Starting phenix.real_space_refine on Wed Mar 4 15:00:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g4d_29717/03_2026/8g4d_29717.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g4d_29717/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/8g4d_29717/03_2026/8g4d_29717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g4d_29717/03_2026/8g4d_29717.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g4d_29717/03_2026/8g4d_29717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g4d_29717/03_2026/8g4d_29717.map" } 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-5986/lib/python3.9/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: 3.22, per 1000 atoms: 0.22 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: 1.16 Conformation dependent library (CDL) restraints added in 460.4 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: 0.39 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: 2.40 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 4573 1.35 - 1.50: 3825 1.50 - 1.65: 6165 1.65 - 1.80: 62 1.80 - 1.95: 54 Bond restraints: 14679 Sorted by residual: bond pdb=" N VAL C 2 " pdb=" CA VAL C 2 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.07e+01 bond pdb=" C LYS A 558 " pdb=" N PRO A 559 " ideal model delta sigma weight residual 1.335 1.373 -0.038 1.19e-02 7.06e+03 1.03e+01 bond pdb=" N VAL B 2 " pdb=" CA VAL B 2 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.78e+00 bond pdb=" N ILE C 3 " pdb=" CA ILE C 3 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.38e-02 5.25e+03 7.51e+00 bond pdb=" N LEU B 4 " pdb=" CA LEU B 4 " ideal model delta sigma weight residual 1.458 1.490 -0.033 1.22e-02 6.72e+03 7.11e+00 ... (remaining 14674 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 19464 2.27 - 4.54: 275 4.54 - 6.81: 38 6.81 - 9.08: 12 9.08 - 11.35: 1 Bond angle restraints: 19790 Sorted by residual: angle pdb=" N TYR A 561 " pdb=" CA TYR A 561 " pdb=" C TYR A 561 " ideal model delta sigma weight residual 113.88 106.09 7.79 1.23e+00 6.61e-01 4.01e+01 angle pdb=" N GLU E 83 " pdb=" CA GLU E 83 " pdb=" C GLU E 83 " ideal model delta sigma weight residual 114.56 108.76 5.80 1.27e+00 6.20e-01 2.08e+01 angle pdb=" C GLN D 162 " pdb=" N GLN D 163 " pdb=" CA GLN D 163 " ideal model delta sigma weight residual 122.06 114.59 7.47 1.86e+00 2.89e-01 1.61e+01 angle pdb=" C ILE D 225 " pdb=" N ARG D 226 " pdb=" CA ARG D 226 " ideal model delta sigma weight residual 121.58 114.03 7.55 1.95e+00 2.63e-01 1.50e+01 angle pdb=" N THR D 69 " pdb=" CA THR D 69 " pdb=" C THR D 69 " ideal model delta sigma weight residual 111.36 107.31 4.05 1.09e+00 8.42e-01 1.38e+01 ... (remaining 19785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.70: 8510 30.70 - 61.40: 300 61.40 - 92.09: 29 92.09 - 122.79: 0 122.79 - 153.49: 1 Dihedral angle restraints: 8840 sinusoidal: 3616 harmonic: 5224 Sorted by residual: dihedral pdb=" O1A AGS C 301 " pdb=" O3A AGS C 301 " pdb=" PA AGS C 301 " pdb=" PB AGS C 301 " ideal model delta sinusoidal sigma weight residual 292.27 138.78 153.49 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" CA GLY A 604 " pdb=" C GLY A 604 " pdb=" N TRP A 605 " pdb=" CA TRP A 605 " ideal model delta harmonic sigma weight residual 180.00 157.72 22.28 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA MET E 140 " pdb=" C MET E 140 " pdb=" N GLU E 141 " pdb=" CA GLU E 141 " ideal model delta harmonic sigma weight residual -180.00 -160.63 -19.37 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 8837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1661 0.042 - 0.085: 443 0.085 - 0.127: 143 0.127 - 0.169: 12 0.169 - 0.212: 3 Chirality restraints: 2262 Sorted by residual: chirality pdb=" CB ILE E 243 " pdb=" CA ILE E 243 " pdb=" CG1 ILE E 243 " pdb=" CG2 ILE E 243 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA GLN D 163 " pdb=" N GLN D 163 " pdb=" C GLN D 163 " pdb=" CB GLN D 163 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.29e-01 chirality pdb=" CB ILE C 3 " pdb=" CA ILE C 3 " pdb=" CG1 ILE C 3 " pdb=" CG2 ILE C 3 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.14e-01 ... (remaining 2259 not shown) Planarity restraints: 2467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 122 " -0.011 2.00e-02 2.50e+03 2.10e-02 1.10e+01 pdb=" CG TRP E 122 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP E 122 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP E 122 " -0.017 2.00e-02 2.50e+03 pdb=" NE1 TRP E 122 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP E 122 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP E 122 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 122 