Starting phenix.real_space_refine on Fri Jul 3 13:41:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8g4d_29717/07_2026/8g4d_29717.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g4d_29717/07_2026/8g4d_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_29717/07_2026/8g4d_29717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g4d_29717/07_2026/8g4d_29717.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8g4d_29717/07_2026/8g4d_29717.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8g4d_29717/07_2026/8g4d_29717.cif" model { file = "/net/cci-nas-00/data/ceres_data/8g4d_29717/07_2026/8g4d_29717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g4d_29717/07_2026/8g4d_29717.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.56, per 1000 atoms: 0.18 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: 1.03 Conformation dependent library (CDL) restraints added in 400.1 milliseconds 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: 0.40 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: 2.37 Time building geometry restraints manager: 1.40 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: 8504 30.70 - 61.40: 284 61.40 - 92.09: 29 92.09 - 122.79: 0 122.79 - 153.49: 1 Dihedral angle restraints: 8818 sinusoidal: 3594 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 8815 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: 4.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 11.990 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 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 : 15.150 153.488 5436 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.50 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (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 ARG 0.016 0.001 ARG E 226 TYR 0.021 0.001 TYR A 638 PHE 0.021 0.001 PHE A 501 TRP 0.050 0.004 TRP E 122 HIS 0.013 0.001 HIS E 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.19 (14679) covalent geometry : angle 0.67943 / 0.38 (19790) hydrogen bonds : bond 0.16044 / 10.48 ( 816) hydrogen bonds : angle 6.00000 / 4.38 ( 2349) *********************** 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 : 0.576 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: 0.8080 (p90) outliers start: 10 outliers final: 0 residues processed: 223 average time/residue: 0.1063 time to fit residues: 36.6940 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 : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.0770 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.0270 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.2980 chunk 149 optimal weight: 0.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 362 ASN A 602 GLN B 105 ASN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4432 r_free = 0.4432 target = 0.188871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.149420 restraints weight = 26144.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.149423 restraints weight = 43672.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.150259 restraints weight = 28050.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.150527 restraints weight = 16705.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.151148 restraints weight = 14149.574| |-----------------------------------------------------------------------------| r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14679 Z= 0.139 Angle : 0.613 9.320 19790 Z= 0.322 Chirality : 0.042 0.176 2262 Planarity : 0.004 0.063 2467 Dihedral : 6.671 156.010 1921 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.02 % Allowed : 7.66 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.21), residues: 1783 helix: 1.60 (0.17), residues: 1016 sheet: -2.53 (0.41), residues: 148 loop : -1.46 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 226 TYR 0.016 0.001 TYR A 623 PHE 0.023 0.001 PHE A 223 TRP 0.031 0.003 TRP E 153 HIS 0.012 0.001 HIS E 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 (14679) covalent geometry : angle 0.61263 / 0.32 (19790) hydrogen bonds : bond 0.06020 / 3.94 ( 816) hydrogen bonds : angle 4.99193 / 3.69 ( 2349) *********************** 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 192 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 MET cc_start: 0.7780 (tpt) cc_final: 0.7235 (tpt) REVERT: A 487 ASN cc_start: 0.8270 (t0) cc_final: 0.8025 (t0) REVERT: C 39 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7326 (ttt) REVERT: E 120 MET cc_start: 0.8554 (tpt) cc_final: 0.8314 (tpp) REVERT: E 157 HIS cc_start: 0.8562 (p90) cc_final: 0.7954 (p-80) outliers start: 16 outliers final: 10 residues processed: 185 average time/residue: 0.1141 time to fit residues: 32.3800 Evaluate side-chains 167 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 9 ILE Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 74 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 97 optimal weight: 0.0060 chunk 149 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 167 optimal weight: 20.0000 chunk 118 optimal weight: 0.7980 chunk 126 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 29 HIS B 105 ASN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN D 165 HIS E 134 HIS E 165 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.188215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.149039 restraints weight = 26126.