Starting phenix.real_space_refine on Fri Jun 13 06:19:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g3a_29690/06_2025/8g3a_29690.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3a_29690/06_2025/8g3a_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8g3a_29690/06_2025/8g3a_29690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3a_29690/06_2025/8g3a_29690.map" model { file = "/net/cci-nas-00/data/ceres_data/8g3a_29690/06_2025/8g3a_29690.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3a_29690/06_2025/8g3a_29690.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14442 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 5000 Classifications: {'peptide': 635} Link IDs: {'PTRANS': 10, 'TRANS': 624} Chain breaks: 1 Chain: "B" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1915 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "C" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1915 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "D" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2738 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 324} Chain: "E" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2738 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 324} Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 116 Unusual residues: {'6OU': 2, 'PLM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'OLA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.17, per 1000 atoms: 0.63 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: 3.49 Conformation dependent library (CDL) restraints added in 1.9 seconds 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3374 Finding SS restraints... Secondary structure from input PDB file: 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: 1.52 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: 4.75 Time building geometry restraints manager: 4.14 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 - 33.00: 8606 33.00 - 66.00: 256 66.00 - 99.00: 35 99.00 - 132.00: 1 132.00 - 165.00: 3 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 47.33 165.00 1 3.00e+01 1.11e-03 2.10e+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 -76.72 162.21 1 3.00e+01 1.11e-03 2.08e+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 301.00 157.38 143.62 1 3.00e+01 1.11e-03 1.93e+01 ... (remaining 8898 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: 3.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 34.960 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 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 : 15.963 165.000 5527 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.21), residues: 1779 helix: 1.62 (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 TRP 0.015 0.001 TRP E 70 HIS 0.005 0.001 HIS A 596 PHE 0.024 0.001 PHE D 63 TYR 0.019 0.001 TYR A 314 ARG 0.002 0.000 ARG C 137 Details of bonding type rmsd hydrogen bonds : bond 0.15904 ( 790) hydrogen bonds : angle 5.06568 ( 2277) covalent geometry : bond 0.00459 (14709) covalent geometry : angle 0.72027 (19778) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 1.415 Fit side-chains REVERT: A 332 MET cc_start: 0.6674 (ppp) cc_final: 0.5683 (ppp) outliers start: 1 outliers final: 0 residues processed: 150 average time/residue: 0.2403 time to fit residues: 54.3468 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 : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 84 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 HIS B 61 HIS C 86 HIS ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN D 37 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.241404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.196600 restraints weight = 18128.357| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 2.54 r_work: 0.3732 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 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 0.048 14709 Z= 0.227 Angle : 0.616 8.066 19778 Z= 0.325 Chirality : 0.043 0.188 2246 Planarity : 0.004 0.058 2468 Dihedral : 10.859 157.882 2018 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.86 % Favored : 93.03 % Rotamer: Outliers : 1.09 % Allowed : 8.45 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.21), residues: 1779 helix: 1.61 (0.17), residues: 999 sheet: -0.13 (0.42), residues: 188 loop : -2.02 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 70 HIS 0.010 0.001 HIS A 596 PHE 0.022 0.002 PHE A 529 TYR 0.016 0.002 TYR A 164 ARG 0.003 0.000 ARG C 137 Details of bonding type rmsd hydrogen bonds : bond 0.07573 ( 790) hydrogen bonds : angle 4.42932 ( 2277) covalent geometry : bond 0.00542 (14709) covalent geometry : angle 0.61647 (19778) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 1.601 Fit side-chains REVERT: A 314 TYR cc_start: 0.6750 (OUTLIER) cc_final: 0.6202 (m-10) REVERT: A 332 MET cc_start: 0.6566 (ppp) cc_final: 0.5350 (ppp) REVERT: C 94 TYR cc_start: 0.7163 (p90) cc_final: 0.6254 (p90) REVERT: E 17 LEU cc_start: 0.8328 (mt) cc_final: 0.7631 (mp) outliers start: 17 outliers final: 13 residues processed: 124 average time/residue: 0.2375 time to fit residues: 46.3360 Evaluate side-chains 121 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE 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 541 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain C residue 242 THR 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 18 optimal weight: 0.0970 chunk 127 optimal weight: 40.0000 chunk 36 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 chunk 130 optimal weight: 30.0000 chunk 49 optimal weight: 7.9990 chunk 139 optimal weight: 40.0000 chunk 159 optimal weight: 40.0000 chunk 131 optimal weight: 8.