Starting phenix.real_space_refine on Tue Mar 11 16:07:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bfr_44504/03_2025/9bfr_44504.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bfr_44504/03_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_44504/03_2025/9bfr_44504.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bfr_44504/03_2025/9bfr_44504.map" model { file = "/net/cci-nas-00/data/ceres_data/9bfr_44504/03_2025/9bfr_44504.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bfr_44504/03_2025/9bfr_44504.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'PHE:plan': 1, 'HIS: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: {'PHE:plan': 1, 'HIS: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: 4.53, per 1000 atoms: 0.72 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: 1.43 Conformation dependent library (CDL) restraints added in 873.8 milliseconds 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: 0.73 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: 1.88 Time building geometry restraints manager: 1.73 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: 0.03 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: 1.400 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.920 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.690 ------------------------------------------------------------------------------- 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 6382 Z= 0.410 Angle : 1.111 9.633 8636 Z= 0.606 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.020 0.003 TRP A 523 HIS 0.007 0.001 HIS A 285 PHE 0.047 0.004 PHE B 495 TYR 0.011 0.002 TYR A 445 ARG 0.006 0.001 ARG B 382 *********************** 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 : 0.644 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: 0.2033 time to fit residues: 17.7717 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 : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 69 optimal weight: 0.0870 overall best weight: 0.9360 ------------------------------------------------------------------------------- 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 ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN B 199 GLN B 248 HIS B 336 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.193500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.172177 restraints weight = 6558.556| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 1.63 r_work: 0.3902 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3763 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6382 Z= 0.230 Angle : 0.535 5.904 8636 Z= 0.285 Chirality : 0.043 0.145 1012 Planarity : 0.005 0.062 1086 Dihedral : 6.173 51.346 936 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.87 % Allowed : 6.40 % Favored : 92.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.26), residues: 746 helix: -3.85 (0.18), residues: 246 sheet: -1.64 (0.42), residues: 142 loop : -1.23 (0.29), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 252 HIS 0.002 0.001 HIS B 285 PHE 0.018 0.002 PHE A 495 TYR 0.014 0.002 TYR A 269 ARG 0.002 0.000 ARG B 382 *********************** 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 78 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.693 Fit side-chains REVERT: A 361 SER cc_start: 0.8732 (p) cc_final: 0.8500 (p) REVERT: A 378 MET cc_start: 0.7297 (mmt) cc_final: 0.6972 (mmm) REVERT: A 411 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6853 (mt-10) REVERT: B 169 MET cc_start: 0.7458 (ptm) cc_final: 0.7240 (ptm) REVERT: B 250 MET cc_start: 0.8115 (ttt) cc_final: 0.7800 (ttm) REVERT: B 361 SER cc_start: 0.8704 (p) cc_final: 0.8472 (p) REVERT: B 378 MET cc_start: 0.7355 (mmt) cc_final: 0.7023 (mmm) REVERT: B 411 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6854 (mt-10) REVERT: B 494 LYS cc_start: 0.8594 (mttt) cc_final: 0.8291 (mmtm) outliers start: 6 outliers final: 4 residues processed: 74 average time/residue: 0.1720 time to fit residues: 17.6332 Evaluate side-chains 74 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 32 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 A 298 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.195085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.168919 restraints weight = 6598.545| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.14 r_work: 0.3780 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6382 Z= 0.209 Angle : 0.487 4.705 8636 Z= 0.257 Chirality : 0.042 0.141 1012 Planarity : 0.004 0.045 1086 Dihedral : 5.798 51.767 936 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.73 % Allowed : 9.01 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.28), residues: 746 helix: -2.38 (0.27), residues: 248 sheet: -1.79 (0.41), residues: 144 loop : -0.85 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 252 HIS 0.002 