Starting phenix.real_space_refine on Fri May 16 12:30:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g4d_29717/05_2025/8g4d_29717.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g4d_29717/05_2025/8g4d_29717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g4d_29717/05_2025/8g4d_29717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g4d_29717/05_2025/8g4d_29717.map" model { file = "/net/cci-nas-00/data/ceres_data/8g4d_29717/05_2025/8g4d_29717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g4d_29717/05_2025/8g4d_29717.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 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 6 5.49 5 S 64 5.16 5 C 9315 2.51 5 N 2390 2.21 5 O 2627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14402 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: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1932 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 5, 'TRANS': 240} Chain: "C" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1932 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 5, 'TRANS': 240} 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: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.10, per 1000 atoms: 0.56 Number of scatterers: 14402 At special positions: 0 Unit cell: (102.896, 124.696, 178.76, 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 64 16.00 P 6 15.00 O 2627 8.00 N 2390 7.00 C 9315 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: 3.34 Conformation dependent library (CDL) restraints added in 1.7 seconds 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3382 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 13 sheets defined 62.4% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 2 through 15 Processing helix chain 'A' and resid 19 through 40 Processing helix chain 'A' and resid 43 through 47 Processing helix chain 'A' and resid 54 through 82 removed outlier: 4.225A pdb=" N LYS A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N THR A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA A 66 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ILE A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N PHE A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ARG A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 94 Processing helix chain 'A' and resid 96 through 127 removed outlier: 3.733A pdb=" N GLU A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 139 Processing helix chain 'A' and resid 149 through 177 removed outlier: 3.673A pdb=" N LEU A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N MET A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 225 removed outlier: 4.291A pdb=" N MET A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 203 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY A 225 " --> pdb=" O GLU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 Processing helix chain 'A' and resid 233 through 252 Processing helix chain 'A' and resid 254 through 267 removed outlier: 3.554A pdb=" N PHE A 258 " --> pdb=" O GLY A 254 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE A 262 " --> pdb=" O PHE A 258 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS A 267 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 286 Processing helix chain 'A' and resid 290 through 316 removed outlier: 3.534A pdb=" N THR A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 325 Processing helix chain 'A' and resid 333 through 344 Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 409 through 414 Processing helix chain 'A' and resid 447 through 452 removed outlier: 3.598A pdb=" N THR A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 472 Processing helix chain 'A' and resid 493 through 505 Processing helix chain 'A' and resid 513 through 556 removed outlier: 4.544A pdb=" N ALA A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLN A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS A 521 " --> pdb=" O SER A 517 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 546 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR A 547 " --> pdb=" O GLY A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 563 Processing helix chain 'A' and resid 571 through 602 Proline residue: A 589 - end of helix Processing helix chain 'A' and resid 613 through 644 removed outlier: 4.539A pdb=" N ILE A 617 " --> pdb=" O TRP A 613 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N MET A 618 " --> pdb=" O ALA A 614 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 644 " --> pdb=" O LYS A 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 19 removed outlier: 4.091A pdb=" N LYS B 19 " --> pdb=" O LYS B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 76 through 86 Processing helix chain 'B' and resid 101 through 108 Processing helix chain 'B' and resid 109 through 112 removed outlier: 4.063A pdb=" N ILE B 112 " --> pdb=" O PRO B 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 109 through 112' Processing helix chain 'B' and resid 117 through 131 removed outlier: 3.656A pdb=" N GLU B 130 " --> pdb=" O GLU B 126 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 160 removed outlier: 4.550A pdb=" N HIS B 160 " --> pdb=" O ARG B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 193 Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 231 through 246 removed outlier: 3.891A pdb=" N LEU B 246 " --> pdb=" O THR B 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 101 through 108 Processing helix chain 'C' and resid 109 through 111 No H-bonds generated for 'chain 'C' and resid 109 through 111' Processing helix chain 'C' and resid 116 through 132 removed outlier: 3.713A pdb=" N ALA C 120 " --> pdb=" O SER C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 