Starting phenix.real_space_refine on Fri May 16 19:04:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g3l_29701/05_2025/8g3l_29701.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3l_29701/05_2025/8g3l_29701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g3l_29701/05_2025/8g3l_29701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3l_29701/05_2025/8g3l_29701.map" model { file = "/net/cci-nas-00/data/ceres_data/8g3l_29701/05_2025/8g3l_29701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3l_29701/05_2025/8g3l_29701.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 62 5.16 5 C 9385 2.51 5 N 2374 2.21 5 O 2619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14442 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 5000 Classifications: {'peptide': 635} Link IDs: {'PTRANS': 10, 'TRANS': 624} Chain breaks: 1 Chain: "B" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1915 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "C" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1915 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "D" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2738 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 324} Chain: "E" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2738 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 324} Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 116 Unusual residues: {'6OU': 2, 'PLM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'OLA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.55, per 1000 atoms: 0.59 Number of scatterers: 14442 At special positions: 0 Unit cell: (93.304, 117.72, 197.072, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 62 16.00 P 2 15.00 O 2619 8.00 N 2374 7.00 C 9385 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.38 Conformation dependent library (CDL) restraints added in 1.7 seconds 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3374 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 12 sheets defined 60.6% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 2 through 18 removed outlier: 4.049A pdb=" N LEU A 6 " --> pdb=" O ASN A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 41 removed outlier: 3.665A pdb=" N TYR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 47 removed outlier: 3.741A pdb=" N VAL A 47 " --> pdb=" O ILE A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 82 removed outlier: 3.974A pdb=" N THR A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A 66 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 94 removed outlier: 3.626A pdb=" N GLY A 94 " --> pdb=" O PHE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 122 Processing helix chain 'A' and resid 126 through 139 removed outlier: 3.632A pdb=" N ILE A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 178 removed outlier: 3.944A pdb=" N LEU A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A 159 " --> pdb=" O GLN A 155 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR A 173 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE A 174 " --> pdb=" O MET A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 220 removed outlier: 4.031A pdb=" N GLY A 205 " --> pdb=" O GLN A 201 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 214 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR A 216 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 253 Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 272 through 286 removed outlier: 3.566A pdb=" N VAL A 276 " --> pdb=" O ASN A 272 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N MET A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N PHE A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET A 286 " --> pdb=" O ILE A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 316 removed outlier: 3.783A pdb=" N TYR A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR A 315 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER A 316 " --> pdb=" O ILE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 325 removed outlier: 3.538A pdb=" N VAL A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 346 removed outlier: 3.905A pdb=" N GLU A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.616A pdb=" N MET A 369 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 416 removed outlier: 3.585A pdb=" N GLN A 413 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS A 414 " --> pdb=" O ASP A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 472 removed outlier: 3.835A pdb=" N GLN A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 518 through 557 removed outlier: 3.622A pdb=" N LYS A 549 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN A 550 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET A 551 " --> pdb=" O TYR A 547 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY A 552 " --> pdb=" O PHE A 548 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 557 " --> pdb=" O GLU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 565 Processing helix chain 'A' and resid 570 through 602 removed outlier: 3.856A pdb=" N ILE A 580 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE A 588 " --> pdb=" O TYR A 584 " (cutoff:3.500A) Proline residue: A 589 - end of helix Processing helix chain 'A' and resid 614 through 633 removed outlier: 3.960A pdb=" N MET A 618 " --> pdb=" O ALA A 614 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE A 629 " --> pdb=" O ALA A 625 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N PHE A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLY A 631 " --> pdb=" O TYR A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 644 removed outlier: 4.234A pdb=" N TYR A 637 " --> pdb=" O LEU A 633 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER A 644 " --> pdb=" O LYS A 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 removed outlier: 3.533A pdb=" N SER B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 101 through 108 Processing helix chain 'B' and resid 109 through 112 removed outlier: 3.894A pdb=" N ILE B 112 " --> pdb=" O PRO B 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 109 through 112' Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 133 through 137 removed outlier: 3.931A pdb=" N ARG B 137 " --> pdb=" O TYR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 144 Processing helix chain 'B' and resid 145 through 158 removed outlier: 3.644A pdb=" N LYS B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 193 Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 231 through 246 Processing helix chain 'C' and resid 45 through 55 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 101 through 108 Processing helix chain 'C' and resid 109 through 111 No H-bonds generated for 'chain 'C' and resid 109 through 111' Processing helix chain 'C' and resid 116 through 132 removed outlier: 3.527A pdb=" N ALA C 120 " --> pdb=" O SER C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 157 removed outlier: 3.673A pdb=" N ALA C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 193 removed outlier: 3.609A pdb=" N GLN C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS C 192 " --> pdb=" O GLN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 208 removed outlier: 3.794A pdb=" N ALA C 207 " --> pdb=" O ASP C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 246 Processing helix chain 'D' and resid 2 through 9 Processing helix chain 'D' and resid 11 through 30 removed outlier: 3.695A pdb=" N ALA D 15 " --> pdb=" O SER D 11 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA D 27 " --> pdb=" O MET D 23 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP D 30 " --> pdb=" O ILE D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 61 removed outlier: 3.869A pdb=" N VAL D 38 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU D 47 " --> pdb=" O TYR D 43 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE D 48 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE D 50 " --> pdb=" O ILE D 46 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 71 Processing helix chain 'D' and resid 84 through 139 removed outlier: 4.065A pdb=" N MET D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N VAL D 90 " --> pdb=" O PHE D 86 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS D 102 " --> pdb=" O THR D 98 " (cutoff:3.500A) Proline residue: D 129 - end of helix Processing helix chain 'D' and resid 142 through 169 Processing helix chain 'D' and resid 170 through 175 removed outlier: 5.630A pdb=" N GLU D 173 " --> pdb=" O SER D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 194 removed outlier: 4.202A pdb=" N LEU D 186 " --> pdb=" O GLN D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 202 Processing helix chain 'D' and resid 217 through 235 Processing helix chain 'D' and resid 264 through 268 Processing helix chain 'D' and resid 281 through 285 Processing helix chain 'D' and resid 289 through 300 removed outlier: 4.331A pdb=" N TYR D 293 " --> pdb=" O GLY D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 327 Processing helix chain 'D' and resid 328 through 334 Processing helix chain 'E' and resid 2 through 9 Processing helix chain 'E' and resid 11 through 30 removed outlier: 3.546A pdb=" N PHE E 16 " --> pdb=" O TRP E 12 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU E 17 " --> pdb=" O ILE E 13 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N GLN E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN E 20 " --> pdb=" O PHE E 16 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA E 21 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE E 28 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL E 29 " --> pdb=" O PHE E 25 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP E 30 " --> pdb=" O ILE E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 61 removed outlier: 3.951A pdb=" N ARG E 58 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS E 59 " --> pdb=" O PHE E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 71 Processing helix chain 'E' and resid 84 through 138 Proline residue: E 129 - end of helix Processing helix chain 'E' and resid 143 through 170 Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 183 through 194 Processing helix chain 'E' and resid 194 through 202 Processing helix chain 'E' and resid 217 through 235 removed outlier: 3.919A pdb=" N LEU E 221 " --> pdb=" O ASP E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 287 Processing helix chain 'E' and resid 289 through 303 removed outlier: 4.064A pdb=" N TYR E 293 " --> pdb=" O GLY E 289 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA E 300 " --> pdb=" O LYS E 296 " (cutoff:3.500A) Proline residue: E 301 - end of helix Processing helix chain 'E' and resid 324 through 327 Processing helix chain 'E' and resid 328 through 333 Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 330 removed outlier: 3.640A pdb=" N LEU A 511 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 353 through 354 removed outlier: 4.002A pdb=" N LYS A 354 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 485 " --> pdb=" O LYS A 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 425 through 426 removed outlier: 3.640A pdb=" N LYS A 425 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N MET A 383 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 9.136A pdb=" N VAL A 458 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ALA A 386 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 457 " --> pdb=" O SER A 406 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 404 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N PHE A 405 " --> pdb=" O LYS A 438 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU A 440 " --> pdb=" O PHE A 405 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 29 through 30 Processing sheet with id=AA5, first strand: chain 'B' and resid 12 through 14 Processing sheet with id=AA6, first strand: chain 'B' and resid 88 through 90 removed outlier: 7.515A pdb=" N GLY B 88 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N ASP B 168 " --> pdb=" O GLY B 88 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE B 90 " --> pdb=" O ASP B 168 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE B 165 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N VAL B 200 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ALA B 167 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE B 35 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ILE B 214 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER B 37 " --> pdb=" O ILE B 214 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 87 through 88 removed outlier: 5.809A pdb=" N GLY C 88 " --> pdb=" O PHE C 166 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE C 198 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA C 167 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET C 199 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 65 through 66 Processing sheet with id=AA9, first strand: chain 'D' and resid 205 through 209 removed outlier: 3.564A pdb=" N LYS D 248 " --> pdb=" O GLN D 251 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN D 251 " --> pdb=" O LYS D 248 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 305 through 311 Processing sheet with id=AB2, first strand: chain 'E' and resid 179 through 182 removed outlier: 4.006A pdb=" N GLU E 179 " --> pdb=" O SER E 216 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER E 216 " --> pdb=" O GLU E 179 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL E 214 " --> pdb=" O ILE E 181 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 205 through 209 removed outlier: 5.819A pdb=" N ASP E 206 " --> pdb=" O ILE E 243 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N SER E 245 " --> pdb=" O ASP E 206 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLN E 208 " --> pdb=" O SER E 245 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N GLN E 247 " --> pdb=" O GLN E 208 " (cutoff:3.500A) 773 hydrogen bonds defined for protein. 2229 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: 4.45 Time building geometry restraints manager: 4.