Starting phenix.real_space_refine (version: dev) on Sun Feb 26 22:50:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6giy_0008/02_2023/6giy_0008.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6giy_0008/02_2023/6giy_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6giy_0008/02_2023/6giy_0008.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6giy_0008/02_2023/6giy_0008.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6giy_0008/02_2023/6giy_0008.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6giy_0008/02_2023/6giy_0008.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped Residue "A TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 511": "NH1" <-> "NH2" Residue "C ARG 218": "NH1" <-> "NH2" Residue "C ARG 229": "NH1" <-> "NH2" Residue "C ARG 239": "NH1" <-> "NH2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C ARG 345": "NH1" <-> "NH2" Residue "D PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 259": "NH1" <-> "NH2" Residue "F PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 94": "NH1" <-> "NH2" Residue "I PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 17.10, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.43 Conformation dependent library (CDL) restraints added in 5.0 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: 1.21 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: 8.31 Time building geometry restraints manager: 12.39 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: 97.80 - 105.60: 948 105.60 - 113.40: 16360 113.40 - 121.20: 14684 121.20 - 129.00: 8082 129.00 - 136.80: 309 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 2.440 nonbonded pdb=" O ALA A 184 " pdb=" OG SER A 188 " model vdw 2.266 2.440 nonbonded pdb=" OE1 GLU D 120 " pdb=" NH1 ARG D 121 " model vdw 2.278 2.520 nonbonded pdb=" OH TYR A 352 " pdb=" O THR A 407 " model vdw 2.280 2.440 nonbonded pdb=" ND1 HIS H 40 " pdb=" O PRO H 41 " model vdw 2.287 2.520 ... (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 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 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. 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: 4.310 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: 22.300 Check model and map are aligned: 0.440 Process input model: 71.520 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.270 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 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= 0.468 Angle : 1.178 15.263 40383 Z= 0.661 Chirality : 0.059 0.481 4527 Planarity : 0.009 0.119 5284 Dihedral : 10.186 75.042 11060 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.67 % Favored : 87.06 % Rotamer Outliers : 0.29 % 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 *********************** 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 fitting. rotamer outliers: 9 poor density : 636 time to evaluate : 3.982 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 outliers start: 9 outliers final: 0 residues processed: 644 average time/residue: 0.4772 time to fit residues: 461.8260 Evaluate side-chains 344 residues out of total 3143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 344 time to evaluate : 3.608 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8813 ------------------------------------------------------------------------------- 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: 0.8980 chunk 275 optimal weight: 10.0000 chunk 152 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 185 optimal weight: 0.0980 chunk 146 optimal weight: 5.9990 chunk 284 optimal weight: 10.0000 chunk 110 optimal weight: 0.0050 chunk 173 optimal weight: 10.0000 chunk 211 optimal weight: 3.9990 chunk 329 optimal weight: 10.0000 overall best weight: 1.1396 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 HIS A 513 GLN A 542 HIS A 549 ASN A 559 ASN ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 208 ASN B 360 HIS ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 HIS B 510 HIS ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN C 127 HIS C 132 GLN ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 ASN C 318 GLN C 350 GLN C 352 HIS D 149 ASN ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN E 206 HIS E 222 ASN ** E 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN F 292 HIS G 157 GLN G 392 HIS I 18 GLN I 28 HIS I 159 ASN I 241 ASN I 282 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 29661 Z= 0.201 Angle : 0.758 14.138 40383 Z= 0.389 Chirality : 0.045 0.213 4527 Planarity : 0.007 0.124 5284 Dihedral : 7.782 62.758 4026 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.49 % Favored : 89.37 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.07 % Twisted General : 0.65 % 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: -4.07 (0.12), residues: 3631 helix: -2.61 (0.13), residues: 997 sheet: -2.00 (0.22), residues: 490 loop : -3.05 (0.12), residues: 2144 *********************** 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 492 residues out of total 3143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 490 time to evaluate : 3.617 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 outliers start: 2 outliers final: 1 residues processed: 491 average time/residue: 0.4997 time to fit residues: 379.2846 Evaluate side-chains 315 residues out of total 3143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 314 time to evaluate : 3.578 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2538 time to fit residues: 5.3258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 183 optimal weight: 6.9990 chunk 102 optimal weight: 0.0050 chunk 274 optimal weight: 3.9990 chunk 224 optimal weight: 0.0570 chunk 90 optimal weight: 3.9990 chunk 330 optimal weight: 9.9990 chunk 356 optimal weight: 2.9990 chunk 294 optimal weight: 3.9990 chunk 327 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 264 optimal weight: 0.9990 overall best weight: 1.