7227 (mt) REVERT: B 17 ARG cc_start: 0.5993 (mtt180) cc_final: 0.4927 (mmp80) REVERT: B 23 PHE cc_start: 0.7620 (m-10) cc_final: 0.7385 (m-80) REVERT: B 102 MET cc_start: 0.7205 (ppp) cc_final: 0.6348 (pmm) REVERT: B 210 GLU cc_start: 0.5277 (tp30) cc_final: 0.4748 (mm-30) REVERT: B 237 PHE cc_start: 0.8090 (t80) cc_final: 0.7748 (t80) REVERT: B 274 ASP cc_start: 0.8118 (m-30) cc_final: 0.7738 (t70) REVERT: B 367 HIS cc_start: 0.7914 (m-70) cc_final: 0.7701 (p-80) REVERT: B 377 ARG cc_start: 0.4814 (mtt180) cc_final: 0.4166 (tmm-80) REVERT: C 66 PHE cc_start: 0.3763 (m-10) cc_final: 0.3490 (m-80) REVERT: C 138 ARG cc_start: 0.7443 (tmt-80) cc_final: 0.7187 (tmm-80) REVERT: C 319 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6720 (mm) REVERT: D 131 ASN cc_start: 0.8134 (t0) cc_final: 0.7820 (t0) REVERT: D 251 LYS cc_start: 0.8609 (tttt) cc_final: 0.8352 (ttpt) REVERT: F 26 ASP cc_start: 0.8712 (m-30) cc_final: 0.8311 (m-30) REVERT: F 290 TYR cc_start: 0.8723 (t80) cc_final: 0.8399 (t80) REVERT: G 125 TRP cc_start: 0.7504 (p-90) cc_final: 0.7138 (p-90) REVERT: G 126 LYS cc_start: 0.8887 (tmtt) cc_final: 0.8574 (tptp) REVERT: G 283 ASN cc_start: 0.7560 (m-40) cc_final: 0.7008 (t0) REVERT: G 356 HIS cc_start: 0.7703 (t70) cc_final: 0.7475 (t-90) REVERT: G 426 PHE cc_start: 0.8232 (m-10) cc_final: 0.7853 (m-10) REVERT: H 340 ARG cc_start: 0.8410 (ptt-90) cc_final: 0.7982 (mtt90) REVERT: I 42 TRP cc_start: 0.6455 (m-10) cc_final: 0.6101 (m-10) REVERT: I 138 HIS cc_start: 0.7796 (p90) cc_final: 0.7414 (p90) outliers start: 3 outliers final: 1 residues processed: 510 average time/residue: 0.5005 time to fit residues: 391.4720 Evaluate side-chains 346 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 344 time to evaluate : 3.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 271 optimal weight: 5.9990 chunk 188 optimal weight: 0.9990 chunk 245 optimal weight: 5.9990 chunk 306 optimal weight: 0.2980 chunk 298 optimal weight: 8.9990 chunk 343 optimal weight: 0.9980 chunk 123 optimal weight: 0.4980 chunk 87 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 217 optimal weight: 0.9980 chunk 214 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 HIS B 581 HIS ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 HIS D 149 ASN ** D 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN G 392 HIS ** I 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 241 ASN ** I 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.112461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.088395 restraints weight = 111075.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.090193 restraints weight = 65844.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.091452 restraints weight = 45338.368| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3173 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= 0.122 Angle : 0.711 14.510 40383 Z= 0.361 Chirality : 0.044 0.209 4527 Planarity : 0.006 0.120 5284 Dihedral : 7.134 62.443 4026 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.44 % Favored : 89.45 % Rotamer: Outliers : 0.06 % Allowed : 2.94 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 1.24 % Twisted General : 0.44 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.13), residues: 3631 helix: -1.70 (0.15), residues: 997 sheet: -1.80 (0.23), residues: 475 loop : -2.86 (0.12), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 283 HIS 0.013 0.001 HIS D 156 PHE 0.020 0.001 PHE B 561 TYR 0.022 0.001 TYR C 346 ARG 0.015 0.000 ARG I 123 Details of bonding type rmsd hydrogen bonds : bond 0.04547 ( 671) hydrogen bonds : angle 5.59903 ( 1851) covalent geometry : bond 0.00266 (29661) covalent geometry : angle 0.71083 (40383) *********************** 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 461 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 459 time to evaluate : 3.502 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: 0.6208 (tmm) cc_final: 0.6006 (tmm) REVERT: A 61 ARG cc_start: 0.9002 (mtp85) cc_final: 0.8777 (mtp85) REVERT: A 62 GLN cc_start: 0.7215 (tt0) cc_final: 0.6796 (pp30) REVERT: A 214 ILE cc_start: 0.7079 (mp) cc_final: 0.6754 (pt) REVERT: A 258 LEU cc_start: 0.7286 (tt) cc_final: 0.6984 (tt) REVERT: A 263 ASN cc_start: 0.6897 (m-40) cc_final: 0.6597 (p0) REVERT: A 342 THR cc_start: 0.8439 (t) cc_final: 0.8236 (p) REVERT: A 361 ARG cc_start: 0.5462 (mmm-85) cc_final: 0.5165 (mmm-85) REVERT: A 364 MET cc_start: 0.6870 (tmm) cc_final: 0.6113 (ttp) REVERT: A 462 TRP cc_start: 0.6783 (m100) cc_final: 0.6338 (m100) REVERT: A 505 LEU cc_start: 0.8136 (tt) cc_final: 0.7098 (mt) REVERT: A 584 ARG cc_start: 0.4964 (mmp-170) cc_final: 0.4040 (mmp80) REVERT: B 13 MET cc_start: 0.6662 (mmm) cc_final: 0.6459 (mmm) REVERT: B 16 LEU cc_start: 0.7674 (mt) cc_final: 0.7375 (mt) REVERT: B 17 ARG cc_start: 0.6207 (mtt180) cc_final: 0.5013 (mmp80) REVERT: B 23 PHE cc_start: 0.7499 (m-10) cc_final: 0.7252 (m-80) REVERT: B 99 LEU cc_start: 0.6857 (pt) cc_final: 0.6571 (pt) REVERT: B 102 MET cc_start: 0.6989 (ppp) cc_final: 0.6415 (pmm) REVERT: B 210 GLU cc_start: 0.4708 (tp30) cc_final: 0.4291 (mm-30) REVERT: B 375 HIS cc_start: 0.6491 (t70) cc_final: 0.6192 (t70) REVERT: B 377 ARG cc_start: 0.4881 (mtt180) cc_final: 0.4529 (tmm-80) REVERT: C 87 HIS cc_start: 0.2554 (t70) cc_final: 0.2178 (p-80) REVERT: C 138 ARG cc_start: 0.7687 (tmt-80) cc_final: 0.7403 (tmm-80) REVERT: C 319 LEU cc_start: 0.6998 (mm) cc_final: 0.6710 (mm) REVERT: D 131 ASN cc_start: 0.8203 (t0) cc_final: 0.7924 (t0) REVERT: D 188 LEU cc_start: 0.8359 (tp) cc_final: 0.8120 (tt) REVERT: D 251 LYS cc_start: 0.8625 (tttt) cc_final: 0.8253 (ttpt) REVERT: F 198 MET cc_start: 0.8791 (mmm) cc_final: 0.8508 (mmm) REVERT: F 290 TYR cc_start: 0.8711 (t80) cc_final: 0.8333 (t80) REVERT: G 283 ASN cc_start: 0.7368 (m-40) cc_final: 0.6826 (t0) REVERT: G 340 ARG cc_start: 0.7351 (mmm-85) cc_final: 0.7087 (mmp80) REVERT: H 185 ILE cc_start: 0.9152 (pt) cc_final: 0.8684 (mp) REVERT: H 309 LEU cc_start: 0.9579 (mt) cc_final: 0.9236 (tt) REVERT: H 340 ARG cc_start: 0.8116 (ptt-90) cc_final: 0.7775 (mtt90) REVERT: I 42 TRP cc_start: 0.6412 (m-10) cc_final: 0.6186 (m-10) outliers start: 2 outliers final: 0 residues processed: 461 average time/residue: 0.4279 time to fit residues: 307.5652 Evaluate side-chains 335 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 3.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 48 optimal weight: 0.0040 chunk 161 optimal weight: 2.9990 chunk 73 optimal weight: 20.0000 chunk 138 optimal weight: 0.9990 chunk 249 optimal weight: 6.9990 chunk 182 optimal weight: 7.9990 chunk 118 optimal weight: 0.9980 chunk 284 optimal weight: 0.0980 chunk 288 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 chunk 297 optimal weight: 5.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN ** 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 510 HIS ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN G 207 HIS H 392 HIS ** I 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 241 ASN ** I 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.103865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.080077 restraints weight = 124862.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.081503 restraints weight = 82335.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.082393 restraints weight = 61269.255| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 29661 Z= 0.114 Angle : 0.683 14.553 40383 Z= 0.345 Chirality : 0.044 0.234 4527 Planarity : 0.006 0.111 5284 Dihedral : 6.651 60.829 4026 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.86 % Favored : 90.06 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 1.24 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.13), residues: 3631 helix: -1.06 (0.16), residues: 1001 sheet: -1.57 (0.23), residues: 477 loop : -2.74 (0.12), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 162 HIS 0.011 0.001 HIS D 156 PHE 0.020 0.001 PHE B 358 TYR 0.019 0.001 TYR C 346 ARG 0.012 0.000 ARG F 94 Details of bonding type rmsd hydrogen bonds : bond 0.03747 ( 671) hydrogen bonds : angle 5.18241 ( 1851) covalent geometry : bond 0.00246 (29661) covalent geometry : angle 0.68273 (40383) *********************** 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 453 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 453 time to evaluate : 3.172 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: A 14 ARG cc_start: 0.8597 (ttt180) cc_final: 0.8187 (ptp-170) REVERT: A 33 MET cc_start: 0.5615 (tmm) cc_final: 0.5309 (tmm) REVERT: A 62 GLN cc_start: 0.6996 (tt0) cc_final: 0.6647 (pp30) REVERT: A 180 LEU cc_start: 0.8165 (pp) cc_final: 0.7964 (pp) REVERT: A 214 ILE cc_start: 0.6748 (mp) cc_final: 0.6414 (pt) REVERT: A 263 ASN cc_start: 0.7257 (m-40) cc_final: 0.6909 (p0) REVERT: A 434 GLN cc_start: 0.6105 (mm-40) cc_final: 0.5874 (pm20) REVERT: A 462 TRP cc_start: 0.7108 (m100) cc_final: 0.6543 (m100) REVERT: A 525 ASP cc_start: 0.7654 (m-30) cc_final: 0.7297 (m-30) REVERT: A 526 VAL cc_start: 0.8869 (m) cc_final: 0.8326 (m) REVERT: A 527 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7775 (mp0) REVERT: A 584 ARG cc_start: 0.4815 (mmp-170) cc_final: 0.3904 (mmp80) REVERT: B 13 MET cc_start: 0.6001 (mmm) cc_final: 0.5790 (mmm) REVERT: B 16 LEU cc_start: 0.7874 (mt) cc_final: 0.7496 (mt) REVERT: B 17 ARG cc_start: 0.5681 (mtt180) cc_final: 0.4872 (mmp80) REVERT: B 23 PHE cc_start: 0.7624 (m-10) cc_final: 0.7418 (m-80) REVERT: B 80 TRP cc_start: 0.7112 (t-100) cc_final: 0.6859 (t-100) REVERT: B 95 LEU cc_start: 0.7024 (mp) cc_final: 0.6293 (tp) REVERT: B 102 MET cc_start: 0.7328 (ppp) cc_final: 0.6639 (pmm) REVERT: B 210 GLU cc_start: 0.5546 (tp30) cc_final: 0.4889 (mm-30) REVERT: B 237 PHE cc_start: 0.7814 (t80) cc_final: 0.7547 (t80) REVERT: B 322 LEU cc_start: 0.8824 (tp) cc_final: 0.8609 (tp) REVERT: B 375 