Starting phenix.real_space_refine on Sat May 17 05:46:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ib2_35329/05_2025/8ib2_35329.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ib2_35329/05_2025/8ib2_35329.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ib2_35329/05_2025/8ib2_35329.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ib2_35329/05_2025/8ib2_35329.map" model { file = "/net/cci-nas-00/data/ceres_data/8ib2_35329/05_2025/8ib2_35329.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ib2_35329/05_2025/8ib2_35329.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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 10 5.49 5 S 113 5.16 5 C 9608 2.51 5 N 2568 2.21 5 O 2930 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15229 Number of models: 1 Model: "" Number of chains: 11 Chain: "5" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 549 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain: "B" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2909 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2909 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Chain: "D" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2909 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Chain: "E" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2909 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Chain: "F" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2909 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.58, per 1000 atoms: 0.56 Number of scatterers: 15229 At special positions: 0 Unit cell: (108.23, 93.16, 190.43, 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 113 16.00 P 10 15.00 O 2930 8.00 N 2568 7.00 C 9608 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.55 Conformation dependent library (CDL) restraints added in 1.9 seconds 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3576 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 30 sheets defined 48.4% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.24 Creating SS restraints... Processing helix chain '5' and resid 344 through 349 removed outlier: 3.906A pdb=" N LEU 5 348 " --> pdb=" O PRO 5 344 " (cutoff:3.500A) Processing helix chain '5' and resid 372 through 381 Processing helix chain '5' and resid 383 through 390 removed outlier: 3.556A pdb=" N LEU 5 390 " --> pdb=" O GLU 5 386 " (cutoff:3.500A) Processing helix chain '5' and resid 391 through 402 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 93 removed outlier: 3.756A pdb=" N MET B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU B 93 " --> pdb=" O THR B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 127 removed outlier: 4.259A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU B 117 " --> pdb=" O LYS B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.524A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 removed outlier: 3.569A pdb=" N SER B 233 " --> pdb=" O THR B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 255 removed outlier: 3.915A pdb=" N ARG B 254 " --> pdb=" O GLY B 251 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE B 255 " --> pdb=" O ASN B 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 251 through 255' Processing helix chain 'B' and resid 258 through 263 removed outlier: 3.944A pdb=" N PHE B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 289 through 296 removed outlier: 3.870A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.653A pdb=" N MET B 305 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 302 through 306' Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 347 removed outlier: 3.826A pdb=" N GLY B 343 " --> pdb=" O VAL B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 4.054A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.567A pdb=" N GLN C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.582A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 113 through 126 removed outlier: 3.965A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.558A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 194 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 216 removed outlier: 3.926A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 260 removed outlier: 4.082A pdb=" N ARG C 256 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Proline residue: C 258 - end of helix No H-bonds generated for 'chain 'C' and resid 252 through 260' Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.782A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 306 removed outlier: 3.853A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.682A pdb=" N ARG C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 347 removed outlier: 4.075A pdb=" N GLY C 343 " --> pdb=" O VAL C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 356 removed outlier: 3.738A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TRP C 356 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 79 through 92 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.730A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.967A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.731A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.810A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 193 removed outlier: 3.512A pdb=" N LEU D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 204 No H-bonds generated