Starting phenix.real_space_refine on Wed Mar 4 16:09:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g3l_29701/03_2026/8g3l_29701.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3l_29701/03_2026/8g3l_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 { model { file = "/net/cci-nas-00/data/ceres_data/8g3l_29701/03_2026/8g3l_29701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3l_29701/03_2026/8g3l_29701.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g3l_29701/03_2026/8g3l_29701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3l_29701/03_2026/8g3l_29701.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 3.33, per 1000 atoms: 0.23 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: 1.55 Conformation dependent library (CDL) restraints added in 762.8 milliseconds 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: 0.45 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: 2.29 Time building geometry restraints manager: 2.03 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: 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: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 15.250 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.570 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.010 0.001 ARG D 226 TYR 0.023 0.002 TYR A 315 PHE 0.026 0.002 PHE A 529 TRP 0.065 0.004 TRP D 153 HIS 0.008 0.001 HIS A 596 Details of bonding type rmsd covalent geometry : bond 0.00622 (14709) covalent geometry : angle 0.80502 (19778) hydrogen bonds : bond 0.15498 ( 773) hydrogen bonds : angle 5.71354 ( 2229) *********************** 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 : 0.569 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: 0.1279 time to fit residues: 31.4536 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 : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4508 r_free = 0.4508 target = 0.228785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.194780 restraints weight = 19046.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.191210 restraints weight = 35915.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.183242 restraints weight = 37939.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.179232 restraints weight = 44375.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.178241 restraints weight = 37576.616| |-----------------------------------------------------------------------------| r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.0990 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= 0.134 Angle : 0.571 12.026 19778 Z= 0.290 Chirality : 0.042 0.261 2246 Planarity : 0.003 0.038 2468 Dihedral : 11.866 164.755 2018 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.61 % Favored : 95.33 % Rotamer: Outliers : 0.38 % Allowed : 7.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.21), residues: 1779 helix: 1.27 (0.17), residues: 1006 sheet: -0.95 (0.45), residues: 165 loop : -1.53 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 226 TYR 0.033 0.002 TYR E 151 PHE 0.020 0.001 PHE A 529 TRP 0.019 0.002 TRP D 153 HIS 0.008 0.001 HIS D 134 Details of bonding type rmsd covalent geometry : bond 0.00286 (14709) covalent geometry : angle 0.57106 (19778) hydrogen bonds : bond 0.06060 ( 773) hydrogen bonds : angle 4.56053 ( 2229) *********************** 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 156 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 150 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.5494 (mtt) cc_final: 0.5229 (mtm) REVERT: B 83 ARG cc_start: 0.8176 (ttm-80) cc_final: 0.7878 (ttm170) REVERT: D 41 MET cc_start: 0.5490 (mmp) cc_final: 0.5284 (mmp) outliers start: 6 outliers final: 6 residues processed: 152 average time/residue: 0.1213 time to fit residues: 27.3923 Evaluate side-chains 143 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 137 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 SER 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 122 optimal weight: 5.9990 chunk 162 optimal weight: 0.0170 chunk 140 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 89 optimal weight: 9.9990 chunk 151 optimal weight: 2.9990 overall best weight: 1.5022 ------------------------------------------------------------------------------- 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 = 0.4478 r_free = 0.4478 target = 0.225440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.189181 restraints weight = 18724.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.184258 restraints weight = 37412.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.181154 restraints weight = 36069.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.178700 restraints weight = 31819.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.174873 restraints weight = 33856.357| |-----------------------------------------------------------------------------| r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14709 Z= 0.189 Angle : 0.603 13.692 19778 Z= 0.306 Chirality : 0.043 0.260 2246 Planarity : 0.003 0.039 2468 Dihedral : 11.376 170.896 2018 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.90 % Allowed : 10.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.21), residues: 1779 helix: 1.19 (0.17), residues: 1006 sheet: -1.08 (0.41), residues: 176 loop : -1.53 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 107 TYR 0.027 0.002 TYR E 151 PHE 0.029 0.002 PHE A 529 TRP 0.016 0.002 TRP E 153 HIS 0.006 0.001 HIS A 596 Details of bonding type rmsd covalent geometry : bond 0.00453 (14709) covalent geometry : angle 0.60327 (19778) hydrogen bonds : bond 0.06942 ( 773) hydrogen bonds : angle 4.48368 ( 2229) *********************** 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 160 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 TYR cc_start: 0.6556 (m-10) cc_final: 0.6334 (m-80) REVERT: B 83 ARG cc_start: 0.8169 (ttm-80) cc_final: 0.7499 (ttm170) outliers start: 14 outliers final: 11 residues processed: 150 average time/residue: 0.1319 time to fit residues: 28.9886 Evaluate side-chains 147 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 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 13 optimal weight: 0.3980 chunk 115 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 0.1980 chunk 167 optimal weight: 0.0670 chunk 26 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 77 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.229607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.196310 restraints weight = 18745.