Starting phenix.real_space_refine on Sat Aug 23 23:10:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ib2_35329/08_2025/8ib2_35329.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ib2_35329/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ib2_35329/08_2025/8ib2_35329.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ib2_35329/08_2025/8ib2_35329.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ib2_35329/08_2025/8ib2_35329.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ib2_35329/08_2025/8ib2_35329.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.24, per 1000 atoms: 0.28 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: 1.33 Conformation dependent library (CDL) restraints added in 712.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.75 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: 3.09 Time building geometry restraints manager: 1.85 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.820 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.890 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.000 ARG E 372 TYR 0.009 0.001 TYR E 143 PHE 0.026 0.001 PHE E 124 TRP 0.011 0.001 TRP C 356 HIS 0.003 0.001 HIS E 371 Details of bonding type rmsd covalent geometry : bond 0.00305 (15566) covalent geometry : angle 0.68761 (21105) hydrogen bonds : bond 0.15686 ( 653) hydrogen bonds : angle 6.76003 ( 1764) *********************** 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 : 0.638 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: 0.1213 time to fit residues: 36.4510 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 : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN D 12 ASN F 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.089947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.077717 restraints weight = 25943.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.079079 restraints weight = 16933.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.080005 restraints weight = 12190.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.080667 restraints weight = 9495.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.081145 restraints weight = 7840.380| |-----------------------------------------------------------------------------| r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15566 Z= 0.161 Angle : 0.594 7.872 21105 Z= 0.291 Chirality : 0.046 0.175 2338 Planarity : 0.005 0.049 2700 Dihedral : 6.490 85.731 2159 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.98 % Allowed : 6.40 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.20), residues: 1919 helix: 0.30 (0.19), residues: 784 sheet: 0.52 (0.28), residues: 331 loop : 0.50 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 177 TYR 0.012 0.001 TYR 5 345 PHE 0.008 0.001 PHE C 124 TRP 0.010 0.001 TRP F 356 HIS 0.004 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00383 (15566) covalent geometry : angle 0.59378 (21105) hydrogen bonds : bond 0.03902 ( 653) hydrogen bonds : angle 4.87945 ( 1764) *********************** 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 161 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.621 Fit side-chains REVERT: B 117 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7656 (tt0) REVERT: C 227 MET cc_start: 0.8867 (mmm) cc_final: 0.8289 (tpp) REVERT: D 283 MET cc_start: 0.8642 (mmt) cc_final: 0.8427 (mpp) REVERT: D 313 MET cc_start: 0.9072 (tpp) cc_final: 0.8411 (ttm) REVERT: E 296 ASN cc_start: 0.8641 (m-40) cc_final: 0.8160 (m-40) REVERT: E 313 MET cc_start: 0.8428 (tpp) cc_final: 0.8070 (tpp) REVERT: F 82 MET cc_start: 0.8867 (tpt) cc_final: 0.8544 (tpt) REVERT: F 113 LYS cc_start: 0.8037 (mtmt) cc_final: 0.7573 (pttm) outliers start: 16 outliers final: 11 residues processed: 153 average time/residue: 0.1120 time to fit residues: 27.3775 Evaluate side-chains 145 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 ASN 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 129 THR 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 77 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 chunk 164 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 117 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.2877 r_free = 0.2877 target = 0.088181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.075556 restraints weight = 26500.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.077063 restraints weight = 16996.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.078333 restraints weight = 11108.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.078676 restraints weight = 8254.