0.001 HIS A 285 PHE 0.020 0.001 PHE B 495 TYR 0.009 0.002 TYR A 398 ARG 0.002 0.000 ARG B 382 *********************** 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 83 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.658 Fit side-chains REVERT: A 250 MET cc_start: 0.8024 (ttt) cc_final: 0.7755 (ttp) REVERT: A 267 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7933 (mt-10) REVERT: A 411 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6824 (mt-10) REVERT: A 435 LYS cc_start: 0.7795 (mttt) cc_final: 0.7534 (mttp) REVERT: B 250 MET cc_start: 0.8042 (ttt) cc_final: 0.7787 (ttm) REVERT: B 267 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7977 (mt-10) REVERT: B 284 MET cc_start: 0.8201 (mmm) cc_final: 0.7969 (mmm) REVERT: B 411 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6824 (mt-10) outliers start: 5 outliers final: 5 residues processed: 80 average time/residue: 0.1767 time to fit residues: 19.2429 Evaluate side-chains 74 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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 136 VAL 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 74 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 73 optimal weight: 0.0970 chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 33 optimal weight: 0.0970 chunk 54 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 270 ASN A 480 HIS ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.194312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.169659 restraints weight = 6678.151| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 1.98 r_work: 0.3798 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6382 Z= 0.137 Angle : 0.426 4.595 8636 Z= 0.226 Chirality : 0.041 0.139 1012 Planarity : 0.003 0.035 1086 Dihedral : 5.469 52.200 936 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.29 % Allowed : 10.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.30), residues: 746 helix: -1.43 (0.31), residues: 248 sheet: -1.70 (0.42), residues: 142 loop : -0.56 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 252 HIS 0.002 0.000 HIS B 285 PHE 0.019 0.001 PHE A 495 TYR 0.005 0.001 TYR A 398 ARG 0.002 0.000 ARG A 317 *********************** 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 70 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.660 Fit side-chains REVERT: A 250 MET cc_start: 0.8270 (ttt) cc_final: 0.8011 (ttp) REVERT: A 435 LYS cc_start: 0.7771 (mttt) cc_final: 0.7560 (mttp) REVERT: B 250 MET cc_start: 0.8201 (ttt) cc_final: 0.7981 (ttm) outliers start: 2 outliers final: 0 residues processed: 68 average time/residue: 0.1854 time to fit residues: 17.2891 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 : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 270 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 = 0.4086 r_free = 0.4086 target = 0.193659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.167176 restraints weight = 6694.860| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.14 r_work: 0.3669 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6382 Z= 0.301 Angle : 0.542 5.355 8636 Z= 0.285 Chirality : 0.044 0.141 1012 Planarity : 0.003 0.035 1086 Dihedral : 5.844 50.733 936 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.16 % Allowed : 12.35 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.30), residues: 746 helix: -1.24 (0.32), residues: 248 sheet: -1.91 (0.42), residues: 132 loop : -0.51 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 252 HIS 0.002 0.001 HIS B 285 PHE 0.018 0.002 PHE B 495 TYR 0.013 0.002 TYR A 398 ARG 0.002 0.000 ARG B 317 *********************** 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 87 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.801 Fit side-chains REVERT: A 250 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7999 (ttp) REVERT: A 426 GLU cc_start: 0.6771 (tt0) cc_final: 0.6475 (tp30) REVERT: B 171 ASP cc_start: 0.6896 (p0) cc_final: 0.6449 (t0) outliers start: 8 outliers final: 3 residues processed: 83 average time/residue: 0.1551 time to fit residues: 18.3301 Evaluate side-chains 79 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 527 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 46 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.4074 r_free = 0.4074 target = 0.193344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.167875 restraints weight = 6646.334| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 2.07 r_work: 0.3746 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6382 Z= 0.234 Angle : 0.490 5.480 8636 Z= 0.258 Chirality : 0.043 0.143 1012 Planarity : 0.003 0.031 1086 Dihedral : 5.695 51.671 936 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.89 % Allowed : 12.35 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.31), residues: 746 helix: -0.87 (0.33), residues: 248 sheet: -1.86 (0.41), residues: 142 loop : -0.47 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 252 HIS 0.002 0.001 HIS B 238 PHE 0.019 0.001 PHE A 495 TYR 0.010 0.001 TYR B 398 ARG 0.002 0.000 ARG A 317 *********************** 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 84 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.696 Fit side-chains REVERT: A 250 MET cc_start: 0.8304 (ttt) cc_final: 0.8025 (ttp) REVERT: A 278 GLN cc_start: 0.6942 (OUTLIER) cc_final: 0.6684 (mp10) REVERT: A 426 GLU cc_start: 0.6742 (tt0) cc_final: 0.6455 (tp30) REVERT: B 171 ASP cc_start: 0.6858 (p0) cc_final: 0.6471 (t0) REVERT: B 250 MET cc_start: 0.8268 (ttt) cc_final: 0.8023 (ttp) REVERT: B 278 GLN cc_start: 0.6951 (OUTLIER) cc_final: 0.6699 (mp10) outliers start: 13 outliers final: 6 residues processed: 81 average time/residue: 0.1488 time to fit residues: 17.1746 Evaluate side-chains 78 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 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 57 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 65 optimal weight: 0.0870 chunk 45 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.6560 ------------------------------------------------------------------------------- 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 = 0.4087 r_free = 0.4087 target = 0.194864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.169764 restraints weight = 6617.948| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.06 r_work: 0.3736 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6382 Z= 0.167 Angle : 0.441 4.781 8636 Z= 0.234 Chirality : 0.041 0.138 1012 Planarity : 0.003 0.031 1086 Dihedral : 5.487 52.079 936 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.32), residues: 746 helix: -0.42 (0.34), residues: 246 sheet: -1.82 (0.37), residues: 166 loop : -0.17 (0.38), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 252 HIS 0.002 0.001 HIS B 285 PHE 0.020 0.001 PHE A 495 TYR 0.007 0.001 TYR A 398 ARG 0.003 0.000 ARG A 464 *********************** 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 82 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.730 Fit side-chains REVERT: A 250 MET cc_start: 0.8294 (ttt) cc_final: 0.8019 (ttp) REVERT: A 278 GLN cc_start: 0.6916 (OUTLIER) cc_final: 0.6522 (mp10) REVERT: B 171 ASP cc_start: 0.6782 (p0) cc_final: 0.6389 (t0) REVERT: B 250 MET cc_start: 0.8242 (ttt) cc_final: 0.8000 (ttp) REVERT: B 278 GLN cc_start: 0.6901 (OUTLIER) cc_final: 0.6507 (mp10) outliers start: 13 outliers final: 7 residues processed: 79 average time/residue: 0.1619 time to fit residues: 18.2797 Evaluate side-chains 77 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 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 37 optimal weight: 2.9990 chunk 66 optimal weight: 0.0770 chunk 32 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 0.0170 chunk 53 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 58 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.4127 r_free = 0.4127 target = 0.198309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.173221 restraints weight = 6432.409| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 2.08 r_work: 0.3837 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3681 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6382 Z= 0.145 Angle : 0.428 4.638 8636 Z= 0.224 Chirality : 0.041 0.139 1012 Planarity : 0.003 0.030 1086 Dihedral : 5.335 52.078 936 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.16 % Allowed : 14.10 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.32), residues: 746 helix: 0.04 (0.36), residues: 234 sheet: -1.83 (0.37), residues: 166 loop : -0.07 (0.37), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 252 HIS 0.001 0.000 HIS B 285 PHE 0.020 0.001 PHE B 495 TYR 0.006 0.001 TYR A 398 ARG 0.002 0.000 ARG A 317 *********************** 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 75 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.693 Fit side-chains REVERT: A 250 MET cc_start: 0.8247 (ttt) cc_final: 0.7951 (ttp) REVERT: A 278 GLN cc_start: 0.6912 (OUTLIER) cc_final: 0.6540 (mp10) REVERT: B 171 ASP cc_start: 0.6743 (p0) cc_final: 0.6344 (t0) REVERT: B 218 LEU cc_start: 0.8320 (mt) cc_final: 0.8084 (mp) REVERT: B 250 MET cc_start: 0.8253 (ttt) cc_final: 0.8000 (ttp) REVERT: B 278 GLN cc_start: 0.6868 (OUTLIER) cc_final: 0.6490 (mp10) outliers start: 8 outliers final: 4 residues processed: 73 average time/residue: 0.1612 time to fit residues: 16.7470 Evaluate side-chains 71 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 332 VAL 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 463 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.8980 chunk 54 optimal weight: 0.3980 chunk 39 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 