HIS cc_start: 0.6658 (t70) cc_final: 0.6392 (t70) REVERT: C 116 GLU cc_start: 0.5264 (mt-10) cc_final: 0.5054 (mm-30) REVERT: C 138 ARG cc_start: 0.7394 (tmt-80) cc_final: 0.7065 (tmm-80) REVERT: C 299 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6320 (pp20) REVERT: C 319 LEU cc_start: 0.6803 (mm) cc_final: 0.6450 (mm) REVERT: D 131 ASN cc_start: 0.8247 (t0) cc_final: 0.7976 (t0) REVERT: D 188 LEU cc_start: 0.8417 (tp) cc_final: 0.8129 (tt) REVERT: D 251 LYS cc_start: 0.8636 (tttt) cc_final: 0.8420 (ttpt) REVERT: F 198 MET cc_start: 0.8959 (mmm) cc_final: 0.8746 (mmm) REVERT: F 290 TYR cc_start: 0.8625 (t80) cc_final: 0.8223 (t80) REVERT: G 218 MET cc_start: 0.8545 (ttm) cc_final: 0.8330 (ttm) REVERT: G 283 ASN cc_start: 0.7508 (m-40) cc_final: 0.6920 (t0) REVERT: H 138 HIS cc_start: 0.6702 (t-90) cc_final: 0.6149 (t-90) REVERT: H 185 ILE cc_start: 0.9180 (pt) cc_final: 0.8867 (mp) REVERT: H 189 LEU cc_start: 0.9316 (mt) cc_final: 0.9063 (mp) REVERT: H 340 ARG cc_start: 0.8309 (ptt-90) cc_final: 0.7827 (mtt90) REVERT: H 426 PHE cc_start: 0.8012 (t80) cc_final: 0.7707 (t80) REVERT: I 277 THR cc_start: 0.7495 (p) cc_final: 0.7244 (m) outliers start: 0 outliers final: 0 residues processed: 453 average time/residue: 0.4280 time to fit residues: 299.6495 Evaluate side-chains 333 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 3.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 24 optimal weight: 0.0060 chunk 151 optimal weight: 2.9990 chunk 272 optimal weight: 0.2980 chunk 206 optimal weight: 5.9990 chunk 153 optimal weight: 0.8980 chunk 247 optimal weight: 3.9990 chunk 225 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 286 optimal weight: 5.9990 overall best weight: 1.4400 ------------------------------------------------------------------------------- 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 A 444 ASN ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 HIS ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN F 149 ASN G 222 ASN H 392 HIS I 18 GLN ** I 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 241 ASN I 244 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.112760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.088826 restraints weight = 110920.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.090665 restraints weight = 65040.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.091881 restraints weight = 44409.169| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29661 Z= 0.131 Angle : 0.687 12.638 40383 Z= 0.346 Chirality : 0.044 0.272 4527 Planarity : 0.005 0.097 5284 Dihedral : 6.498 60.028 4026 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.91 % Favored : 89.04 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 1.24 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.13), residues: 3631 helix: -0.54 (0.17), residues: 985 sheet: -1.53 (0.23), residues: 485 loop : -2.60 (0.13), residues: 2161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP I 42 HIS 0.008 0.001 HIS D 156 PHE 0.020 0.001 PHE B 561 TYR 0.021 0.001 TYR C 346 ARG 0.011 0.000 ARG B 550 Details of bonding type rmsd hydrogen bonds : bond 0.03610 ( 671) hydrogen bonds : angle 5.06555 ( 1851) covalent geometry : bond 0.00300 (29661) covalent geometry : angle 0.68693 (40383) *********************** 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 418 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 3.102 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: A 33 MET cc_start: 0.5971 (tmm) cc_final: 0.5665 (tmm) REVERT: A 62 GLN cc_start: 0.7278 (tt0) cc_final: 0.7017 (pp30) REVERT: A 214 ILE cc_start: 0.7063 (mp) cc_final: 0.6770 (pt) REVERT: A 263 ASN cc_start: 0.6870 (m-40) cc_final: 0.6543 (p0) REVERT: A 320 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8112 (mp0) REVERT: A 385 MET cc_start: 0.1596 (ttt) cc_final: 0.1339 (ttt) REVERT: A 462 TRP cc_start: 0.6936 (m100) cc_final: 0.6226 (m100) REVERT: A 526 VAL cc_start: 0.8788 (m) cc_final: 0.8238 (m) REVERT: A 527 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7806 (mp0) REVERT: B 13 MET cc_start: 0.6674 (mmm) cc_final: 0.6279 (mmm) REVERT: B 16 LEU cc_start: 0.7738 (mt) cc_final: 0.7455 (mt) REVERT: B 17 ARG cc_start: 0.6099 (mtt180) cc_final: 0.4897 (mmp80) REVERT: B 237 PHE cc_start: 0.7785 (t80) cc_final: 0.7552 (t80) REVERT: B 321 TYR cc_start: 0.6852 (p90) cc_final: 0.6597 (p90) REVERT: B 375 HIS cc_start: 0.6464 (t70) cc_final: 0.6114 (t70) REVERT: C 116 GLU cc_start: 0.6122 (mt-10) cc_final: 0.5744 (mm-30) REVERT: C 138 ARG cc_start: 0.7819 (tmt-80) cc_final: 0.6590 (tmm-80) REVERT: C 147 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6819 (tp30) REVERT: C 299 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6519 (pp20) REVERT: C 319 LEU cc_start: 0.6719 (mm) cc_final: 0.6417 (mm) REVERT: D 188 LEU cc_start: 0.8334 (tp) cc_final: 0.8060 (tt) REVERT: D 240 LEU cc_start: 0.9068 (mt) cc_final: 0.8841 (mt) REVERT: D 256 MET cc_start: 0.7935 (mpp) cc_final: 0.7665 (mmt) REVERT: E 81 ASN cc_start: 0.7244 (m110) cc_final: 0.6843 (t0) REVERT: E 198 MET cc_start: 0.7936 (mmm) cc_final: 0.7609 (mmm) REVERT: F 198 MET cc_start: 0.8849 (mmm) cc_final: 0.8635 (mmm) REVERT: F 290 TYR cc_start: 0.8681 (t80) cc_final: 0.8296 (t80) REVERT: G 198 MET cc_start: 0.8610 (mpp) cc_final: 0.8100 (mtm) REVERT: G 233 ASP cc_start: 0.7485 (m-30) cc_final: 0.7042 (t0) REVERT: G 283 ASN cc_start: 0.7111 (m-40) cc_final: 0.6778 (t0) REVERT: H 185 ILE cc_start: 0.9220 (pt) cc_final: 0.8896 (mp) REVERT: H 340 ARG cc_start: 0.8069 (ptt-90) cc_final: 0.7699 (mtt90) REVERT: H 426 PHE cc_start: 0.8015 (t80) cc_final: 0.7739 (t80) REVERT: I 42 TRP cc_start: 0.6005 (m-10) cc_final: 0.5794 (m-10) outliers start: 0 outliers final: 0 residues processed: 418 average time/residue: 0.4163 time to fit residues: 273.3599 Evaluate side-chains 329 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 3.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 287 optimal weight: 7.9990 chunk 294 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 250 optimal weight: 0.0870 chunk 209 optimal weight: 0.9990 chunk 349 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 295 optimal weight: 0.9980 chunk 244 optimal weight: 9.9990 chunk 242 optimal weight: 0.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- 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 444 ASN ** 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** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 392 HIS ** I 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 177 GLN I 241 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.099733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.075476 restraints weight = 112855.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.077337 restraints weight = 65403.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.078575 restraints weight = 44462.963| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.4155 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= 0.123 Angle : 0.691 12.303 40383 Z= 0.344 Chirality : 0.045 0.394 4527 Planarity : 0.005 0.081 5284 Dihedral : 6.357 59.233 4026 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.82 % Favored : 89.15 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 1.24 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.14), residues: 3631 helix: -0.32 (0.17), residues: 981 sheet: -1.40 (0.23), residues: 472 loop : -2.55 (0.13), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 389 HIS 0.008 0.001 HIS D 156 PHE 0.017 0.001 PHE B 358 TYR 0.022 0.001 TYR C 140 ARG 0.011 0.000 ARG A 361 Details of bonding type rmsd hydrogen bonds : bond 0.03398 ( 671) hydrogen bonds : angle 4.96126 ( 1851) covalent geometry : bond 0.00282 (29661) covalent geometry : angle 0.69060 (40383) *********************** 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 412 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 3.428 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: 0.5740 (tmm) cc_final: 0.5510 (tmm) REVERT: A 62 GLN cc_start: 0.7182 (tt0) cc_final: 0.6932 (pp30) REVERT: A 202 TYR cc_start: 0.6417 (m-80) cc_final: 0.6143 (m-10) REVERT: A 214 ILE cc_start: 0.7053 (mp) cc_final: 0.6827 (pt) REVERT: A 263 ASN cc_start: 0.6862 (m-40) cc_final: 0.6538 (p0) REVERT: A 320 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8148 (mp0) REVERT: A 462 TRP cc_start: 0.6868 (m100) cc_final: 0.6360 (m100) REVERT: A 526 VAL cc_start: 0.8782 (m) cc_final: 0.8398 (m) REVERT: A 527 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7814 (mp0) REVERT: A 550 ARG cc_start: 0.8018 (tpp80) cc_final: 0.7758 (tpt170) REVERT: B 16 LEU cc_start: 0.7668 (mt) cc_final: 0.6463 (pp) REVERT: B 17 ARG cc_start: 0.6077 (mtt180) cc_final: 0.5682 (mtt90) REVERT: B 102 MET cc_start: 0.7070 (ppp) cc_final: 0.6389 (pmm) REVERT: B 237 PHE cc_start: 0.7894 (t80) cc_final: 0.7610 (t80) REVERT: B 375 HIS cc_start: 0.6588 (t70) cc_final: 0.6263 (t70) REVERT: B 390 LEU cc_start: 0.9079 (pt) cc_final: 0.8464 (tp) REVERT: C 116 GLU cc_start: 0.6003 (mt-10) cc_final: 0.5654 (mm-30) REVERT: C 138 ARG cc_start: 0.7850 (tmt-80) cc_final: 0.7519 (tmm-80) REVERT: C 299 GLU cc_start: 0.6854 (mt-10) cc_final: 0.6572 (pp20) REVERT: D 188 LEU cc_start: 0.8318 (tp) cc_final: 0.8114 (tp) REVERT: D 237 PHE cc_start: 0.8148 (p90) cc_final: 0.7681 (p90) REVERT: D 238 TRP cc_start: 0.6018 (m100) cc_final: 0.5745 (m100) REVERT: D 240 LEU cc_start: 0.9134 (mt) cc_final: 0.8911 (mt) REVERT: D 256 MET cc_start: 0.8002 (mpp) cc_final: 0.7660 (mmt) REVERT: E 81 ASN cc_start: 0.7278 (m110) cc_final: 0.6934 (t0) REVERT: E 198 MET cc_start: 0.7890 (mmm) cc_final: 0.7650 (mmm) REVERT: F 198 MET cc_start: 0.8839 (mmm) cc_final: 0.8626 (mmm) REVERT: F 290 TYR cc_start: 0.8671 (t80) cc_final: 0.8293 (t80) REVERT: G 75 ASP cc_start: 0.8401 (p0) cc_final: 0.8188 (p0) REVERT: G 198 MET cc_start: 0.8498 (mpp) cc_final: 0.8169 (mtt) REVERT: G 233 ASP cc_start: 0.7809 (m-30) cc_final: 0.6893 (t0) REVERT: G 283 ASN cc_start: 0.7130 (m-40) cc_final: 0.6791 (t0) REVERT: H 185 ILE cc_start: 0.9220 (pt) cc_final: 0.8923 (mp) REVERT: H 340 ARG cc_start: 0.8127 (ptt-90) cc_final: 0.7743 (mtt90) REVERT: H 426 PHE cc_start: 0.7939 (t80) cc_final: 0.7643 (t80) REVERT: I 31 ASP cc_start: 0.8387 (p0) cc_final: 0.7920 (t70) outliers start: 0 outliers final: 0 residues processed: 412 average time/residue: 0.4069 time to fit residues: 265.6312 Evaluate side-chains 322 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 3.