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.078783 restraints weight = 6953.616| |-----------------------------------------------------------------------------| r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 15566 Z= 0.167 Angle : 0.580 7.104 21105 Z= 0.283 Chirality : 0.045 0.156 2338 Planarity : 0.004 0.045 2700 Dihedral : 6.381 89.113 2159 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.10 % Allowed : 8.17 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.20), residues: 1919 helix: 0.62 (0.19), residues: 777 sheet: 0.41 (0.28), residues: 331 loop : 0.50 (0.23), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 116 TYR 0.010 0.001 TYR C 143 PHE 0.008 0.001 PHE E 262 TRP 0.014 0.001 TRP E 340 HIS 0.004 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00399 (15566) covalent geometry : angle 0.57990 (21105) hydrogen bonds : bond 0.03717 ( 653) hydrogen bonds : angle 4.69623 ( 1764) *********************** 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 161 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.640 Fit side-chains REVERT: 5 396 ASN cc_start: 0.8779 (m-40) cc_final: 0.8479 (m-40) REVERT: B 44 MET cc_start: 0.7578 (mmm) cc_final: 0.7261 (mmm) REVERT: B 117 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7704 (tt0) REVERT: C 227 MET cc_start: 0.8864 (mmm) cc_final: 0.8272 (tpp) REVERT: D 227 MET cc_start: 0.8841 (mmm) cc_final: 0.8409 (tpt) REVERT: E 296 ASN cc_start: 0.8628 (m-40) cc_final: 0.8410 (m-40) REVERT: E 313 MET cc_start: 0.8486 (tpp) cc_final: 0.8142 (tpp) REVERT: E 326 LYS cc_start: 0.8701 (tttt) cc_final: 0.8305 (pttp) REVERT: F 82 MET cc_start: 0.8918 (tpt) cc_final: 0.8619 (tpt) REVERT: F 113 LYS cc_start: 0.8116 (mtmt) cc_final: 0.7575 (pttt) REVERT: F 328 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7779 (mmpt) outliers start: 18 outliers final: 12 residues processed: 157 average time/residue: 0.1163 time to fit residues: 28.7388 Evaluate side-chains 149 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 162 THR 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 31 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 108 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 122 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 chunk 155 optimal weight: 0.0770 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN D 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.090844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.078295 restraints weight = 26458.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.079775 restraints weight = 16972.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.081234 restraints weight = 11137.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.081611 restraints weight = 7899.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.081645 restraints weight = 6557.883| |-----------------------------------------------------------------------------| r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15566 Z= 0.088 Angle : 0.522 7.161 21105 Z= 0.249 Chirality : 0.043 0.140 2338 Planarity : 0.004 0.044 2700 Dihedral : 6.105 89.857 2159 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.79 % Allowed : 9.63 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.20), residues: 1919 helix: 1.05 (0.20), residues: 772 sheet: 0.27 (0.28), residues: 355 loop : 0.55 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 177 TYR 0.007 0.001 TYR B 362 PHE 0.016 0.001 PHE 5 376 TRP 0.010 0.001 TRP E 340 HIS 0.002 0.000 HIS D 101 Details of bonding type rmsd covalent geometry : bond 0.00198 (15566) covalent geometry : angle 0.52183 (21105) hydrogen bonds : bond 0.02745 ( 653) hydrogen bonds : angle 4.37328 ( 1764) *********************** 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 173 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.635 Fit side-chains REVERT: 5 365 MET cc_start: 0.8024 (tpp) cc_final: 0.7599 (tpp) REVERT: B 117 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7633 (tt0) REVERT: C 227 MET cc_start: 0.8826 (mmm) cc_final: 0.8237 (tpp) REVERT: D 227 MET cc_start: 0.8763 (mmm) cc_final: 0.8370 (tpt) REVERT: D 283 MET cc_start: 0.8563 (mmt) cc_final: 0.8237 (mpp) REVERT: D 313 MET cc_start: 0.9041 (tpp) cc_final: 0.8438 (ttm) REVERT: E 132 MET cc_start: 0.8083 (ttp) cc_final: 0.7810 (ttp) REVERT: E 296 ASN cc_start: 0.8527 (m-40) cc_final: 0.8301 (m-40) REVERT: E 313 MET cc_start: 0.8385 (tpp) cc_final: 0.8071 (tpp) REVERT: E 326 LYS cc_start: 0.8723 (tttt) cc_final: 0.8343 (pttp) REVERT: F 82 MET cc_start: 0.8832 (tpt) cc_final: 0.8502 (tpt) REVERT: F 113 LYS cc_start: 0.8030 (mtmt) cc_final: 0.7494 (pttt) REVERT: F 328 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7686 (mmpt) outliers start: 13 outliers final: 9 residues processed: 167 average time/residue: 0.1169 time to fit residues: 30.6400 Evaluate