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.146375 restraints weight = 42282.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.148774 restraints weight = 29150.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.149097 restraints weight = 17414.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.149856 restraints weight = 14952.578| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14679 Z= 0.133 Angle : 0.588 11.275 19790 Z= 0.306 Chirality : 0.041 0.170 2262 Planarity : 0.003 0.054 2467 Dihedral : 6.609 155.910 1921 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.60 % Allowed : 10.40 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.21), residues: 1783 helix: 1.68 (0.17), residues: 1021 sheet: -2.39 (0.42), residues: 148 loop : -1.50 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 226 TYR 0.014 0.001 TYR A 623 PHE 0.028 0.001 PHE A 223 TRP 0.026 0.002 TRP A 605 HIS 0.013 0.001 HIS E 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (14679) covalent geometry : angle 0.58788 / 0.31 (19790) hydrogen bonds : bond 0.05733 / 3.79 ( 816) hydrogen bonds : angle 4.77921 / 3.53 ( 2349) *********************** 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 187 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 487 ASN cc_start: 0.8272 (t0) cc_final: 0.8003 (t0) REVERT: B 9 ILE cc_start: 0.8174 (mm) cc_final: 0.7783 (mm) REVERT: C 39 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.7451 (ttt) REVERT: C 71 MET cc_start: 0.7902 (mmp) cc_final: 0.6217 (tmm) REVERT: E 120 MET cc_start: 0.8650 (tpt) cc_final: 0.8342 (tpp) REVERT: E 157 HIS cc_start: 0.8742 (p90) cc_final: 0.8155 (p-80) outliers start: 25 outliers final: 16 residues processed: 177 average time/residue: 0.1120 time to fit residues: 30.6213 Evaluate side-chains 171 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 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 2 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 101 THR 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 E residue 84 THR 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 169 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 166 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 165 optimal weight: 8.9990 chunk 2 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 ASN E 157 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.187797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.146708 restraints weight = 26140.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.142506 restraints weight = 38171.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.144303 restraints weight = 28168.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.146342 restraints weight = 16048.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.146749 restraints weight = 12263.597| |-----------------------------------------------------------------------------| r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14679 Z= 0.134 Angle : 0.586 10.885 19790 Z= 0.304 Chirality : 0.042 0.322 2262 Planarity : 0.003 0.052 2467 Dihedral : 6.589 155.827 1921 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.53 % Allowed : 12.95 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.21), residues: 1783 helix: 1.71 (0.17), residues: 1021 sheet: -2.30 (0.44), residues: 136 loop : -1.51 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 122 TYR 0.015 0.001 TYR A 623 PHE 0.029 0.001 PHE A 223 TRP 0.026 0.002 TRP A 605 HIS 0.006 0.001 HIS E 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (14679) covalent geometry : angle 0.58584 / 0.30 (19790) hydrogen bonds : bond 0.05661 / 3.74 ( 816) hydrogen bonds : angle 4.71649 / 3.49 ( 2349) *********************** 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 183 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 487 ASN cc_start: 0.8365 (t0) cc_final: 0.8072 (t0) REVERT: B 9 ILE cc_start: 0.8174 (mm) cc_final: 0.7764 (mm) REVERT: C 39 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7433 (ttt) REVERT: C 117 LYS cc_start: 0.7495 (mmmt) cc_final: 0.7071 (tppt) REVERT: E 120 MET cc_start: 0.8738 (tpt) cc_final: 0.8413 (tpp) REVERT: E 153 TRP cc_start: 0.7589 (t60) cc_final: 0.7345 (t60) REVERT: E 157 HIS cc_start: 0.8807 (p-80) cc_final: 0.8386 (p-80) outliers start: 24 outliers final: 17 residues processed: 172 average time/residue: 0.1139 time to fit residues: 30.0668 Evaluate side-chains 169 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 107 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 384 GLN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 ASN ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN ** D 165 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.185886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.143872 restraints weight = 25824.