Starting phenix.real_space_refine on Fri Jul 3 15:12:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8g3a_29690/07_2026/8g3a_29690.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3a_29690/07_2026/8g3a_29690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g3a_29690/07_2026/8g3a_29690.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3a_29690/07_2026/8g3a_29690.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8g3a_29690/07_2026/8g3a_29690.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8g3a_29690/07_2026/8g3a_29690.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g3a_29690/07_2026/8g3a_29690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3a_29690/07_2026/8g3a_29690.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 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 Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 3.35, per 1000 atoms: 0.23 Number of scatterers: 14442 At special positions: 0 Unit cell: (106.384, 116.848, 199.688, 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: 1.28 Conformation dependent library (CDL) restraints added in 611.0 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: 77 helices and 11 sheets defined 61.6% alpha, 9.5% 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: 3.743A pdb=" N ARG A 16 " --> pdb=" O LYS A 12 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN A 17 " --> pdb=" O LYS A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 40 removed outlier: 3.939A pdb=" N VAL A 22 " --> pdb=" O TYR A 18 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 47 removed outlier: 4.074A pdb=" N ASN A 45 " --> pdb=" O PRO A 42 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A 46 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 47 " --> pdb=" O ILE A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 81 removed outlier: 3.518A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 66 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 71 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 73 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE A 80 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 94 removed outlier: 3.590A pdb=" N ILE A 87 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 89 " --> pdb=" O LYS A 85 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY A 94 " --> pdb=" O PHE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 105 removed outlier: 4.069A pdb=" N ILE A 100 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ARG A 102 " --> pdb=" O HIS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 126 removed outlier: 3.598A pdb=" N ALA A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.651A pdb=" N LEU A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS A 136 " --> pdb=" O MET A 132 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 178 removed outlier: 3.731A pdb=" N VAL A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 220 removed outlier: 3.919A pdb=" N MET A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 219 " --> pdb=" O GLY A 215 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 254 removed outlier: 3.802A pdb=" N VAL A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR A 252 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A 253 " --> pdb=" O PHE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 265 removed outlier: 4.021A pdb=" N ILE A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 290 through 325 removed outlier: 3.506A pdb=" N THR A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TYR A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR A 315 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 346 removed outlier: 3.654A pdb=" N GLU A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.854A pdb=" N MET A 369 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 382 Processing helix chain 'A' and resid 409 through 416 removed outlier: 3.604A pdb=" N LYS A 414 " --> pdb=" O ASP A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 472 removed outlier: 3.688A pdb=" N GLN A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 505 removed outlier: 4.151A pdb=" N ALA A 497 " --> pdb=" O GLN A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 557 removed outlier: 3.747A pdb=" N LYS A 549 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN A 550 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET A 551 " --> pdb=" O TYR A 547 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY A 552 " --> pdb=" O PHE A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 565 Processing helix chain 'A' and resid 570 through 602 removed outlier: 4.065A pdb=" N LYS A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE A 580 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 581 " --> pdb=" O GLY A 577 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE A 586 " --> pdb=" O GLN A 582 " (cutoff:3.500A) removed outlier: 3.919A 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 603 through 605 No H-bonds generated for 'chain 'A' and resid 603 through 605' Processing helix chain 'A' and resid 614 through 