Starting phenix.real_space_refine on Fri Aug 22 17:07:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bfr_44504/08_2025/9bfr_44504.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bfr_44504/08_2025/9bfr_44504.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bfr_44504/08_2025/9bfr_44504.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bfr_44504/08_2025/9bfr_44504.map" model { file = "/net/cci-nas-00/data/ceres_data/9bfr_44504/08_2025/9bfr_44504.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bfr_44504/08_2025/9bfr_44504.cif" } resolution = 3.19 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= 0.000 sd= 0.033 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: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 4006 2.51 5 N 1026 2.21 5 O 1192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 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: 6266 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3091 Classifications: {'peptide': 383} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 372} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 3091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3091 Classifications: {'peptide': 383} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 372} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.76, per 1000 atoms: 0.28 Number of scatterers: 6266 At special positions: 0 Unit cell: (97.11, 98.77, 89.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1192 8.00 N 1026 7.00 C 4006 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 112 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 501 " distance=2.04 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 403 " distance=2.03 Simple disulfide: pdb=" SG CYS B 112 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 501 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 403 " distance=2.03 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 183 " " NAG A 602 " - " ASN A 474 " " NAG A 603 " - " ASN A 485 " " NAG B 601 " - " ASN B 183 " " NAG B 602 " - " ASN B 474 " " NAG B 603 " - " ASN B 485 " Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 377.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1480 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 9 sheets defined 37.1% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 109 through 115 removed outlier: 3.685A pdb=" N LEU A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 135 removed outlier: 3.667A pdb=" N GLU A 134 " --> pdb=" O LYS A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 166 removed outlier: 3.525A pdb=" N LEU A 156 " --> pdb=" O PRO A 152 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 157 " --> pdb=" O ASP A 153 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 199 removed outlier: 3.683A pdb=" N ILE A 192 " --> pdb=" O GLU A 188 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN A 199 " --> pdb=" O VAL A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 218 removed outlier: 3.644A pdb=" N GLN A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 226 removed outlier: 3.996A pdb=" N LYS A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 226 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 249 Proline residue: A 241 - end of helix removed outlier: 3.505A pdb=" N LEU A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN A 249 " --> pdb=" O HIS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 279 removed outlier: 3.602A pdb=" N GLU A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 369 Processing helix chain 'A' and resid 370 through 385 removed outlier: 3.653A pdb=" N ILE A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP A 376 " --> pdb=" O GLY A 372 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TRP A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY A 383 " --> pdb=" O ASN A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 403 Processing helix chain 'A' and resid 409 through 414 removed outlier: 4.036A pdb=" N TRP A 413 " --> pdb=" O ILE A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 431 Processing helix chain 'A' and resid 433 through 438 removed outlier: 3.777A pdb=" N GLY A 437 " --> pdb=" O ARG A 434 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR A 438 " --> pdb=" O LYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 499 Processing helix chain 'B' and resid 109 through 115 removed outlier: 3.703A pdb=" N LEU B 113 " --> pdb=" O PRO B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 