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.193055 restraints weight = 34832.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.187863 restraints weight = 35222.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.185347 restraints weight = 36377.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.181817 restraints weight = 34087.529| |-----------------------------------------------------------------------------| r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 14709 Z= 0.111 Angle : 0.520 11.880 19778 Z= 0.261 Chirality : 0.040 0.245 2246 Planarity : 0.003 0.035 2468 Dihedral : 10.544 169.893 2018 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.22 % Allowed : 12.09 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.21), residues: 1779 helix: 1.52 (0.17), residues: 1013 sheet: -1.02 (0.41), residues: 176 loop : -1.48 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 107 TYR 0.024 0.001 TYR E 151 PHE 0.017 0.001 PHE A 529 TRP 0.016 0.002 TRP D 122 HIS 0.006 0.001 HIS A 510 Details of bonding type rmsd covalent geometry : bond 0.00224 (14709) covalent geometry : angle 0.51953 (19778) hydrogen bonds : bond 0.05151 ( 773) hydrogen bonds : angle 4.12216 ( 2229) *********************** 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 170 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 83 ARG cc_start: 0.8098 (ttm-80) cc_final: 0.7407 (ttm170) outliers start: 19 outliers final: 13 residues processed: 161 average time/residue: 0.1227 time to fit residues: 29.2262 Evaluate side-chains 152 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 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 D residue 30 ASP Chi-restraints excluded: chain D residue 113 GLU 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 64 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 104 optimal weight: 0.3980 chunk 162 optimal weight: 50.0000 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 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 = 0.4490 r_free = 0.4490 target = 0.226657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.191534 restraints weight = 18745.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.186331 restraints weight = 37263.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.181616 restraints weight = 37110.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.180241 restraints weight = 36140.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.177037 restraints weight = 31534.836| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.1551 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= 0.160 Angle : 0.565 10.520 19778 Z= 0.286 Chirality : 0.042 0.221 2246 Planarity : 0.003 0.037 2468 Dihedral : 10.589 169.909 2018 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.21), residues: 1779 helix: 1.38 (0.17), residues: 1017 sheet: -1.02 (0.41), residues: 176 loop : -1.60 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 107 TYR 0.022 0.002 TYR E 151 PHE 0.028 0.001 PHE A 529 TRP 0.020 0.002 TRP E 122 HIS 0.004 0.001 HIS A 596 Details of bonding type rmsd covalent geometry : bond 0.00378 (14709) covalent geometry : angle 0.56510 (19778) hydrogen bonds : bond 0.06117 ( 773) hydrogen bonds : angle 4.16911 ( 2229) *********************** 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 160 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 TYR cc_start: 0.6488 (m-10) cc_final: 0.6141 (m-80) REVERT: B 83 ARG cc_start: 0.8151 (ttm-80) cc_final: 0.7790 (ttm170) outliers start: 21 outliers final: 15 residues processed: 150 average time/residue: 0.1228 time to fit residues: 27.3658 Evaluate side-chains 149 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 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 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 104 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 41 optimal weight: 30.0000 chunk 89 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 86 optimal weight: 0.4980 chunk 69 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** 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 = 0.4505 r_free = 0.4505 target = 0.228289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.195634 restraints weight = 18826.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.192886 restraints weight = 35009.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.189139 restraints weight = 34036.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.185751 restraints weight = 37728.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.182611 restraints weight = 37097.205| |-----------------------------------------------------------------------------| r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.1745 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= 0.122 Angle : 0.540 9.667 19778 Z= 0.271 Chirality : 0.041 0.238 2246 Planarity : 0.003 0.036 2468 Dihedral : 10.334 171.835 2018 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.92 % Allowed : 13.82 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.21), residues: 1779 helix: 1.52 (0.17), residues: 1017 sheet: -0.82 (0.41), residues: 167 loop : -1.53 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 107 TYR 0.020 0.001 TYR E 151 PHE 0.021 0.001 PHE A 529 TRP 0.013 0.001 TRP E 122 HIS 0.004 0.001 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00264 (14709) covalent geometry : angle 0.54019 (19778) hydrogen bonds : bond 0.05394 ( 773) hydrogen bonds : angle 4.04195 ( 2229) *********************** 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 