139 removed outlier: 4.682A pdb=" N ASP C 138 " --> pdb=" O GLU C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 157 Processing helix chain 'C' and resid 175 through 193 removed outlier: 4.050A pdb=" N GLN C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS C 192 " --> pdb=" O GLN C 188 " (cutoff:3.500A) removed outlier: 4.036A 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: 3.986A 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 10 through 30 Processing helix chain 'D' and resid 35 through 72 removed outlier: 4.047A pdb=" N ILE D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE D 52 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 79 removed outlier: 3.870A pdb=" N ALA D 78 " --> pdb=" O ASP D 75 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE D 79 " --> pdb=" O VAL D 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 75 through 79' Processing helix chain 'D' and resid 84 through 138 Proline residue: D 129 - end of helix Processing helix chain 'D' and resid 143 through 169 Processing helix chain 'D' and resid 170 through 175 removed outlier: 5.034A 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 Processing helix chain 'D' and resid 217 through 236 Processing helix chain 'D' and resid 264 through 273 removed outlier: 3.522A pdb=" N VAL D 268 " --> pdb=" O PRO D 265 " (cutoff:3.500A) Proline residue: D 269 - end of helix removed outlier: 4.167A pdb=" N PHE D 272 " --> pdb=" O PRO D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 285 Processing helix chain 'D' and resid 289 through 303 removed outlier: 3.808A pdb=" N TYR D 293 " --> pdb=" O GLY D 289 " (cutoff:3.500A) Proline residue: D 301 - end of helix Processing helix chain 'D' and resid 327 through 334 removed outlier: 3.766A pdb=" N VAL D 331 " --> pdb=" O GLN D 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 9 Processing helix chain 'E' and resid 9 through 30 removed outlier: 3.569A pdb=" N ILE E 13 " --> pdb=" O ARG E 9 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL E 29 " --> pdb=" O PHE E 25 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP E 30 " --> pdb=" O ILE E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 37 Processing helix chain 'E' and resid 38 through 61 Processing helix chain 'E' and resid 62 through 70 Processing helix chain 'E' and resid 75 through 79 removed outlier: 4.308A pdb=" N ILE E 79 " --> pdb=" O VAL E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 138 removed outlier: 4.093A pdb=" N VAL E 90 " --> pdb=" O PHE E 86 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU E 91 " --> pdb=" O GLU E 87 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N HIS E 100 " --> pdb=" O GLY E 96 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LEU E 101 " --> pdb=" O GLN E 97 " (cutoff:3.500A) Proline residue: E 129 - end of helix Processing helix chain 'E' and resid 143 through 170 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.526A pdb=" N ASP E 175 " --> pdb=" O ILE E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 193 Processing helix chain 'E' and resid 195 through 202 Processing helix chain 'E' and resid 218 through 236 Processing helix chain 'E' and resid 264 through 268 Processing helix chain 'E' and resid 281 through 286 removed outlier: 3.520A pdb=" N ASP E 284 " --> pdb=" O ASP E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 300 removed outlier: 4.059A pdb=" N TYR E 293 " --> pdb=" O GLY E 289 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA E 300 " --> pdb=" O LYS E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 334 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 356 removed outlier: 3.630A pdb=" N LYS A 354 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY A 485 " --> pdb=" O LYS A 354 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR A 356 " --> pdb=" O PHE A 483 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE A 484 " --> pdb=" O PHE A 331 " (cutoff:3.500A) removed outlier: 3.752A 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 360 removed outlier: 3.638A pdb=" N LEU A 359 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL A 458 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 26 removed outlier: 6.385A pdb=" N LYS B 11 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS B 24 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE B 9 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE B 26 " --> pdb=" O ASN B 7 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN B 7 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU B 4 " --> pdb=" O ILE B 30 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 20 through 26 removed outlier: 6.385A pdb=" N LYS B 11 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS B 24 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE B 9 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE B 26 " --> pdb=" O ASN B 7 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN B 7 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ALA B 6 " --> pdb=" O HIS B 65 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N HIS B 65 " --> pdb=" O ALA B 6 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N LYS B 8 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N THR B 63 " --> pdb=" O LYS B 8 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.419A pdb=" N GLY B 88 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ASP B 168 " --> pdb=" O GLY B 88 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE B 165 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N VAL B 200 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ALA B 167 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR B 201 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N