for 'chain 'D' and resid 202 through 204' Processing helix chain 'D' and resid 205 through 216 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 251 through 256 removed outlier: 3.960A pdb=" N ARG D 254 " --> pdb=" O GLY D 251 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE D 255 " --> pdb=" O ASN D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 262 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.691A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 removed outlier: 4.120A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 347 removed outlier: 3.801A pdb=" N GLY D 343 " --> pdb=" O VAL D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 356 removed outlier: 6.316A pdb=" N THR D 351 " --> pdb=" O SER D 348 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE D 352 " --> pdb=" O LEU D 349 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET D 355 " --> pdb=" O PHE D 352 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TRP D 356 " --> pdb=" O GLN D 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 348 through 356' Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 55 through 61 removed outlier: 3.543A pdb=" N LYS E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 93 removed outlier: 3.626A pdb=" N GLU E 93 " --> pdb=" O THR E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 126 removed outlier: 4.037A pdb=" N GLU E 117 " --> pdb=" O LYS E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.541A pdb=" N ILE E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.737A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 216 Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 removed outlier: 4.119A pdb=" N ARG E 256 " --> pdb=" O ASN E 252 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 252 through 257' Processing helix chain 'E' and resid 258 through 261 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 289 through 295 Processing helix chain 'E' and resid 301 through 306 removed outlier: 4.066A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 removed outlier: 3.718A pdb=" N ARG E 312 " --> pdb=" O GLY E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 347 Processing helix chain 'E' and resid 348 through 349 No H-bonds generated for 'chain 'E' and resid 348 through 349' Processing helix chain 'E' and resid 350 through 355 removed outlier: 3.677A pdb=" N GLN E 353 " --> pdb=" O SER E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 368 through 374 removed outlier: 4.023A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 61 removed outlier: 3.583A pdb=" N LYS F 61 " --> pdb=" O GLU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 92 Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.690A pdb=" N HIS F 101 " --> pdb=" O PRO F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.839A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 146 Processing helix chain 'F' and resid 172 through 175 Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 202 through 216 Processing helix chain 'F' and resid 222 through 233 Processing helix chain 'F' and resid 251 through 256 removed outlier: 3.962A pdb=" N PHE F 255 " --> pdb=" O ASN F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 262 removed outlier: 3.643A pdb=" N LEU F 261 " --> pdb=" O PRO F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 267 Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 289 through 296 Processing helix chain 'F' and resid 301 through 306 removed outlier: 4.074A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 removed outlier: 3.509A pdb=" N ARG F 312 " --> pdb=" O GLY F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 336 No H-bonds generated for 'chain 'F' and resid 334 through 336' Processing helix chain 'F' and resid 337 through 349 removed outlier: 3.920A pdb=" N GLY F 343 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU F 349 " --> pdb=" O ILE F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 355 Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 368 through 374 removed outlier: 4.405A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.841A pdb=" N THR B 106 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ALA B 135 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET B 132 " --> pdb=" O ILE B 357 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'B' and resid 176 through 178 removed outlier: 7.477A pdb=" N VAL B 298 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.736A pdb=" N ALA B 170 " --> pdb=" O GLN D 41 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 239 through 241 Processing sheet with id=AA7, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.725A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N VAL C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ALA C 135 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.566A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N MET C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THR C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 176 through 178 removed outlier: 3.641A pdb=" N GLN E 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 239 through 241 Processing sheet with id=AB4, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.559A pdb=" N LEU D 104 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR D 106 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET D 132 " --> pdb=" O ILE D 357 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.505A pdb=" N THR D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 239 through 241 Processing sheet with id=AC1, first strand: chain 'E' and resid 29 through 32 removed outlier: 4.018A pdb=" N THR E 106 " --> pdb=" O VAL E 10 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ASN E 12 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N ALA E 135 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.407A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N MET E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N THR E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 239 through 241 Processing sheet with id=AC7, first strand: chain 'F' and resid 29 through 32 removed outlier: 4.175A pdb=" N THR F 106 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ASN F 12 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ALA F 135 " --> pdb=" O VAL F 103 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET F 132 " --> pdb=" O ILE F 357 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'F' and resid 169 through 170 removed outlier: 6.507A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N MET F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 239 through 241 667 hydrogen bonds defined for protein. 1764 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.97 Time building geometry restraints manager: 4.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4945 1.34 - 1.46: 3223 1.46 - 1.58: 7187 1.58 - 1.70: 15 1.70 - 1.82: 196 Bond restraints: 15566 Sorted by residual: bond pdb=" CA VAL F 43 " pdb=" CB VAL F 43 " ideal model delta sigma weight residual 1.531 1.551 -0.020 1.11e-02 8.12e+03 3.32e+00 bond pdb=" CB GLN B 354 " pdb=" CG GLN B 354 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.09e+00 bond pdb=" CB ASN C 252 " pdb=" CG ASN C 252 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.83e+00 bond pdb=" CA THR E 201 " pdb=" CB THR E 201 " ideal model delta sigma weight residual 1.530 1.550 -0.020 1.69e-02 3.50e+03 1.42e+00 bond pdb=" CG GLN B 354 " pdb=" CD GLN B 354 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.41e+00 ... (remaining 15561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 20683 2.16 - 4.31: 344 4.31 - 6.47: 67 6.47 - 8.63: 9 8.63 - 10.79: 2 Bond angle restraints: 21105 Sorted by residual: angle pdb=" C GLY B 42 " pdb=" N VAL B 43 " pdb=" CA VAL B 43 " ideal model delta sigma weight residual 121.97 128.58 -6.61 1.80e+00 3.09e-01 1.35e+01 angle pdb=" CB GLN B 354 " pdb=" CG GLN B 354 " pdb=" CD GLN B 354 " ideal model delta sigma weight residual 112.60 118.46 -5.86 1.70e+00 3.46e-01 1.19e+01 angle pdb=" CA GLU E 364 " pdb=" CB GLU E 364 " pdb=" CG GLU E 364 " ideal model delta sigma weight residual 114.10 120.59 -6.49 2.00e+00 2.50e-01 1.05e+01 angle pdb=" CB MET 5 365 " pdb=" CG MET 5 365 " pdb=" SD MET 5 365 " ideal model delta sigma weight residual 112.70 103.03 9.67 3.00e+00 1.11e-01 1.04e+01 angle pdb=" N GLU D 83 " pdb=" CA GLU D 83 " pdb=" CB GLU D 83 " ideal model delta sigma weight residual 110.28 115.17 -4.89 1.55e+00 4.16e-01 9.95e+00 ... (remaining 21100 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8466 17.94 - 35.89: 768 35.89 - 53.83: 119 53.83 - 71.77: 21 71.77 - 89.72: 12 Dihedral angle restraints: 9386 sinusoidal: 3808 harmonic: 5578 Sorted by residual: dihedral pdb=" CA VAL D 152 " pdb=" C VAL D 152 " pdb=" N MET D 153 " pdb=" CA MET D 153 " ideal model delta harmonic sigma weight residual 180.00 155.85 24.15 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA GLN F 353 " pdb=" C GLN F 353 " pdb=" N GLN F 354 " pdb=" CA GLN F 354 " ideal model delta harmonic sigma weight residual 180.00 155.90 24.10 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" O1B ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PB ADP E 401 " pdb=" PA ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 -134.83 74.83 1 2.00e+01 2.50e-03 1.77e+01 ... (remaining 9383 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1846 0.054 - 0.107: 401 0.107 - 0.161: 86 0.161 - 0.215: 3 0.215 - 0.268: 2 Chirality restraints: 2338 Sorted by residual: chirality pdb=" CB ILE F 250 " pdb=" CA ILE F 250 " pdb=" CG1 ILE F 250 " pdb=" CG2 ILE F 250 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CB ILE D 250 " pdb=" CA ILE D 250 " pdb=" CG1 ILE D 250 " pdb=" CG2 ILE D 250 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA MET C 123 " pdb=" N MET C 123 " pdb=" C MET C 123 " pdb=" CB MET C 123 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 2335 not shown) Planarity restraints: 2700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP 5 363 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.59e+00 pdb=" CG ASP 5 363 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASP 5 363 " -0.017 2.00e-02 2.50e+03 pdb=" OD2 ASP 5 363 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 111 " 0.041 5.00e-02 4.00e+02 6.17e-02 6.09e+00 pdb=" N PRO C 112 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 112 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 112 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 242 " 0.029 5.00e-02 4.00e+02 4.31e-02 2.98e+00 pdb=" N PRO E 243 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO E 243 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 