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.236035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.185171 restraints weight = 18186.106| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 2.93 r_work: 0.3618 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.072 14709 Z= 0.405 Angle : 0.770 8.237 19778 Z= 0.406 Chirality : 0.049 0.250 2246 Planarity : 0.005 0.058 2468 Dihedral : 11.113 160.719 2018 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.70 % Favored : 92.19 % Rotamer: Outliers : 2.56 % Allowed : 10.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.21), residues: 1779 helix: 1.14 (0.17), residues: 1005 sheet: -0.55 (0.41), residues: 200 loop : -2.13 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 12 HIS 0.011 0.001 HIS A 596 PHE 0.030 0.002 PHE A 71 TYR 0.021 0.003 TYR E 43 ARG 0.006 0.001 ARG C 156 Details of bonding type rmsd hydrogen bonds : bond 0.09458 ( 790) hydrogen bonds : angle 4.78006 ( 2277) covalent geometry : bond 0.01009 (14709) covalent geometry : angle 0.76961 (19778) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 106 time to evaluate : 1.637 Fit side-chains REVERT: A 314 TYR cc_start: 0.7417 (OUTLIER) cc_final: 0.6502 (m-80) REVERT: A 332 MET cc_start: 0.6582 (ppp) cc_final: 0.5248 (ppp) REVERT: A 574 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8181 (mp) outliers start: 40 outliers final: 25 residues processed: 135 average time/residue: 0.2579 time to fit residues: 53.0688 Evaluate side-chains 129 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 486 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 562 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain C residue 242 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 1.9990 chunk 27 optimal weight: 0.0270 chunk 153 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 146 optimal weight: 0.8980 chunk 171 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 HIS B 61 HIS C 65 HIS C 86 HIS ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN D 37 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.243142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.200712 restraints weight = 17968.692| |-----------------------------------------------------------------------------| r_work (start): 0.4229 rms_B_bonded: 2.51 r_work: 0.3774 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1577 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= 0.151 Angle : 0.548 7.757 19778 Z= 0.288 Chirality : 0.041 0.176 2246 Planarity : 0.003 0.055 2468 Dihedral : 10.286 157.755 2018 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.46 % Favored : 93.42 % Rotamer: Outliers : 1.60 % Allowed : 13.37 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.21), residues: 1779 helix: 1.64 (0.17), residues: 1001 sheet: -0.35 (0.42), residues: 191 loop : -2.07 (0.24), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 613 HIS 0.004 0.001 HIS A 596 PHE 0.021 0.001 PHE D 63 TYR 0.012 0.001 TYR A 164 ARG 0.003 0.000 ARG C 156 Details of bonding type rmsd hydrogen bonds : bond 0.06424 ( 790) hydrogen bonds : angle 4.17793 ( 2277) covalent geometry : bond 0.00339 (14709) covalent geometry : angle 0.54752 (19778) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 1.661 Fit side-chains REVERT: A 35 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.8293 (m-10) REVERT: A 314 TYR cc_start: 0.7221 (OUTLIER) cc_final: 0.6385 (m-80) REVERT: A 332 MET cc_start: 0.6720 (ppp) cc_final: 0.5450 (ppp) REVERT: E 17 LEU cc_start: 0.8148 (mt) cc_final: 0.7592 (mp) REVERT: E 47 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7831 (mt) REVERT: E 57 TYR cc_start: 0.8228 (t80) cc_final: 0.7995 (t80) outliers start: 25 outliers final: 18 residues processed: 138 average time/residue: 0.2397 time to fit residues: 51.5958 Evaluate side-chains 136 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 168 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 562 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 39 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 70 optimal weight: 1.9990 chunk 136 optimal weight: 40.0000 chunk 151 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 165 optimal weight: 20.0000 chunk 65 optimal weight: 7.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 HIS C 65 HIS C 86 HIS ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN D 37 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.241974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.199587 restraints weight = 18142.073| |-----------------------------------------------------------------------------| r_work (start): 0.4220 rms_B_bonded: 2.50 r_work: 0.3767 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14709 Z= 0.188 Angle : 0.568 7.326 19778 Z= 0.299 Chirality : 0.041 0.187 2246 Planarity : 0.003 0.054 2468 Dihedral : 10.202 158.513 2018 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.03 % Favored : 92.86 % Rotamer: Outliers : 2.75 % Allowed : 13.76 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.21), residues: 1779 helix: 1.70 (0.17), residues: 1001 sheet: -0.38 (0.42), residues: 191 loop : -2.06 (0.24), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 613 HIS 0.005 0.001 HIS C 65 PHE 0.021 0.001 PHE A 529 TYR 0.015 0.002 TYR A 164 ARG 0.003 0.000 ARG C 156 Details of bonding type rmsd hydrogen