29 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 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 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 = 0.4140 r_free = 0.4140 target = 0.199046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.173828 restraints weight = 6554.305| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.10 r_work: 0.3763 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6382 Z= 0.167 Angle : 0.441 4.682 8636 Z= 0.231 Chirality : 0.042 0.140 1012 Planarity : 0.003 0.029 1086 Dihedral : 5.396 51.920 936 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.60 % Allowed : 14.10 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.32), residues: 746 helix: 0.00 (0.35), residues: 246 sheet: -1.86 (0.37), residues: 162 loop : -0.08 (0.38), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 252 HIS 0.002 0.000 HIS A 285 PHE 0.019 0.001 PHE B 495 TYR 0.007 0.001 TYR B 398 ARG 0.002 0.000 ARG A 317 *********************** 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 76 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.656 Fit side-chains REVERT: A 250 MET cc_start: 0.8255 (ttt) cc_final: 0.7953 (ttp) REVERT: A 278 GLN cc_start: 0.6863 (OUTLIER) cc_final: 0.6481 (mp10) REVERT: B 171 ASP cc_start: 0.6775 (p0) cc_final: 0.6371 (t0) REVERT: B 278 GLN cc_start: 0.6879 (OUTLIER) cc_final: 0.6485 (mp10) outliers start: 11 outliers final: 8 residues processed: 74 average time/residue: 0.1714 time to fit residues: 18.2519 Evaluate side-chains 75 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 463 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 281 MET 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 74 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 60 optimal weight: 0.1980 chunk 68 optimal weight: 5.9990 chunk 35 optimal weight: 0.0770 chunk 58 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 44 optimal weight: 0.0980 chunk 66 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.8742 ------------------------------------------------------------------------------- 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 = 0.4047 r_free = 0.4047 target = 0.191123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.166802 restraints weight = 6637.622| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.01 r_work: 0.3727 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6382 Z= 0.207 Angle : 0.474 4.781 8636 Z= 0.247 Chirality : 0.042 0.141 1012 Planarity : 0.003 0.029 1086 Dihedral : 5.557 51.435 936 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.89 % Allowed : 13.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.32), residues: 746 helix: -0.13 (0.34), residues: 248 sheet: -1.89 (0.37), residues: 162 loop : -0.09 (0.38), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 252 HIS 0.002 0.001 HIS A 285 PHE 0.020 0.001 PHE B 495 TYR 0.009 0.001 TYR A 398 ARG 0.002 0.000 ARG A 317 ********************** 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 82 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.659 Fit side-chains REVERT: A 250 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7966 (ttp) REVERT: A 278 GLN cc_start: 0.6846 (OUTLIER) cc_final: 0.6587 (mp10) REVERT: B 171 ASP cc_start: 0.6852 (p0) cc_final: 0.6454 (t0) REVERT: B 278 GLN cc_start: 0.6879 (OUTLIER) cc_final: 0.6478 (mp10) outliers start: 13 outliers final: 9 residues processed: 80 average time/residue: 0.1679 time to fit residues: 18.7976 Evaluate side-chains 80 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 250 MET 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 281 MET 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 45 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 7 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 73 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4035 r_free = 0.4035 target = 0.190721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.166749 restraints weight = 6669.340| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 1.98 r_work: 0.3832 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3678 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6382 Z= 0.184 Angle : 0.456 4.763 8636 Z= 0.240 Chirality : 0.042 0.140 1012 Planarity : 0.003 0.030 1086 Dihedral : 5.513 51.778 936 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.89 % Allowed : 13.95 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.32), residues: 746 helix: -0.04 (0.35), residues: 248 sheet: -1.86 (0.37), residues: 162 loop : -0.07 (0.38), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 252 HIS 0.002 0.001 HIS B 285 PHE 0.020 0.001 PHE A 495 TYR 0.013 0.001 TYR B 204 ARG 0.006 0.000 ARG B 277 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3500.84 seconds wall clock time: 60 minutes 36.38 seconds (3636.38 seconds total)