side-chains 159 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 355 MET 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 D residue 372 ARG 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 328 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 31 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 189 optimal weight: 10.0000 chunk 113 optimal weight: 0.0470 chunk 78 optimal weight: 0.3980 chunk 161 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 overall best weight: 1.0882 ------------------------------------------------------------------------------- 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 F 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.089248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.076777 restraints weight = 26583.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.078117 restraints weight = 16957.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.079510 restraints weight = 11563.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.079770 restraints weight = 8516.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.079964 restraints weight = 7184.425| |-----------------------------------------------------------------------------| r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15566 Z= 0.121 Angle : 0.545 7.196 21105 Z= 0.261 Chirality : 0.044 0.242 2338 Planarity : 0.004 0.045 2700 Dihedral : 5.959 88.616 2159 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.34 % Allowed : 10.30 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.20), residues: 1919 helix: 1.08 (0.20), residues: 783 sheet: 0.42 (0.29), residues: 331 loop : 0.62 (0.23), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 256 TYR 0.007 0.001 TYR F 53 PHE 0.008 0.001 PHE B 200 TRP 0.011 0.001 TRP E 340 HIS 0.003 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00287 (15566) covalent geometry : angle 0.54476 (21105) hydrogen bonds : bond 0.03098 ( 653) hydrogen bonds : angle 4.33719 ( 1764) *********************** 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: 22 poor density : 153 time to evaluate : 0.628 Fit side-chains REVERT: 5 365 MET cc_start: 0.7772 (tpp) cc_final: 0.7382 (tpp) REVERT: B 117 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7653 (tt0) REVERT: B 313 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8296 (ttp) REVERT: C 227 MET cc_start: 0.8886 (mmm) cc_final: 0.8278 (tpp) REVERT: D 227 MET cc_start: 0.8743 (mmm) cc_final: 0.8342 (tpt) REVERT: E 296 ASN cc_start: 0.8511 (m-40) cc_final: 0.8295 (m-40) REVERT: E 313 MET cc_start: 0.8464 (tpp) cc_final: 0.8154 (tpp) REVERT: E 326 LYS cc_start: 0.8700 (tttt) cc_final: 0.8446 (pttt) REVERT: F 82 MET cc_start: 0.8885 (tpt) cc_final: 0.8582 (tpt) REVERT: F 113 LYS cc_start: 0.8093 (mtmt) cc_final: 0.7572 (pttt) REVERT: F 328 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7730 (mmpt) outliers start: 22 outliers final: 15 residues processed: 165 average time/residue: 0.1164 time to fit residues: 29.6895 Evaluate side-chains 162 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 313 MET 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 153 MET Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain D residue 372 ARG 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 257 CYS 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 20 optimal weight: 0.0070 chunk 25 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 166 optimal weight: 6.9990 chunk 87 optimal weight: 0.4980 chunk 135 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 111 optimal weight: 0.7980 chunk 155 optimal weight: 0.5980 chunk 142 optimal weight: 0.8980 chunk 143 optimal weight: 0.7980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN D 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.090934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.078393 restraints weight = 26288.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.080015 restraints weight = 17135.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.081415 restraints weight = 11058.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.081769 restraints weight = 7517.