633 removed outlier: 4.100A pdb=" N MET A 618 " --> pdb=" O ALA A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 644 removed outlier: 3.940A pdb=" N LYS A 640 " --> pdb=" O LEU A 636 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A 644 " --> pdb=" O LYS A 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 101 through 106 removed outlier: 3.659A pdb=" N ILE B 106 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 113 removed outlier: 4.061A pdb=" N ILE B 112 " --> pdb=" O PRO B 109 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR B 113 " --> pdb=" O LEU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 133 through 137 removed outlier: 4.095A pdb=" N ARG B 137 " --> pdb=" O TYR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 144 removed outlier: 3.786A pdb=" N ILE B 144 " --> pdb=" O PRO B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 159 removed outlier: 3.744A pdb=" N SER B 153 " --> pdb=" O LYS B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 193 Processing helix chain 'B' and resid 203 through 209 removed outlier: 4.085A pdb=" N TYR B 209 " --> pdb=" O VAL B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 246 Processing helix chain 'C' and resid 45 through 54 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 101 through 108 removed outlier: 3.920A pdb=" N ILE C 106 " --> pdb=" O VAL C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 112 removed outlier: 4.054A pdb=" N ILE C 112 " --> pdb=" O PRO C 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 109 through 112' Processing helix chain 'C' and resid 116 through 132 removed outlier: 3.711A pdb=" N ALA C 120 " --> pdb=" O SER C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 157 removed outlier: 3.651A pdb=" N LYS C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 193 removed outlier: 3.573A pdb=" N GLN C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS C 192 " --> pdb=" O GLN C 188 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 208 Processing helix chain 'C' and resid 233 through 246 removed outlier: 3.794A pdb=" N LEU C 246 " --> pdb=" O THR C 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 9 Processing helix chain 'D' and resid 12 through 29 Processing helix chain 'D' and resid 34 through 61 removed outlier: 4.033A pdb=" N VAL D 38 " --> pdb=" O SER D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 72 removed outlier: 4.401A pdb=" N ASN D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 79 removed outlier: 4.155A pdb=" N ILE D 79 " --> pdb=" O VAL D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 138 removed outlier: 3.760A pdb=" N ALA D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N VAL D 90 " --> pdb=" O PHE D 86 " (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: 5.490A pdb=" N GLU D 173 " --> pdb=" O SER D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 194 Processing helix chain 'D' and resid 194 through 202 removed outlier: 3.505A pdb=" N CYS D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 236 Processing helix chain 'D' and resid 264 through 271 Proline residue: D 269 - end of helix Processing helix chain 'D' and resid 281 through 285 removed outlier: 3.526A pdb=" N ASP D 284 " --> pdb=" O ASP D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 300 removed outlier: 3.579A pdb=" N ALA D 300 " --> pdb=" O LYS D 296 " (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 9 through 30 removed outlier: 4.329A pdb=" N ILE E 13 " --> pdb=" O ARG E 9 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA E 14 " --> pdb=" O ARG E 10 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA E 15 " --> pdb=" O SER E 11 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE E 16 " --> pdb=" O TRP E 12 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL E 29 " --> pdb=" O PHE E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 61 removed outlier: 4.065A pdb=" N ARG E 58 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS E 59 " --> pdb=" O PHE E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 72 removed outlier: 3.762A pdb=" N LYS E 68 " --> pdb=" O TYR E 64 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ASN E 72 " --> pdb=" O LYS E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 138 Proline residue: E 129 - end of helix Processing helix chain 'E' and resid 143 through 169 Processing helix chain 'E' and resid 170 through 175 removed outlier: 5.281A pdb=" N GLU E 173 " --> pdb=" O SER E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 194 Processing helix chain 'E' and resid 194 through 202 Processing helix chain 'E' and resid 218 through 235 Processing helix chain 'E' and resid 267 through 271 Processing helix chain 'E' and resid 281 through 286 removed outlier: 3.586A pdb=" N ALA E 286 " --> pdb=" O HIS E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 300 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: 3.700A pdb=" N LEU A 511 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 359 through 364 removed outlier: 3.591A pdb=" N MET A 383 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N