PHE B 35 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ILE B 214 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER B 37 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ILE B 216 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET B 39 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL B 213 " --> pdb=" O GLN B 224 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLN B 224 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE B 215 " --> pdb=" O TYR B 222 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 18 through 26 removed outlier: 6.815A pdb=" N LYS C 11 " --> pdb=" O VAL C 22 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LYS C 24 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ILE C 9 " --> pdb=" O LYS C 24 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE C 26 " --> pdb=" O ASN C 7 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ASN C 7 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ALA C 6 " --> pdb=" O HIS C 65 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N HIS C 65 " --> pdb=" O ALA C 6 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LYS C 8 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N THR C 63 " --> pdb=" O LYS C 8 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 37 through 39 Processing sheet with id=AA8, first strand: chain 'C' and resid 164 through 166 removed outlier: 7.366A pdb=" N ILE C 165 " --> pdb=" O ILE C 198 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 179 through 182 removed outlier: 3.560A pdb=" N GLU D 179 " --> pdb=" O SER D 216 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER D 216 " --> pdb=" O GLU D 179 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE D 181 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL D 214 " --> pdb=" O ILE D 181 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 206 through 208 removed outlier: 6.650A pdb=" N ASP D 206 " --> pdb=" O ILE D 243 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL D 256 " --> pdb=" O PHE D 318 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU D 311 " --> pdb=" O GLY D 315 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL D 317 " --> pdb=" O GLU D 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 180 through 182 Processing sheet with id=AB3, first strand: chain 'E' and resid 205 through 209 removed outlier: 3.663A pdb=" N SER E 245 " --> pdb=" O GLN E 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 305 through 311 removed outlier: 3.802A pdb=" N HIS E 305 " --> pdb=" O THR E 321 " (cutoff:3.500A) 819 hydrogen bonds defined for protein. 2349 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: 3.94 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 4573 1.35 - 1.50: 3825 1.50 - 1.65: 6165 1.65 - 1.80: 62 1.80 - 1.95: 54 Bond restraints: 14679 Sorted by residual: bond pdb=" N VAL C 2 " pdb=" CA VAL C 2 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.07e+01 bond pdb=" C LYS A 558 " pdb=" N PRO A 559 " ideal model delta sigma weight residual 1.335 1.373 -0.038 1.19e-02 7.06e+03 1.03e+01 bond pdb=" N VAL B 2 " pdb=" CA VAL B 2 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.78e+00 bond pdb=" N ILE C 3 " pdb=" CA ILE C 3 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.38e-02 5.25e+03 7.51e+00 bond pdb=" N LEU B 4 " pdb=" CA LEU B 4 " ideal model delta sigma weight residual 1.458 1.490 -0.033 1.22e-02 6.72e+03 7.11e+00 ... (remaining 14674 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 19464 2.27 - 4.54: 275 4.54 - 6.81: 38 6.81 - 9.08: 12 9.08 - 11.35: 1 Bond angle restraints: 19790 Sorted by residual: angle pdb=" N TYR A 561 " pdb=" CA TYR A 561 " pdb=" C TYR A 561 " ideal model delta sigma weight residual 113.88 106.09 7.79 1.23e+00 6.61e-01 4.01e+01 angle pdb=" N GLU E 83 " pdb=" CA GLU E 83 " pdb=" C GLU E 83 " ideal model delta sigma weight residual 114.56 108.76 5.80 1.27e+00 6.20e-01 2.08e+01 angle pdb=" C GLN D 162 " pdb=" N GLN D 163 " pdb=" CA GLN D 163 " ideal model delta sigma weight residual 122.06 114.59 7.47 1.86e+00 2.89e-01 1.61e+01 angle pdb=" C ILE D 225 " pdb=" N ARG D 226 " pdb=" CA ARG D 226 " ideal model delta sigma weight residual 121.58 114.03 7.55 1.95e+00 2.63e-01 1.50e+01 angle pdb=" N THR D 69 " pdb=" CA THR D 69 " pdb=" C THR D 69 " ideal model delta sigma weight residual 111.36 107.31 4.05 1.09e+00 8.42e-01 1.38e+01 ... (remaining 19785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.70: 8510 30.70 - 61.40: 300 61.40 - 92.09: 29 92.09 - 122.79: 0 122.79 - 153.49: 1 Dihedral angle restraints: 8840 sinusoidal: 3616 harmonic: 5224 Sorted by residual: dihedral pdb=" O1A AGS C 301 " pdb=" O3A AGS C 301 " pdb=" PA AGS C 301 " pdb=" PB AGS C 301 " ideal model delta sinusoidal sigma weight residual 292.27 138.78 153.49 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" CA GLY A 604 " pdb=" C GLY A 604 " pdb=" N TRP A 605 " pdb=" CA TRP A 605 " ideal model delta harmonic sigma weight residual 180.00 157.72 22.28 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA MET E 140 " pdb=" C MET E 140 " pdb=" N GLU E 141 " pdb=" CA GLU E 141 " ideal model delta harmonic sigma weight residual -180.00 -160.63 -19.37 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 8837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1661 0.042 - 0.085: 443 0.085 - 0.127: 143 0.127 - 0.169: 12 0.169 - 0.212: 3 Chirality restraints: 2262 Sorted by residual: chirality pdb=" CB ILE E 243 " pdb=" CA ILE E 243 " pdb=" CG1 ILE E 243 " pdb=" CG2 ILE E 243 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA GLN D 163 " pdb=" N GLN D 163 " pdb=" C GLN D 163 " pdb=" CB GLN D 163 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.29e-01 chirality pdb=" CB ILE C 3 " pdb=" CA ILE C 3 " pdb=" CG1 ILE C 3 " pdb=" CG2 ILE C 3 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.14e-01 ... (remaining 2259 not shown) Planarity restraints: 2467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 122 " -0.011 2.00e-02 2.50e+03 2.10e-02 1.10e+01 pdb=" CG TRP E 122 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP E 122 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP E 122 " -0.017 2.00e-02 2.50e+03 pdb=" NE1 TRP E 122 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP E 122 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP E 122 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 122 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 122 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP E 122 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 605 " 0.021 2.00e-02 2.50e+03 1.59e-02 6.35e+00 pdb=" CG TRP A 605 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP A 605 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 605 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 605 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 605 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 605 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 605 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 605 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 605 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 153 " -0.022 2.00e-02 2.50e+03 1.43e-02 5.14e+00 pdb=" CG TRP E 153 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP E 153 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP E 153 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 153 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 153 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 153 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 153 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 153 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 153 " -0.003 2.00e-02 2.50e+03 ... (remaining 2464 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2290 2.76 - 3.30: 14519 3.30 - 3.83: 23360 3.83 - 4.37: 25816 4.37 - 4.90: 44532 Nonbonded interactions: 110517 Sorted by model distance: nonbonded pdb=" OE1 GLN E 247 " pdb=" OG1 THR E 252 " model vdw 2.228 3.040 nonbonded pdb=" O THR D 128 " pdb=" OG1 THR D 131 " model vdw 2.236 3.040 nonbonded pdb=" OD1 ASN C 95 " pdb=" NH2 ARG C 156 " model vdw 2.248 3.120 nonbonded pdb=" NH2 ARG A 9 " pdb=" O THR C 99 " model vdw 2.249 3.120 nonbonded pdb=" O ARG E 226 " pdb=" OG1 THR E 230 " model vdw 2.251 3.040 ... (remaining 110512 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 31.150 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 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 : 0.003 0.061 14679 Z= 0.189 Angle : 0.679 11.346 19790 Z= 0.383 Chirality : 0.043 0.212 2262 Planarity : 0.004 0.067 2467 Dihedral : 15.325 153.488 5458 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.64 % Allowed : 0.45 % Favored : 98.92 % 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: 0.05 (0.21), residues: 1783 helix: 1.43 (0.17), residues: 1017 sheet: -2.67 (0.45), residues: 116 loop : -1.72 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.004 TRP E 122 HIS 0.013 0.001 HIS E 157 PHE 0.021 0.001 PHE A 501 TYR 0.021 0.001 TYR A 638 ARG 0.016 0.001 ARG E 226 Details of bonding type rmsd hydrogen bonds : bond 0.16044 ( 816) hydrogen bonds : angle 6.00000 ( 2349) covalent geometry : bond 0.00319 (14679) covalent geometry : angle 0.67943 (19790) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 219 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 487 ASN cc_start: 0.8205 (t0) cc_final: 0.7860 (t0) REVERT: C 95 ASN cc_start: 0.7965 (p0) cc_final: 0.7749 (p0) REVERT: C 117 LYS cc_start: 0.6903 (mmmt) cc_final: 0.6569 (tppt) REVERT: D 23 MET cc_start: 0.7397 (ptm) cc_final: 0.6957 (ptt) REVERT: D 169 ILE cc_start: 0.7642 (pt) cc_final: 0.7326 (tp) REVERT: E 112 LEU cc_start: 0.7911 (tp) cc_final: 0.7695 (tt) REVERT: E 120 MET cc_start: 0.8340 (tpt) cc_final: 0.7997 (tpp) REVERT: E 157 HIS cc_start: 0.8354 (p90) cc_final: 0.8079 (p90) outliers start: 10 outliers final: 0 residues processed: 223 average time/residue: 0.2407 time to fit residues: 81.2391 Evaluate side-chains 159 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.762 ------------------------------------------------------------------------------- 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: 8.9990 chunk 74 optimal weight: 0.8980 chunk 45 optimal weight: 20.0000 chunk 90 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 138 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 160 optimal weight: 9.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 GLN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 160 HIS ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 HIS ** E 165 HIS ** 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 = 0.4408 r_free = 0.4408 target = 0.186537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.144286 restraints weight = 26036.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.141157 restraints weight = 39045.