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2344 1.31 - 1.44: 3764 1.44 - 1.56: 8465 1.56 - 1.69: 22 1.69 - 1.81: 114 Bond restraints: 14709 Sorted by residual: bond pdb=" C10 OLA E 401 " pdb=" C9 OLA E 401 " ideal model delta sigma weight residual 1.332 1.470 -0.138 2.00e-02 2.50e+03 4.75e+01 bond pdb=" C16 6OU A 702 " pdb=" O18 6OU A 702 " ideal model delta sigma weight residual 1.327 1.455 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C16 6OU A 703 " pdb=" O18 6OU A 703 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.02e+01 bond pdb=" C14 6OU A 702 " pdb=" C15 6OU A 702 " ideal model delta sigma weight residual 1.521 1.607 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C31 6OU A 703 " pdb=" O30 6OU A 703 " ideal model delta sigma weight residual 1.331 1.417 -0.086 2.00e-02 2.50e+03 1.84e+01 ... (remaining 14704 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.18: 19726 5.18 - 10.36: 45 10.36 - 15.54: 3 15.54 - 20.72: 2 20.72 - 25.90: 2 Bond angle restraints: 19778 Sorted by residual: angle pdb=" C40 6OU A 702 " pdb=" C41 6OU A 702 " pdb=" C42 6OU A 702 " ideal model delta sigma weight residual 127.56 153.46 -25.90 3.00e+00 1.11e-01 7.45e+01 angle pdb=" C40 6OU A 703 " pdb=" C41 6OU A 703 " pdb=" C42 6OU A 703 " ideal model delta sigma weight residual 127.56 151.55 -23.99 3.00e+00 1.11e-01 6.40e+01 angle pdb=" O22 6OU A 702 " pdb=" P23 6OU A 702 " pdb=" O26 6OU A 702 " ideal model delta sigma weight residual 93.95 110.61 -16.66 3.00e+00 1.11e-01 3.08e+01 angle pdb=" C39 6OU A 703 " pdb=" C40 6OU A 703 " pdb=" C41 6OU A 703 " ideal model delta sigma weight residual 127.60 111.71 15.89 3.00e+00 1.11e-01 2.81e+01 angle pdb=" O22 6OU A 703 " pdb=" P23 6OU A 703 " pdb=" O26 6OU A 703 " ideal model delta sigma weight residual 93.95 108.87 -14.92 3.00e+00 1.11e-01 2.47e+01 ... (remaining 19773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 8672 35.85 - 71.70: 202 71.70 - 107.55: 21 107.55 - 143.40: 4 143.40 - 179.25: 2 Dihedral angle restraints: 8901 sinusoidal: 3689 harmonic: 5212 Sorted by residual: dihedral pdb=" C19 6OU A 703 " pdb=" C20 6OU A 703 " pdb=" O30 6OU A 703 " pdb=" C31 6OU A 703 " ideal model delta sinusoidal sigma weight residual 212.33 33.08 179.25 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C21 6OU A 703 " pdb=" C20 6OU A 703 " pdb=" O30 6OU A 703 " pdb=" C31 6OU A 703 " ideal model delta sinusoidal sigma weight residual 85.49 -88.88 174.37 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C19 6OU A 703 " pdb=" C20 6OU A 703 " pdb=" C21 6OU A 703 " pdb=" O22 6OU A 703 " ideal model delta sinusoidal sigma weight residual 301.00 158.85 142.15 1 3.00e+01 1.11e-03 1.91e+01 ... (remaining 8898 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1880 0.060 - 0.120: 335 0.120 - 0.180: 28 0.180 - 0.240: 2 0.240 - 0.300: 1 Chirality restraints: 2246 Sorted by residual: chirality pdb=" C20 6OU A 702 " pdb=" C19 6OU A 702 " pdb=" C21 6OU A 702 " pdb=" O30 6OU A 702 " both_signs ideal model delta sigma weight residual False 2.35 2.65 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CB ILE C 198 " pdb=" CA ILE C 198 " pdb=" CG1 ILE C 198 " pdb=" CG2 ILE C 198 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ILE A 563 " pdb=" N ILE A 563 " pdb=" C ILE A 563 " pdb=" CB ILE A 563 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.78e-01 ... (remaining 2243 not shown) Planarity restraints: 2468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA E 401 " 0.287 2.00e-02 2.50e+03 2.20e-01 4.82e+02 pdb=" C11 OLA E 401 " -0.112 2.00e-02 2.50e+03 pdb=" C8 OLA E 401 " 0.116 2.00e-02 2.50e+03 pdb=" C9 OLA E 401 " -0.291 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 153 " 0.031 2.00e-02 2.50e+03 2.44e-02 1.49e+01 pdb=" CG TRP D 153 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP D 153 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP D 153 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 153 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 153 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 153 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 153 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 153 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 153 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 197 " -0.008 2.00e-02 2.50e+03 1.56e-02 6.06e+00 pdb=" CG TRP D 197 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP D 197 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP D 197 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 197 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP D 197 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 197 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 197 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 197 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP D 197 " 0.001 2.00e-02 2.50e+03 ... (remaining 2465 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 982 2.73 - 3.27: 14476 3.27 - 3.82: 22689 3.82 - 4.36: 25463 4.36 - 4.90: 44529 Nonbonded interactions: 108139 Sorted by model distance: nonbonded pdb=" ND2 ASN A 362 " pdb=" OD1 ASN A 382 " model vdw 2.191 3.120 nonbonded pdb=" NH2 ARG D 9 " pdb=" OE2 GLU D 60 " model vdw 2.226 3.120 nonbonded pdb=" OG SER C 145 " pdb=" OE1 GLN C 148 " model vdw 2.227 3.040 nonbonded pdb=" OG SER A 406 " pdb=" O ALA A 457 " model vdw 2.241 3.040 nonbonded pdb=" OG1 THR A 451 " pdb=" O MET A 455 " model vdw 2.268 3.040 ... (remaining 108134 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = (chain 'E' and resid 1 through 334) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.840 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: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 32.770 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 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 : 0.006 0.138 14709 Z= 0.284 Angle : 0.805 25.896 19778 Z= 0.387 Chirality : 0.045 0.300 2246 Planarity : 0.006 0.220 2468 Dihedral : 16.626 179.254 5527 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.21), residues: 1779 helix: 0.99 (0.17), residues: 1003 sheet: -1.02 (0.45), residues: 169 loop : -1.60 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.004 TRP D 153 HIS 0.008 0.001 HIS A 596 PHE 0.026 0.002 PHE A 529 TYR 0.023 0.002 TYR A 315 ARG 0.010 0.001 ARG D 226 Details of bonding type rmsd hydrogen bonds : bond 0.15498 ( 773) hydrogen bonds : angle 5.71354 ( 2229) covalent geometry : bond 0.00622 (14709) covalent geometry : angle 0.80502 (19778) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 57 TYR cc_start: 0.8347 (t80) cc_final: 0.8086 (t80) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2713 time to fit residues: 65.9912 Evaluate side-chains 144 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 0.5980 chunk 134 optimal weight: 10.0000 chunk 74 optimal weight: 0.2980 chunk 45 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 138 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 160 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 GLN ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.227517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.189947 restraints weight = 18538.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.186711 restraints weight = 31262.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.183154 restraints weight = 26628.467| |-----------------------------------------------------------------------------| r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14709 Z= 0.148 Angle : 0.584 11.643 19778 Z= 0.298 Chirality : 0.043 0.259 2246 Planarity : 0.003 0.039 2468 Dihedral : 11.996 165.934 2018 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.95 % Favored : 95.00 % Rotamer: Outliers : 0.51 % Allowed : 7.42 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.21), residues: 1779 helix: 1.20 (0.17), residues: 1006 sheet: -0.96 (0.45), residues: 165 loop : -1.55 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 153 HIS 0.008 0.001 HIS D 134 PHE 0.022 0.001 PHE A 529 TYR 0.033 0.002 TYR E 151 ARG 0.005 0.000 ARG D 226 Details of bonding type rmsd hydrogen bonds : bond 0.06453 ( 773) hydrogen bonds : angle 4.64104 ( 2229) covalent geometry : bond 0.00332 (14709) covalent geometry : angle 0.58358 (19778) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.5747 (mtt) cc_final: 0.5421 (mtm) REVERT: D 41 MET cc_start: 0.5700 (mmp) cc_final: 0.5464 (mmp) outliers start: 8 outliers final: 8 residues processed: 149 average time/residue: 0.2637 time to fit residues: 58.1914 Evaluate side-chains 144 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 290 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 18 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 109 optimal weight: 0.0570 chunk 33 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 139 optimal weight: 40.0000 chunk 159 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.226590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.195889 restraints weight = 19011.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.191912 restraints weight = 35229.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.187338 restraints weight = 38589.118| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14709 Z= 0.161 Angle : 0.578 13.874 19778 Z= 0.293 Chirality : 0.042 0.235 2246 Planarity : 0.003 0.038 2468 Dihedral : 11.280 170.453 2018 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.83 % Allowed : 10.94 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.21), residues: 1779 helix: 1.24 (0.17), residues: 1006 sheet: -1.09 (0.42), residues: 174 loop : -1.54 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 153 HIS 0.006 0.001 HIS A 596 PHE 0.026 0.001 PHE A 529 TYR 0.028 0.002 TYR E 151 ARG 0.006 0.000 ARG D 107 Details of bonding type rmsd hydrogen bonds : bond 0.06524 ( 773) hydrogen bonds : angle 4.42869 ( 2229) covalent geometry : bond 0.00377 (14709) covalent geometry : angle 0.57801 (19778) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 83 ARG cc_start: 0.8157 (ttm-80) cc_final: 0.7527 (ttm170) outliers start: 13 outliers final: 10 residues processed: 149 average time/residue: 0.2751 time to fit residues: 60.7112 Evaluate side-chains 146 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 130 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 153 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 146 optimal weight: 0.7980 chunk 171 optimal weight: 50.0000 chunk 44 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.226702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.190309 restraints weight = 18543.