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 122 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP E 122 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 605 " 0.021 2.00e-02 2.50e+03 1.59e-02 6.35e+00 pdb=" CG TRP A 605 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP A 605 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 605 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 605 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 605 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 605 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 605 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 605 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 605 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 153 " -0.022 2.00e-02 2.50e+03 1.43e-02 5.14e+00 pdb=" CG TRP E 153 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP E 153 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP E 153 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 153 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 153 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 153 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 153 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 153 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 153 " -0.003 2.00e-02 2.50e+03 ... (remaining 2464 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2290 2.76 - 3.30: 14519 3.30 - 3.83: 23360 3.83 - 4.37: 25816 4.37 - 4.90: 44532 Nonbonded interactions: 110517 Sorted by model distance: nonbonded pdb=" OE1 GLN E 247 " pdb=" OG1 THR E 252 " model vdw 2.228 3.040 nonbonded pdb=" O THR D 128 " pdb=" OG1 THR D 131 " model vdw 2.236 3.040 nonbonded pdb=" OD1 ASN C 95 " pdb=" NH2 ARG C 156 " model vdw 2.248 3.120 nonbonded pdb=" NH2 ARG A 9 " pdb=" O THR C 99 " model vdw 2.249 3.120 nonbonded pdb=" O ARG E 226 " pdb=" OG1 THR E 230 " model vdw 2.251 3.040 ... (remaining 110512 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.300 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14679 Z= 0.189 Angle : 0.679 11.346 19790 Z= 0.383 Chirality : 0.043 0.212 2262 Planarity : 0.004 0.067 2467 Dihedral : 15.325 153.488 5458 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.50 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 covalent geometry : bond 0.00319 (14679) covalent geometry : angle 0.67943 (19790) hydrogen bonds : bond 0.16044 ( 816) hydrogen bonds : angle 6.00000 ( 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 : 0.396 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: 0.0995 time to fit residues: 34.5378 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 : 0.516 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4431 r_free = 0.4431 target = 0.188821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.148139 restraints weight = 26132.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.146025 restraints weight = 43148.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.148377 restraints weight = 28409.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.148247 restraints weight = 16379.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.149798 restraints weight = 13998.205| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14679 Z= 0.139 Angle : 0.613 9.357 19790 Z= 0.322 Chirality : 0.042 0.197 2262 Planarity : 0.004 0.068 2467 Dihedral : 7.779 154.821 1943 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.08 % Allowed : 7.72 % Favored : 91.19 % 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: 0.22 (0.21), residues: 1783 helix: 1.55 (0.17), residues: 1022 sheet: -2.54 (0.41), residues: 148 loop : -1.58 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 226 TYR 0.016 0.001 TYR A 623 PHE 0.024 0.001 PHE A 223 TRP 0.029 0.003 TRP E 153 HIS 0.010 0.001 HIS E 134 Details of bonding type rmsd covalent geometry : bond 0.00271 (14679) covalent geometry : angle 0.61298 (19790) hydrogen bonds : bond 0.06158 ( 816) hydrogen bonds : angle 5.01656 ( 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 190 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 MET cc_start: 0.7850 (tpt) cc_final: 0.7314 (tpt) REVERT: A 487 ASN cc_start: 0.8318 (t0) cc_final: 0.8045 (t0) REVERT: A 500 LEU cc_start: 0.9226 (pp) cc_final: 0.9018 (pp) REVERT: E 120 MET cc_start: 0.8641 (tpt) cc_final: 0.8383 (tpp) REVERT: E 157 HIS cc_start: 0.8663 (p90) cc_final: 0.8207 (p90) outliers start: 17 outliers final: 10 residues processed: 184 average time/residue: 0.1080 time to fit residues: 30.4587 Evaluate side-chains 167 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 157 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 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: 0.0980 chunk 149 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 8 optimal weight: 0.0060 chunk 167 optimal weight: 20.0000 chunk 118 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 HIS B 105 ASN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 HIS E 134 HIS E 165 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.188685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.148253 restraints weight = 26084.