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.142910 restraints weight = 27538.278| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14679 Z= 0.155 Angle : 0.632 9.025 19790 Z= 0.332 Chirality : 0.043 0.179 2262 Planarity : 0.004 0.064 2467 Dihedral : 7.821 153.041 1943 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.02 % Allowed : 7.98 % Favored : 91.00 % 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: 0.21 (0.21), residues: 1783 helix: 1.54 (0.17), residues: 1015 sheet: -2.67 (0.40), residues: 148 loop : -1.50 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP E 153 HIS 0.010 0.001 HIS E 134 PHE 0.025 0.001 PHE A 223 TYR 0.019 0.001 TYR A 623 ARG 0.008 0.001 ARG D 226 Details of bonding type rmsd hydrogen bonds : bond 0.06481 ( 816) hydrogen bonds : angle 5.06567 ( 2349) covalent geometry : bond 0.00327 (14679) covalent geometry : angle 0.63161 (19790) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 487 ASN cc_start: 0.8359 (t0) cc_final: 0.8075 (t0) REVERT: A 500 LEU cc_start: 0.9269 (pp) cc_final: 0.9068 (pp) REVERT: C 39 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7428 (ttt) REVERT: C 71 MET cc_start: 0.6186 (tmm) cc_final: 0.5933 (mmp) REVERT: D 107 ARG cc_start: 0.8123 (ttp80) cc_final: 0.7872 (ttp80) REVERT: E 120 MET cc_start: 0.8709 (tpt) cc_final: 0.8447 (tpp) REVERT: E 157 HIS cc_start: 0.8737 (p90) cc_final: 0.8015 (p-80) outliers start: 16 outliers final: 11 residues processed: 179 average time/residue: 0.2392 time to fit residues: 64.7219 Evaluate side-chains 166 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain E residue 84 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 133 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 101 optimal weight: 0.2980 chunk 4 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 HIS ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 HIS ** E 165 HIS ** 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 = 0.4405 r_free = 0.4405 target = 0.186331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.145332 restraints weight = 25976.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.144501 restraints weight = 46166.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.146439 restraints weight = 29451.302| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14679 Z= 0.144 Angle : 0.599 9.539 19790 Z= 0.313 Chirality : 0.042 0.171 2262 Planarity : 0.003 0.054 2467 Dihedral : 7.770 153.282 1943 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.91 % Allowed : 10.98 % Favored : 87.11 % 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: 0.28 (0.21), residues: 1783 helix: 1.59 (0.17), residues: 1021 sheet: -2.54 (0.41), residues: 148 loop : -1.51 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 605 HIS 0.008 0.001 HIS C 86 PHE 0.029 0.001 PHE A 223 TYR 0.016 0.001 TYR A 623 ARG 0.005 0.000 ARG D 9 Details of bonding type rmsd hydrogen bonds : bond 0.06146 ( 816) hydrogen bonds : angle 4.88585 ( 2349) covalent geometry : bond 0.00303 (14679) covalent geometry : angle 0.59850 (19790) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 487 ASN cc_start: 0.8299 (t0) cc_final: 0.8049 (t0) REVERT: B 9 ILE cc_start: 0.8189 (mm) cc_final: 0.7805 (mm) REVERT: C 39 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7435 (ttt) REVERT: E 120 MET cc_start: 0.8670 (tpt) cc_final: 0.8380 (tpp) REVERT: E 157 HIS cc_start: 0.8747 (p90) cc_final: 0.8361 (p90) outliers start: 30 outliers final: 21 residues processed: 184 average time/residue: 0.2338 time to fit residues: 65.3167 Evaluate side-chains 174 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 165 HIS Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 151 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 58 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 23 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 46 optimal weight: 0.0670 chunk 34 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 87 optimal weight: 0.0000 chunk 32 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 overall best weight: 0.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.188288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.146944 restraints weight = 25758.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.146323 restraints weight = 37535.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.147996 restraints weight = 27315.573| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14679 Z= 0.126 Angle : 0.591 11.778 19790 Z= 0.304 Chirality : 0.041 0.310 2262 Planarity : 0.003 0.053 2467 Dihedral : 7.685 155.085 1943 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.28 % Allowed : 13.91 % Favored : 84.81 % 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: 1783 helix: 1.70 (0.17), residues: 1018 sheet: -2.30 (0.43), residues: 136 loop : -1.49 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 122 HIS 0.006 0.001 HIS D 165 PHE 0.031 0.001 PHE E 63 TYR 0.013 0.001 TYR A 623 ARG 0.006 0.000 ARG D 107 Details of bonding type rmsd hydrogen bonds : bond 0.05594 ( 816) hydrogen bonds : angle 4.75546 ( 2349) covalent geometry : bond 0.00244 (14679) covalent geometry : angle 0.59142 (19790) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 487 ASN cc_start: 0.8291 (t0) cc_final: 0.8044 (t0) REVERT: B 9 ILE cc_start: 0.8179 (mm) cc_final: 0.7779 (mm) REVERT: C 39 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.7377 (ttt) REVERT: C 117 LYS cc_start: 0.7448 (mmmt) cc_final: 0.7029 (tppt) REVERT: D 107 ARG cc_start: 0.7996 (ttp80) cc_final: 0.7757 (ttp80) REVERT: E 63 PHE cc_start: 0.7685 (t80) cc_final: 0.7443 (t80) REVERT: E 120 MET cc_start: 0.8681 (tpt) cc_final: 0.8380 (tpp) REVERT: E 153 TRP cc_start: 0.7406 (t60) cc_final: 0.7145 (t60) REVERT: E 157 HIS cc_start: 0.8652 (p-80) cc_final: 0.8331 (p-80) outliers start: 20 outliers final: 13 residues processed: 177 average time/residue: 0.2391 time to fit residues: 63.9031 Evaluate side-chains 172 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 37 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 94 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 36 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 167 optimal weight: 20.0000 chunk 40 optimal weight: 6.9990 chunk 38 optimal weight: 0.0470 chunk 170 optimal weight: 0.1980 chunk 34 optimal weight: 0.7980 chunk 174 optimal weight: 4.9990 chunk 107 optimal weight: 0.0980 overall best weight: 0.3478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN B 105 ASN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 ASN C 160 HIS D 80 ASN ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.189446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.148185 restraints weight = 26048.