243 " 0.024 5.00e-02 4.00e+02 ... (remaining 2697 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2432 2.77 - 3.30: 13542 3.30 - 3.83: 23805 3.83 - 4.37: 27944 4.37 - 4.90: 49784 Nonbonded interactions: 117507 Sorted by model distance: nonbonded pdb=" OG1 THR F 202 " pdb=" OE1 GLU F 205 " model vdw 2.232 3.040 nonbonded pdb=" OG SER F 141 " pdb=" OG SER F 300 " model vdw 2.262 3.040 nonbonded pdb=" OD1 ASP F 157 " pdb=" O3' ADP F 401 " model vdw 2.306 3.040 nonbonded pdb=" OD1 ASP B 157 " pdb=" O3' ADP B 401 " model vdw 2.319 3.040 nonbonded pdb=" NZ LYS C 213 " pdb=" O2' ADP C 401 " model vdw 2.329 3.120 ... (remaining 117502 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' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 34.440 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 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 0.043 15566 Z= 0.142 Angle : 0.688 10.786 21105 Z= 0.354 Chirality : 0.047 0.268 2338 Planarity : 0.005 0.062 2700 Dihedral : 13.903 89.718 5810 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.19), residues: 1919 helix: -0.37 (0.18), residues: 750 sheet: 0.74 (0.28), residues: 332 loop : 0.26 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 356 HIS 0.003 0.001 HIS E 371 PHE 0.026 0.001 PHE E 124 TYR 0.009 0.001 TYR E 143 ARG 0.009 0.000 ARG E 372 Details of bonding type rmsd hydrogen bonds : bond 0.15686 ( 653) hydrogen bonds : angle 6.76003 ( 1764) covalent geometry : bond 0.00305 (15566) covalent geometry : angle 0.68761 (21105) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 1.617 Fit side-chains revert: symmetry clash REVERT: 5 376 PHE cc_start: 0.8161 (t80) cc_final: 0.7868 (t80) REVERT: B 122 ILE cc_start: 0.7942 (mt) cc_final: 0.7682 (mt) REVERT: B 195 GLU cc_start: 0.7678 (tp30) cc_final: 0.7418 (tp30) REVERT: C 72 GLU cc_start: 0.7447 (pp20) cc_final: 0.7214 (pp20) REVERT: C 269 MET cc_start: 0.8282 (mtt) cc_final: 0.7882 (mtp) REVERT: D 117 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7692 (mt-10) REVERT: E 296 ASN cc_start: 0.8844 (m-40) cc_final: 0.8389 (m-40) REVERT: E 313 MET cc_start: 0.8058 (tpp) cc_final: 0.7709 (tpp) REVERT: F 16 MET cc_start: 0.8169 (mmp) cc_final: 0.7950 (mmm) REVERT: F 113 LYS cc_start: 0.7382 (mtmt) cc_final: 0.6828 (pttm) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.2450 time to fit residues: 73.4735 Evaluate side-chains 152 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 57 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 173 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN F 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.090934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.078162 restraints weight = 25990.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.079729 restraints weight = 16794.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.080390 restraints weight = 11188.956| |-----------------------------------------------------------------------------| r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15566 Z= 0.139 Angle : 0.575 7.710 21105 Z= 0.281 Chirality : 0.045 0.163 2338 Planarity : 0.004 0.049 2700 Dihedral : 6.454 84.629 2159 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.79 % Allowed : 5.98 % Favored : 93.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.20), residues: 1919 helix: 0.32 (0.19), residues: 784 sheet: 0.54 (0.28), residues: 331 loop : 0.53 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 356 HIS 0.004 0.001 HIS C 88 PHE 0.008 0.001 PHE C 255 TYR 0.012 0.001 TYR 5 345 ARG 0.003 0.000 ARG E 177 Details of bonding type rmsd hydrogen bonds : bond 0.03866 ( 653) hydrogen bonds : angle 4.91114 ( 1764) covalent geometry : bond 0.00326 (15566) covalent geometry : angle 0.57473 (21105) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 1.644 Fit side-chains REVERT: B 117 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7653 (tt0) REVERT: C 227 MET cc_start: 0.8814 (mmm) cc_final: 0.8215 (tpp) REVERT: D 283 MET cc_start: 0.8641 (mmt) cc_final: 0.8130 (mmt) REVERT: D 313 MET cc_start: 0.9079 (tpp) cc_final: 0.8415 (ttm) REVERT: E 45 VAL cc_start: 0.9196 (p) cc_final: 0.8979 (p) REVERT: E 132 MET cc_start: 0.7922 (ptm) cc_final: 0.7705 (ttp) REVERT: E 296 ASN cc_start: 0.8635 (m-40) cc_final: 0.8127 (m-40) REVERT: E 313 MET cc_start: 0.8403 (tpp) cc_final: 0.8049 (tpp) REVERT: F 82 MET cc_start: 0.8937 (tpt) cc_final: 0.8613 (tpt) REVERT: F 113 LYS cc_start: 0.8027 (mtmt) cc_final: 0.7506 (pttm) outliers start: 13 outliers final: 9 residues processed: 159 average time/residue: 0.2230 time to fit residues: 56.4166 Evaluate side-chains 146 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 272 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 176 optimal weight: 0.2980 chunk 150 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 169 optimal weight: 10.0000 chunk 187 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN D 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.089293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.076728 restraints weight = 26496.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.078285 restraints weight = 17807.