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 HIS A 508 GLN ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 HIS B 581 HIS ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN ** D 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 ASN ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN G 392 HIS I 18 GLN I 241 ASN ** I 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 29661 Z= 0.217 Angle : 0.734 14.472 40383 Z= 0.371 Chirality : 0.045 0.226 4527 Planarity : 0.006 0.124 5284 Dihedral : 7.308 62.243 4026 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.35 % Favored : 88.52 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.07 % Twisted General : 0.50 % 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: -3.55 (0.13), residues: 3631 helix: -1.67 (0.15), residues: 999 sheet: -1.80 (0.23), residues: 462 loop : -2.96 (0.12), residues: 2170 *********************** 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 418 residues out of total 3143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 416 time to evaluate : 3.749 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 outliers start: 2 outliers final: 0 residues processed: 417 average time/residue: 0.4528 time to fit residues: 294.2735 Evaluate side-chains 312 residues out of total 3143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 3.253 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 326 optimal weight: 7.9990 chunk 248 optimal weight: 0.6980 chunk 171 optimal weight: 0.9990 chunk 36 optimal weight: 40.0000 chunk 157 optimal weight: 0.9980 chunk 221 optimal weight: 5.9990 chunk 331 optimal weight: 3.9990 chunk 350 optimal weight: 0.8980 chunk 173 optimal weight: 7.9990 chunk 314 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 HIS ** 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 149 ASN E 206 HIS F 40 HIS F 149 ASN G 207 HIS G 359 GLN I 138 HIS I 241 ASN ** I 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 29661 Z= 0.175 Angle : 0.687 14.561 40383 Z= 0.345 Chirality : 0.044 0.223 4527 Planarity : 0.006 0.119 5284 Dihedral : 6.848 61.783 4026 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.77 % Favored : 89.15 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 1.66 % Twisted General : 0.41 % 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: -3.13 (0.13), residues: 3631 helix: -1.03 (0.16), residues: 998 sheet: -1.69 (0.23), residues: 469 loop : -2.82 (0.12), residues: 2164 *********************** 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 408 residues out of total 3143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 407 time to evaluate : 3.357 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 outliers start: 1 outliers final: 0 residues processed: 407 average time/residue: 0.4482 time to fit residues: 286.4736 Evaluate side-chains 302 residues out of total 3143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 3.889 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 292 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 261 optimal weight: 6.9990 chunk 144 optimal weight: 7.9990 chunk 299 optimal weight: 0.8980 chunk 242 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 179 optimal weight: 6.9990 chunk 314 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN C 232 HIS ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 222 ASN G 359 GLN I 138 HIS I 177 GLN I 241 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 29661 Z= 0.241 Angle : 0.724 13.440 40383 Z= 0.363 Chirality : 0.045 0.243 4527 Planarity : 0.006 0.112 5284 Dihedral : 6.801 60.621 4026 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.65 % Favored : 88.24 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 1.66 % Twisted General : 0.32 % 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: -2.89 (0.13), residues: 3631 helix: -0.67 (0.17), residues: 999 sheet: -1.57 (0.23), residues: 460 loop : -2.75 (0.12), residues: 2172 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7262 Ramachandran restraints generated. 3631 Oldfield, 0 Emsley, 3631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7262 Ramachandran restraints generated. 3631 Oldfield, 0 Emsley, 3631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 382 time to evaluate : 3.448 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 outliers start: 1 outliers final: 0 residues processed: 382 average time/residue: 0.4297 time to fit residues: 261.3943 Evaluate side-chains 291 residues out of total 3143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 3.627 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 118 optimal weight: 5.9990 chunk 315 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 206 optimal weight: 0.0770 chunk 86 optimal weight: 20.0000 chunk 351 optimal weight: 0.2980 chunk 291 optimal weight: 0.0050 chunk 162 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 116 optimal weight: 0.0070 chunk 184 optimal weight: 0.9990 overall best weight: 0.2772 ------------------------------------------------------------------------------- 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 513 GLN ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 HIS C 42 GLN ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 HIS C 245 HIS C 283 HIS ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN E 206 HIS ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 359 GLN I 138 HIS I 241 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.051 29661 Z= 0.165 Angle : 0.683 13.058 40383 Z= 0.341 Chirality : 0.044 0.323 4527 Planarity : 0.005 0.098 5284 Dihedral : 6.465 60.116 4026 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.02 % Favored : 89.87 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 1.66 % 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: -2.69 (0.13), residues: 3631 helix: -0.39 (0.17), residues: 974 sheet: -1.45 (0.23), residues: 445 loop : -2.67 (0.12), residues: 2212 *********************** 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 402 residues out of total 3143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 400 time to evaluate : 3.985 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 outliers start: 2 outliers final: 0 residues processed: 401 average time/residue: 0.4340 time to fit residues: 275.1634 Evaluate side-chains 292 residues out of total 3143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 3.669 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 338 optimal weight: 2.9990 chunk 39 optimal weight: 20.0000 chunk 200 optimal weight: 3.9990 chunk 256 optimal weight: 6.9990 chunk 198 optimal weight: 0.9990 chunk 295 optimal weight: 1.9990 chunk 196 optimal weight: 3.9990 chunk 349 optimal weight: 6.9990 chunk 218 optimal weight: 5.9990 chunk 213 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 GLN C 232 HIS D 148 HIS D 149 ASN ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 138 HIS I 241 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 29661 Z= 0.208 Angle : 0.709 12.475 40383 Z= 0.352 Chirality : 0.045 0.293 4527 Planarity : 0.006 0.087 5284 Dihedral : 6.372 59.241 4026 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.32 % Favored : 88.60 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 1.24 % Twisted General : 0.32 % 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: -2.56 (0.14), residues: 3631 helix: -0.18 (0.17), residues: 966 sheet: -1.46 (0.23), residues: 469 loop : -2.61 (0.12), residues: 2196 *********************** 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 386 residues out of total 3143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 386 time to evaluate : 3.487 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 outliers start: 0 outliers final: 0 residues processed: 386 average time/residue: 0.4606 time to fit residues: 281.5621 Evaluate side-chains 292 residues out of total 3143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 3.658 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 216 optimal weight: 0.5980 chunk 139 optimal weight: 9.9990 chunk 208 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 222 optimal weight: 2.9990 chunk 238 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 275 optimal weight: 6.