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.139618 restraints weight = 36604.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.141500 restraints weight = 26876.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.143835 restraints weight = 15015.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.144075 restraints weight = 12215.800| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14679 Z= 0.149 Angle : 0.608 11.650 19790 Z= 0.312 Chirality : 0.042 0.214 2262 Planarity : 0.004 0.075 2467 Dihedral : 6.576 154.564 1921 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.43 % Allowed : 14.17 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.21), residues: 1783 helix: 1.75 (0.17), residues: 1018 sheet: -2.35 (0.43), residues: 136 loop : -1.50 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 226 TYR 0.016 0.001 TYR A 314 PHE 0.031 0.001 PHE A 223 TRP 0.028 0.002 TRP E 122 HIS 0.005 0.001 HIS E 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (14679) covalent geometry : angle 0.60751 / 0.31 (19790) hydrogen bonds : bond 0.05956 / 3.93 ( 816) hydrogen bonds : angle 4.66517 / 3.45 ( 2349) *********************** 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 195 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6688 (mp0) REVERT: A 487 ASN cc_start: 0.8348 (t0) cc_final: 0.8038 (t0) REVERT: B 9 ILE cc_start: 0.8194 (mm) cc_final: 0.7766 (mm) REVERT: C 39 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7522 (ttt) REVERT: E 120 MET cc_start: 0.8774 (tpt) cc_final: 0.8460 (tpp) REVERT: E 154 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8501 (mt) outliers start: 38 outliers final: 26 residues processed: 183 average time/residue: 0.1078 time to fit residues: 30.6419 Evaluate side-chains 178 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 214 THR Chi-restraints excluded: chain A residue 275 GLU 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 131 LEU 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 67 LEU Chi-restraints excluded: chain D residue 108 HIS Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 272 PHE Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain E residue 151 TYR Chi-restraints excluded: chain E residue 154 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 118 optimal weight: 0.0060 chunk 131 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 76 optimal weight: 0.0670 chunk 23 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 overall best weight: 0.7136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 367 ASN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 HIS D 165 HIS ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.187323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.144843 restraints weight = 25719.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.141055 restraints weight = 37861.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.142916 restraints weight = 27415.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.145347 restraints weight = 15564.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.145614 restraints weight = 11716.801| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2120 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= 0.130 Angle : 0.593 11.546 19790 Z= 0.304 Chirality : 0.041 0.232 2262 Planarity : 0.004 0.079 2467 Dihedral : 6.546 155.748 1921 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.43 % Allowed : 15.44 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.21), residues: 1783 helix: 1.77 (0.17), residues: 1019 sheet: -2.27 (0.44), residues: 136 loop : -1.44 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 226 TYR 0.014 0.001 TYR A 623 PHE 0.035 0.001 PHE A 501 TRP 0.038 0.003 TRP E 122 HIS 0.007 0.001 HIS E 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (14679) covalent geometry : angle 0.59290 / 0.30 (19790) hydrogen bonds : bond 0.05642 / 3.74 ( 816) hydrogen bonds : angle 4.59264 / 3.40 ( 2349) *********************** 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 194 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.6621 (mp0) REVERT: A 369 MET