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.079796 restraints weight = 11295.479| |-----------------------------------------------------------------------------| r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15566 Z= 0.144 Angle : 0.565 8.572 21105 Z= 0.273 Chirality : 0.045 0.149 2338 Planarity : 0.004 0.045 2700 Dihedral : 6.282 88.208 2159 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.10 % Allowed : 7.99 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.20), residues: 1919 helix: 0.71 (0.19), residues: 777 sheet: 0.41 (0.28), residues: 331 loop : 0.54 (0.23), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 340 HIS 0.004 0.001 HIS E 87 PHE 0.008 0.001 PHE 5 380 TYR 0.009 0.001 TYR E 143 ARG 0.002 0.000 ARG C 116 Details of bonding type rmsd hydrogen bonds : bond 0.03483 ( 653) hydrogen bonds : angle 4.60706 ( 1764) covalent geometry : bond 0.00344 (15566) covalent geometry : angle 0.56538 (21105) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 1.667 Fit side-chains REVERT: B 117 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7691 (tt0) REVERT: C 227 MET cc_start: 0.8836 (mmm) cc_final: 0.8253 (tpp) REVERT: D 227 MET cc_start: 0.8818 (mmm) cc_final: 0.8387 (tpt) REVERT: D 283 MET cc_start: 0.8611 (mmt) cc_final: 0.8264 (mpp) REVERT: E 132 MET cc_start: 0.7993 (ptm) cc_final: 0.7629 (ttp) REVERT: E 296 ASN cc_start: 0.8657 (m-40) cc_final: 0.8406 (m-40) REVERT: E 313 MET cc_start: 0.8408 (tpp) cc_final: 0.8062 (tpp) REVERT: E 326 LYS cc_start: 0.8670 (tttt) cc_final: 0.8251 (pttp) REVERT: F 82 MET cc_start: 0.8886 (tpt) cc_final: 0.8556 (tpt) REVERT: F 113 LYS cc_start: 0.8076 (mtmt) cc_final: 0.7541 (pttt) REVERT: F 132 MET cc_start: 0.7822 (tmm) cc_final: 0.7597 (tmm) REVERT: F 328 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7747 (mmpt) outliers start: 18 outliers final: 13 residues processed: 164 average time/residue: 0.2393 time to fit residues: 61.6113 Evaluate side-chains 153 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 328 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 107 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 11 optimal weight: 0.0270 chunk 51 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN E 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.089686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.077564 restraints weight = 26271.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.078849 restraints weight = 16371.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.080132 restraints weight = 11367.611| |-----------------------------------------------------------------------------| r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 15566 Z= 0.194 Angle : 0.605 7.193 21105 Z= 0.295 Chirality : 0.047 0.157 2338 Planarity : 0.004 0.048 2700 Dihedral : 6.307 87.083 2159 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.52 % Allowed : 9.94 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.20), residues: 1919 helix: 0.82 (0.20), residues: 777 sheet: 0.31 (0.28), residues: 331 loop : 0.45 (0.23), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 340 HIS 0.005 0.001 HIS E 87 PHE 0.018 0.001 PHE 5 376 TYR 0.010 0.001 TYR E 143 ARG 0.003 0.000 ARG C 256 Details of bonding type rmsd hydrogen bonds : bond 0.03815 ( 653) hydrogen bonds : angle 4.63345 ( 1764) covalent geometry : bond 0.00466 (15566) covalent geometry : angle 0.60456 (21105) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 1.435 Fit side-chains REVERT: 5 396 ASN cc_start: 0.8782 (m-40) cc_final: 0.8442 (m-40) REVERT: B 117 GLU cc_start: 0.8378 (mt-10) cc_final: 0.7710 (tt0) REVERT: C 227 MET cc_start: 0.8929 (mmm) cc_final: 0.8327 (tpp) REVERT: D 227 MET cc_start: 0.8791 (mmm) cc_final: 0.8375 (tpt) REVERT: E 132 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7721 (ttp) REVERT: E 313 MET cc_start: 0.8529 (tpp) cc_final: 0.8204 (tpp) REVERT: E 326 LYS cc_start: 0.8728 (tttt) cc_final: 0.8461 (pttt) REVERT: F 44 MET cc_start: 0.7939 (mmm) cc_final: 0.7469 (mmt) REVERT: F 113 LYS cc_start: 0.8209 (mtmt) cc_final: 0.7636 (pttt) REVERT: F 283 MET cc_start: 0.9023 (mmt) cc_final: 0.8799 (mmt) REVERT: F 328 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7766 (mmpt) outliers start: 25 outliers final: 18 residues processed: 160 average time/residue: 0.2416 time to fit residues: 60.6442 Evaluate side-chains 159 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 328 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 72 optimal weight: 0.8980 chunk 189 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN E 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.088698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.075933 restraints weight = 26637.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.077522 restraints weight = 16336.