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.081884 restraints weight = 6599.049| |-----------------------------------------------------------------------------| r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15566 Z= 0.086 Angle : 0.514 7.933 21105 Z= 0.244 Chirality : 0.042 0.186 2338 Planarity : 0.004 0.045 2700 Dihedral : 5.769 88.021 2159 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.22 % Allowed : 11.04 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.20), residues: 1919 helix: 1.33 (0.20), residues: 775 sheet: 0.28 (0.28), residues: 355 loop : 0.70 (0.23), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 177 TYR 0.007 0.001 TYR C 143 PHE 0.009 0.001 PHE 5 376 TRP 0.010 0.001 TRP E 340 HIS 0.002 0.000 HIS D 101 Details of bonding type rmsd covalent geometry : bond 0.00195 (15566) covalent geometry : angle 0.51426 (21105) hydrogen bonds : bond 0.02588 ( 653) hydrogen bonds : angle 4.21173 ( 1764) *********************** 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 174 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 0.674 Fit side-chains REVERT: B 117 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7612 (tt0) REVERT: B 313 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8343 (ttp) REVERT: C 227 MET cc_start: 0.8862 (mmm) cc_final: 0.8222 (tpp) REVERT: D 123 MET cc_start: 0.8991 (tpp) cc_final: 0.8597 (tpp) REVERT: D 227 MET cc_start: 0.8728 (mmm) cc_final: 0.8315 (tpt) REVERT: E 132 MET cc_start: 0.7844 (ttp) cc_final: 0.7249 (ttp) REVERT: E 296 ASN cc_start: 0.8492 (m-40) cc_final: 0.8286 (m-40) REVERT: E 313 MET cc_start: 0.8406 (tpp) cc_final: 0.8104 (tpp) REVERT: F 82 MET cc_start: 0.8859 (tpt) cc_final: 0.8584 (tpt) REVERT: F 113 LYS cc_start: 0.8038 (mtmt) cc_final: 0.7496 (pttt) outliers start: 20 outliers final: 15 residues processed: 164 average time/residue: 0.1117 time to fit residues: 29.2343 Evaluate side-chains 161 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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 162 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 153 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 D residue 372 ARG 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 272 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 147 optimal weight: 0.7980 chunk 106 optimal weight: 0.0870 chunk 99 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 137 optimal weight: 0.9980 chunk 13 optimal weight: 0.0570 chunk 189 optimal weight: 9.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- 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 F 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.091166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.078535 restraints weight = 26077.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.080184 restraints weight = 17484.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.081511 restraints weight = 11157.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.081850 restraints weight = 7848.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.081970 restraints weight = 6963.260| |-----------------------------------------------------------------------------| r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1792 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= 0.087 Angle : 0.521 8.660 21105 Z= 0.244 Chirality : 0.042 0.165 2338 Planarity : 0.003 0.045 2700 Dihedral : 5.626 87.188 2159 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.34 % Allowed : 11.83 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.20), residues: 1919 helix: 1.42 (0.20), residues: 774 sheet: 0.30 (0.28), residues: 355 loop : 0.76 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 256 TYR 0.007 0.001 TYR C 143 PHE 0.007 0.001 PHE B 255 TRP 0.009 0.001 TRP E 340 HIS 0.002 0.000 HIS D 101 Details of bonding type rmsd covalent geometry : bond 0.00201 (15566) covalent geometry : angle 0.52088 (21105) hydrogen bonds : bond 0.02578 ( 653) hydrogen bonds : angle 4.18124 ( 1764) *********************** 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 176 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.637 Fit side-chains REVERT: 5 365 MET cc_start: 0.7950 (tpp) cc_final: 0.7442 (tpp) REVERT: B 117 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7543 (tt0) REVERT: B 313 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8355 (ttp) REVERT: D 123 MET cc_start: 0.8983 (tpp) cc_final: 0.8581 (tpp) REVERT: D 227 MET cc_start: 0.8714 (mmm) cc_final: 0.8299 (tpt) REVERT: E 132 MET cc_start: 0.7917 (ttp) cc_final: 0.7456 (ttp) REVERT: E 296 ASN cc_start: 0.8477 (m-40) cc_final: 0.8264 (m-40) REVERT: F 113 LYS cc_start: 0.8010 (mtmt) cc_final: 0.7467 (pttt) REVERT: F 328 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7520 (mmpt) outliers start: 22 outliers final: 15 residues processed: 164 average time/residue: 0.1066 time to fit residues: 27.9586 Evaluate side-chains 163 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 162 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 153 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 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 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 174 optimal weight: 6.9990 chunk 170 optimal weight: 3.9990 chunk 126 optimal weight: 0.4980 chunk 11 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- 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 = 0.2834 r_free = 0.2834 target = 0.085148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.072444 restraints weight = 27170.