166 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 TYR cc_start: 0.6402 (m-10) cc_final: 0.6154 (m-80) REVERT: B 83 ARG cc_start: 0.8124 (ttm-80) cc_final: 0.7783 (ttp-170) REVERT: C 71 MET cc_start: 0.3359 (ppp) cc_final: 0.3132 (ppp) REVERT: C 74 MET cc_start: -0.0783 (pmm) cc_final: -0.3143 (tmm) outliers start: 30 outliers final: 15 residues processed: 155 average time/residue: 0.1218 time to fit residues: 28.4494 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 : 0.540 ------------------------------------------------------------------------------- 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 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 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 E residue 308 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 124 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 125 optimal weight: 20.0000 chunk 55 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 76 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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** 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 = 0.4490 r_free = 0.4490 target = 0.226757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.190292 restraints weight = 18727.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.187038 restraints weight = 38365.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.183904 restraints weight = 35866.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.181767 restraints weight = 34722.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.177805 restraints weight = 31641.591| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.1768 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= 0.150 Angle : 0.555 9.192 19778 Z= 0.281 Chirality : 0.042 0.246 2246 Planarity : 0.003 0.037 2468 Dihedral : 10.427 173.648 2018 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.66 % Allowed : 15.23 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.21), residues: 1779 helix: 1.42 (0.17), residues: 1016 sheet: -0.80 (0.41), residues: 165 loop : -1.56 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 107 TYR 0.018 0.001 TYR E 151 PHE 0.027 0.001 PHE A 529 TRP 0.010 0.001 TRP D 122 HIS 0.004 0.001 HIS A 596 Details of bonding type rmsd covalent geometry : bond 0.00352 (14709) covalent geometry : angle 0.55464 (19778) hydrogen bonds : bond 0.06019 ( 773) hydrogen bonds : angle 4.05266 ( 2229) *********************** 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 164 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 TYR cc_start: 0.6598 (m-10) cc_final: 0.6294 (m-80) REVERT: B 83 ARG cc_start: 0.8121 (ttm-80) cc_final: 0.7785 (ttm170) REVERT: E 140 MET cc_start: 0.6224 (pmm) cc_final: 0.5890 (pmm) outliers start: 26 outliers final: 20 residues processed: 154 average time/residue: 0.1213 time to fit residues: 28.0802 Evaluate side-chains 152 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 445 LEU Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain B residue 9 ILE 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 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 141 optimal weight: 50.0000 chunk 12 optimal weight: 0.9990 chunk 112 optimal weight: 0.4980 chunk 73 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 130 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 9 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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** A 510 HIS B 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.228730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.192372 restraints weight = 18565.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.187984 restraints weight = 38442.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.184656 restraints weight = 37309.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.183169 restraints weight = 32441.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.179069 restraints weight = 32615.964| |-----------------------------------------------------------------------------| r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.1957 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= 0.117 Angle : 0.541 11.836 19778 Z= 0.272 Chirality : 0.041 0.262 2246 Planarity : 0.003 0.035 2468 Dihedral : 10.114 171.633 2018 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.41 % Allowed : 16.31 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.21), residues: 1779 helix: 1.57 (0.17), residues: 1023 sheet: -0.69 (0.43), residues: 151 loop : -1.47 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 107 TYR 0.017 0.001 TYR E 151 PHE 0.020 0.001 PHE A 529 TRP 0.008 0.001 TRP E 122 HIS 0.003 0.000 HIS D 134 Details of bonding type rmsd covalent geometry : bond 0.00251 (14709) covalent geometry : angle 0.54097 (19778) hydrogen bonds : bond 0.05172 ( 773) hydrogen bonds : angle 3.92148 ( 2229) *********************** 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 161 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.6412 (mtt) cc_final: 0.6061 (ttm) REVERT: A 315 TYR cc_start: 0.6609 (m-10) cc_final: 0.6352 (m-80) REVERT: A 505 ASN cc_start: 0.7355 (OUTLIER) cc_final: 0.6250 (p0) REVERT: B 83 ARG cc_start: 0.8122 (ttm-80) cc_final: 0.7783 (ttm170) REVERT: C 74 MET cc_start: -0.0554 (pmm) cc_final: -0.3033 (tmm) outliers start: 22 outliers final: 17 residues processed: 152 average time/residue: 0.1257 time to fit residues: 28.6144 Evaluate side-chains 151 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 77 optimal weight: 0.9990 chunk 129 optimal weight: 0.0020 chunk 117 optimal weight: 0.9980 chunk 156 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 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 = 0.4503 r_free = 0.4503 target = 0.228364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.191052 restraints weight = 18789.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.188282 restraints weight = 39350.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.184518 restraints weight = 33725.