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 83 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 269 optimal weight: 0.0670 chunk 74 optimal weight: 0.0470 chunk 110 optimal weight: 8.9990 chunk 155 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 304 optimal weight: 2.9990 chunk 257 optimal weight: 5.9990 chunk 209 optimal weight: 0.9990 overall best weight: 0.5616 ------------------------------------------------------------------------------- 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 ** 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 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 392 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 = 0.3838 r_free = 0.3838 target = 0.100846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.076887 restraints weight = 111680.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.078694 restraints weight = 66054.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.079906 restraints weight = 45556.716| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29661 Z= 0.114 Angle : 0.688 12.248 40383 Z= 0.341 Chirality : 0.044 0.509 4527 Planarity : 0.005 0.067 5284 Dihedral : 6.149 58.700 4026 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.00 % Favored : 89.98 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 1.24 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.14), residues: 3631 helix: -0.16 (0.17), residues: 986 sheet: -1.23 (0.24), residues: 452 loop : -2.45 (0.13), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP B 389 HIS 0.008 0.001 HIS D 156 PHE 0.031 0.001 PHE A 515 TYR 0.022 0.001 TYR A 15 ARG 0.006 0.000 ARG B 522 Details of bonding type rmsd hydrogen bonds : bond 0.03195 ( 671) hydrogen bonds : angle 4.74413 ( 1851) covalent geometry : bond 0.00257 (29661) covalent geometry : angle 0.68751 (40383) *********************** 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 423 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 423 time to evaluate : 3.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.5524 (tmm) cc_final: 0.5256 (tmm) REVERT: A 61 ARG cc_start: 0.8995 (mtp180) cc_final: 0.8683 (mtp85) REVERT: A 62 GLN cc_start: 0.7091 (tt0) cc_final: 0.6658 (pp30) REVERT: A 194 MET cc_start: 0.8093 (mmp) cc_final: 0.7713 (mmm) REVERT: A 214 ILE cc_start: 0.7064 (mp) cc_final: 0.6853 (pt) REVERT: A 263 ASN cc_start: 0.7057 (m-40) cc_final: 0.6667 (p0) REVERT: A 320 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7917 (mp0) REVERT: A 527 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7780 (mp0) REVERT: B 17 ARG cc_start: 0.6035 (mtt180) cc_final: 0.5266 (tpp80) REVERT: B 23 PHE cc_start: 0.7606 (m-80) cc_final: 0.7348 (m-80) REVERT: B 102 MET cc_start: 0.6930 (ppp) cc_final: 0.6308 (pmm) REVERT: B 375 HIS cc_start: 0.6611 (t70) cc_final: 0.6345 (t70) REVERT: B 377 ARG cc_start: 0.4878 (mtt180) cc_final: 0.4334 (tmm-80) REVERT: B 390 LEU cc_start: 0.8914 (pt) cc_final: 0.8299 (tt) REVERT: B 551 PHE cc_start: 0.7446 (m-10) cc_final: 0.5676 (m-80) REVERT: C 116 GLU cc_start: 0.6009 (mt-10) cc_final: 0.5660 (mm-30) REVERT: C 138 ARG cc_start: 0.7765 (tmt-80) cc_final: 0.7135 (tmm160) REVERT: C 147 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6903 (tp30) REVERT: D 237 PHE cc_start: 0.7985 (p90) cc_final: 0.7547 (p90) REVERT: E 81 ASN cc_start: 0.7225 (m110) cc_final: 0.6924 (t0) REVERT: F 290 TYR cc_start: 0.8630 (t80) cc_final: 0.8257 (t80) REVERT: G 283 ASN cc_start: 0.7029 (m-40) cc_final: 0.6749 (t0) REVERT: H 185 ILE cc_start: 0.9212 (pt) cc_final: 0.8940 (mp) REVERT: H 340 ARG cc_start: 0.8030 (ptt-90) cc_final: 0.7695 (mtt90) REVERT: I 31 ASP cc_start: 0.8189 (p0) cc_final: 0.7796 (t70) REVERT: I 42 TRP cc_start: 0.5696 (m-10) cc_final: 0.5340 (m-10) REVERT: I 113 LEU cc_start: 0.5848 (tp) cc_final: 0.5571 (tp) outliers start: 0 outliers final: 0 residues processed: 423 average time/residue: 0.4099 time to fit residues: 274.4704 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 : 3.