135 removed outlier: 4.314A pdb=" N PHE B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 131 through 135' Processing helix chain 'B' and resid 151 through 166 removed outlier: 3.908A pdb=" N ALA B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA B 165 " --> pdb=" O ARG B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 199 removed outlier: 3.694A pdb=" N ILE B 192 " --> pdb=" O GLU B 188 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN B 199 " --> pdb=" O VAL B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 218 removed outlier: 3.634A pdb=" N GLN B 217 " --> pdb=" O GLU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 226 removed outlier: 4.019A pdb=" N LYS B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP B 224 " --> pdb=" O SER B 220 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU B 226 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 249 Proline residue: B 241 - end of helix removed outlier: 3.506A pdb=" N LEU B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN B 249 " --> pdb=" O HIS B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 279 removed outlier: 3.595A pdb=" N GLU B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 385 removed outlier: 3.694A pdb=" N PHE B 370 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER B 373 " --> pdb=" O SER B 369 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B 375 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP B 376 " --> pdb=" O GLY B 372 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TRP B 380 " --> pdb=" O ASP B 376 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY B 383 " --> pdb=" O ASN B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 403 Processing helix chain 'B' and resid 409 through 414 removed outlier: 4.042A pdb=" N TRP B 413 " --> pdb=" O ILE B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 431 Processing helix chain 'B' and resid 433 through 439 removed outlier: 3.882A pdb=" N GLY B 437 " --> pdb=" O ARG B 434 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N THR B 438 " --> pdb=" O LYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 499 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA2, first strand: chain 'A' and resid 137 through 139 removed outlier: 3.757A pdb=" N ALA A 178 " --> pdb=" O LYS A 137 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL A 147 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 251 through 252 removed outlier: 3.717A pdb=" N THR A 493 " --> pdb=" O TRP A 252 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 476 through 478 removed outlier: 6.384A pdb=" N MET A 444 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N SER A 468 " --> pdb=" O PHE A 442 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N PHE A 442 " --> pdb=" O SER A 468 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA A 330 " --> pdb=" O LYS A 447 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU A 310 " --> pdb=" O PHE A 331 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N LEU A 333 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N SER A 312 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N GLU A 335 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN A 291 " --> pdb=" O THR A 309 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N PHE A 311 " --> pdb=" O ASN A 291 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N TYR A 293 " --> pdb=" O PHE A 311 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL A 313 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N MET A 295 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N SER A 258 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ILE A 294 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLU A 260 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N PHE A 296 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA A 262 " --> pdb=" O PHE A 296 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL A 259 " --> pdb=" O MET B 527 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N MET B 527 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N MET A 527 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL B 259 " --> pdb=" O MET A 527 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N SER B 258 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ILE B 294 " --> pdb=" O SER B 258 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLU B 260 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N