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.186154 restraints weight = 34416.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.180330 restraints weight = 36194.307| |-----------------------------------------------------------------------------| r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14709 Z= 0.149 Angle : 0.559 11.465 19778 Z= 0.281 Chirality : 0.042 0.240 2246 Planarity : 0.003 0.038 2468 Dihedral : 10.908 171.407 2018 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.41 % Allowed : 12.03 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.21), residues: 1779 helix: 1.31 (0.17), residues: 1015 sheet: -1.10 (0.40), residues: 176 loop : -1.53 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 122 HIS 0.006 0.001 HIS D 124 PHE 0.024 0.001 PHE A 529 TYR 0.024 0.002 TYR E 151 ARG 0.004 0.000 ARG D 107 Details of bonding type rmsd hydrogen bonds : bond 0.06185 ( 773) hydrogen bonds : angle 4.27978 ( 2229) covalent geometry : bond 0.00344 (14709) covalent geometry : angle 0.55853 (19778) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 ARG cc_start: 0.8189 (ttm-80) cc_final: 0.7869 (ttm170) REVERT: E 140 MET cc_start: 0.6264 (pmm) cc_final: 0.5796 (pmm) outliers start: 22 outliers final: 16 residues processed: 159 average time/residue: 0.2597 time to fit residues: 60.6901 Evaluate side-chains 152 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 70 optimal weight: 5.9990 chunk 136 optimal weight: 20.0000 chunk 151 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 83 optimal weight: 0.0020 chunk 150 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.228377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.195698 restraints weight = 18779.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.191835 restraints weight = 34401.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.186542 restraints weight = 37255.640| |-----------------------------------------------------------------------------| r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14709 Z= 0.123 Angle : 0.535 10.022 19778 Z= 0.269 Chirality : 0.041 0.223 2246 Planarity : 0.003 0.036 2468 Dihedral : 10.500 168.295 2018 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.34 % Allowed : 13.44 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.21), residues: 1779 helix: 1.51 (0.17), residues: 1005 sheet: -1.03 (0.40), residues: 176 loop : -1.47 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 122 HIS 0.003 0.001 HIS D 134 PHE 0.022 0.001 PHE A 529 TYR 0.022 0.001 TYR E 151 ARG 0.007 0.000 ARG D 107 Details of bonding type rmsd hydrogen bonds : bond 0.05523 ( 773) hydrogen bonds : angle 4.11494 ( 2229) covalent geometry : bond 0.00267 (14709) covalent geometry : angle 0.53544 (19778) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 TYR cc_start: 0.6401 (m-10) cc_final: 0.6019 (m-80) outliers start: 21 outliers final: 15 residues processed: 157 average time/residue: 0.2793 time to fit residues: 64.7636 Evaluate side-chains 150 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 53 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 chunk 144 optimal weight: 0.0570 chunk 77 optimal weight: 0.0060 chunk 12 optimal weight: 1.9990 chunk 106 optimal weight: 0.3980 chunk 62 optimal weight: 0.9990 overall best weight: 0.3914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.230017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.197425 restraints weight = 19004.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.194062 restraints weight = 34574.