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.143637 restraints weight = 37453.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.145885 restraints weight = 26687.040| |-----------------------------------------------------------------------------| r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14679 Z= 0.118 Angle : 0.573 11.966 19790 Z= 0.294 Chirality : 0.041 0.219 2262 Planarity : 0.003 0.058 2467 Dihedral : 7.559 156.594 1943 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.85 % Allowed : 14.93 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.21), residues: 1783 helix: 1.80 (0.17), residues: 1019 sheet: -2.16 (0.44), residues: 136 loop : -1.48 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 122 HIS 0.010 0.001 HIS E 134 PHE 0.035 0.001 PHE A 501 TYR 0.012 0.001 TYR A 623 ARG 0.010 0.000 ARG D 226 Details of bonding type rmsd hydrogen bonds : bond 0.05170 ( 816) hydrogen bonds : angle 4.57954 ( 2349) covalent geometry : bond 0.00225 (14679) covalent geometry : angle 0.57308 (19790) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6582 (mp0) REVERT: A 487 ASN cc_start: 0.8379 (t0) cc_final: 0.8071 (t0) REVERT: B 9 ILE cc_start: 0.8128 (mm) cc_final: 0.7722 (mm) REVERT: B 105 ASN cc_start: 0.8105 (OUTLIER) cc_final: 0.7865 (t0) REVERT: C 39 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7373 (ttt) REVERT: D 107 ARG cc_start: 0.8055 (ttp80) cc_final: 0.7738 (ttp80) REVERT: E 63 PHE cc_start: 0.7404 (t80) cc_final: 0.7135 (t80) REVERT: E 120 MET cc_start: 0.8855 (tpt) cc_final: 0.8545 (tpp) outliers start: 29 outliers final: 17 residues processed: 185 average time/residue: 0.2573 time to fit residues: 71.7352 Evaluate side-chains 180 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 105 ASN Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 272 PHE Chi-restraints excluded: chain E residue 151 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 93 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 47 optimal weight: 30.0000 chunk 28 optimal weight: 0.6980 chunk 148 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 157 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 ASN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 HIS ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 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 = 0.4414 r_free = 0.4414 target = 0.186761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.144980 restraints weight = 26013.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.140872 restraints weight = 39115.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.142913 restraints weight = 27565.859| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14679 Z= 0.148 Angle : 0.604 14.412 19790 Z= 0.309 Chirality : 0.041 0.218 2262 Planarity : 0.004 0.088 2467 Dihedral : 7.533 155.212 1943 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.04 % Allowed : 15.76 % Favored : 82.20 % 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: 0.52 (0.21), residues: 1783 helix: 1.75 (0.17), residues: 1019 sheet: -2.25 (0.44), residues: 136 loop : -1.43 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP E 122 HIS 0.007 0.001 HIS E 134 PHE 0.030 0.001 PHE A 223 TYR 0.016 0.001 TYR A 314 ARG 0.017 0.001 ARG D 226 Details of bonding type rmsd hydrogen bonds : bond 0.05718 ( 816) hydrogen bonds : angle 4.62434 ( 2349) covalent geometry : bond 0.00324 (14679) covalent geometry : angle 0.60377 (19790) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6701 (mp0) REVERT: A 369 MET cc_start: 0.5064 (mmm) cc_final: 0.4667 (mmp) REVERT: A 416 MET cc_start: 0.3024 (tpt) cc_final: 0.2786 (tpt) REVERT: A 487 ASN cc_start: 0.8411 (t0) cc_final: 0.8121 (t0) REVERT: B 9 ILE cc_start: 0.8149 (mm) cc_final: 0.7742 (mm) REVERT: B 105 ASN cc_start: 0.7960 (OUTLIER) cc_final: 0.7661 (t0) REVERT: C 39 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7524 (ttt) REVERT: C 71 MET cc_start: 0.7702 (mmp) cc_final: 0.5966 (tmm) REVERT: D 294 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7489 (pp) REVERT: E 63 PHE cc_start: 0.7432 (t80) cc_final: 0.7120 (t80) REVERT: E 112 LEU cc_start: 0.7883 (tp) cc_final: 0.7676 (tt) REVERT: E 120 MET cc_start: 0.8898 (tpt) cc_final: 0.8599 (tpp) REVERT: E 157 HIS cc_start: 0.8883 (p90) cc_final: 0.8594 (p-80) outliers start: 32 outliers final: 25 residues processed: 176 average time/residue: 0.2462 time to fit residues: 65.8332 Evaluate side-chains 184 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 105 ASN Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 272 PHE Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain E residue 81 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 130 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 165 optimal weight: 20.0000 chunk 125 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 157 optimal weight: 10.0000 chunk 57 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 ASN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 HIS ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 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 = 0.4404 r_free = 0.4404 target = 0.185901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.143594 restraints weight = 25776.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.138980 restraints weight = 40111.