PHE B 296 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA B 262 " --> pdb=" O PHE B 296 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASN B 291 " --> pdb=" O THR B 309 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N PHE B 311 " --> pdb=" O ASN B 291 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TYR B 293 " --> pdb=" O PHE B 311 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL B 313 " --> pdb=" O TYR B 293 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N MET B 295 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU B 310 " --> pdb=" O PHE B 331 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU B 333 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N SER B 312 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N GLU B 335 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA B 330 " --> pdb=" O LYS B 447 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE B 442 " --> pdb=" O SER B 468 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N SER B 468 " --> pdb=" O PHE B 442 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N MET B 444 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 338 through 339 Processing sheet with id=AA6, first strand: chain 'B' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'B' and resid 136 through 139 removed outlier: 3.732A pdb=" N ALA B 178 " --> pdb=" O LYS B 137 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL B 147 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 251 through 252 removed outlier: 3.725A pdb=" N THR B 493 " --> pdb=" O TRP B 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 338 through 339 182 hydrogen bonds defined for protein. 477 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: 0.89 Time building geometry restraints manager: 0.70 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: 1970 1.34 - 1.46: 1328 1.46 - 1.58: 3012 1.58 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 6382 Sorted by residual: bond pdb=" C5 NAG B 603 " pdb=" O5 NAG B 603 " ideal model delta sigma weight residual 1.413 1.450 -0.037 2.00e-02 2.50e+03 3.41e+00 bond pdb=" C5 NAG A 603 " pdb=" O5 NAG A 603 " ideal model delta sigma weight residual 1.413 1.449 -0.036 2.00e-02 2.50e+03 3.27e+00 bond pdb=" N MET A 169 " pdb=" CA MET A 169 " ideal model delta sigma weight residual 1.460 1.486 -0.027 1.54e-02 4.22e+03 3.01e+00 bond pdb=" CB LYS B 131 " pdb=" CG LYS B 131 " ideal model delta sigma weight residual 1.520 1.570 -0.050 3.00e-02 1.11e+03 2.83e+00 bond pdb=" N MET B 169 " pdb=" CA MET B 169 " ideal model delta sigma weight residual 1.460 1.485 -0.026 1.54e-02 4.22e+03 2.75e+00 ... (remaining 6377 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 8061 1.93 - 3.85: 462 3.85 - 5.78: 70 5.78 - 7.71: 30 7.71 - 9.63: 13 Bond angle restraints: 8636 Sorted by residual: angle pdb=" C ILE B 168 " pdb=" N MET B 169 " pdb=" CA MET B 169 " ideal model delta sigma weight residual 122.46 130.62 -8.16 1.41e+00 5.03e-01 3.35e+01 angle pdb=" C ILE A 168 " pdb=" N MET A 169 " pdb=" CA MET A 169 " ideal model delta sigma weight residual 122.46 130.40 -7.94 1.41e+00 5.03e-01 3.17e+01 angle pdb=" N ILE B 232 " pdb=" CA ILE B 232 " pdb=" C ILE B 232 " ideal model delta sigma weight residual 109.02 103.98 5.04 9.30e-01 1.16e+00 2.94e+01 angle pdb=" N ILE A 232 " pdb=" CA ILE A 232 " pdb=" C ILE A 232 " ideal model delta sigma weight residual 109.02 104.10 4.92 9.30e-01 1.16e+00 2.80e+01 angle pdb=" C GLU A 279 " pdb=" N HIS A 280 " pdb=" CA HIS A 280 " ideal model delta sigma weight residual 122.19 129.62 -7.43 1.41e+00 5.03e-01 2.78e+01 ... (remaining 8631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 3558 17.50 - 35.01: 315 35.01 - 52.51: 47 52.51 - 70.01: 8 70.01 - 87.51: 4 Dihedral angle restraints: 3932 sinusoidal: 1674 harmonic: 2258 Sorted by residual: dihedral pdb=" CB CYS B 282 " pdb=" SG CYS B 282 " pdb=" SG CYS B 501 " pdb=" CB CYS B 501 " ideal model delta sinusoidal sigma weight residual -86.00 -173.51 87.51 1 1.00e+01 1.00e-02 9.18e+01 dihedral pdb=" CB CYS A 282 " pdb=" SG CYS A 282 " pdb=" SG CYS A 501 " pdb=" CB CYS A 501 " ideal model delta sinusoidal sigma weight residual -86.00 -172.66 86.66 1 1.00e+01 1.00e-02 9.04e+01 dihedral pdb=" CA PHE A 240 " pdb=" C PHE A 240 " pdb=" N PRO A 241 " pdb=" CA PRO A 241 " ideal model delta harmonic sigma weight residual 180.00 158.07 21.93 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 