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.191477 restraints weight = 36033.154| |-----------------------------------------------------------------------------| r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 14709 Z= 0.107 Angle : 0.519 10.188 19778 Z= 0.261 Chirality : 0.040 0.252 2246 Planarity : 0.003 0.034 2468 Dihedral : 10.117 171.784 2018 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.54 % Allowed : 14.14 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.21), residues: 1779 helix: 1.72 (0.17), residues: 1008 sheet: -0.84 (0.41), residues: 167 loop : -1.41 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 122 HIS 0.004 0.001 HIS A 510 PHE 0.018 0.001 PHE A 529 TYR 0.019 0.001 TYR E 151 ARG 0.005 0.000 ARG D 107 Details of bonding type rmsd hydrogen bonds : bond 0.04830 ( 773) hydrogen bonds : angle 3.92508 ( 2229) covalent geometry : bond 0.00219 (14709) covalent geometry : angle 0.51934 (19778) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 TYR cc_start: 0.6460 (m-10) cc_final: 0.6139 (m-80) REVERT: C 71 MET cc_start: 0.3261 (ppp) cc_final: 0.2466 (ppp) REVERT: C 74 MET cc_start: -0.0631 (pmm) cc_final: -0.3239 (tmm) REVERT: E 92 ARG cc_start: 0.7313 (mmm160) cc_final: 0.7107 (mmm160) outliers start: 24 outliers final: 12 residues processed: 157 average time/residue: 0.2449 time to fit residues: 58.1004 Evaluate side-chains 150 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 90 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 168 optimal weight: 20.0000 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 125 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.226259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.188228 restraints weight = 18905.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.186485 restraints weight = 36315.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.182513 restraints weight = 33690.878| |-----------------------------------------------------------------------------| r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14709 Z= 0.164 Angle : 0.578 8.756 19778 Z= 0.292 Chirality : 0.042 0.234 2246 Planarity : 0.003 0.036 2468 Dihedral : 10.412 173.792 2018 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.47 % Allowed : 15.36 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.45 (0.21), residues: 1779 helix: 1.47 (0.17), residues: 1017 sheet: -0.83 (0.41), residues: 165 loop : -1.41 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 122 HIS 0.005 0.001 HIS B 86 PHE 0.041 0.002 PHE B 82 TYR 0.018 0.002 TYR E 151 ARG 0.005 0.000 ARG D 107 Details of bonding type rmsd hydrogen bonds : bond 0.06158 ( 773) hydrogen bonds : angle 4.04023 ( 2229) covalent geometry : bond 0.00389 (14709) covalent geometry : angle 0.57771 (19778) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 TYR cc_start: 0.6605 (m-10) cc_final: 0.6386 (m-80) outliers start: 23 outliers final: 16 residues processed: 154 average time/residue: 0.2618 time to fit residues: 59.8808 Evaluate side-chains 149 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 132 optimal weight: 40.0000 chunk 170 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 151 optimal weight: 0.0770 chunk 4 optimal weight: 0.9980 chunk 174 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 84 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.228228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.192796 restraints weight = 18637.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.187709 restraints weight = 38850.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.184065 restraints weight = 37950.097| |-----------------------------------------------------------------------------| r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14709 Z= 0.126 Angle : 0.543 11.802 19778 Z= 0.273 Chirality : 0.041 0.269 2246 Planarity : 0.003 0.034 2468 Dihedral : 10.158 173.685 2018 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.54 % Allowed : 15.87 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.55 (0.21), residues: 1779 helix: 1.55 (0.17), residues: 1024 sheet: -0.72 (0.42), residues: 151 loop : -1.43 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 122 HIS 0.011 0.001 HIS B 86 PHE 0.023 0.001 PHE B 82 TYR 0.017 0.001 TYR E 151 ARG 0.008 0.000 ARG D 107 Details of bonding type rmsd hydrogen bonds : bond 0.05353 ( 773) hydrogen bonds : angle 3.90786 ( 2229) covalent geometry : bond 0.00282 (14709) covalent geometry : angle 0.54275 (19778) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.6319 (mtt) cc_final: 0.5972 (ttm) REVERT: A 315 TYR cc_start: 0.6613 (m-10) cc_final: 0.6362 (m-80) REVERT: C 71 MET cc_start: 0.3332 (ppp) cc_final: 0.2496 (ppp) REVERT: C 74 MET cc_start: -0.0722 (pmm) cc_final: -0.3345 (tmm) outliers start: 24 outliers final: 20 residues processed: 150 average time/residue: 0.2467 time to fit residues: 56.7539 Evaluate side-chains 149 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 510 HIS Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 116 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 42 optimal weight: 20.0000 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.226570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.193562 restraints weight = 18979.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.189291 restraints weight = 38632.