VAL A 458 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA A 386 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA A 457 " --> pdb=" O SER A 406 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA A 403 " --> pdb=" O TYR A 437 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLY A 439 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 425 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 19 through 26 removed outlier: 6.321A pdb=" N LYS B 11 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LYS B 24 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ILE B 9 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ILE B 26 " --> pdb=" O ASN B 7 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ASN B 7 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B 63 " --> pdb=" O ASN B 7 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE B 9 " --> pdb=" O HIS B 61 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N HIS B 61 " --> pdb=" O ILE B 9 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 89 through 90 removed outlier: 3.548A pdb=" N MET B 199 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG B 212 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL B 213 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 6 through 10 removed outlier: 5.213A pdb=" N ILE C 9 " --> pdb=" O HIS C 61 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N HIS C 61 " --> pdb=" O ILE C 9 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 37 through 40 removed outlier: 7.093A pdb=" N SER C 37 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ILE C 216 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N MET C 39 " --> pdb=" O ILE C 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 87 through 90 removed outlier: 6.179A pdb=" N GLY C 88 " --> pdb=" O PHE C 166 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 167 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 179 through 182 Processing sheet with id=AA9, first strand: chain 'D' and resid 204 through 209 removed outlier: 6.738A pdb=" N GLY D 204 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ILE D 243 " --> pdb=" O GLY D 204 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASP D 206 " --> pdb=" O ILE D 243 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N SER D 245 " --> pdb=" O ASP D 206 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N GLN D 208 " --> pdb=" O SER D 245 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N GLN D 247 " --> pdb=" O GLN D 208 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 178 through 182 removed outlier: 3.748A pdb=" N SER E 216 " --> pdb=" O GLU E 179 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 205 through 209 removed outlier: 5.851A pdb=" N ASP E 206 " --> pdb=" O ILE E 243 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N SER E 245 " --> pdb=" O ASP E 206 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLN E 208 " --> pdb=" O SER E 245 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N GLN E 247 " --> pdb=" O GLN E 208 " (cutoff:3.500A) 790 hydrogen bonds defined for protein. 2277 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: 2.49 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2342 1.32 - 1.44: 3764 1.44 - 1.56: 8463 1.56 - 1.69: 26 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 4.74e+01 bond pdb=" C16 6OU A 702 " pdb=" O18 6OU A 702 " ideal model delta sigma weight residual 1.327 1.462 -0.135 2.00e-02 2.50e+03 4.56e+01 bond pdb=" C16 6OU A 703 " pdb=" O18 6OU A 703 " ideal model delta sigma weight residual 1.327 1.461 -0.134 2.00e-02 2.50e+03 4.50e+01 bond pdb=" C31 6OU A 703 " pdb=" O30 6OU A 703 " ideal model delta sigma weight residual 1.331 1.424 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" C14 6OU A 702 " pdb=" C15 6OU A 702 " ideal model delta sigma weight residual 1.521 1.608 -0.087 2.00e-02 2.50e+03 1.90e+01 ... (remaining 14704 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.02: 19730 5.02 - 10.04: 41 10.04 - 15.06: 3 15.06 - 20.07: 2 20.07 - 25.09: 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 127.56 152.65 -25.09 3.00e+00 1.11e-01 7.00e+01 angle pdb=" C40 6OU A 703 " pdb=" C41 6OU A 703 " pdb=" C42 6OU A 703 " ideal model delta sigma weight residual 127.56 152.26 -24.70 3.00e+00 1.11e-01 6.78e+01 angle pdb=" O22 6OU A 702 " pdb=" P23 6OU A 702 " pdb=" O26 6OU A 702 " ideal model delta sigma weight residual 93.95 111.25 -17.30 3.00e+00 1.11e-01 3.33e+01 angle pdb=" C39 6OU A 702 " pdb=" C40 6OU A 702 " pdb=" C41 6OU A 702 " ideal model delta sigma weight residual 127.60 112.20 15.40 3.00e+00 1.11e-01 2.64e+01 angle pdb=" C39 6OU A 703 " pdb=" C40 6OU A 703 " pdb=" C41 6OU A 703 " ideal model delta sigma weight residual 127.60 112.92 14.68 3.00e+00 1.11e-01 2.39e+01 ... (remaining 19773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.60: 8370 25.60 - 51.20: 442 51.20 - 76.79: 53 76.79 - 102.39: 13 102.39 - 127.99: 1 Dihedral angle restraints: 8879 sinusoidal: 3667 harmonic: 5212 Sorted by residual: dihedral pdb=" CA ILE A 282 " pdb=" C ILE A 282 " pdb=" N MET A 283 " pdb=" CA MET A 283 " ideal model delta harmonic sigma weight residual 180.00 158.57 21.43 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" C07 6OU A 702 " pdb=" C08 6OU A 702 " pdb=" C09 6OU A 702 " pdb=" C10 6OU A 702 " ideal model delta sinusoidal sigma weight residual 179.90 -52.11 -127.99 1 3.00e+01 1.11e-03 1.72e+01 dihedral pdb=" CA TRP E 70 " pdb=" C TRP E 70 " pdb=" N GLU E 71 " pdb=" CA GLU E 71 " ideal model delta harmonic sigma weight residual -180.00 -159.30 -20.70 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 8876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1884 0.054 - 0.108: 309 0.108 - 0.162: 51 0.162 - 0.216: 1 0.216 - 0.270: 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 2.62 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CB ILE B 112 " pdb=" CA ILE B 112 " pdb=" CG1 ILE B 112 " pdb=" CG2 ILE B 112 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.71e-01 chirality pdb=" CB THR A 541 " pdb=" CA THR A 541 " pdb=" OG1 THR A 541 " pdb=" CG2 THR A 541 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 2243 not shown) Planarity restraints: 2468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA E 401 " 0.177 2.00e-02 2.50e+03 1.38e-01 1.89e+02 pdb=" C11 OLA E 401 " -0.081 2.00e-02 2.50e+03 pdb=" C8 OLA E 401 " 0.081 2.00e-02 2.50e+03 pdb=" C9 OLA E 401 " -0.177 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR E 128 " 0.040 5.00e-02 4.00e+02 6.03e-02 5.81e+00 pdb=" N PRO E 129 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO E 129 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 129 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 84 " 0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO E 85 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO E 85 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 85 " 0.020 5.00e-02 4.00e+02 ... (remaining 2465 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 135 2.65 - 3.21: 12976 3.21 - 3.78: 20564 3.78 - 4.34: 27215 4.34 - 4.90: 45915 Nonbonded interactions: 106805 Sorted by model distance: nonbonded pdb=" OG1 THR A 451 " pdb=" O MET A 455 " model vdw 2.088 3.040 nonbonded pdb=" OE2 GLU A 555 " pdb=" OH TYR A 637 " model vdw 2.210 3.040 nonbonded pdb=" NE2 GLN A 91 " pdb=" OG SER A 179 " model vdw 2.210 3.120 nonbonded pdb=" O SER A 125 " pdb=" OH TYR E 40 " model vdw 2.224 3.040 nonbonded pdb=" O ALA E 211 " pdb=" OG SER E 245 " model vdw 2.233 3.040 ... (remaining 106800 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 individual isotropic 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: 4.300 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.510 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 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 : 0.005 0.138 14709 Z= 0.231 Angle : 0.720 25.093 19778 Z= 0.341 Chirality : 0.041 0.270 2246 Planarity : 0.004 0.138 2468 Dihedral : 15.302 127.990 5505 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.85 % Favored : 94.04 % Rotamer: Outliers : 0.06 % Allowed : 0.26 % Favored : 99.68 % 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: 0.42 (0.21), residues: 1779 helix: 1.62 (0.17), residues: 1005 sheet: -0.22 (0.42), residues: 188 loop : -1.99 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 137 TYR 0.019 0.001 TYR A 314 PHE 0.024 0.001 PHE D 63 TRP 0.015 0.001 TRP E 70 HIS 0.005 0.001 HIS A 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.23 (14709) covalent geometry : angle 0.72027 / 0.34 (19778) hydrogen bonds : bond 0.15904 / 10.09 ( 790) hydrogen bonds : angle 5.06568 / 3.63 ( 2277) *********************** 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 150 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 0.471 Fit side-chains REVERT: A 332 MET cc_start: 0.6674 (ppp) cc_final: 0.5684 (ppp) outliers start: 1 outliers final: 0 residues processed: 150 average time/residue: 0.1043 time to fit residues: 23.8687 Evaluate side-chains 118 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.1980 chunk 103 optimal weight: 0.0040 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 GLN A 510 HIS B 61 HIS C 86 HIS ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.245517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.196769 restraints weight = 18152.183| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 3.04 r_work: 0.3812 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14709 Z= 0.143 Angle : 0.536 7.252 19778 Z= 0.283 Chirality : 0.041 0.155 2246 Planarity : 0.003 0.058 2468 Dihedral : 8.483 113.154 1996 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.35 % Favored : 93.54 % Rotamer: Outliers : 1.02 % Allowed : 6.40 % Favored : 92.58 % 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: 0.69 (0.21), residues: 1779 helix: 1.86 (0.17), residues: 999 sheet: 0.09 (0.43), residues: 177 loop : -1.93 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 137 TYR 0.012 0.001 TYR E 43 PHE 0.017 0.001 PHE A 529 TRP 0.012 0.001 TRP E 70 HIS 0.006 0.001 HIS A 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (14709) covalent