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.073955 restraints weight = 16878.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.075008 restraints weight = 11733.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.075678 restraints weight = 8919.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.076208 restraints weight = 7338.932| |-----------------------------------------------------------------------------| r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 15566 Z= 0.272 Angle : 0.679 10.034 21105 Z= 0.332 Chirality : 0.049 0.163 2338 Planarity : 0.004 0.046 2700 Dihedral : 6.076 84.254 2159 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.46 % Allowed : 12.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.20), residues: 1919 helix: 0.97 (0.20), residues: 776 sheet: 0.32 (0.28), residues: 343 loop : 0.50 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 312 TYR 0.016 0.002 TYR C 143 PHE 0.013 0.002 PHE B 200 TRP 0.010 0.002 TRP E 340 HIS 0.006 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00652 (15566) covalent geometry : angle 0.67862 (21105) hydrogen bonds : bond 0.04397 ( 653) hydrogen bonds : angle 4.70344 ( 1764) *********************** 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 166 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.620 Fit side-chains REVERT: 5 365 MET cc_start: 0.7723 (tpp) cc_final: 0.7290 (tpp) REVERT: 5 381 SER cc_start: 0.8285 (m) cc_final: 0.7963 (p) REVERT: 5 396 ASN cc_start: 0.8760 (m-40) cc_final: 0.8428 (m-40) REVERT: B 117 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7722 (tt0) REVERT: D 227 MET cc_start: 0.8817 (mmm) cc_final: 0.8410 (tpt) REVERT: E 132 MET cc_start: 0.8132 (ttp) cc_final: 0.7587 (ttp) REVERT: F 113 LYS cc_start: 0.8209 (mtmt) cc_final: 0.7780 (pttt) REVERT: F 201 THR cc_start: 0.9131 (p) cc_final: 0.8903 (t) outliers start: 24 outliers final: 20 residues processed: 154 average time/residue: 0.1165 time to fit residues: 27.7611 Evaluate side-chains 155 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 162 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain D residue 47 MET 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 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 154 ASP Chi-restraints excluded: chain F residue 257 CYS Chi-restraints excluded: chain F residue 272 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 31 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN D 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 = 0.088615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.076100 restraints weight = 26315.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.077766 restraints weight = 16778.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.078834 restraints weight = 10859.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.079254 restraints weight = 8010.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.079265 restraints weight = 7070.062| |-----------------------------------------------------------------------------| r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15566 Z= 0.112 Angle : 0.563 10.771 21105 Z= 0.268 Chirality : 0.044 0.154 2338 Planarity : 0.004 0.045 2700 Dihedral : 5.841 83.456 2159 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.28 % Allowed : 13.60 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.20), residues: 1919 helix: 1.40 (0.20), residues: 752 sheet: 0.39 (0.29), residues: 331 loop : 0.57 (0.23), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 116 TYR 0.008 0.001 TYR F 53 PHE 0.012 0.001 PHE D 279 TRP 0.012 0.001 TRP E 340 HIS 0.003 0.001 HIS F 161 Details of bonding type rmsd covalent geometry : bond 0.00265 (15566) covalent geometry : angle 0.56284 (21105) hydrogen bonds : bond 0.03012 ( 653) hydrogen bonds : angle 4.38731 ( 1764) *********************** 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 168 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.634 Fit side-chains REVERT: 5 365 MET cc_start: 0.7648 (tpp) cc_final: 0.7170 (tpp) REVERT: 5 381 SER cc_start: 0.8314 (m) cc_final: 0.8003 (p) REVERT: B 117 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7660 (tt0) REVERT: B 132 MET cc_start: 0.8608 (tmm) cc_final: 0.8347 (tmm) REVERT: B 313 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8384 (ttp) REVERT: D 227 MET cc_start: 0.8746 (mmm) cc_final: 0.8342 (tpt) REVERT: D 283 MET cc_start: 0.8537 (tpp) cc_final: 0.7597 (mpp) REVERT: F 113 LYS cc_start: 0.8045 (mtmt) cc_final: 0.7523 (pttt) REVERT: F 283 MET cc_start: 0.8957 (mmt) cc_final: 0.8681 (mmt) outliers start: 21 outliers final: 17 residues processed: 159 average time/residue: 0.1117 time to fit residues: 28.2756 Evaluate side-chains 162 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 382 MET Chi-restraints excluded: chain B residue 313 MET 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 58 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN D 12 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.086813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.074231 restraints weight = 26765.