3929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 732 0.056 - 0.111: 211 0.111 - 0.167: 48 0.167 - 0.223: 15 0.223 - 0.279: 6 Chirality restraints: 1012 Sorted by residual: chirality pdb=" CB VAL A 136 " pdb=" CA VAL A 136 " pdb=" CG1 VAL A 136 " pdb=" CG2 VAL A 136 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CB ILE A 176 " pdb=" CA ILE A 176 " pdb=" CG1 ILE A 176 " pdb=" CG2 ILE A 176 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CB ILE B 176 " pdb=" CA ILE B 176 " pdb=" CG1 ILE B 176 " pdb=" CG2 ILE B 176 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 1009 not shown) Planarity restraints: 1092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 485 " 0.031 2.00e-02 2.50e+03 2.83e-02 9.98e+00 pdb=" CG ASN B 485 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN B 485 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B 485 " -0.033 2.00e-02 2.50e+03 pdb=" C1 NAG B 603 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 485 " -0.030 2.00e-02 2.50e+03 2.79e-02 9.70e+00 pdb=" CG ASN A 485 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN A 485 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 485 " 0.033 2.00e-02 2.50e+03 pdb=" C1 NAG A 603 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 240 " -0.050 5.00e-02 4.00e+02 7.41e-02 8.78e+00 pdb=" N PRO B 241 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO B 241 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 241 " -0.042 5.00e-02 4.00e+02 ... (remaining 1089 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 2423 2.93 - 3.42: 5270 3.42 - 3.92: 9889 3.92 - 4.41: 11138 4.41 - 4.90: 19454 Nonbonded interactions: 48174 Sorted by model distance: nonbonded pdb=" OE2 GLU B 335 " pdb=" OG SER B 365 " model vdw 2.440 3.040 nonbonded pdb=" OE2 GLU A 335 " pdb=" OG SER A 365 " model vdw 2.440 3.040 nonbonded pdb=" ND2 ASN B 482 " pdb=" O HIS B 486 " model vdw 2.472 3.120 nonbonded pdb=" ND2 ASN A 482 " pdb=" O HIS A 486 " model vdw 2.474 3.120 nonbonded pdb=" O VAL B 120 " pdb=" N THR B 127 " model vdw 2.481 3.120 ... (remaining 48169 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 individual isotropic 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: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.760 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 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 : 0.006 0.062 6394 Z= 0.302 Angle : 1.122 9.633 8666 Z= 0.608 Chirality : 0.060 0.279 1012 Planarity : 0.008 0.074 1086 Dihedral : 13.105 83.190 2434 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % 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: -4.21 (0.24), residues: 746 helix: -4.99 (0.10), residues: 228 sheet: -1.35 (0.42), residues: 126 loop : -1.80 (0.25), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 382 TYR 0.011 0.002 TYR A 445 PHE 0.047 0.004 PHE B 495 TRP 0.020 0.003 TRP A 523 HIS 0.007 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00633 ( 6382) covalent geometry : angle 1.11052 ( 8636) SS BOND : bond 0.00283 ( 6) SS BOND : angle 1.38930 ( 12) hydrogen bonds : bond 0.30238 ( 182) hydrogen bonds : angle 10.85439 ( 477) link_NAG-ASN : bond 0.00411 ( 6) link_NAG-ASN : angle 3.63269 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.183 Fit side-chains REVERT: A 361 SER cc_start: 0.8541 (p) cc_final: 0.8336 (p) REVERT: A 378 MET cc_start: 0.7483 (mmt) cc_final: 0.7216 (mmm) REVERT: A 411 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7061 (mt-10) REVERT: B 169 MET cc_start: 0.7198 (ptm) cc_final: 0.6943 (ptp) REVERT: B 284 MET cc_start: 0.8038 (mmm) cc_final: 0.7797 (mmm) REVERT: B 361 SER cc_start: 0.8636 (p) cc_final: 0.8410 (p) REVERT: B 378 MET cc_start: 0.7503 (mmt) cc_final: 0.7241 (mmm) REVERT: B 411 GLU cc_start: 0.7417 (mm-30) cc_final: 0.7082 (mt-10) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0786 time to fit residues: 6.8886 Evaluate side-chains 58 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 199 GLN A 248 HIS A 336 ASN A 480 HIS ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN B 199 GLN B 248 HIS B 336 ASN B 480 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.192654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.170867 restraints weight = 6695.641| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 1.71 r_work: 0.3920 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3781 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6394 Z= 0.126 Angle : 0.510 5.023 8666 Z= 0.269 