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.078614 restraints weight = 11263.610| |-----------------------------------------------------------------------------| r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15566 Z= 0.109 Angle : 0.543 7.441 21105 Z= 0.260 Chirality : 0.044 0.138 2338 Planarity : 0.004 0.046 2700 Dihedral : 6.091 86.220 2159 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.28 % Allowed : 11.34 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.20), residues: 1919 helix: 1.06 (0.20), residues: 777 sheet: 0.34 (0.28), residues: 331 loop : 0.53 (0.23), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 340 HIS 0.002 0.001 HIS E 87 PHE 0.008 0.001 PHE B 255 TYR 0.007 0.001 TYR F 53 ARG 0.003 0.000 ARG 5 366 Details of bonding type rmsd hydrogen bonds : bond 0.03036 ( 653) hydrogen bonds : angle 4.41938 ( 1764) covalent geometry : bond 0.00256 (15566) covalent geometry : angle 0.54308 (21105) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 1.758 Fit side-chains REVERT: 5 365 MET cc_start: 0.7767 (tpp) cc_final: 0.7353 (tpp) REVERT: 5 396 ASN cc_start: 0.8781 (m-40) cc_final: 0.8466 (m-40) REVERT: B 117 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7677 (tt0) REVERT: B 313 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8410 (ttp) REVERT: C 82 MET cc_start: 0.8492 (tpp) cc_final: 0.8215 (tpt) REVERT: C 227 MET cc_start: 0.8899 (mmm) cc_final: 0.8264 (tpp) REVERT: D 227 MET cc_start: 0.8723 (mmm) cc_final: 0.8337 (tpt) REVERT: D 283 MET cc_start: 0.8777 (tpp) cc_final: 0.7550 (mpp) REVERT: E 12 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8487 (t160) REVERT: E 132 MET cc_start: 0.7981 (ptm) cc_final: 0.7661 (ttp) REVERT: F 113 LYS cc_start: 0.8159 (mtmt) cc_final: 0.7574 (pttt) REVERT: F 283 MET cc_start: 0.8897 (mmt) cc_final: 0.8660 (mmt) REVERT: F 328 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7727 (mmpt) outliers start: 21 outliers final: 13 residues processed: 166 average time/residue: 0.2512 time to fit residues: 65.9993 Evaluate side-chains 163 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 328 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 128 optimal weight: 3.9990 chunk 171 optimal weight: 10.0000 chunk 133 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 178 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 50 optimal weight: 0.0470 chunk 130 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.089481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.076989 restraints weight = 26511.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.078506 restraints weight = 17195.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.079689 restraints weight = 11340.200| |-----------------------------------------------------------------------------| r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15566 Z= 0.097 Angle : 0.529 7.746 21105 Z= 0.252 Chirality : 0.043 0.273 2338 Planarity : 0.004 0.046 2700 Dihedral : 5.962 85.399 2159 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.40 % Allowed : 11.71 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.20), residues: 1919 helix: 1.24 (0.20), residues: 777 sheet: 0.35 (0.29), residues: 331 loop : 0.60 (0.23), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 340 HIS 0.003 0.000 HIS F 161 PHE 0.008 0.001 PHE 5 376 TYR 0.007 0.001 TYR F 53 ARG 0.002 0.000 ARG B 116 Details of bonding type rmsd hydrogen bonds : bond 0.02833 ( 653) hydrogen bonds : angle 4.30461 ( 1764) covalent geometry : bond 0.00224 (15566) covalent geometry : angle 0.52865 (21105) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 1.668 Fit side-chains REVERT: B 117 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7650 (tt0) REVERT: B 313 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8392 (ttp) REVERT: C 227 MET cc_start: 0.8876 (mmm) cc_final: 0.8256 (tpp) REVERT: D 123 MET cc_start: 0.8961 (tpp) cc_final: 0.8643 (tpp) REVERT: D 227 MET cc_start: 0.8720 (mmm) cc_final: 0.8309 (tpt) REVERT: D 283 MET cc_start: 0.8818 (tpp) cc_final: 0.7432 (mpp) REVERT: E 132 MET cc_start: 0.7975 (ptm) cc_final: 0.7646 (ttp) REVERT: F 113 LYS cc_start: 0.8117 (mtmt) cc_final: 0.7554 (pttt) REVERT: F 328 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7685 (mmpt) outliers start: 23 outliers final: 16 residues processed: 161 average time/residue: 0.2237 time to fit residues: 57.4089 Evaluate side-chains 160 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 257 CYS Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 328 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 61 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 94 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 157 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN E 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.088443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.075897 restraints weight = 26716.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.077503 restraints weight = 17734.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.078378 restraints weight = 11597.814| |-----------------------------------------------------------------------------| r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15566 Z= 0.131 Angle : 0.550 8.162 21105 Z= 0.263 Chirality : 0.044 0.222 2338 Planarity : 0.004 0.047 2700 Dihedral : 5.872 83.894 2159 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.40 % Allowed : 12.56 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.20), residues: 1919 helix: 1.40 (0.20), residues: 753 sheet: 0.36 (0.29), residues: 331 loop : 0.56 (0.23), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 340 HIS 0.003 0.001 HIS E 87 PHE 0.008 0.001 PHE B 255 TYR 0.008 0.001 TYR C 143 ARG 0.002 0.000 ARG C 256 Details of bonding type rmsd hydrogen bonds : bond 0.03140 ( 653) hydrogen bonds : angle 4.32776 ( 1764) covalent geometry : bond 0.00314 (15566) covalent geometry : angle 0.55033 (21105) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 1.627 Fit side-chains REVERT: 5 348 LEU cc_start: 