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.075846 restraints weight = 17297.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.077194 restraints weight = 11190.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.077552 restraints weight = 7796.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.077559 restraints weight = 6898.320| |-----------------------------------------------------------------------------| r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15566 Z= 0.184 Angle : 0.610 12.821 21105 Z= 0.293 Chirality : 0.046 0.145 2338 Planarity : 0.004 0.047 2700 Dihedral : 5.898 81.911 2159 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.16 % Allowed : 13.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.20), residues: 1919 helix: 1.32 (0.20), residues: 752 sheet: 0.35 (0.28), residues: 331 loop : 0.52 (0.23), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 335 TYR 0.011 0.001 TYR C 143 PHE 0.028 0.001 PHE C 223 TRP 0.010 0.001 TRP E 340 HIS 0.004 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00446 (15566) covalent geometry : angle 0.61009 (21105) hydrogen bonds : bond 0.03617 ( 653) hydrogen bonds : angle 4.49527 ( 1764) ********************** 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 163 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.648 Fit side-chains REVERT: 5 365 MET cc_start: 0.7661 (tpp) cc_final: 0.7196 (tpp) REVERT: 5 381 SER cc_start: 0.8343 (m) cc_final: 0.8038 (p) REVERT: B 117 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7696 (tt0) REVERT: B 132 MET cc_start: 0.8611 (tmm) cc_final: 0.8338 (tmm) REVERT: B 369 ILE cc_start: 0.9060 (tp) cc_final: 0.8832 (tt) REVERT: D 227 MET cc_start: 0.8770 (mmm) cc_final: 0.8366 (tpt) REVERT: D 283 MET cc_start: 0.8693 (tpp) cc_final: 0.7635 (mpp) REVERT: E 132 MET cc_start: 0.8133 (ttp) cc_final: 0.7589 (ttp) REVERT: F 113 LYS cc_start: 0.8113 (mtmt) cc_final: 0.7700 (pttt) outliers start: 19 outliers final: 19 residues processed: 155 average time/residue: 0.1153 time to fit residues: 27.9552 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 : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 382 MET Chi-restraints excluded: chain B residue 313 MET 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 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 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 201 THR Chi-restraints excluded: chain F residue 257 CYS Chi-restraints excluded: chain F residue 272 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 116 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN D 12 ASN E 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.088379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.075761 restraints weight = 26546.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.077298 restraints weight = 16448.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.078340 restraints weight = 11439.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.079078 restraints weight = 8682.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.079537 restraints weight = 7093.508| |-----------------------------------------------------------------------------| r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15566 Z= 0.172 Angle : 0.606 13.818 21105 Z= 0.291 Chirality : 0.046 0.149 2338 Planarity : 0.004 0.045 2700 Dihedral : 5.926 80.611 2159 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.28 % Allowed : 13.78 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.20), residues: 1919 helix: 1.30 (0.20), residues: 752 sheet: 0.34 (0.28), residues: 331 loop : 0.50 (0.23), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 335 TYR 0.009 0.001 TYR F 53 PHE 0.027 0.001 PHE C 223 TRP 0.011 0.001 TRP E 340 HIS 0.004 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00417 (15566) covalent geometry : angle 0.60585 (21105) hydrogen bonds : bond 0.03475 ( 653) hydrogen bonds : angle 4.49149 ( 1764) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2103.39 seconds wall clock time: 37 minutes 29.11 seconds (2249.11 seconds total)