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.184245 restraints weight = 36239.711| |-----------------------------------------------------------------------------| r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14709 Z= 0.158 Angle : 0.582 10.722 19778 Z= 0.294 Chirality : 0.042 0.233 2246 Planarity : 0.003 0.036 2468 Dihedral : 10.335 173.779 2018 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.66 % Allowed : 16.25 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.42 (0.21), residues: 1779 helix: 1.43 (0.17), residues: 1020 sheet: -0.74 (0.42), residues: 151 loop : -1.43 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 122 HIS 0.014 0.001 HIS A 510 PHE 0.028 0.001 PHE A 529 TYR 0.017 0.002 TYR E 151 ARG 0.006 0.000 ARG D 107 Details of bonding type rmsd hydrogen bonds : bond 0.06056 ( 773) hydrogen bonds : angle 3.96990 ( 2229) covalent geometry : bond 0.00372 (14709) covalent geometry : angle 0.58249 (19778) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.6927 (mt0) REVERT: A 315 TYR cc_start: 0.6675 (m-10) cc_final: 0.6346 (m-80) REVERT: C 74 MET cc_start: -0.0664 (pmm) cc_final: -0.3217 (tmm) outliers start: 26 outliers final: 20 residues processed: 150 average time/residue: 0.2456 time to fit residues: 55.8981 Evaluate side-chains 154 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 135 optimal weight: 30.0000 chunk 62 optimal weight: 0.0980 chunk 173 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.228616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.193204 restraints weight = 18557.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.189025 restraints weight = 35054.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.184477 restraints weight = 32807.952| |-----------------------------------------------------------------------------| r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14709 Z= 0.118 Angle : 0.561 13.489 19778 Z= 0.278 Chirality : 0.041 0.283 2246 Planarity : 0.003 0.034 2468 Dihedral : 10.037 172.206 2018 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.34 % Allowed : 16.76 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.21), residues: 1779 helix: 1.54 (0.17), residues: 1024 sheet: -0.69 (0.42), residues: 151 loop : -1.38 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 122 HIS 0.003 0.001 HIS A 510 PHE 0.023 0.001 PHE B 82 TYR 0.016 0.001 TYR E 151 ARG 0.006 0.000 ARG D 107 Details of bonding type rmsd hydrogen bonds : bond 0.05208 ( 773) hydrogen bonds : angle 3.85065 ( 2229) covalent geometry : bond 0.00255 (14709) covalent geometry : angle 0.56052 (19778) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 TYR cc_start: 0.6542 (m-10) cc_final: 0.6282 (m-80) REVERT: A 505 ASN cc_start: 0.7155 (OUTLIER) cc_final: 0.6158 (p0) REVERT: C 74 MET cc_start: -0.0465 (pmm) cc_final: -0.3072 (tmm) REVERT: E 92 ARG cc_start: 0.7384 (mmm160) cc_final: 0.7140 (mmm160) outliers start: 21 outliers final: 19 residues processed: 145 average time/residue: 0.2411 time to fit residues: 53.5736 Evaluate side-chains 148 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 510 HIS Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 36 optimal weight: 0.0970 chunk 56 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 108 optimal weight: 0.0670 chunk 132 optimal weight: 30.0000 chunk 128 optimal weight: 0.0270 chunk 28 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 163 optimal weight: 30.0000 chunk 142 optimal weight: 4.9990 overall best weight: 0.2774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.230654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.195081 restraints weight = 18757.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.190519 restraints weight = 36151.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.184718 restraints weight = 35815.277| |-----------------------------------------------------------------------------| r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 14709 Z= 0.109 Angle : 0.556 12.596 19778 Z= 0.276 Chirality : 0.041 0.250 2246 Planarity : 0.003 0.034 2468 Dihedral : 9.757 170.965 2018 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.22 % Allowed : 16.89 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.21), residues: 1779 helix: 1.70 (0.17), residues: 1021 sheet: -0.59 (0.43), residues: 150 loop : -1.37 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 122 HIS 0.008 0.001 HIS A 510 PHE 0.060 0.001 PHE C 35 TYR 0.016 0.001 TYR E 151 ARG 0.006 0.000 ARG D 107 Details of bonding type rmsd hydrogen bonds : bond 0.04655 ( 773) hydrogen bonds : angle 3.75520 ( 2229) covalent geometry : bond 0.00219 (14709) covalent geometry : angle 0.55588 (19778) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4008.74 seconds wall clock time: 71 minutes 26.01 seconds (4286.01 seconds total)