Chirality : 0.042 0.143 1012 Planarity : 0.005 0.061 1086 Dihedral : 6.066 51.770 936 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.87 % Allowed : 6.10 % Favored : 93.02 % 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: -3.30 (0.26), residues: 746 helix: -3.80 (0.19), residues: 240 sheet: -1.55 (0.42), residues: 142 loop : -1.10 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 317 TYR 0.014 0.001 TYR B 269 PHE 0.016 0.001 PHE A 495 TRP 0.007 0.001 TRP B 252 HIS 0.002 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 6382) covalent geometry : angle 0.49660 ( 8636) SS BOND : bond 0.00152 ( 6) SS BOND : angle 0.66170 ( 12) hydrogen bonds : bond 0.03558 ( 182) hydrogen bonds : angle 5.14257 ( 477) link_NAG-ASN : bond 0.00076 ( 6) link_NAG-ASN : angle 2.53417 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.231 Fit side-chains REVERT: A 355 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7352 (tm-30) REVERT: A 361 SER cc_start: 0.8734 (p) cc_final: 0.8510 (p) REVERT: A 378 MET cc_start: 0.7307 (mmt) cc_final: 0.6984 (mmm) REVERT: A 411 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6815 (mt-10) REVERT: B 361 SER cc_start: 0.8709 (p) cc_final: 0.8484 (p) REVERT: B 378 MET cc_start: 0.7358 (mmt) cc_final: 0.7022 (mmm) REVERT: B 411 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6804 (mt-10) outliers start: 6 outliers final: 4 residues processed: 73 average time/residue: 0.0658 time to fit residues: 6.9392 Evaluate side-chains 72 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 464 ARG Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 464 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 3 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 48 optimal weight: 0.0980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 270 ASN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN B 270 ASN B 298 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.194623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.170218 restraints weight = 6582.732| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 1.97 r_work: 0.3717 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6394 Z= 0.146 Angle : 0.499 4.971 8666 Z= 0.261 Chirality : 0.042 0.144 1012 Planarity : 0.004 0.044 1086 Dihedral : 5.766 51.721 936 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.58 % Allowed : 8.87 % Favored : 90.55 % 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: -2.52 (0.28), residues: 746 helix: -2.38 (0.26), residues: 248 sheet: -1.81 (0.41), residues: 144 loop : -0.85 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 419 TYR 0.009 0.002 TYR A 398 PHE 0.017 0.002 PHE A 495 TRP 0.009 0.001 TRP A 252 HIS 0.002 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 6382) covalent geometry : angle 0.48715 ( 8636) SS BOND : bond 0.00231 ( 6) SS BOND : angle 0.55323 ( 12) hydrogen bonds : bond 0.03059 ( 182) hydrogen bonds : angle 4.79640 ( 477) link_NAG-ASN : bond 0.00197 ( 6) link_NAG-ASN : angle 2.41077 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.211 Fit side-chains REVERT: A 164 GLN cc_start: 0.7972 (mm-40) cc_final: 0.7761 (mm-40) REVERT: A 250 MET cc_start: 0.8233 (ttt) cc_final: 0.7956 (ttp) REVERT: A 411 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6925 (mt-10) REVERT: A 435 LYS cc_start: 0.7827 (mttt) cc_final: 0.7592 (mttp) REVERT: B 250 MET cc_start: 0.8247 (ttt) cc_final: 0.7989 (ttm) REVERT: B 411 GLU cc_start: 0.7296 (mm-30) cc_final: 0.6922 (mt-10) REVERT: B 494 LYS cc_start: 0.8783 (mttt) cc_final: 0.8556 (mmtm) outliers start: 4 outliers final: 4 residues processed: 73 average time/residue: 0.0748 time to fit residues: 7.4074 Evaluate side-chains 70 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 464 ARG Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 464 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 3 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 298 ASN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.194721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.168178 restraints weight = 6641.046| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 2.13 r_work: 0.3777 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6394 Z= 0.201 Angle : 0.559 5.711 8666 Z= 0.289 Chirality : 0.044 0.142 1012 Planarity : 0.004 0.038 1086 Dihedral : 5.940 50.906 936 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.73 % Allowed : 10.32 % Favored : 88.95 % 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: -2.07 (0.30), residues: 746 helix: -1.76 (0.30), residues: 248 sheet: -1.90 (0.42), residues: 132 loop : -0.68 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 277 TYR 0.013 0.002 TYR A 398 PHE 0.019 0.002 PHE A 495 TRP 0.010 0.001 TRP B 252 HIS 0.002 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 6382) covalent geometry : angle 0.54556 ( 8636) SS BOND : bond 0.00283 ( 6) SS BOND : angle 0.72140 ( 12) hydrogen bonds : bond 0.03025 ( 182) hydrogen bonds : angle 4.95656 ( 477) link_NAG-ASN : bond 0.00290 ( 6) link_NAG-ASN : angle 2.69431 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.243 Fit side-chains REVERT: A 250 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7771 (ttp) REVERT: A 411 GLU cc_start: 0.7076 (mm-30) cc_final: 0.6793 (mt-10) REVERT: A 435 LYS cc_start: 0.7869 (mttt) cc_final: 0.7556 (mttp) REVERT: B 171 ASP cc_start: 0.6858 (p0) cc_final: 0.6424 (t0) REVERT: B 411 GLU cc_start: 0.7060 (mm-30) cc_final: 0.6789 (mt-10) outliers start: 5 outliers final: 2 residues processed: 85 average time/residue: 0.0851 time to fit residues: 9.5229 Evaluate side-chains 80 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain B residue 342 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 4 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.194564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.168487 restraints weight = 6728.917| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.11 r_work: 0.3699 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6394 Z= 0.127 Angle : 0.474 5.065 8666 Z= 0.247 Chirality : 0.042 0.138 1012 Planarity : 0.003 0.033 1086 Dihedral : 5.651 51.865 936 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.73 % Allowed : 12.21 % Favored : 87.06 % 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: -1.72 (0.30), residues: 746 helix: -1.17 (0.32), residues: 248 sheet: -1.85 (0.40), residues: 148 loop : -0.57 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 317 TYR 0.008 0.001 TYR A 398 PHE 0.020 0.001 PHE B 495 TRP 0.009 0.001 TRP B 252 HIS 0.002 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 6382) covalent geometry : angle 0.46412 ( 8636) SS BOND : bond 0.00190 ( 6) SS BOND : angle 0.61059 ( 12) hydrogen bonds : bond 0.02608 ( 182) hydrogen bonds : angle 4.62541 ( 477) link_NAG-ASN : bond 0.00169 ( 6) link_NAG-ASN : angle 2.13169 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.230 Fit side-chains REVERT: A 250 MET cc_start: 0.8297 (ttt) cc_final: 0.8013 (ttp) REVERT: A 435 LYS cc_start: 0.7827 (mttt) cc_final: 0.7527 (mttp) REVERT: B 171 ASP cc_start: 0.6837 (p0) cc_final: 0.6400 (t0) REVERT: B 218 LEU cc_start: 0.8241 (mt) cc_final: 0.8039 (mp) outliers start: 5 outliers final: 1 residues processed: 78 average time/residue: 0.0699 time to fit residues: 7.6262 Evaluate side-chains 74 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 73 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 66 optimal weight: 0.1980 chunk 25 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.196251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.171233 restraints weight = 6659.973| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.05 r_work: 0.3745 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6394 Z= 0.107 Angle : 0.440 4.708 8666 Z= 0.230 Chirality : 0.041 0.140 1012 Planarity : 0.003 0.030 1086 Dihedral : 5.417 51.969 936 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.60 % Allowed : 12.21 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.31), residues: 746 helix: -0.64 (0.33), residues: 248 sheet: -1.78 (0.41), residues: 146 loop : -0.37 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 317 TYR 0.007 0.001 TYR A 398 PHE 0.020 0.001 PHE B 495 TRP 0.008 0.001 TRP B 252 HIS 0.001 0.000 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 6382) covalent geometry : angle 0.43184 ( 8636) SS BOND : bond 0.00167 ( 6) SS BOND : angle 0.56132 ( 12) hydrogen bonds : bond 0.02428 ( 182) hydrogen bonds : angle 4.33713 ( 477) link_NAG-ASN : bond 0.00150 ( 6) link_NAG-ASN : angle 1.86462 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.262 Fit side-chains REVERT: A 250 MET cc_start: 0.8265 (ttt) cc_final: 0.7987 (ttp) REVERT: A 278 GLN cc_start: 0.7009 (OUTLIER) cc_final: 0.6667 (mp10) REVERT: B 171 ASP cc_start: 0.6819 (p0) cc_final: 0.6373 (t0) REVERT: B 278 GLN cc_start: 0.7021 (OUTLIER) cc_final: 0.6681 (mp10) outliers start: 11 outliers final: 6 residues processed: 