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.141068 restraints weight = 28349.994| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14679 Z= 0.154 Angle : 0.612 12.805 19790 Z= 0.315 Chirality : 0.042 0.223 2262 Planarity : 0.004 0.090 2467 Dihedral : 7.550 154.588 1943 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.30 % Allowed : 16.40 % Favored : 81.30 % 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: 0.48 (0.21), residues: 1783 helix: 1.70 (0.17), residues: 1021 sheet: -2.31 (0.44), residues: 136 loop : -1.40 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP E 122 HIS 0.005 0.001 HIS E 134 PHE 0.032 0.001 PHE A 223 TYR 0.017 0.001 TYR A 314 ARG 0.017 0.001 ARG D 226 Details of bonding type rmsd hydrogen bonds : bond 0.05957 ( 816) hydrogen bonds : angle 4.63152 ( 2349) covalent geometry : bond 0.00341 (14679) covalent geometry : angle 0.61172 (19790) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.6698 (mp0) REVERT: A 369 MET cc_start: 0.5277 (mmm) cc_final: 0.3942 (mmm) REVERT: A 416 MET cc_start: 0.3086 (tpt) cc_final: 0.2671 (tpt) REVERT: A 487 ASN cc_start: 0.8454 (t0) cc_final: 0.8189 (t0) REVERT: B 9 ILE cc_start: 0.8174 (mm) cc_final: 0.7761 (mm) REVERT: C 39 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7547 (ttt) REVERT: C 71 MET cc_start: 0.7813 (mmp) cc_final: 0.5987 (tmm) REVERT: E 63 PHE cc_start: 0.7445 (t80) cc_final: 0.7166 (t80) REVERT: E 112 LEU cc_start: 0.7934 (tp) cc_final: 0.7697 (tt) REVERT: E 120 MET cc_start: 0.8938 (tpt) cc_final: 0.8634 (tpp) REVERT: E 157 HIS cc_start: 0.8912 (p90) cc_final: 0.8512 (p-80) outliers start: 36 outliers final: 26 residues processed: 178 average time/residue: 0.2465 time to fit residues: 66.1518 Evaluate side-chains 177 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 272 PHE Chi-restraints excluded: chain E residue 81 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 24 optimal weight: 0.9990 chunk 110 optimal weight: 0.4980 chunk 96 optimal weight: 1.9990 chunk 107 optimal weight: 0.0970 chunk 142 optimal weight: 0.3980 chunk 36 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 137 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 HIS ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.187684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.144138 restraints weight = 25586.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.140809 restraints weight = 34994.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.142711 restraints weight = 24545.984| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14679 Z= 0.126 Angle : 0.603 13.039 19790 Z= 0.307 Chirality : 0.041 0.229 2262 Planarity : 0.003 0.071 2467 Dihedral : 7.494 156.603 1943 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.16 % Favored : 94.78 % Rotamer: Outliers : 1.98 % Allowed : 17.23 % Favored : 80.79 % 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: 0.59 (0.21), residues: 1783 helix: 1.81 (0.17), residues: 1016 sheet: -2.31 (0.42), residues: 145 loop : -1.34 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP E 122 HIS 0.013 0.001 HIS D 108 PHE 0.033 0.001 PHE A 223 TYR 0.014 0.001 TYR A 623 ARG 0.016 0.001 ARG D 226 Details of bonding type rmsd hydrogen bonds : bond 0.05431 ( 816) hydrogen bonds : angle 4.50029 ( 2349) covalent geometry : bond 0.00255 (14679) covalent geometry : angle 0.60301 (19790) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.7948 (ptmt) cc_final: 0.7507 (ptmt) REVERT: A 275 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6634 (mp0) REVERT: A 369 MET cc_start: 0.5155 (mmm) cc_final: 0.3822 (mmm) REVERT: A 416 MET cc_start: 0.3163 (tpt) cc_final: 0.2752 (tpt) REVERT: A 487 ASN cc_start: 0.8392 (t0) cc_final: 0.8162 (t0) REVERT: B 9 ILE cc_start: 0.8102 (mm) cc_final: 0.7690 (mm) REVERT: C 39 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7470 (ttt) REVERT: C 71 MET cc_start: 0.7834 (mmp) cc_final: 0.5827 (tmm) REVERT: C 101 THR cc_start: 0.7220 (p) cc_final: 0.6938 (p) REVERT: C 117 LYS cc_start: 0.7544 (mmmt) cc_final: 0.7145 (tppt) REVERT: E 120 MET cc_start: 0.8842 (tpt) cc_final: 0.8533 (tpp) REVERT: E 157 HIS cc_start: 0.8889 (p90) cc_final: 0.8439 (p-80) outliers start: 31 outliers final: 23 residues processed: 178 average time/residue: 0.2649 time to fit residues: 71.4899 Evaluate side-chains 184 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 272 PHE Chi-restraints excluded: chain E residue 81 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 64 optimal weight: 0.0010 chunk 160 optimal weight: 0.9980 chunk 45 optimal weight: 0.0670 chunk 157 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 165 optimal weight: 30.0000 chunk 87 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 170 optimal weight: 30.0000 chunk 69 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 overall best weight: 0.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 ASN B 29 HIS ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 ASN C 160 HIS ** E 208 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 = 0.4428 r_free = 0.4428 target = 0.188190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.145798 restraints weight = 25558.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.145785 restraints weight = 40391.