cc_start: 0.5055 (mmm) cc_final: 0.4669 (mmp) REVERT: A 416 MET cc_start: 0.2983 (tpt) cc_final: 0.2749 (tpt) REVERT: A 487 ASN cc_start: 0.8403 (t0) cc_final: 0.8095 (t0) REVERT: B 9 ILE cc_start: 0.8140 (mm) cc_final: 0.7712 (mm) REVERT: C 39 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7474 (ttt) REVERT: D 294 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7544 (pp) REVERT: E 113 GLU cc_start: 0.7158 (mp0) cc_final: 0.6701 (mp0) REVERT: E 120 MET cc_start: 0.8822 (tpt) cc_final: 0.8458 (tpp) REVERT: E 154 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8514 (mt) REVERT: E 157 HIS cc_start: 0.8897 (OUTLIER) cc_final: 0.8560 (p-80) outliers start: 38 outliers final: 25 residues processed: 177 average time/residue: 0.1087 time to fit residues: 29.7466 Evaluate side-chains 183 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 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 484 ILE 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 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 108 HIS 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 Chi-restraints excluded: chain E residue 151 TYR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 157 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 70 optimal weight: 0.3980 chunk 138 optimal weight: 20.0000 chunk 128 optimal weight: 9.9990 chunk 69 optimal weight: 0.6980 chunk 143 optimal weight: 0.1980 chunk 5 optimal weight: 0.1980 chunk 163 optimal weight: 20.0000 chunk 168 optimal weight: 10.0000 chunk 46 optimal weight: 0.0970 chunk 44 optimal weight: 0.0870 chunk 0 optimal weight: 5.9990 overall best weight: 0.1956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 105 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.189590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.148607 restraints weight = 25524.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.143917 restraints weight = 36069.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.145734 restraints weight = 28440.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.147879 restraints weight = 15932.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.148178 restraints weight = 12115.750| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14679 Z= 0.119 Angle : 0.586 12.728 19790 Z= 0.298 Chirality : 0.041 0.231 2262 Planarity : 0.004 0.099 2467 Dihedral : 6.518 157.441 1921 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.91 % Allowed : 16.53 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.21), residues: 1783 helix: 1.88 (0.17), residues: 1022 sheet: -2.12 (0.45), residues: 134 loop : -1.39 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG D 226 TYR 0.011 0.001 TYR A 164 PHE 0.032 0.001 PHE A 223 TRP 0.038 0.002 TRP E 122 HIS 0.007 0.001 HIS E 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.12 (14679) covalent geometry : angle 0.58636 / 0.30 (19790) hydrogen bonds : bond 0.05114 / 3.40 ( 816) hydrogen bonds : angle 4.47097 / 3.31 ( 2349) *********************** 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: 30 poor density : 163 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6546 (mp0) REVERT: A 369 MET cc_start: 0.4998 (mmm) cc_final: 0.3693 (mmm) REVERT: A 416 MET cc_start: 0.2873 (tpt) cc_final: 0.2449 (tpt) REVERT: A 487 ASN cc_start: 0.8345 (t0) cc_final: 0.8093 (t0) REVERT: B 9 ILE cc_start: 0.8148 (mm) cc_final: 0.7739 (mm) REVERT: C 39 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7370 (ttt) REVERT: C 71 MET cc_start: 0.7504 (mmp) cc_final: 0.5953 (tmm) REVERT: E 120 MET cc_start: 0.8708 (tpt) cc_final: 0.8391 (tpp) REVERT: E 154 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8505 (mt) REVERT: E 157 HIS cc_start: 0.8838 (OUTLIER) cc_final: 0.8509 (p-80) outliers start: 30 outliers final: 18 residues processed: 179 average time/residue: 0.1113 time to fit residues: 30.5995 Evaluate side-chains 179 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 393 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 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 37 ASN Chi-restraints excluded: chain D residue 108 HIS 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 151 TYR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 157 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 141 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 166 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 170 optimal weight: 0.4980 chunk 79 optimal weight: 0.9980 chunk 86 optimal weight: 0.2980 chunk 27 optimal weight: 0.0970 chunk 33 optimal weight: 7.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 105 ASN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4433 r_free = 0.4433 target = 0.188456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.144946 restraints weight = 25559.