77 average time/residue: 0.0611 time to fit residues: 6.6431 Evaluate side-chains 77 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 342 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 65 optimal weight: 0.0070 chunk 6 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.194084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.169033 restraints weight = 6666.473| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.06 r_work: 0.3783 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3632 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6394 Z= 0.112 Angle : 0.451 7.264 8666 Z= 0.232 Chirality : 0.041 0.143 1012 Planarity : 0.003 0.029 1086 Dihedral : 5.400 51.769 936 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.89 % Allowed : 12.79 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.32), residues: 746 helix: -0.41 (0.34), residues: 250 sheet: -1.82 (0.37), residues: 166 loop : -0.12 (0.38), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 317 TYR 0.007 0.001 TYR A 398 PHE 0.018 0.001 PHE A 495 TRP 0.008 0.001 TRP B 252 HIS 0.002 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 6382) covalent geometry : angle 0.44326 ( 8636) SS BOND : bond 0.00168 ( 6) SS BOND : angle 0.55245 ( 12) hydrogen bonds : bond 0.02399 ( 182) hydrogen bonds : angle 4.31529 ( 477) link_NAG-ASN : bond 0.00146 ( 6) link_NAG-ASN : angle 1.86267 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.257 Fit side-chains REVERT: A 250 MET cc_start: 0.8269 (ttt) cc_final: 0.7984 (ttp) REVERT: A 278 GLN cc_start: 0.7009 (OUTLIER) cc_final: 0.6695 (mp10) REVERT: B 171 ASP cc_start: 0.6734 (p0) cc_final: 0.6308 (t0) REVERT: B 278 GLN cc_start: 0.7031 (OUTLIER) cc_final: 0.6716 (mp10) outliers start: 13 outliers final: 9 residues processed: 77 average time/residue: 0.0629 time to fit residues: 6.9497 Evaluate side-chains 78 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 463 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 67 optimal weight: 0.1980 chunk 65 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.192403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.167820 restraints weight = 6614.850| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.01 r_work: 0.3734 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3584 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6394 Z= 0.143 Angle : 0.476 5.046 8666 Z= 0.247 Chirality : 0.042 0.141 1012 Planarity : 0.003 0.029 1086 Dihedral : 5.561 51.371 936 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.74 % Allowed : 13.37 % Favored : 84.88 % 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: -1.08 (0.32), residues: 746 helix: -0.44 (0.34), residues: 250 sheet: -1.84 (0.37), residues: 166 loop : -0.05 (0.38), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 464 TYR 0.009 0.001 TYR A 398 PHE 0.019 0.001 PHE A 495 TRP 0.010 0.001 TRP B 252 HIS 0.002 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 6382) covalent geometry : angle 0.46682 ( 8636) SS BOND : bond 0.00206 ( 6) SS BOND : angle 0.59746 ( 12) hydrogen bonds : bond 0.02529 ( 182) hydrogen bonds : angle 4.47725 ( 477) link_NAG-ASN : bond 0.00176 ( 6) link_NAG-ASN : angle 2.09991 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.247 Fit side-chains REVERT: A 250 MET cc_start: 0.8265 (ttt) cc_final: 0.7965 (ttp) REVERT: A 278 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.6658 (mp10) REVERT: B 171 ASP cc_start: 0.6823 (p0) cc_final: 0.6398 (t0) REVERT: B 278 GLN cc_start: 0.7015 (OUTLIER) cc_final: 0.6656 (mp10) outliers start: 12 outliers final: 9 residues processed: 82 average time/residue: 0.0683 time to fit residues: 7.8113 Evaluate side-chains 83 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 463 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 45 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 0.0980 chunk 4 optimal weight: 0.0670 chunk 37 optimal weight: 0.7980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.205723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.179688 restraints weight = 6528.601| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.17 r_work: 0.3766 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6394 Z= 0.098 Angle : 0.427 4.691 8666 Z= 0.223 Chirality : 0.041 0.140 1012 Planarity : 0.003 0.029 1086 Dihedral : 5.321 52.346 936 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.03 % Allowed : 13.37 % Favored : 84.59 % 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: -0.85 (0.32), residues: 746 helix: -0.11 (0.34), residues: 250 sheet: -1.82 (0.37), residues: 166 loop : 0.04 (0.38), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 317 TYR 0.006 0.001 TYR A 398 PHE 0.019 0.001 PHE A 495 TRP 0.007 0.001 TRP B 252 HIS 0.002 0.000 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 6382) covalent geometry : angle 0.41939 ( 8636) SS BOND : bond 0.00141 ( 6) SS BOND : angle 0.55805 ( 12) hydrogen bonds : bond 0.02294 ( 182) hydrogen bonds : angle 4.22238 ( 477) link_NAG-ASN : bond 0.00140 ( 6) link_NAG-ASN : angle 1.75166 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.206 Fit side-chains REVERT: A 250 MET cc_start: 0.8290 (ttt) cc_final: 0.7988 (ttp) REVERT: A 278 GLN cc_start: 0.6972 (OUTLIER) cc_final: 0.6643 (mp10) REVERT: B 171 ASP cc_start: 0.6787 (p0) cc_final: 0.6351 (t0) REVERT: B 250 MET cc_start: 0.8269 (ttt) cc_final: 0.8010 (ttp) REVERT: B 278 GLN cc_start: 0.6948 (OUTLIER) cc_final: 0.6620 (mp10) outliers start: 14 outliers final: 9 residues processed: 79 average time/residue: 0.0688 time to fit residues: 7.7442 Evaluate side-chains 77 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 463 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 21 optimal weight: 0.4980 chunk 60 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.197724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.172701 restraints weight = 6435.104| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 2.07 r_work: 0.3762 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3609 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6394 Z= 0.117 Angle : 0.448 4.670 8666 Z= 0.232 Chirality : 0.041 0.143 1012 Planarity : 0.003 0.029 1086 Dihedral : 5.383 51.655 936 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.74 % Allowed : 13.66 % Favored : 84.59 % 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: -0.77 (0.32), residues: 746 helix: 0.03 (0.35), residues: 238 sheet: -1.85 (0.37), residues: 166 loop : 0.06 (0.38), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 317 TYR 0.007 0.001 TYR A 398 PHE 0.019 0.001 PHE A 495 TRP 0.008 0.001 TRP B 252 HIS 0.002 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 6382) covalent geometry : angle 0.43999 ( 8636) SS BOND : bond 0.00172 ( 6) SS BOND : angle 0.55047 ( 12) hydrogen bonds : bond 0.02377 ( 182) hydrogen bonds : angle 4.27975 ( 477) link_NAG-ASN : bond 0.00160 ( 6) link_NAG-ASN : angle 1.87082 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.239 Fit side-chains REVERT: A 250 MET cc_start: 0.8250 (ttt) cc_final: 0.7957 (ttp) REVERT: A 278 GLN cc_start: 0.6975 (OUTLIER) cc_final: 0.6644 (mp10) REVERT: B 171 ASP cc_start: 0.6818 (p0) cc_final: 0.6385 (t0) REVERT: B 250 MET cc_start: 0.8247 (ttt) cc_final: 0.7987 (ttp) REVERT: B 278 GLN cc_start: 0.7012 (OUTLIER) cc_final: 0.6687 (mp10) outliers start: 12 outliers final: 8 residues processed: 77 average time/residue: 0.0616 time to fit residues: 6.7174 Evaluate side-chains 76 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 463 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 7 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 0.1980 chunk 63 optimal weight: 0.6980 chunk 6 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.197759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.172589 restraints weight = 6565.298| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.11 r_work: 0.3776 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6394 Z= 0.092 Angle : 0.419 4.645 8666 Z= 0.219 Chirality : 0.041 0.139 1012 Planarity : 0.003 0.029 1086 Dihedral : 5.251 52.210 936 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.45 % Allowed : 14.10 % Favored : 84.45 % 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: -0.67 (0.32), residues: 746 helix: 0.15 (0.34), residues: 250 sheet: -1.80 (0.37), residues: 166 loop : 0.08 (0.38), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 317 TYR 0.005 0.001 TYR A 398 PHE 0.019 0.001 PHE A 495 TRP 0.006 0.001 TRP B 252 HIS 0.002 0.000 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 6382) covalent geometry : angle 0.41205 ( 8636) SS BOND : bond 0.00147 ( 6) SS BOND : angle 0.52692 ( 12) hydrogen bonds : bond 0.02235 ( 182) hydrogen bonds : angle 4.15373 ( 477) link_NAG-ASN : bond 0.00144 ( 6) link_NAG-ASN : angle 1.69778 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1558.65 seconds wall clock time: 27 minutes 20.53 seconds (1640.53 seconds total)