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 85 optimal weight: 3.9990 chunk 340 optimal weight: 0.9990 chunk 303 optimal weight: 0.0030 chunk 307 optimal weight: 3.9990 chunk 258 optimal weight: 10.0000 chunk 273 optimal weight: 3.9990 chunk 163 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 117 optimal weight: 30.0000 chunk 207 optimal weight: 1.9990 chunk 251 optimal weight: 0.0030 overall best weight: 0.8004 ------------------------------------------------------------------------------- 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 ** 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** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 ASN ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 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 = 0.3840 r_free = 0.3840 target = 0.100903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.076926 restraints weight = 112262.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.078730 restraints weight = 66087.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.079919 restraints weight = 45464.871| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29661 Z= 0.114 Angle : 0.677 12.880 40383 Z= 0.336 Chirality : 0.044 0.262 4527 Planarity : 0.005 0.097 5284 Dihedral : 6.023 58.701 4026 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.30 % Favored : 89.67 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.83 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.14), residues: 3631 helix: 0.04 (0.18), residues: 980 sheet: -1.22 (0.24), residues: 449 loop : -2.36 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP B 577 HIS 0.007 0.001 HIS D 156 PHE 0.031 0.001 PHE B 55 TYR 0.020 0.001 TYR C 346 ARG 0.008 0.000 ARG B 576 Details of bonding type rmsd hydrogen bonds : bond 0.03037 ( 671) hydrogen bonds : angle 4.64409 ( 1851) covalent geometry : bond 0.00260 (29661) covalent geometry : angle 0.67726 (40383) *********************** 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 410 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 3.373 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 14 ARG cc_start: 0.8532 (ttt180) cc_final: 0.8248 (ptp-170) REVERT: A 33 MET cc_start: 0.5335 (tmm) cc_final: 0.5092 (tmm) REVERT: A 61 ARG cc_start: 0.9011 (mtp180) cc_final: 0.8711 (mtp85) REVERT: A 62 GLN cc_start: 0.7119 (tt0) cc_final: 0.6541 (pp30) REVERT: A 194 MET cc_start: 0.8085 (mmp) cc_final: 0.7692 (mmm) REVERT: A 214 ILE cc_start: 0.7010 (mp) cc_final: 0.6786 (pt) REVERT: A 263 ASN cc_start: 0.7100 (m-40) cc_final: 0.6699 (p0) REVERT: A 320 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8145 (mp0) REVERT: A 527 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7779 (mp0) REVERT: B 16 LEU cc_start: 0.7204 (mt) cc_final: 0.6056 (pp) REVERT: B 17 ARG cc_start: 0.6206 (mtt180) cc_final: 0.5728 (mtt90) REVERT: B 23 PHE cc_start: 0.7379 (m-80) cc_final: 0.7139 (m-80) REVERT: B 80 TRP cc_start: 0.6919 (t-100) cc_final: 0.6713 (t-100) REVERT: B 102 MET cc_start: 0.6934 (ppp) cc_final: 0.6313 (pmm) REVERT: B 375 HIS cc_start: 0.6582 (t70) cc_final: 0.6370 (t70) REVERT: B 377 ARG cc_start: 0.4864 (mtt180) cc_final: 0.4419 (tmm-80) REVERT: B 390 LEU cc_start: 0.8841 (pt) cc_final: 0.8220 (tt) REVERT: C 116 GLU cc_start: 0.5984 (mt-10) cc_final: 0.5596 (mm-30) REVERT: C 157 TYR cc_start: 0.6400 (m-10) cc_final: 0.5626 (m-10) REVERT: C 347 GLN cc_start: 0.5154 (tp-100) cc_final: 0.4560 (tp40) REVERT: D 198 MET cc_start: 0.8638 (mmp) cc_final: 0.8319 (mmt) REVERT: D 237 PHE cc_start: 0.8114 (p90) cc_final: 0.7602 (p90) REVERT: E 81 ASN cc_start: 0.7068 (m110) cc_final: 0.6865 (t0) REVERT: F 290 TYR cc_start: 0.8675 (t80) cc_final: 0.8289 (t80) REVERT: G 75 ASP cc_start: 0.8400 (p0) cc_final: 0.8117 (p0) REVERT: G 283 ASN cc_start: 0.6934 (m-40) cc_final: 0.6661 (t0) REVERT: H 185 ILE cc_start: 0.9220 (pt) cc_final: 0.8942 (mp) REVERT: H 340 ARG cc_start: 0.8008 (ptt-90) cc_final: 0.7739 (mtt90) REVERT: H 362 PHE cc_start: 0.6494 (m-10) cc_final: 0.6283 (m-80) REVERT: I 31 ASP cc_start: 0.8198 (p0) cc_final: 0.7923 (t70) REVERT: I 113 LEU cc_start: 0.5625 (tp) cc_final: 0.5396 (tp) outliers start: 0 outliers final: 0 residues processed: 410 average time/residue: 0.4090 time to fit residues: 264.4129 Evaluate side-chains 317 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 3.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 65 optimal weight: 5.9990 chunk 272 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 217 optimal weight: 5.9990 chunk 273 optimal weight: 0.0070 chunk 71 optimal weight: 4.9990 chunk 274 optimal weight: 0.8980 chunk 182 optimal weight: 3.9990 chunk 356 optimal weight: 0.9990 chunk 162 optimal weight: 4.9990 chunk 159 optimal weight: 10.0000 overall best weight: 0.7202 ------------------------------------------------------------------------------- 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 A 513 GLN ** 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 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 ASN H 148 HIS H 392 HIS ** I 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 241 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.101460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.077462 restraints weight = 113059.