bonds : bond 0.06855 ( 790) hydrogen bonds : angle 4.14215 ( 2277) covalent geometry : bond 0.00446 (14709) covalent geometry : angle 0.56812 (19778) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 111 time to evaluate : 1.490 Fit side-chains REVERT: A 8 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8264 (mp) REVERT: A 35 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.8246 (m-10) REVERT: A 314 TYR cc_start: 0.7451 (OUTLIER) cc_final: 0.6534 (m-80) REVERT: A 332 MET cc_start: 0.6597 (ppp) cc_final: 0.5284 (ppp) REVERT: A 412 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7446 (mm) REVERT: A 574 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8051 (mp) REVERT: C 94 TYR cc_start: 0.8574 (OUTLIER) cc_final: 0.6309 (p90) REVERT: D 63 PHE cc_start: 0.7513 (t80) cc_final: 0.7241 (t80) REVERT: E 17 LEU cc_start: 0.8441 (mt) cc_final: 0.7826 (mp) REVERT: E 47 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7925 (mt) REVERT: E 57 TYR cc_start: 0.8497 (t80) cc_final: 0.8285 (t80) outliers start: 43 outliers final: 29 residues processed: 144 average time/residue: 0.2267 time to fit residues: 51.4827 Evaluate side-chains 145 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 1.628 ------------------------------------------------------------------------------- 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 65 VAL 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 168 MET Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 486 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 554 SER Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 39 LEU 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 38 VAL Chi-restraints excluded: chain E residue 47 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 53 optimal weight: 0.9980 chunk 131 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 156 optimal weight: 20.0000 chunk 117 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 77 optimal weight: 0.2980 chunk 12 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 62 optimal weight: 0.0670 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 HIS C 65 HIS C 86 HIS ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.243339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.193828 restraints weight = 18565.368| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 2.85 r_work: 0.3683 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1667 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= 0.118 Angle : 0.502 7.070 19778 Z= 0.264 Chirality : 0.039 0.160 2246 Planarity : 0.003 0.053 2468 Dihedral : 9.788 156.487 2018 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.13 % Favored : 93.76 % Rotamer: Outliers : 2.30 % Allowed : 13.82 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.21), residues: 1779 helix: 1.94 (0.17), residues: 1002 sheet: -0.30 (0.42), residues: 191 loop : -1.92 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 613 HIS 0.007 0.001 HIS C 65 PHE 0.015 0.001 PHE A 529 TYR 0.012 0.001 TYR D 64 ARG 0.002 0.000 ARG B 83 Details of bonding type rmsd hydrogen bonds : bond 0.05504 ( 790) hydrogen bonds : angle 3.88137 ( 2277) covalent geometry : bond 0.00245 (14709) covalent geometry : angle 0.50157 (19778) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 121 time to evaluate : 1.700 Fit side-chains REVERT: A 8 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8115 (mp) REVERT: A 35 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.8374 (m-10) REVERT: A 314 TYR cc_start: 0.7087 (OUTLIER) cc_final: 0.6328 (m-80) REVERT: A 332 MET cc_start: 0.6757 (ppp) cc_final: 0.5407 (ppp) REVERT: A 574 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7951 (mp) REVERT: C 94 TYR cc_start: 0.8481 (OUTLIER) cc_final: 0.6187 (p90) outliers start: 36 outliers final: 26 residues processed: 145 average time/residue: 0.2485 time to fit residues: 55.8882 Evaluate side-chains 147 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 1.619 ------------------------------------------------------------------------------- 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 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 512 SER 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 574 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 90 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 168 optimal weight: 20.0000 chunk 63 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 125 optimal weight: 0.0970 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 HIS C 65 HIS C 86 HIS C 202 HIS ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.243726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.200701 restraints weight = 18582.902| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 2.64 r_work: 0.3695 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14709 Z= 0.122 Angle : 0.505 8.842 19778 Z= 0.264 Chirality : 0.039 0.155 2246 Planarity : 0.003 0.052 2468 Dihedral : 9.625 156.066 2018 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.30 % Favored : 93.59 % Rotamer: Outliers : 2.30 % Allowed : 14.27 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.21), residues: 1779 helix: 2.04 (0.17), residues: 1002 sheet: -0.26 (0.43), residues: 191 loop : -1.88 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 613 HIS 0.008 0.001 HIS C 65 PHE 0.017 0.001 PHE A 529 TYR 0.016 0.001 TYR E 57 ARG 0.002 0.000 ARG C 137 Details of bonding type rmsd hydrogen bonds : bond 0.05411 ( 790) hydrogen bonds : angle 3.79906 ( 