0.8593 (mt) cc_final: 0.8387 (mt) REVERT: 5 365 MET cc_start: 0.7915 (tpp) cc_final: 0.7481 (tpp) REVERT: 5 396 ASN cc_start: 0.8790 (m-40) cc_final: 0.8449 (m-40) REVERT: B 117 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7673 (tt0) REVERT: B 313 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8448 (ttp) REVERT: C 227 MET cc_start: 0.8910 (mmm) cc_final: 0.8301 (tpp) REVERT: D 227 MET cc_start: 0.8764 (mmm) cc_final: 0.8358 (tpt) REVERT: D 283 MET cc_start: 0.8849 (tpp) cc_final: 0.8227 (mpp) REVERT: E 12 ASN cc_start: 0.8709 (OUTLIER) cc_final: 0.8447 (t160) REVERT: E 132 MET cc_start: 0.8150 (ptm) cc_final: 0.7650 (ttp) REVERT: F 113 LYS cc_start: 0.8151 (mtmt) cc_final: 0.7642 (pttt) REVERT: F 328 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7578 (mmpt) outliers start: 23 outliers final: 16 residues processed: 160 average time/residue: 0.2349 time to fit residues: 59.2061 Evaluate side-chains 160 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 257 CYS Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 328 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 140 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 154 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 49 optimal weight: 0.1980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.089203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.076641 restraints weight = 26387.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.078280 restraints weight = 17425.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.079186 restraints weight = 11271.696| |-----------------------------------------------------------------------------| r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15566 Z= 0.106 Angle : 0.541 9.015 21105 Z= 0.256 Chirality : 0.043 0.203 2338 Planarity : 0.004 0.047 2700 Dihedral : 5.826 83.110 2159 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.34 % Allowed : 12.93 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.20), residues: 1919 helix: 1.49 (0.20), residues: 752 sheet: 0.40 (0.29), residues: 331 loop : 0.59 (0.23), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 340 HIS 0.002 0.001 HIS E 87 PHE 0.009 0.001 PHE 5 376 TYR 0.007 0.001 TYR F 53 ARG 0.002 0.000 ARG C 256 Details of bonding type rmsd hydrogen bonds : bond 0.02873 ( 653) hydrogen bonds : angle 4.27291 ( 1764) covalent geometry : bond 0.00249 (15566) covalent geometry : angle 0.54109 (21105) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 1.660 Fit side-chains REVERT: 5 348 LEU cc_start: 0.8574 (mt) cc_final: 0.8368 (mt) REVERT: 5 365 MET cc_start: 0.7819 (tpp) cc_final: 0.7393 (tpp) REVERT: B 117 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7647 (tt0) REVERT: B 132 MET cc_start: 0.8580 (tmm) cc_final: 0.8314 (tmm) REVERT: B 313 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8414 (ttp) REVERT: C 227 MET cc_start: 0.8892 (mmm) cc_final: 0.8271 (tpp) REVERT: D 107 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8055 (pt0) REVERT: D 227 MET cc_start: 0.8759 (mmm) cc_final: 0.8359 (tpt) REVERT: D 283 MET cc_start: 0.8836 (tpp) cc_final: 0.7698 (mpp) REVERT: E 123 MET cc_start: 0.8730 (mmm) cc_final: 0.8301 (mmt) REVERT: F 113 LYS cc_start: 0.8073 (mtmt) cc_final: 0.7572 (pttt) REVERT: F 328 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7549 (mmpt) outliers start: 22 outliers final: 18 residues processed: 161 average time/residue: 0.2454 time to fit residues: 61.3850 Evaluate side-chains 166 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 382 MET Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 328 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 130 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 166 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 78 optimal weight: 0.1980 chunk 171 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 118 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN E 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.088282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.075776 restraints weight = 26586.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.077504 restraints weight = 17008.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.078468 restraints weight = 10916.220| |-----------------------------------------------------------------------------| r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15566 Z= 0.140 Angle : 0.566 9.845 21105 Z= 0.269 Chirality : 0.045 0.184 2338 Planarity : 0.004 0.047 2700 Dihedral : 5.830 81.718 2159 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.59 % Allowed : 13.35 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.20), residues: 1919 helix: 1.43 (0.20), residues: 752 sheet: 0.39 (0.28), residues: 331 loop : 0.58 (0.23), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 340 HIS 0.003 0.001 HIS E 87 PHE 0.013 0.001 PHE F 223 TYR 0.008 0.001 TYR C 143 ARG 0.003 0.000 ARG C 256 Details of bonding type rmsd hydrogen bonds : bond 0.03176 ( 653) hydrogen bonds : angle 4.33009 ( 1764) covalent geometry : bond 0.00336 (15566) covalent geometry : angle 0.56617 (21105) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 1.753 Fit side-chains REVERT: 5 348 LEU cc_start: 0.8633 (mt) cc_final: 0.8406 (mt) REVERT: 5 365 MET cc_start: 0.7660 (tpp) cc_final: 0.7151 (tpp) REVERT: 5 396 ASN cc_start: 0.8785 (m-40) cc_final: 