geometry : angle 0.53613 / 0.28 (19778) hydrogen bonds : bond 0.06058 / 3.97 ( 790) hydrogen bonds : angle 4.19553 / 2.98 ( 2277) *********************** 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 144 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.424 Fit side-chains REVERT: A 332 MET cc_start: 0.6596 (ppp) cc_final: 0.5409 (ppp) outliers start: 16 outliers final: 10 residues processed: 134 average time/residue: 0.0981 time to fit residues: 20.7559 Evaluate side-chains 129 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 101 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 122 optimal weight: 9.9990 chunk 162 optimal weight: 6.9990 chunk 140 optimal weight: 8.9990 chunk 115 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 89 optimal weight: 0.0170 chunk 151 optimal weight: 0.4980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 510 HIS B 61 HIS ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.247724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.200549 restraints weight = 18643.621| |-----------------------------------------------------------------------------| r_work (start): 0.4222 rms_B_bonded: 2.93 r_work: 0.3837 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1139 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= 0.111 Angle : 0.482 7.173 19778 Z= 0.253 Chirality : 0.039 0.144 2246 Planarity : 0.003 0.055 2468 Dihedral : 7.753 90.388 1996 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.73 % Favored : 94.15 % Rotamer: Outliers : 1.34 % Allowed : 8.00 % Favored : 90.66 % 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: 0.89 (0.21), residues: 1779 helix: 2.04 (0.17), residues: 999 sheet: -0.02 (0.42), residues: 189 loop : -1.86 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 137 TYR 0.011 0.001 TYR D 64 PHE 0.029 0.001 PHE D 63 TRP 0.011 0.001 TRP E 70 HIS 0.003 0.000 HIS A 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (14709) covalent geometry : angle 0.48152 / 0.25 (19778) hydrogen bonds : bond 0.05154 / 3.37 ( 790) hydrogen bonds : angle 3.90397 / 2.76 ( 2277) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.373 Fit side-chains REVERT: A 181 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6983 (tt) REVERT: A 314 TYR cc_start: 0.6523 (OUTLIER) cc_final: 0.6069 (m-10) REVERT: A 332 MET cc_start: 0.6559 (ppp) cc_final: 0.5285 (ppp) REVERT: D 7 ILE cc_start: 0.8468 (tt) cc_final: 0.8174 (tt) REVERT: E 33 ILE cc_start: 0.7876 (mt) cc_final: 0.7607 (mm) outliers start: 21 outliers final: 14 residues processed: 144 average time/residue: 0.0868 time to fit residues: 20.2083 Evaluate side-chains 141 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 MET Chi-restraints excluded: chain E residue 79 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 13 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 4 optimal weight: 0.6980 chunk 167 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 89 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 510 HIS ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.245504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.196684 restraints weight = 18407.702| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 2.96 r_work: 0.3829 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 14709 Z= 0.115 Angle : 0.477 7.315 19778 Z= 0.250 Chirality : 0.039 0.141 2246 Planarity : 0.003 0.054 2468 Dihedral : 7.438 82.924 1996 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.18 % Favored : 93.70 % Rotamer: Outliers : 1.47 % Allowed : 10.43 % Favored : 88.10 % 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: 0.92 (0.21), residues: 1779 helix: 2.08 (0.17), residues: 1005 sheet: -0.02 (0.42), residues: 189 loop : -1.90 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 156 TYR 0.012 0.001 TYR E 57 PHE 0.018 0.001 PHE A 258 TRP 0.009 0.001 TRP E 70 HIS 0.004 0.000 HIS A 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (14709) covalent geometry : angle 0.47710 / 0.25 (19778) hydrogen bonds : bond 0.05165 / 3.39 ( 790) hydrogen bonds : angle 3.79494 / 2.68 ( 2277) *********************** 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 154 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.551 Fit side-chains REVERT: A 35 PHE cc_start: 0.8871 (OUTLIER) cc_final: 0.8369 (m-10) REVERT: A 181 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.7079 (tt) REVERT: A 314 TYR cc_start: 0.6680 (OUTLIER) cc_final: 0.6195 (m-10) REVERT: A 332 MET cc_start: 0.6723 (ppp) cc_final: 0.5430 (ppp) REVERT: D 63 PHE cc_start: 0.7592 (t80) cc_final: 0.7366 (t80) REVERT: E 33 ILE cc_start: 0.7887 (mt) cc_final: 0.7603 (mm) outliers start: 23 outliers final: 15 residues processed: 141 average time/residue: 0.0871 time to fit residues: 19.6065 Evaluate side-chains 142 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 MET Chi-restraints excluded: chain E residue 79 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 64 optimal weight: 9.9990 chunk 101 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 161 optimal weight: 30.0000 chunk 104 