2277) covalent geometry : bond 0.00264 (14709) covalent geometry : angle 0.50470 (19778) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 2.563 Fit side-chains REVERT: A 8 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8124 (mp) REVERT: A 35 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.8349 (m-10) REVERT: A 181 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7174 (tt) REVERT: A 314 TYR cc_start: 0.7074 (OUTLIER) cc_final: 0.6293 (m-80) REVERT: A 332 MET cc_start: 0.6675 (ppp) cc_final: 0.5318 (ppp) REVERT: A 574 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7958 (mp) REVERT: B 221 MET cc_start: 0.7425 (tpp) cc_final: 0.7091 (tpp) REVERT: C 94 TYR cc_start: 0.8531 (OUTLIER) cc_final: 0.6089 (p90) outliers start: 36 outliers final: 26 residues processed: 141 average time/residue: 0.2462 time to fit residues: 55.0532 Evaluate side-chains 147 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 1.525 ------------------------------------------------------------------------------- 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 168 MET Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 512 SER 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 574 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 39 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 132 optimal weight: 0.8980 chunk 170 optimal weight: 0.5980 chunk 47 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 174 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 HIS C 65 HIS C 86 HIS C 202 HIS ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.244071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.192693 restraints weight = 18360.710| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 3.12 r_work: 0.3685 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14709 Z= 0.118 Angle : 0.499 7.766 19778 Z= 0.260 Chirality : 0.040 0.154 2246 Planarity : 0.003 0.052 2468 Dihedral : 9.424 155.387 2018 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.01 % Favored : 93.87 % Rotamer: Outliers : 2.62 % Allowed : 14.08 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.21), residues: 1779 helix: 2.11 (0.17), residues: 1002 sheet: -0.23 (0.43), residues: 191 loop : -1.87 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 613 HIS 0.010 0.001 HIS C 65 PHE 0.025 0.001 PHE D 63 TYR 0.015 0.001 TYR E 57 ARG 0.002 0.000 ARG C 137 Details of bonding type rmsd hydrogen bonds : bond 0.05281 ( 790) hydrogen bonds : angle 3.72616 ( 2277) covalent geometry : bond 0.00256 (14709) covalent geometry : angle 0.49909 (19778) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 117 time to evaluate : 1.701 Fit side-chains REVERT: A 8 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8127 (mp) REVERT: A 35 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.8338 (m-10) REVERT: A 181 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7225 (tt) REVERT: A 314 TYR cc_start: 0.7119 (OUTLIER) cc_final: 0.6391 (m-10) REVERT: A 332 MET cc_start: 0.6819 (ppp) cc_final: 0.5444 (ppp) REVERT: A 412 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7276 (mm) REVERT: A 574 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7940 (mp) REVERT: B 221 MET cc_start: 0.7400 (tpp) cc_final: 0.7123 (tpp) REVERT: C 94 TYR cc_start: 0.8547 (OUTLIER) cc_final: 0.6026 (p90) outliers start: 41 outliers final: 30 residues processed: 146 average time/residue: 0.2369 time to fit residues: 54.4786 Evaluate side-chains 152 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 115 time to evaluate : 1.599 ------------------------------------------------------------------------------- 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 84 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 512 SER 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 574 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 39 LEU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 116 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 118 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 chunk 9 optimal weight: 0.0670 chunk 37 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 129 optimal weight: 20.0000 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 HIS C 65 HIS C 86 HIS ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.247223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.199395 restraints weight = 18091.192| |-----------------------------------------------------------------------------| r_work (start): 0.4214 rms_B_bonded: 3.10 r_work: 0.3838 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3741 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 14709 Z= 0.114 Angle : 0.495 8.720 19778 Z= 0.258 Chirality : 0.039 0.157 2246 Planarity : 0.003 0.052 2468 Dihedral : 9.239 154.703 2018 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.79 % Favored : 94.10 % Rotamer: Outliers : 2.37 % Allowed : 14.