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.145780 restraints weight = 39096.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.148060 restraints weight = 27038.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.147902 restraints weight = 16438.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.149781 restraints weight = 13757.975| |-----------------------------------------------------------------------------| r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14679 Z= 0.129 Angle : 0.592 9.646 19790 Z= 0.309 Chirality : 0.041 0.191 2262 Planarity : 0.004 0.059 2467 Dihedral : 7.694 155.056 1943 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.53 % Allowed : 10.15 % Favored : 88.32 % 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: 0.38 (0.21), residues: 1783 helix: 1.67 (0.17), residues: 1021 sheet: -2.36 (0.42), residues: 148 loop : -1.51 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 226 TYR 0.014 0.001 TYR A 623 PHE 0.030 0.001 PHE A 223 TRP 0.027 0.003 TRP E 122 HIS 0.013 0.001 HIS E 134 Details of bonding type rmsd covalent geometry : bond 0.00254 (14679) covalent geometry : angle 0.59249 (19790) hydrogen bonds : bond 0.05658 ( 816) hydrogen bonds : angle 4.81303 ( 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 193 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.6663 (mmt) cc_final: 0.6092 (mmt) REVERT: A 487 ASN cc_start: 0.8292 (t0) cc_final: 0.8009 (t0) REVERT: B 9 ILE cc_start: 0.8170 (mm) cc_final: 0.7779 (mm) REVERT: C 39 MET cc_start: 0.7489 (ttt) cc_final: 0.7277 (ttt) REVERT: C 71 MET cc_start: 0.7840 (mmp) cc_final: 0.6105 (tmm) REVERT: E 120 MET cc_start: 0.8672 (tpt) cc_final: 0.8351 (tpp) REVERT: E 157 HIS cc_start: 0.8758 (p90) cc_final: 0.8119 (p-80) outliers start: 24 outliers final: 16 residues processed: 184 average time/residue: 0.1014 time to fit residues: 28.9628 Evaluate side-chains 174 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 76 optimal weight: 0.4980 chunk 166 optimal weight: 8.9990 chunk 28 optimal weight: 0.7980 chunk 86 optimal weight: 0.4980 chunk 165 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 ASN ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.186441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.145083 restraints weight = 26002.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.140935 restraints weight = 41063.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.142943 restraints weight = 29692.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.145230 restraints weight = 16530.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.145509 restraints weight = 12730.561| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14679 Z= 0.154 Angle : 0.611 10.918 19790 Z= 0.316 Chirality : 0.042 0.288 2262 Planarity : 0.004 0.052 2467 Dihedral : 7.669 153.741 1943 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.66 % Allowed : 12.76 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.21), residues: 1783 helix: 1.64 (0.17), residues: 1024 sheet: -2.41 (0.43), residues: 136 loop : -1.51 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 226 TYR 0.017 0.001 TYR A 314 PHE 0.030 0.001 PHE A 223 TRP 0.027 0.002 TRP A 605 HIS 0.011 0.001 HIS D 165 Details of bonding type rmsd covalent geometry : bond 0.00341 (14679) covalent geometry : angle 0.61086 (19790) hydrogen bonds : bond 0.06048 ( 816) hydrogen bonds : angle 4.81290 ( 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 185 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 487 ASN cc_start: 0.8367 (t0) cc_final: 0.8087 (t0) REVERT: B 9 ILE cc_start: 0.8205 (mm) cc_final: 0.7778 (mm) REVERT: C 39 MET cc_start: 0.7703 (ttt) cc_final: 0.7488 (ttt) REVERT: C 117 LYS cc_start: 0.7520 (mmmt) cc_final: 0.7113 (tppt) REVERT: E 120 MET cc_start: 0.8759 (tpt) cc_final: 0.8433 (tpp) REVERT: E 153 TRP cc_start: 0.7557 (t60) cc_final: 0.7285 (t60) REVERT: E 157 HIS cc_start: 0.8790 (p-80) cc_final: 0.8403 (p-80) outliers start: 26 outliers final: 19 residues processed: 176 average time/residue: 0.1097 time to fit residues: 29.5809 Evaluate side-chains 169 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 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 54 SER Chi-restraints excluded: chain C residue 101 THR 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: 0.7980 chunk 51 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 chunk 46 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 73 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 ASN ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 HIS ** E 165 HIS ** 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 = 0.4417 r_free = 0.4417 target = 0.187383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.146022 restraints weight = 26083.