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.181104 restraints weight = 36359.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.177426 restraints weight = 33115.959| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14709 Z= 0.125 Angle : 0.555 10.591 19778 Z= 0.277 Chirality : 0.041 0.256 2246 Planarity : 0.003 0.036 2468 Dihedral : 10.080 171.577 2018 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.41 % Allowed : 16.38 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.21), residues: 1779 helix: 1.56 (0.17), residues: 1023 sheet: -0.70 (0.42), residues: 151 loop : -1.46 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 107 TYR 0.017 0.001 TYR E 151 PHE 0.023 0.001 PHE A 529 TRP 0.011 0.001 TRP D 122 HIS 0.012 0.001 HIS A 510 Details of bonding type rmsd covalent geometry : bond 0.00279 (14709) covalent geometry : angle 0.55498 (19778) hydrogen bonds : bond 0.05323 ( 773) hydrogen bonds : angle 3.90359 ( 2229) *********************** 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 157 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 TYR cc_start: 0.6608 (m-10) cc_final: 0.6386 (m-80) REVERT: B 83 ARG cc_start: 0.8145 (ttm-80) cc_final: 0.7859 (ttm170) REVERT: C 74 MET cc_start: -0.0632 (pmm) cc_final: -0.3135 (tmm) REVERT: E 92 ARG cc_start: 0.7310 (mmm160) cc_final: 0.7091 (mmm160) outliers start: 22 outliers final: 20 residues processed: 148 average time/residue: 0.1207 time to fit residues: 26.8667 Evaluate side-chains 152 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 95 MET 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 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 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 C residue 136 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 23 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 41 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 160 optimal weight: 8.9990 chunk 144 optimal weight: 0.0060 chunk 117 optimal weight: 0.3980 chunk 14 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 159 optimal weight: 8.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.229343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.192427 restraints weight = 18662.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.188817 restraints weight = 37955.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.185495 restraints weight = 33286.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.184973 restraints weight = 30256.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.183573 restraints weight = 23171.491| |-----------------------------------------------------------------------------| r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.2129 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= 0.114 Angle : 0.556 15.976 19778 Z= 0.274 Chirality : 0.041 0.271 2246 Planarity : 0.003 0.035 2468 Dihedral : 9.896 170.992 2018 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.41 % Allowed : 16.44 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.21), residues: 1779 helix: 1.64 (0.17), residues: 1023 sheet: -0.70 (0.42), residues: 151 loop : -1.41 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 107 TYR 0.016 0.001 TYR E 151 PHE 0.020 0.001 PHE A 529 TRP 0.009 0.001 TRP D 122 HIS 0.004 0.000 HIS A 510 Details of bonding type rmsd covalent geometry : bond 0.00245 (14709) covalent geometry : angle 0.55599 (19778) hydrogen bonds : bond 0.04990 ( 773) hydrogen bonds : angle 3.83509 ( 2229) ********************** 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 161 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 ASN cc_start: 0.7108 (OUTLIER) cc_final: 0.6083 (p0) REVERT: C 74 MET cc_start: -0.0439 (pmm) cc_final: -0.2975 (tmm) REVERT: E 92 ARG cc_start: 0.7268 (mmm160) cc_final: 0.7064 (mmm160) outliers start: 22 outliers final: 21 residues processed: 153 average time/residue: 0.1143 time to fit residues: 26.5830 Evaluate side-chains 158 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 95 MET 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 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 94 TYR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain D residue 7 ILE 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 58 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 135 optimal weight: 10.0000 chunk 168 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 159 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 38 optimal weight: 20.0000 chunk 6 optimal weight: 0.9990 chunk 172 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 HIS D 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.223973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.187276 restraints weight = 18601.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.184156 restraints weight = 39082.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.178855 restraints weight = 32204.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.175692 restraints weight = 37292.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.172079 restraints weight = 36891.431| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 14709 Z= 0.245 Angle : 0.687 18.731 19778 Z= 0.343 Chirality : 0.045 0.254 2246 Planarity : 0.004 0.039 2468 Dihedral : 10.584 170.125 2018 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.54 % Allowed : 16.25 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.21), residues: 1779 helix: 1.13 (0.17), residues: 1023 sheet: -0.67 (0.42), residues: 146 loop : -1.49 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 107 TYR 0.030 0.002 TYR A 311 PHE 0.034 0.002 PHE A 529 TRP 0.010 0.002 TRP E 54 HIS 0.007 0.001 HIS A 510 Details of bonding type rmsd covalent geometry : bond 0.00607 (14709) covalent geometry : angle 0.68736 (19778) hydrogen bonds : bond 0.07385 ( 773) hydrogen bonds : angle 4.19737 ( 2229) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2154.55 seconds wall clock time: 38 minutes 8.52 seconds (2288.52 seconds total)