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.079317 restraints weight = 66087.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.080551 restraints weight = 45118.821| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29661 Z= 0.111 Angle : 0.680 12.641 40383 Z= 0.336 Chirality : 0.045 0.371 4527 Planarity : 0.005 0.092 5284 Dihedral : 5.931 58.537 4026 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.64 % Favored : 90.33 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.83 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.14), residues: 3631 helix: 0.16 (0.18), residues: 979 sheet: -1.11 (0.24), residues: 448 loop : -2.34 (0.13), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP D 238 HIS 0.007 0.001 HIS D 156 PHE 0.036 0.001 PHE A 515 TYR 0.018 0.001 TYR G 265 ARG 0.008 0.000 ARG A 396 Details of bonding type rmsd hydrogen bonds : bond 0.02959 ( 671) hydrogen bonds : angle 4.59695 ( 1851) covalent geometry : bond 0.00254 (29661) covalent geometry : angle 0.68015 (40383) *********************** 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 411 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 411 time to evaluate : 3.915 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: 0.8572 (ttt180) cc_final: 0.8249 (ptp-170) REVERT: A 61 ARG cc_start: 0.8990 (mtp180) cc_final: 0.8704 (mtp85) REVERT: A 62 GLN cc_start: 0.7026 (tt0) cc_final: 0.6392 (pp30) REVERT: A 104 MET cc_start: 0.3090 (mmp) cc_final: 0.2535 (mmp) REVERT: A 194 MET cc_start: 0.8016 (mmp) cc_final: 0.7550 (mmm) REVERT: A 214 ILE cc_start: 0.7058 (mp) cc_final: 0.6840 (pt) REVERT: A 263 ASN cc_start: 0.6988 (m-40) cc_final: 0.6691 (p0) REVERT: A 320 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8143 (mp0) REVERT: A 527 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7776 (mp0) REVERT: B 16 LEU cc_start: 0.7160 (mt) cc_final: 0.6088 (pp) REVERT: B 17 ARG cc_start: 0.6178 (mtt180) cc_final: 0.5393 (tpp80) REVERT: B 23 PHE cc_start: 0.7364 (m-80) cc_final: 0.7120 (m-80) REVERT: B 102 MET cc_start: 0.6961 (ppp) cc_final: 0.6305 (pmm) REVERT: B 276 GLU cc_start: 0.8650 (pm20) cc_final: 0.8394 (mp0) REVERT: B 377 ARG cc_start: 0.4780 (mtt180) cc_final: 0.4359 (tmm-80) REVERT: B 390 LEU cc_start: 0.8799 (pt) cc_final: 0.8212 (tt) REVERT: B 551 PHE cc_start: 0.6940 (m-10) cc_final: 0.6559 (m-80) REVERT: C 116 GLU cc_start: 0.5976 (mt-10) cc_final: 0.5589 (mm-30) REVERT: C 157 TYR cc_start: 0.6502 (m-10) cc_final: 0.5662 (m-10) REVERT: C 347 GLN cc_start: 0.5274 (tp-100) cc_final: 0.4779 (tp40) REVERT: E 189 LEU cc_start: 0.8307 (tp) cc_final: 0.7975 (tp) REVERT: F 290 TYR cc_start: 0.8676 (t80) cc_final: 0.8295 (t80) REVERT: G 75 ASP cc_start: 0.8431 (p0) cc_final: 0.8180 (p0) REVERT: G 283 ASN cc_start: 0.7011 (m-40) cc_final: 0.6701 (t0) REVERT: H 185 ILE cc_start: 0.9218 (pt) cc_final: 0.8943 (mp) REVERT: H 340 ARG cc_start: 0.8040 (ptt-90) cc_final: 0.7771 (mtt90) REVERT: H 362 PHE cc_start: 0.6461 (m-10) cc_final: 0.6252 (m-80) REVERT: I 31 ASP cc_start: 0.8298 (p0) cc_final: 0.7989 (t70) REVERT: I 113 LEU cc_start: 0.5888 (tp) cc_final: 0.5591 (tp) outliers start: 0 outliers final: 0 residues processed: 411 average time/residue: 0.4261 time to fit residues: 279.1274 Evaluate side-chains 318 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 3.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 30 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 143 optimal weight: 0.0980 chunk 247 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 chunk 113 optimal weight: 0.9990 chunk 188 optimal weight: 0.0570 chunk 332 optimal weight: 0.8980 chunk 198 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 overall best weight: 0.5700 ------------------------------------------------------------------------------- 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 ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 581 HIS ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 392 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 = 0.3852 r_free = 0.3852 target = 0.101607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.077498 restraints weight = 111961.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.079378 restraints weight = 65466.