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.21), residues: 1779 helix: 2.21 (0.17), residues: 1000 sheet: -0.18 (0.43), residues: 191 loop : -1.90 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 613 HIS 0.009 0.001 HIS C 65 PHE 0.016 0.001 PHE A 529 TYR 0.015 0.001 TYR E 57 ARG 0.002 0.000 ARG C 137 Details of bonding type rmsd hydrogen bonds : bond 0.05071 ( 790) hydrogen bonds : angle 3.67730 ( 2277) covalent geometry : bond 0.00244 (14709) covalent geometry : angle 0.49524 (19778) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 1.492 Fit side-chains revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8205 (mp) REVERT: A 35 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.8354 (m-10) REVERT: A 181 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7304 (tt) REVERT: A 314 TYR cc_start: 0.7240 (OUTLIER) cc_final: 0.6538 (m-80) REVERT: A 332 MET cc_start: 0.6709 (ppp) cc_final: 0.5395 (ppp) REVERT: A 412 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7444 (mm) REVERT: A 574 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7958 (mp) REVERT: B 221 MET cc_start: 0.7544 (tpp) cc_final: 0.7324 (tpp) REVERT: C 94 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.6101 (p90) outliers start: 37 outliers final: 28 residues processed: 144 average time/residue: 0.2328 time to fit residues: 52.2923 Evaluate side-chains 150 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 115 time to evaluate : 1.452 ------------------------------------------------------------------------------- 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 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 512 SER 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 574 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 39 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 9.9990 chunk 56 optimal weight: 0.8980 chunk 27 optimal weight: 0.0570 chunk 46 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 135 optimal weight: 40.0000 chunk 62 optimal weight: 0.7980 chunk 173 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 overall best weight: 1.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 HIS C 86 HIS ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.241563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.178575 restraints weight = 18142.200| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 3.51 r_work: 0.3203 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14709 Z= 0.188 Angle : 0.561 8.803 19778 Z= 0.293 Chirality : 0.041 0.168 2246 Planarity : 0.003 0.052 2468 Dihedral : 9.404 156.106 2018 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.63 % Favored : 93.25 % Rotamer: Outliers : 2.50 % Allowed : 14.33 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.21), residues: 1779 helix: 1.98 (0.17), residues: 1007 sheet: -0.18 (0.44), residues: 182 loop : -1.95 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 122 HIS 0.009 0.001 HIS C 65 PHE 0.022 0.001 PHE A 529 TYR 0.015 0.002 TYR E 57 ARG 0.003 0.000 ARG C 156 Details of bonding type rmsd hydrogen bonds : bond 0.06529 ( 790) hydrogen bonds : angle 3.90009 ( 2277) covalent geometry : bond 0.00451 (14709) covalent geometry : angle 0.56122 (19778) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 109 time to evaluate : 1.552 Fit side-chains REVERT: A 8 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8074 (mp) REVERT: A 35 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.8311 (m-10) REVERT: A 181 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7548 (tt) REVERT: A 314 TYR cc_start: 0.7139 (OUTLIER) cc_final: 0.6359 (m-80) REVERT: A 332 MET cc_start: 0.6129 (ppp) cc_final: 0.4826 (ppp) REVERT: A 376 MET cc_start: 0.4301 (mpp) cc_final: 0.4025 (mpp) REVERT: A 412 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6691 (mm) REVERT: A 455 MET cc_start: 0.7088 (tpp) cc_final: 0.6801 (tpp) REVERT: A 574 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7731 (mp) REVERT: C 94 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.5884 (p90) outliers start: 39 outliers final: 28 residues processed: 136 average time/residue: 0.2471 time to fit residues: 52.6799 Evaluate side-chains 144 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 1.478 ------------------------------------------------------------------------------- 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 84 SER Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 512 SER 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 574 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 39 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 36 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 128 optimal weight: 20.0000 chunk 28 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 105 optimal weight: 0.2980 chunk 163 optimal weight: 8.9990 chunk 142 optimal weight: 40.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 HIS C 86 HIS ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.242327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.175164 restraints weight = 18233.748| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 3.72 r_work: 0.3202 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14709 Z= 0.146 Angle : 0.534 8.973 19778 Z= 0.277 Chirality : 0.040 0.164 2246 Planarity : 0.003 0.052 2468 Dihedral : 9.293 155.008 2018 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.30 % Favored : 93.59 % Rotamer: Outliers : 2.37 % Allowed : 14.65 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.21), residues: 1779 helix: 2.03 (0.17), residues: 1007 sheet: -0.15 (0.44), residues: 182 loop : -1.93 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 613 HIS 0.005 0.001 HIS E 124 PHE 0.020 0.001 PHE A 529 TYR 0.015 0.001 TYR E 57 ARG 0.002 0.000 ARG C 156 Details of bonding type rmsd hydrogen bonds : bond 0.05944 ( 790) hydrogen bonds : angle 3.81835 ( 2277) covalent geometry : bond 0.00339 (14709) covalent geometry : angle 0.53366 (19778) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7956.23 seconds wall clock time: 140 minutes 2.68 seconds (8402.68 seconds total)