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 549 ASN ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 HIS ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN D 149 ASN E 206 HIS ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 138 HIS I 241 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 29661 Z= 0.265 Angle : 0.754 12.853 40383 Z= 0.374 Chirality : 0.046 0.447 4527 Planarity : 0.006 0.081 5284 Dihedral : 6.549 57.888 4026 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.95 % Favored : 87.96 % Rotamer Outliers : 0.06 % 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: -2.56 (0.14), residues: 3631 helix: -0.29 (0.17), residues: 996 sheet: -1.38 (0.23), residues: 472 loop : -2.61 (0.13), residues: 2163 *********************** 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 370 residues out of total 3143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 368 time to evaluate : 4.032 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 outliers start: 2 outliers final: 1 residues processed: 370 average time/residue: 0.4432 time to fit residues: 262.3607 Evaluate side-chains 287 residues out of total 3143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 286 time to evaluate : 3.573 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3478 time to fit residues: 5.5152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 318 optimal weight: 0.8980 chunk 335 optimal weight: 7.9990 chunk 305 optimal weight: 1.9990 chunk 326 optimal weight: 9.9990 chunk 196 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 256 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 294 optimal weight: 7.9990 chunk 308 optimal weight: 1.9990 chunk 324 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 549 ASN ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS C 252 GLN D 149 ASN ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 241 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 29661 Z= 0.255 Angle : 0.750 12.788 40383 Z= 0.372 Chirality : 0.046 0.379 4527 Planarity : 0.006 0.080 5284 Dihedral : 6.564 57.522 4026 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.15 % Favored : 87.77 % Rotamer Outliers : 0.00 % 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: -2.51 (0.14), residues: 3631 helix: -0.22 (0.17), residues: 982 sheet: -1.41 (0.23), residues: 466 loop : -2.55 (0.13), residues: 2183 *********************** 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 367 residues out of total 3143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 3.497 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 outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.4567 time to fit residues: 266.3016 Evaluate side-chains 287 residues out of total 3143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 3.710 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 214 optimal weight: 2.9990 chunk 344 optimal weight: 0.7980 chunk 210 optimal weight: 3.9990 chunk 163 optimal weight: 0.7980 chunk 239 optimal weight: 0.6980 chunk 361 optimal weight: 0.9990 chunk 332 optimal weight: 7.9990 chunk 287 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 222 optimal weight: 4.9990 chunk 176 optimal weight: 0.2980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 549 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 HIS ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 HIS D 149 ASN E 206 HIS ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 HIS H 282 HIS I 138 HIS I 241 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.080 29661 Z= 0.176 Angle : 0.709 13.007 40383 Z= 0.349 Chirality : 0.044 0.249 4527 Planarity : 0.005 0.076 5284 Dihedral : 6.286 57.302 4026 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.41 % Favored : 89.53 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 1.24 % Twisted General : 0.32 % 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: -2.35 (0.14), residues: 3631 helix: 0.04 (0.18), residues: 979 sheet: -1.33 (0.24), residues: 449 loop : -2.51 (0.13), residues: 2203 ********************** 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 385 residues out of total 3143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 384 time to evaluate : 3.494 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 outliers start: 1 outliers final: 0 residues processed: 385 average time/residue: 0.4355 time to fit residues: 266.4127 Evaluate side-chains 298 residues out of total 3143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 3.398 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 228 optimal weight: 0.1980 chunk 306 optimal weight: 0.7980 chunk 88 optimal weight: 8.9990 chunk 265 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 288 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 296 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 HIS D 149 ASN ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 403 ASN H 282 HIS I 241 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.100099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.076509 restraints weight = 113905.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.078179 restraints weight = 69375.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.079305 restraints weight = 48842.208| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 29661 Z= 0.170 Angle : 0.691 12.542 40383 Z= 0.340 Chirality : 0.044 0.270 4527 Planarity : 0.005 0.071 5284 Dihedral : 6.039 57.400 4026 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.41 % Favored : 89.51 % Rotamer Outliers : 0.00 % 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: -2.19 (0.14), residues: 3631 helix: 0.23 (0.18), residues: 985 sheet: -1.27 (0.23), residues: 456 loop : -2.44 (0.13), residues: 2190 =============================================================================== Job complete usr+sys time: 6140.46 seconds wall clock time: 112 minutes 33.87 seconds (6753.87 seconds total)