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.080626 restraints weight = 44643.309| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 29661 Z= 0.108 Angle : 0.672 12.363 40383 Z= 0.330 Chirality : 0.044 0.317 4527 Planarity : 0.005 0.088 5284 Dihedral : 5.803 58.102 4026 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.69 % Favored : 90.28 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.83 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.14), residues: 3631 helix: 0.30 (0.18), residues: 975 sheet: -1.11 (0.24), residues: 449 loop : -2.27 (0.13), residues: 2207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 389 HIS 0.007 0.001 HIS D 156 PHE 0.031 0.001 PHE H 278 TYR 0.019 0.001 TYR C 104 ARG 0.007 0.000 ARG A 396 Details of bonding type rmsd hydrogen bonds : bond 0.02885 ( 671) hydrogen bonds : angle 4.53004 ( 1851) covalent geometry : bond 0.00247 (29661) covalent geometry : angle 0.67176 (40383) ********************** 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 405 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 3.044 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 14 ARG cc_start: 0.8575 (ttt180) cc_final: 0.8254 (ptp-170) REVERT: A 62 GLN cc_start: 0.7006 (tt0) cc_final: 0.6424 (pp30) REVERT: A 104 MET cc_start: 0.3041 (mmp) cc_final: 0.2491 (mmp) REVERT: A 194 MET cc_start: 0.8096 (mmp) cc_final: 0.7675 (mmm) REVERT: A 214 ILE cc_start: 0.7110 (mp) cc_final: 0.6876 (pt) REVERT: A 263 ASN cc_start: 0.6956 (m-40) cc_final: 0.6675 (p0) REVERT: A 320 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8098 (mp0) REVERT: A 527 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7790 (mp0) REVERT: B 16 LEU cc_start: 0.7196 (mt) cc_final: 0.6174 (pp) REVERT: B 17 ARG cc_start: 0.6357 (mtt180) cc_final: 0.5867 (mtt90) REVERT: B 80 TRP cc_start: 0.6573 (t-100) cc_final: 0.6261 (t60) REVERT: B 102 MET cc_start: 0.6976 (ppp) cc_final: 0.6350 (pmm) REVERT: B 377 ARG cc_start: 0.4773 (mtt180) cc_final: 0.4406 (tmm-80) REVERT: B 390 LEU cc_start: 0.8732 (pt) cc_final: 0.8105 (tt) REVERT: B 547 MET cc_start: 0.6947 (mpp) cc_final: 0.6285 (mpp) REVERT: B 551 PHE cc_start: 0.6761 (m-10) cc_final: 0.6365 (m-80) REVERT: C 116 GLU cc_start: 0.6034 (mt-10) cc_final: 0.5618 (mm-30) REVERT: C 121 PHE cc_start: 0.3817 (t80) cc_final: 0.3614 (t80) REVERT: C 157 TYR cc_start: 0.6393 (m-10) cc_final: 0.5564 (m-10) REVERT: D 216 MET cc_start: 0.7274 (tmm) cc_final: 0.7070 (tmm) REVERT: E 189 LEU cc_start: 0.8255 (tp) cc_final: 0.7942 (tp) REVERT: E 238 TRP cc_start: 0.7998 (m100) cc_final: 0.7424 (m100) REVERT: E 278 PHE cc_start: 0.7748 (t80) cc_final: 0.7523 (t80) REVERT: F 290 TYR cc_start: 0.8684 (t80) cc_final: 0.8302 (t80) REVERT: G 75 ASP cc_start: 0.8506 (p0) cc_final: 0.8215 (p0) REVERT: G 198 MET cc_start: 0.8506 (mpp) cc_final: 0.8022 (mtt) REVERT: G 283 ASN cc_start: 0.7030 (m-40) cc_final: 0.6725 (t0) REVERT: H 185 ILE cc_start: 0.9240 (pt) cc_final: 0.8986 (mp) REVERT: H 236 LEU cc_start: 0.9237 (tt) cc_final: 0.9021 (tt) REVERT: H 340 ARG cc_start: 0.7971 (ptt-90) cc_final: 0.7768 (mtt90) REVERT: H 362 PHE cc_start: 0.6588 (m-10) cc_final: 0.6337 (m-80) REVERT: I 31 ASP cc_start: 0.8296 (p0) cc_final: 0.7993 (t70) REVERT: I 113 LEU cc_start: 0.5904 (tp) cc_final: 0.5545 (tp) REVERT: I 254 LEU cc_start: 0.9186 (mt) cc_final: 0.8985 (mm) outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.4352 time to fit residues: 281.0125 Evaluate side-chains 318 residues out of total 3143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 3.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 116 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 252 optimal weight: 6.9990 chunk 133 optimal weight: 0.0000 chunk 13 optimal weight: 0.5980 chunk 196 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 281 optimal weight: 0.7980 chunk 83 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 chunk 101 optimal weight: 30.0000 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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 ** 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 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 392 HIS ** 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 = 0.3857 r_free = 0.3857 target = 0.101795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.077633 restraints weight = 112839.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.079453 restraints weight = 66822.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.080679 restraints weight = 46117.506| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.5106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 29661 Z= 0.108 Angle : 0.671 12.311 40383 Z= 0.330 Chirality : 0.044 0.303 4527 Planarity : 0.005 0.085 5284 Dihedral : 5.694 58.177 4026 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.64 % Favored : 90.33 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.83 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.14), residues: 3631 helix: 0.41 (0.18), residues: 973 sheet: -1.08 (0.24), residues: 459 loop : -2.27 (0.13), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 389 HIS 0.007 0.001 HIS D 156 PHE 0.047 0.001 PHE B 55 TYR 0.017 0.001 TYR C 346 ARG 0.008 0.000 ARG A 61 Details of bonding type rmsd hydrogen bonds : bond 0.02813 ( 671) hydrogen bonds : angle 4.50893 ( 1851) covalent geometry : bond 0.00247 (29661) covalent geometry : angle 0.67097 (40383) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10254.74 seconds wall clock time: 178 minutes 33.22 seconds (10713.22 seconds total)