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.141600 restraints weight = 38581.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.143484 restraints weight = 29023.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.145964 restraints weight = 15941.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.146179 restraints weight = 11805.388| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.1909 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= 0.131 Angle : 0.598 10.710 19790 Z= 0.306 Chirality : 0.041 0.217 2262 Planarity : 0.004 0.063 2467 Dihedral : 7.602 154.889 1943 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.04 % Allowed : 14.55 % 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: 0.48 (0.21), residues: 1783 helix: 1.74 (0.17), residues: 1018 sheet: -2.28 (0.44), residues: 136 loop : -1.49 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 226 TYR 0.015 0.001 TYR A 623 PHE 0.032 0.001 PHE A 501 TRP 0.049 0.002 TRP E 122 HIS 0.014 0.001 HIS D 165 Details of bonding type rmsd covalent geometry : bond 0.00268 (14679) covalent geometry : angle 0.59833 (19790) hydrogen bonds : bond 0.05667 ( 816) hydrogen bonds : angle 4.67029 ( 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 197 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.6613 (mp0) REVERT: A 487 ASN cc_start: 0.8384 (t0) cc_final: 0.8069 (t0) REVERT: B 9 ILE cc_start: 0.8133 (mm) cc_final: 0.7716 (mm) REVERT: C 39 MET cc_start: 0.7706 (ttt) cc_final: 0.7463 (ttt) REVERT: E 63 PHE cc_start: 0.7576 (t80) cc_final: 0.7243 (t80) REVERT: E 120 MET cc_start: 0.8834 (tpt) cc_final: 0.8559 (tpp) REVERT: E 153 TRP cc_start: 0.7548 (t60) cc_final: 0.7338 (t60) REVERT: E 154 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8533 (mt) REVERT: E 157 HIS cc_start: 0.8726 (p-80) cc_final: 0.8416 (p-80) outliers start: 32 outliers final: 23 residues processed: 184 average time/residue: 0.1162 time to fit residues: 32.8184 Evaluate side-chains 177 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 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 54 SER Chi-restraints excluded: chain C residue 101 THR 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 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: 0.0000 chunk 131 optimal weight: 30.0000 chunk 107 optimal weight: 3.9990 chunk 76 optimal weight: 0.0020 chunk 23 optimal weight: 0.9980 chunk 49 optimal weight: 0.0010 chunk 122 optimal weight: 4.9990 chunk 142 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 34 optimal weight: 8.9990 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 ASN B 105 ASN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN ** 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 = 0.4435 r_free = 0.4435 target = 0.189135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.148356 restraints weight = 25859.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.143915 restraints weight = 38198.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.145830 restraints weight = 28706.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.147888 restraints weight = 16181.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.148285 restraints weight = 12338.770| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14679 Z= 0.120 Angle : 0.581 12.052 19790 Z= 0.298 Chirality : 0.041 0.215 2262 Planarity : 0.004 0.085 2467 Dihedral : 7.510 156.896 1943 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.98 % Allowed : 15.63 % Favored : 82.39 % 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: 0.59 (0.21), residues: 1783 helix: 1.83 (0.17), residues: 1020 sheet: -2.18 (0.45), residues: 136 loop : -1.46 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 226 TYR 0.012 0.001 TYR A 623 PHE 0.033 0.001 PHE A 501 TRP 0.032 0.002 TRP E 122 HIS 0.007 0.001 HIS E 134 Details of bonding type rmsd covalent geometry : bond 0.00234 (14679) covalent geometry : angle 0.58102 (19790) hydrogen bonds : bond 0.05231 ( 816) hydrogen bonds : angle 4.54302 ( 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 192 