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.144622 restraints weight = 35775.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.146509 restraints weight = 23023.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.146018 restraints weight = 14440.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.147983 restraints weight = 12540.100| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14679 Z= 0.122 Angle : 0.603 14.833 19790 Z= 0.303 Chirality : 0.041 0.227 2262 Planarity : 0.003 0.062 2467 Dihedral : 6.487 156.833 1921 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.79 % Allowed : 17.17 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.21), residues: 1783 helix: 1.85 (0.17), residues: 1024 sheet: -2.11 (0.46), residues: 133 loop : -1.30 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 226 TYR 0.012 0.001 TYR A 623 PHE 0.034 0.001 PHE A 223 TRP 0.045 0.002 TRP E 122 HIS 0.005 0.001 HIS C 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (14679) covalent geometry : angle 0.60311 / 0.30 (19790) hydrogen bonds : bond 0.05182 / 3.43 ( 816) hydrogen bonds : angle 4.43336 / 3.28 ( 2349) *********************** 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 186 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6404 (mp0) REVERT: A 338 LYS cc_start: 0.9316 (tptp) cc_final: 0.9091 (tptp) REVERT: A 369 MET cc_start: 0.4936 (mmm) cc_final: 0.3631 (mmm) REVERT: A 416 MET cc_start: 0.2885 (tpt) cc_final: 0.2493 (tpt) REVERT: A 487 ASN cc_start: 0.8364 (t0) cc_final: 0.8119 (t0) REVERT: B 9 ILE cc_start: 0.8079 (mm) cc_final: 0.7674 (mm) REVERT: C 39 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.7473 (ttt) REVERT: C 71 MET cc_start: 0.7650 (mmp) cc_final: 0.5915 (tmm) REVERT: C 117 LYS cc_start: 0.7433 (mmmt) cc_final: 0.7002 (tppt) REVERT: E 113 GLU cc_start: 0.7183 (mp0) cc_final: 0.6837 (mp0) REVERT: E 120 MET cc_start: 0.8676 (tpt) cc_final: 0.8363 (tpp) REVERT: E 157 HIS cc_start: 0.8820 (OUTLIER) cc_final: 0.8345 (p-80) outliers start: 28 outliers final: 22 residues processed: 172 average time/residue: 0.1105 time to fit residues: 29.4822 Evaluate side-chains 178 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 393 VAL 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 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 108 HIS 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 124 HIS Chi-restraints excluded: chain E residue 151 TYR Chi-restraints excluded: chain E residue 157 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 72 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 45 optimal weight: 0.3980 chunk 13 optimal weight: 0.7980 chunk 160 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 23 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 29 HIS ** B 194 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.188735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.145392 restraints weight = 25755.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.141213 restraints weight = 35087.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.143325 restraints weight = 24977.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.145669 restraints weight = 14056.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.145829 restraints weight = 11941.910| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14679 Z= 0.128 Angle : 0.614 14.591 19790 Z= 0.308 Chirality : 0.041 0.234 2262 Planarity : 0.003 0.053 2467 Dihedral : 6.472 156.322 1921 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.27 % Favored : 94.67 % Rotamer: Outliers : 1.85 % Allowed : 17.29 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.21), residues: 1783 helix: 1.83 (0.17), residues: 1022 sheet: -2.25 (0.42), residues: 149 loop : -1.18 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 226 TYR 0.013 0.001 TYR A 623 PHE 0.032 0.001 PHE A 223 TRP 0.048 0.002 TRP E 122 HIS 0.005 0.001 HIS C 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (14679) covalent geometry : angle 0.61369 / 0.31 (19790) hydrogen bonds : bond 0.05308 / 3.51 ( 816) hydrogen bonds : angle 4.42326 / 3.26 ( 2349) *********************** 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 187 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6490 (mp0) REVERT: A 369 MET cc_start: 0.5239 (mmm) cc_final: 0.3900 (mmm) REVERT: A 416 MET cc_start: 0.3018 (tpt) cc_final: 0.2526 (tpt) REVERT: A 487 ASN cc_start: 0.8388 (t0) cc_final: 0.8153 (t0) REVERT: A 551 MET cc_start: 0.8189 (ptm) cc_final: 0.7902 (ptp) REVERT: B 9 ILE cc_start: 0.8114 (mm) cc_final: 0.7699 (mm) REVERT: C 39 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7503 (ttt) REVERT: C 71 MET cc_start: 0.7696 (mmp) cc_final: 0.5789 (tmm) REVERT: E 120 MET cc_start: 0.8730 (tpt) cc_final: 0.8385 (tpp) REVERT: E 157 HIS cc_start: 0.8844 (OUTLIER) cc_final: 0.8249 (p-80) outliers start: 29 outliers final: 21 residues processed: 174 average time/residue: 0.1107 time to fit residues: 29.9791 Evaluate side-chains 179 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 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 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 108 HIS 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 157 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 29 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 76 optimal weight: 0.0050 chunk 116 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 10 optimal weight: 0.0870 chunk 65 optimal weight: 0.9980 chunk 170 optimal weight: 20.0000 chunk 49 optimal weight: 4.9990 overall best weight: 1.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.184695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.141836 restraints weight = 25344.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.137145 restraints weight = 39763.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.139113 restraints weight = 28386.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.141898 restraints weight = 15713.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.141990 restraints weight = 12185.221| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14679 Z= 0.170 Angle : 0.673 14.276 19790 Z= 0.338 Chirality : 0.043 0.230 2262 Planarity : 0.004 0.055 2467 Dihedral : 6.541 152.824 1921 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.47 % Allowed : 18.12 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.21), residues: 1783 helix: 1.64 (0.16), residues: 1020 sheet: -2.47 (0.41), residues: 151 loop : -1.19 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 226 TYR 0.022 0.002 TYR A 314 PHE 0.031 0.001 PHE A 223 TRP 0.049 0.003 TRP E 122 HIS 0.008 0.001 HIS C 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (14679) covalent geometry : angle 0.67320 / 0.34 (19790) hydrogen bonds : bond 0.06277 / 4.14 ( 816) hydrogen bonds : angle 4.56575 / 3.35 ( 2349) ********************** 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 176 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6646 (mp0) REVERT: A 369 MET cc_start: 0.5341 (mmm) cc_final: 0.3979 (mmm) REVERT: A 416 MET cc_start: 0.3266 (tpt) cc_final: 0.2781 (tpt) REVERT: A 487 ASN cc_start: 0.8395 (t0) cc_final: 0.8127 (t0) REVERT: B 9 ILE cc_start: 0.8256 (mm) cc_final: 0.7849 (mm) REVERT: C 39 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7523 (ttt) REVERT: C 71 MET cc_start: 0.7810 (mmp) cc_final: 0.5941 (ttp) REVERT: E 120 MET cc_start: 0.8718 (tpt) cc_final: 0.8353 (tpp) REVERT: E 157 HIS cc_start: 0.8897 (OUTLIER) cc_final: 0.8135 (p-80) outliers start: 23 outliers final: 20 residues processed: 168 average time/residue: 0.1115 time to fit residues: 29.2038 Evaluate side-chains 172 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 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 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 108 HIS 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 157 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 162 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 160 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.186281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.145223 restraints weight = 25699.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.142753 restraints weight = 44457.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.145035 restraints weight = 30343.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.145120 restraints weight = 17877.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.146896 restraints weight = 14725.331| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14679 Z= 0.139 Angle : 0.632 14.046 19790 Z= 0.318 Chirality : 0.042 0.228 2262 Planarity : 0.003 0.055 2467 Dihedral : 6.538 154.148 1921 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.53 % Allowed : 18.19 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.21), residues: 1783 helix: 1.74 (0.17), residues: 1014 sheet: -2.46 (0.39), residues: 165 loop : -1.14 (0.27), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 226 TYR 0.016 0.001 TYR A 623 PHE 0.032 0.001 PHE A 223 TRP 0.045 0.003 TRP E 122 HIS 0.006 0.001 HIS C 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (14679) covalent geometry : angle 0.63153 / 0.32 (19790) hydrogen bonds : bond 0.05768 / 3.81 ( 816) hydrogen bonds : angle 4.47160 / 3.29 ( 2349) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2404.07 seconds wall clock time: 42 minutes 36.88 seconds (2556.88 seconds total)