0.8434 (m-40) REVERT: B 117 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7668 (tt0) REVERT: B 313 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8465 (ttp) REVERT: C 227 MET cc_start: 0.8912 (mmm) cc_final: 0.8283 (tpp) REVERT: D 107 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8002 (pt0) REVERT: D 227 MET cc_start: 0.8751 (mmm) cc_final: 0.8352 (tpt) REVERT: D 283 MET cc_start: 0.8920 (tpp) cc_final: 0.8043 (mpp) REVERT: E 12 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.8469 (t160) REVERT: E 25 ASP cc_start: 0.7444 (t0) cc_final: 0.7239 (t0) REVERT: E 132 MET cc_start: 0.8258 (ttp) cc_final: 0.7712 (ttp) REVERT: F 113 LYS cc_start: 0.8114 (mtmt) cc_final: 0.7595 (pttt) REVERT: F 328 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7502 (mmpt) outliers start: 26 outliers final: 21 residues processed: 162 average time/residue: 0.2337 time to fit residues: 59.3001 Evaluate side-chains 169 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 382 MET Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 257 CYS Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 328 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 147 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 127 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 164 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.088790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.076372 restraints weight = 26590.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.077865 restraints weight = 16893.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.079193 restraints weight = 11190.732| |-----------------------------------------------------------------------------| r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15566 Z= 0.121 Angle : 0.559 12.530 21105 Z= 0.265 Chirality : 0.044 0.185 2338 Planarity : 0.004 0.046 2700 Dihedral : 5.811 80.832 2159 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.40 % Allowed : 13.41 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.20), residues: 1919 helix: 1.47 (0.20), residues: 752 sheet: 0.41 (0.28), residues: 331 loop : 0.61 (0.23), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 340 HIS 0.003 0.001 HIS E 87 PHE 0.010 0.001 PHE 5 376 TYR 0.007 0.001 TYR F 53 ARG 0.002 0.000 ARG C 256 Details of bonding type rmsd hydrogen bonds : bond 0.03020 ( 653) hydrogen bonds : angle 4.30210 ( 1764) covalent geometry : bond 0.00289 (15566) covalent geometry : angle 0.55941 (21105) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 1.635 Fit side-chains REVERT: 5 348 LEU cc_start: 0.8627 (mt) cc_final: 0.8411 (mt) REVERT: 5 396 ASN cc_start: 0.8779 (m-40) cc_final: 0.8416 (m-40) REVERT: B 117 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7645 (tt0) REVERT: B 313 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8428 (ttp) REVERT: C 227 MET cc_start: 0.8912 (mmm) cc_final: 0.8302 (tpp) REVERT: D 107 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7985 (pt0) REVERT: D 227 MET cc_start: 0.8762 (mmm) cc_final: 0.8367 (tpt) REVERT: D 283 MET cc_start: 0.8918 (tpp) cc_final: 0.8044 (mpp) REVERT: E 25 ASP cc_start: 0.7426 (t0) cc_final: 0.7221 (t0) REVERT: E 132 MET cc_start: 0.8223 (ttp) cc_final: 0.7659 (ttp) REVERT: E 325 MET cc_start: 0.7646 (mmt) cc_final: 0.7316 (mmt) REVERT: F 113 LYS cc_start: 0.8088 (mtmt) cc_final: 0.7604 (pttt) REVERT: F 283 MET cc_start: 0.8872 (mmt) cc_final: 0.8662 (mmt) REVERT: F 328 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7446 (mmpt) outliers start: 23 outliers final: 20 residues processed: 160 average time/residue: 0.2348 time to fit residues: 58.6154 Evaluate side-chains 166 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 382 MET Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 257 CYS Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 328 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 147 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 149 optimal weight: 0.0270 chunk 85 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.090002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.077618 restraints weight = 26224.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.078966 restraints weight = 16864.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.080413 restraints weight = 11505.553| |-----------------------------------------------------------------------------| r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15566 Z= 0.099 Angle : 0.553 14.016 21105 Z= 0.258 Chirality : 0.043 0.184 2338 Planarity : 0.004 0.047 2700 Dihedral : 5.688 79.117 2159 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.24 % Favored : 97.71 % Rotamer: Outliers : 1.52 % Allowed : 13.48 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.20), residues: 1919 helix: 1.57 (0.20), residues: 751 sheet: 0.43 (0.29), residues: 336 loop : 0.65 (0.23), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 340 HIS 0.002 0.000 HIS E 87 PHE 0.011 0.001 PHE F 223 TYR 0.007 0.001 TYR F 53 ARG 0.004 0.000 ARG F 335 Details of bonding type rmsd hydrogen bonds : bond 0.02740 ( 653) hydrogen bonds : angle 4.23170 ( 1764) covalent geometry : bond 0.00233 (15566) covalent geometry : angle 0.55299 (21105) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3845.05 seconds wall clock time: 68 minutes 40.50 seconds (4120.50 seconds total)