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6567 (mp0) REVERT: A 369 MET cc_start: 0.4765 (mmm) cc_final: 0.4371 (mmp) REVERT: A 416 MET cc_start: 0.2886 (tpt) cc_final: 0.2649 (tpt) REVERT: A 487 ASN cc_start: 0.8371 (t0) cc_final: 0.8079 (t0) REVERT: B 9 ILE cc_start: 0.8147 (mm) cc_final: 0.7727 (mm) REVERT: C 39 MET cc_start: 0.7676 (ttt) cc_final: 0.7444 (ttt) REVERT: E 112 LEU cc_start: 0.8010 (tp) cc_final: 0.7749 (tt) REVERT: E 113 GLU cc_start: 0.7065 (mp0) cc_final: 0.6674 (mp0) REVERT: E 120 MET cc_start: 0.8769 (tpt) cc_final: 0.8484 (tpp) REVERT: E 154 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8455 (mt) REVERT: E 157 HIS cc_start: 0.8796 (p-80) cc_final: 0.8567 (p-80) outliers start: 31 outliers final: 20 residues processed: 181 average time/residue: 0.1086 time to fit residues: 30.5950 Evaluate side-chains 180 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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 393 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 101 THR 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 70 optimal weight: 0.8980 chunk 138 optimal weight: 30.0000 chunk 128 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 143 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 163 optimal weight: 20.0000 chunk 168 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 44 optimal weight: 0.0170 chunk 0 optimal weight: 5.9990 overall best weight: 1.7022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** 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 = 0.4387 r_free = 0.4387 target = 0.184022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.140333 restraints weight = 25695.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.135311 restraints weight = 35372.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.137515 restraints weight = 24749.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.139353 restraints weight = 14536.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.139821 restraints weight = 12585.866| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14679 Z= 0.194 Angle : 0.666 13.597 19790 Z= 0.339 Chirality : 0.043 0.296 2262 Planarity : 0.004 0.052 2467 Dihedral : 7.603 153.107 1943 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.85 % Allowed : 16.98 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.37 (0.21), residues: 1783 helix: 1.59 (0.16), residues: 1022 sheet: -2.38 (0.45), residues: 126 loop : -1.44 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 226 TYR 0.026 0.002 TYR A 314 PHE 0.031 0.002 PHE A 223 TRP 0.031 0.002 TRP E 122 HIS 0.009 0.001 HIS C 202 Details of bonding type rmsd covalent geometry : bond 0.00451 (14679) covalent geometry : angle 0.66626 (19790) hydrogen bonds : bond 0.06560 ( 816) hydrogen bonds : angle 4.73123 ( 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 186 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.6734 (mp0) REVERT: A 369 MET cc_start: 0.5348 (mmm) cc_final: 0.3995 (mmm) REVERT: A 416 MET cc_start: 0.3078 (tpt) cc_final: 0.2678 (tpt) REVERT: A 487 ASN cc_start: 0.8463 (t0) cc_final: 0.8205 (t0) REVERT: B 9 ILE cc_start: 0.8265 (mm) cc_final: 0.7835 (mm) REVERT: C 39 MET cc_start: 0.7869 (ttt) cc_final: 0.7664 (ttt) REVERT: C 71 MET cc_start: 0.7702 (mmp) cc_final: 0.6001 (tmm) REVERT: E 120 MET cc_start: 0.8933 (tpt) cc_final: 0.8625 (tpp) REVERT: E 154 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8596 (mt) REVERT: E 157 HIS cc_start: 0.8956 (p-80) cc_final: 0.8709 (p-80) outliers start: 29 outliers final: 20 residues processed: 177 average time/residue: 0.1117 time to fit residues: 30.3416 Evaluate side-chains 171 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 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 B residue 245 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 54 SER 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 160 LEU Chi-restraints excluded: chain D residue 272 PHE Chi-restraints excluded: chain E residue 151 TYR Chi-restraints excluded: chain E residue 154 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 141 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 166 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 170 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 HIS ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** 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 = 0.4415 r_free = 0.4415 target = 0.186803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.144422 restraints weight = 25626.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.140345 restraints weight = 38144.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.142311 restraints weight = 27701.