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.147231 restraints weight = 25660.777| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14679 Z= 0.124 Angle : 0.604 13.362 19790 Z= 0.307 Chirality : 0.041 0.223 2262 Planarity : 0.003 0.054 2467 Dihedral : 7.416 157.519 1943 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.50 % Favored : 94.45 % Rotamer: Outliers : 1.79 % Allowed : 17.61 % Favored : 80.60 % 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: 0.68 (0.21), residues: 1783 helix: 1.87 (0.17), residues: 1015 sheet: -2.27 (0.42), residues: 151 loop : -1.25 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP E 122 HIS 0.005 0.001 HIS C 202 PHE 0.033 0.001 PHE A 223 TYR 0.014 0.001 TYR E 64 ARG 0.013 0.000 ARG C 122 Details of bonding type rmsd hydrogen bonds : bond 0.05264 ( 816) hydrogen bonds : angle 4.43225 ( 2349) covalent geometry : bond 0.00251 (14679) covalent geometry : angle 0.60358 (19790) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6589 (mp0) REVERT: A 369 MET cc_start: 0.4959 (mmm) cc_final: 0.3645 (mmm) REVERT: A 416 MET cc_start: 0.2887 (tpt) cc_final: 0.2476 (tpt) REVERT: A 551 MET cc_start: 0.8213 (ptm) cc_final: 0.7773 (ptp) REVERT: B 9 ILE cc_start: 0.8098 (mm) cc_final: 0.7697 (mm) REVERT: C 39 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7429 (ttt) REVERT: C 71 MET cc_start: 0.7824 (mmp) cc_final: 0.5840 (tmm) REVERT: C 101 THR cc_start: 0.7222 (p) cc_final: 0.6894 (p) REVERT: E 120 MET cc_start: 0.8731 (tpt) cc_final: 0.8448 (tpp) REVERT: E 122 TRP cc_start: 0.7480 (t60) cc_final: 0.6849 (t60) REVERT: E 157 HIS cc_start: 0.8748 (p90) cc_final: 0.8235 (p-80) outliers start: 28 outliers final: 21 residues processed: 179 average time/residue: 0.2304 time to fit residues: 63.1021 Evaluate side-chains 182 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 272 PHE Chi-restraints excluded: chain E residue 81 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 153 optimal weight: 0.9990 chunk 146 optimal weight: 0.3980 chunk 110 optimal weight: 0.0970 chunk 128 optimal weight: 0.1980 chunk 117 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 56 optimal weight: 0.6980 chunk 158 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 172 optimal weight: 9.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 HIS ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.189082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.145865 restraints weight = 25723.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.142836 restraints weight = 34960.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.144690 restraints weight = 24464.741| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14679 Z= 0.122 Angle : 0.612 14.244 19790 Z= 0.310 Chirality : 0.041 0.224 2262 Planarity : 0.003 0.055 2467 Dihedral : 7.350 158.737 1943 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.10 % Favored : 94.84 % Rotamer: Outliers : 1.47 % Allowed : 17.93 % Favored : 80.60 % 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: 0.69 (0.21), residues: 1783 helix: 1.88 (0.17), residues: 1015 sheet: -2.28 (0.41), residues: 163 loop : -1.21 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP E 122 HIS 0.006 0.001 HIS E 108 PHE 0.033 0.001 PHE A 223 TYR 0.013 0.001 TYR E 64 ARG 0.013 0.000 ARG C 122 Details of bonding type rmsd hydrogen bonds : bond 0.05115 ( 816) hydrogen bonds : angle 4.35794 ( 2349) covalent geometry : bond 0.00244 (14679) covalent geometry : angle 0.61243 (19790) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 1.776 Fit side-chains revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6591 (mp0) REVERT: A 369 MET cc_start: 0.5161 (mmm) cc_final: 0.3826 (mmm) REVERT: A 416 MET cc_start: 0.3156 (tpt) cc_final: 0.2657 (tpt) REVERT: B 9 ILE cc_start: 0.8164 (mm) cc_final: 0.7748 (mm) REVERT: C 39 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.7435 (ttt) REVERT: C 71 MET cc_start: 0.7839 (mmp) cc_final: 0.5842 (tmm) REVERT: C 101 THR cc_start: 0.7150 (p) cc_final: 0.6799 (p) REVERT: C 117 LYS cc_start: 0.7436 (mmmt) cc_final: 0.7099 (tppt) REVERT: E 120 MET cc_start: 0.8814 (tpt) cc_final: 0.8514 (tpp) REVERT: E 122 TRP cc_start: 0.7667 (t60) cc_final: 0.6982 (t60) REVERT: E 157 HIS cc_start: 0.8795 (p90) cc_final: 0.7978 (p-80) outliers start: 23 outliers final: 21 residues processed: 173 average time/residue: 0.2582 time to fit residues: 67.0184 Evaluate side-chains 181 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 272 PHE Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 172 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 138 optimal weight: 20.0000 chunk 47 optimal weight: 30.0000 chunk 31 optimal weight: 0.9990 chunk 136 optimal weight: 9.9990 chunk 139 optimal weight: 30.0000 chunk 86 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 77 optimal weight: 0.3980 chunk 161 optimal weight: 30.0000 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 HIS ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.188319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.145809 restraints weight = 25890.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.142097 restraints weight = 37462.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.144004 restraints weight = 27275.037| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14679 Z= 0.134 Angle : 0.621 13.474 19790 Z= 0.315 Chirality : 0.041 0.227 2262 Planarity : 0.003 0.054 2467 Dihedral : 7.324 158.173 1943 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.72 % Favored : 94.22 % Rotamer: Outliers : 1.66 % Allowed : 18.38 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.21), residues: 1783 helix: 1.84 (0.17), residues: 1015 sheet: -2.32 (0.41), residues: 165 loop : -1.16 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP E 122 HIS 0.005 0.001 HIS C 202 PHE 0.033 0.001 PHE A 223 TYR 0.013 0.001 TYR A 623 ARG 0.013 0.001 ARG C 122 Details of bonding type rmsd hydrogen bonds : bond 0.05382 ( 816) hydrogen bonds : angle 4.38594 ( 2349) covalent geometry : bond 0.00286 (14679) covalent geometry : angle 0.62113 (19790) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4413.31 seconds wall clock time: 78 minutes 29.99 seconds (4709.99 seconds total)