optimal weight: 0.7980 chunk 162 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 GLN A 510 HIS ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.241862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.192547 restraints weight = 18187.141| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 2.66 r_work: 0.3830 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3751 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14709 Z= 0.169 Angle : 0.526 7.557 19778 Z= 0.276 Chirality : 0.041 0.144 2246 Planarity : 0.003 0.054 2468 Dihedral : 7.426 70.188 1996 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.41 % Favored : 93.48 % Rotamer: Outliers : 1.86 % Allowed : 11.58 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.76 (0.21), residues: 1779 helix: 1.92 (0.17), residues: 1011 sheet: -0.16 (0.42), residues: 192 loop : -1.93 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 156 TYR 0.014 0.001 TYR E 43 PHE 0.020 0.001 PHE A 529 TRP 0.011 0.001 TRP E 70 HIS 0.007 0.001 HIS A 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (14709) covalent geometry : angle 0.52591 / 0.28 (19778) hydrogen bonds : bond 0.06466 / 4.27 ( 790) hydrogen bonds : angle 3.94965 / 2.80 ( 2277) *********************** 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 145 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.490 Fit side-chains REVERT: A 8 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8356 (mp) REVERT: A 35 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8274 (m-10) REVERT: A 314 TYR cc_start: 0.7211 (OUTLIER) cc_final: 0.6474 (m-10) REVERT: A 332 MET cc_start: 0.6674 (ppp) cc_final: 0.5311 (ppp) REVERT: A 574 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8031 (mp) REVERT: D 63 PHE cc_start: 0.7739 (t80) cc_final: 0.7528 (t80) outliers start: 29 outliers final: 16 residues processed: 135 average time/residue: 0.0965 time to fit residues: 20.5032 Evaluate side-chains 134 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 MET Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 79 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 104 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 510 HIS ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.241557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.196577 restraints weight = 18112.177| |-----------------------------------------------------------------------------| r_work (start): 0.4204 rms_B_bonded: 2.56 r_work: 0.3830 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3710 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14709 Z= 0.175 Angle : 0.538 13.613 19778 Z= 0.281 Chirality : 0.041 0.144 2246 Planarity : 0.003 0.054 2468 Dihedral : 7.369 68.873 1996 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.46 % Favored : 93.42 % Rotamer: Outliers : 1.66 % Allowed : 12.86 % Favored : 85.48 % 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: 0.69 (0.21), residues: 1779 helix: 1.89 (0.17), residues: 1010 sheet: -0.18 (0.42), residues: 192 loop : -2.00 (0.24), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 156 TYR 0.014 0.001 TYR E 43 PHE 0.020 0.001 PHE A 529 TRP 0.010 0.001 TRP E 70 HIS 0.006 0.001 HIS A 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 (14709) covalent geometry : angle 0.53800 / 0.28 (19778) hydrogen bonds : bond 0.06394 / 4.21 ( 790) hydrogen bonds : angle 3.93461 / 2.79 ( 2277) *********************** 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 141 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.343 Fit side-chains REVERT: A 8 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8322 (mp) REVERT: A 35 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.8266 (m-10) REVERT: A 314 TYR cc_start: 0.7338 (OUTLIER) cc_final: 0.6494 (m-80) REVERT: A 332 MET cc_start: 0.6652 (ppp) cc_final: 0.5379 (ppp) REVERT: A 574 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8008 (mp) REVERT: D 7 ILE cc_start: 0.8646 (tt) cc_final: 0.8358 (tt) outliers start: 26 outliers final: 18 residues processed: 131 average time/residue: 0.0910 time to fit residues: 18.8855 Evaluate side-chains 134 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 MET Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 79 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 124 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 125 optimal weight: 40.0000 chunk 55 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 510 HIS ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.243028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.198718 restraints weight = 18071.086| |-----------------------------------------------------------------------------| r_work (start): 0.4222 rms_B_bonded: 2.56 r_work: 0.3850 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3737 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1624 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= 0.139 Angle : 0.512 7.908 19778 Z= 0.267 Chirality : 0.040 0.141 2246 Planarity : 0.003 0.053 2468 Dihedral : 7.256 67.436 1996 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.30 % Favored : 93.59 % Rotamer: Outliers : 1.79 % Allowed : 12.99 % 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: 0.80 (0.21), residues: 1779 helix: 1.99 (0.17), residues: 1010 sheet: -0.16 (0.42), residues: 192 loop : -1.98 (0.24), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 156 TYR 0.011 0.001 TYR E 43 PHE 0.018 0.001 PHE A 351 TRP 0.008 0.001 TRP E 70 HIS 0.005 0.001 HIS A 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (14709) covalent geometry : angle 0.51209 / 0.27 (19778) hydrogen bonds : bond 0.05860 / 3.85 ( 790) hydrogen bonds : angle 3.83103 / 2.71 ( 2277) *********************** 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 144 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.346 Fit side-chains REVERT: A 8 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8266 (mp) REVERT: A 35 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.8322 (m-10) REVERT: A 314 TYR cc_start: 0.7347 (OUTLIER) cc_final: 0.6483 (m-80) REVERT: A 332 MET cc_start: 0.6537 (ppp) cc_final: 0.5272 (ppp) REVERT: A 574 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8032 (mp) outliers start: 28 outliers final: 22 residues processed: 133 average time/residue: 0.0984 time to fit residues: 20.5552 Evaluate side-chains 137 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 MET Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 79 ILE 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: 1.9990 chunk 112 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 130 optimal weight: 30.0000 chunk 64 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 510 HIS ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.243506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.199640 restraints weight = 17978.888| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 2.56 r_work: 0.3854 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3699 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14709 Z= 0.129 Angle : 0.497 7.373 19778 Z= 0.260 Chirality : 0.039 0.150 2246 Planarity : 0.003 0.053 2468 Dihedral : 7.019 65.960 1996 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.01 % Favored : 93.87 % Rotamer: Outliers : 1.79 % Allowed : 13.37 % Favored : 84.84 % 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: 0.87 (0.21), residues: 1779 helix: 2.05 (0.17), residues: 1010 sheet: -0.14 (0.42), residues: 192 loop : -1.95 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 156 TYR 0.011 0.001 TYR E 43 PHE 0.018 0.001 PHE A 351 TRP 0.008 0.001 TRP A 613 HIS 0.004 0.001 HIS E 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (14709) covalent geometry : angle 0.49699 / 0.26 (19778) hydrogen bonds : bond 0.05581 / 3.66 ( 790) hydrogen bonds : angle 3.77122 / 2.66 ( 2277) *********************** 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 142 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.369 Fit side-chains REVERT: A 8 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8231 (mp) REVERT: A 35 PHE cc_start: 0.8896 (OUTLIER) cc_final: 0.8315 (m-10) REVERT: A 314 TYR cc_start: 0.7360 (OUTLIER) cc_final: 0.6554 (m-80) REVERT: A 332 MET cc_start: 0.6584 (ppp) cc_final: 0.5318 (ppp) REVERT: A 574 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8026 (mp) REVERT: E 47 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7926 (mt) outliers start: 28 outliers final: 23 residues processed: 131 average time/residue: 0.0939 time to fit residues: 19.7136 Evaluate side-chains 140 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 MET Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 79 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 77 optimal weight: 1.9990 chunk 129 optimal weight: 8.9990 chunk 117 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 chunk 21 optimal weight: 0.2980 chunk 106 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 15 optimal weight: 0.0980 chunk 133 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 510 HIS ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.243417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.199870 restraints weight = 18201.805| |-----------------------------------------------------------------------------| r_work (start): 0.4227 rms_B_bonded: 2.56 r_work: 0.3867 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3736 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14709 Z= 0.136 Angle : 0.501 7.920 19778 Z= 0.261 Chirality : 0.040 0.160 2246 Planarity : 0.003 0.053 2468 Dihedral : 6.932 65.103 1996 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.07 % Favored : 93.82 % Rotamer: Outliers : 2.18 % Allowed : 12.99 % Favored : 84.84 % 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: 0.88 (0.21), residues: 1779 helix: 2.04 (0.17), residues: 1012 sheet: -0.14 (0.42), residues: 192 loop : -1.92 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 156 TYR 0.011 0.001 TYR E 43 PHE 0.018 0.001 PHE A 529 TRP 0.007 0.001 TRP E 70 HIS 0.004 0.001 HIS A 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (14709) covalent geometry : angle 0.50121 / 0.26 (19778) hydrogen bonds : bond 0.05646 / 3.71 ( 790) hydrogen bonds : angle 3.75998 / 2.66 ( 2277) *********************** 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 148 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 114 time to evaluate : 0.426 Fit side-chains REVERT: A 8 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8243 (mp) REVERT: A 35 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.8323 (m-10) REVERT: A 314 TYR cc_start: 0.7401 (OUTLIER) cc_final: 0.6548 (m-80) REVERT: A 332 MET cc_start: 0.6589 (ppp) cc_final: 0.5322 (ppp) REVERT: A 376 MET cc_start: 0.4280 (mpp) cc_final: 0.4060 (mpp) REVERT: A 574 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7998 (mp) REVERT: E 47 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7916 (mt) outliers start: 34 outliers final: 27 residues processed: 136 average time/residue: 0.0931 time to fit residues: 20.3976 Evaluate side-chains 144 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 MET Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 79 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 23 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 160 optimal weight: 0.0070 chunk 144 optimal weight: 0.0270 chunk 117 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 65 optimal weight: 0.1980 chunk 159 optimal weight: 5.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 510 HIS D 97 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.246718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.201971 restraints weight = 18445.582| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 2.65 r_work: 0.3784 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 14709 Z= 0.102 Angle : 0.478 8.849 19778 Z= 0.248 Chirality : 0.039 0.168 2246 Planarity : 0.003 0.052 2468 Dihedral : 6.503 70.030 1996 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.40 % Favored : 94.44 % Rotamer: Outliers : 1.66 % Allowed : 13.44 % Favored : 84.90 % 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: 1.11 (0.21), residues: 1779 helix: 2.23 (0.17), residues: 1012 sheet: 0.01 (0.42), residues: 189 loop : -1.86 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 156 TYR 0.009 0.001 TYR D 64 PHE 0.015 0.001 PHE A 351 TRP 0.010 0.001 TRP A 613 HIS 0.005 0.000 HIS E 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.10 (14709) covalent geometry : angle 0.47771 / 0.25 (19778) hydrogen bonds : bond 0.04574 / 2.99 ( 790) hydrogen bonds : angle 3.57432 / 2.52 ( 2277) ********************** 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 148 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.615 Fit side-chains REVERT: A 8 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8082 (mp) REVERT: A 35 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.8427 (m-10) REVERT: A 314 TYR cc_start: 0.7070 (OUTLIER) cc_final: 0.6345 (m-10) REVERT: A 332 MET cc_start: 0.6761 (ppp) cc_final: 0.5444 (ppp) REVERT: A 574 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7893 (mp) REVERT: D 55 PHE cc_start: 0.6896 (OUTLIER) cc_final: 0.6135 (t80) REVERT: E 47 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7792 (mt) outliers start: 26 outliers final: 19 residues processed: 137 average time/residue: 0.0996 time to fit residues: 21.8398 Evaluate side-chains 140 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 57 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 58 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 135 optimal weight: 20.0000 chunk 168 optimal weight: 20.0000 chunk 25 optimal weight: 0.9980 chunk 159 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 38 optimal weight: 0.0980 chunk 6 optimal weight: 1.9990 chunk 172 optimal weight: 30.0000 chunk 50 optimal weight: 0.0770 overall best weight: 0.5140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 510 HIS C 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.249196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.200645 restraints weight = 18615.486| |-----------------------------------------------------------------------------| r_work (start): 0.4220 rms_B_bonded: 2.95 r_work: 0.3747 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 14709 Z= 0.103 Angle : 0.469 8.913 19778 Z= 0.243 Chirality : 0.039 0.171 2246 Planarity : 0.003 0.052 2468 Dihedral : 6.159 73.003 1996 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.23 % Favored : 94.60 % Rotamer: Outliers : 1.60 % Allowed : 13.69 % Favored : 84.71 % 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: 1.21 (0.21), residues: 1779 helix: 2.31 (0.17), residues: 1013 sheet: 0.06 (0.42), residues: 189 loop : -1.83 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 156 TYR 0.011 0.001 TYR A 164 PHE 0.019 0.001 PHE A 351 TRP 0.007 0.001 TRP A 613 HIS 0.004 0.000 HIS E 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (14709) covalent geometry : angle 0.46908 / 0.24 (19778) hydrogen bonds : bond 0.04595 / 3.02 ( 790) hydrogen bonds : angle 3.49359 / 2.47 ( 2277) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3166.96 seconds wall clock time: 55 minutes 4.50 seconds (3304.50 seconds total)