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.144761 restraints weight = 15481.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.144921 restraints weight = 12401.334| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14679 Z= 0.137 Angle : 0.624 13.688 19790 Z= 0.317 Chirality : 0.042 0.242 2262 Planarity : 0.003 0.052 2467 Dihedral : 7.559 155.180 1943 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.44 % Favored : 94.50 % Rotamer: Outliers : 1.85 % Allowed : 17.80 % Favored : 80.34 % 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: 0.52 (0.21), residues: 1783 helix: 1.70 (0.17), residues: 1020 sheet: -2.35 (0.44), residues: 135 loop : -1.31 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 226 TYR 0.015 0.001 TYR A 623 PHE 0.033 0.001 PHE A 223 TRP 0.037 0.003 TRP D 220 HIS 0.006 0.001 HIS C 202 Details of bonding type rmsd covalent geometry : bond 0.00287 (14679) covalent geometry : angle 0.62424 (19790) hydrogen bonds : bond 0.05834 ( 816) hydrogen bonds : angle 4.59910 ( 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 177 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6649 (mp0) REVERT: A 369 MET cc_start: 0.5168 (mmm) cc_final: 0.3830 (mmm) REVERT: A 416 MET cc_start: 0.3081 (tpt) cc_final: 0.2632 (tpt) REVERT: A 487 ASN cc_start: 0.8356 (t0) cc_final: 0.8141 (t0) REVERT: B 9 ILE cc_start: 0.8172 (mm) cc_final: 0.7747 (mm) REVERT: C 39 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7536 (ttt) REVERT: C 71 MET cc_start: 0.7661 (mmp) cc_final: 0.5934 (tmm) REVERT: D 294 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7513 (pp) REVERT: E 120 MET cc_start: 0.8836 (tpt) cc_final: 0.8543 (tpp) REVERT: E 154 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8464 (mt) REVERT: E 157 HIS cc_start: 0.8855 (p-80) cc_final: 0.8648 (p-80) outliers start: 29 outliers final: 24 residues processed: 164 average time/residue: 0.1064 time to fit residues: 27.0897 Evaluate side-chains 179 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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 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 B residue 221 MET Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 205 VAL 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 172 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 72 optimal weight: 0.0870 chunk 26 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 13 optimal weight: 0.2980 chunk 160 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN C 190 ASN ** 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 = 0.4431 r_free = 0.4431 target = 0.188428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.146074 restraints weight = 25796.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.140864 restraints weight = 37970.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.143202 restraints weight = 26494.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.145341 restraints weight = 15031.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.145717 restraints weight = 11851.754| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 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 : 0.002 0.037 14679 Z= 0.124 Angle : 0.608 13.792 19790 Z= 0.307 Chirality : 0.041 0.223 2262 Planarity : 0.003 0.053 2467 Dihedral : 7.459 157.336 1943 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.61 % Favored : 94.34 % Rotamer: Outliers : 1.85 % Allowed : 17.68 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.58 (0.21), residues: 1783 helix: 1.79 (0.17), residues: 1020 sheet: -2.44 (0.40), residues: 165 loop : -1.24 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 226 TYR 0.013 0.001 TYR A 623 PHE 0.033 0.001 PHE A 223 TRP 0.039 0.002 TRP D 220 HIS 0.005 0.001 HIS C 202 Details of bonding type rmsd covalent geometry : bond 0.00250 (14679) covalent geometry : angle 0.60818 (19790) hydrogen bonds : bond 0.05293 ( 816) hydrogen bonds : angle 4.46022 ( 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 185 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6606 (mp0) REVERT: A 338 LYS cc_start: 0.9344 (tptp) cc_final: 0.9123 (tptp) REVERT: A 369 MET cc_start: 0.5275 (mmm) cc_final: 0.3918 (mmm) REVERT: A 416 MET cc_start: 0.3065 (tpt) cc_final: 0.2542 (tpt) REVERT: A 487 ASN cc_start: 0.8377 (t0) cc_final: 0.8160 (t0) REVERT: B 9 ILE cc_start: 0.8124 (mm) cc_final: 0.7704 (mm) REVERT: C 39 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.7445 (ttt) REVERT: C 71 MET cc_start: 0.7701 (mmp) cc_final: 0.5977 (tmm) REVERT: E 120 MET cc_start: 0.8841 (tpt) cc_final: 0.8553 (tpp) outliers start: 29 outliers final: 21 residues processed: 174 average time/residue: 0.1081 time to fit residues: 29.0508 Evaluate side-chains 175 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 205 VAL 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 151 TYR Chi-restraints excluded: chain E residue 172 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 29 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 76 optimal weight: 0.0770 chunk 116 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 170 optimal weight: 30.0000 chunk 49 optimal weight: 0.6980 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 GLN A 582 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.186233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.142692 restraints weight = 25467.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.139905 restraints weight = 38099.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.142466 restraints weight = 26484.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.142182 restraints weight = 15569.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.144389 restraints weight = 13640.069| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14679 Z= 0.140 Angle : 0.641 16.598 19790 Z= 0.320 Chirality : 0.042 0.233 2262 Planarity : 0.003 0.055 2467 Dihedral : 7.431 156.701 1943 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.66 % Favored : 94.28 % Rotamer: Outliers : 1.53 % Allowed : 18.12 % Favored : 80.34 % 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: 1.76 (0.17), residues: 1020 sheet: -2.45 (0.40), residues: 165 loop : -1.20 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 226 TYR 0.014 0.001 TYR A 314 PHE 0.033 0.001 PHE A 223 TRP 0.029 0.002 TRP D 220 HIS 0.006 0.001 HIS C 202 Details of bonding type rmsd covalent geometry : bond 0.00301 (14679) covalent geometry : angle 0.64091 (19790) hydrogen bonds : bond 0.05634 ( 816) hydrogen bonds : angle 4.48045 ( 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 180 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.6655 (mp0) REVERT: A 369 MET cc_start: 0.5217 (mmm) cc_final: 0.3849 (mmm) REVERT: A 416 MET cc_start: 0.3090 (tpt) cc_final: 0.2595 (tpt) REVERT: A 487 ASN cc_start: 0.8364 (t0) cc_final: 0.8091 (t0) REVERT: B 9 ILE cc_start: 0.8173 (mm) cc_final: 0.7751 (mm) REVERT: C 39 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7458 (ttt) REVERT: C 71 MET cc_start: 0.7753 (mmp) cc_final: 0.6000 (tmm) REVERT: D 41 MET cc_start: 0.6685 (tmm) cc_final: 0.6470 (tmm) REVERT: E 120 MET cc_start: 0.8805 (tpt) cc_final: 0.8526 (tpp) REVERT: E 157 HIS cc_start: 0.8769 (p-80) cc_final: 0.8428 (p-80) outliers start: 24 outliers final: 21 residues processed: 172 average time/residue: 0.1057 time to fit residues: 28.0225 Evaluate side-chains 177 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 205 VAL Chi-restraints excluded: chain D residue 8 GLU 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 172 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 162 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 46 optimal weight: 9.9990 chunk 160 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 97 optimal weight: 0.0770 chunk 54 optimal weight: 0.7980 overall best weight: 1.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 = 0.4407 r_free = 0.4407 target = 0.186059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.143957 restraints weight = 25940.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.144439 restraints weight = 42465.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.145465 restraints weight = 27374.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.145511 restraints weight = 17807.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.147791 restraints weight = 14570.840| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14679 Z= 0.148 Angle : 0.639 14.752 19790 Z= 0.323 Chirality : 0.042 0.232 2262 Planarity : 0.003 0.054 2467 Dihedral : 7.445 155.911 1943 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.00 % Favored : 93.94 % Rotamer: Outliers : 1.85 % Allowed : 18.00 % Favored : 80.15 % 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: 1.70 (0.17), residues: 1021 sheet: -2.50 (0.39), residues: 165 loop : -1.14 (0.27), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 226 TYR 0.017 0.001 TYR A 314 PHE 0.033 0.001 PHE A 223 TRP 0.030 0.002 TRP D 220 HIS 0.006 0.001 HIS C 202 Details of bonding type rmsd covalent geometry : bond 0.00324 (14679) covalent geometry : angle 0.63867 (19790) hydrogen bonds : bond 0.05918 ( 816) hydrogen bonds : angle 4.50770 ( 2349) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2292.57 seconds wall clock time: 40 minutes 29.47 seconds (2429.47 seconds total)