Starting phenix.real_space_refine on Sun May 11 08:02:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gw7_34304/05_2025/8gw7_34304_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gw7_34304/05_2025/8gw7_34304.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gw7_34304/05_2025/8gw7_34304.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gw7_34304/05_2025/8gw7_34304.map" model { file = "/net/cci-nas-00/data/ceres_data/8gw7_34304/05_2025/8gw7_34304_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gw7_34304/05_2025/8gw7_34304_trim.cif" } resolution = 3.3 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= 0.002 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 39 5.16 5 Cl 6 4.86 5 C 5169 2.51 5 N 1128 2.21 5 O 1182 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7524 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2471 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 20, 'TRANS': 294} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {' CL': 2, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: C, B Time building chain proxies: 4.44, per 1000 atoms: 0.59 Number of scatterers: 7524 At special positions: 0 Unit cell: (106.68, 97.44, 66.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 6 17.00 S 39 16.00 O 1182 8.00 N 1128 7.00 C 5169 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 1.0 seconds 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1806 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 0 sheets defined 81.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 189 through 191 No H-bonds generated for 'chain 'A' and resid 189 through 191' Processing helix chain 'A' and resid 192 through 212 removed outlier: 4.310A pdb=" N CYS A 196 " --> pdb=" O CYS A 192 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 205 " --> pdb=" O SER A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 219 removed outlier: 3.752A pdb=" N LEU A 218 " --> pdb=" O THR A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 250 removed outlier: 3.842A pdb=" N LEU A 226 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 260 removed outlier: 3.757A pdb=" N PHE A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N HIS A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 267 removed outlier: 3.526A pdb=" N VAL A 264 " --> pdb=" O PRO A 261 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASN A 265 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE A 266 " --> pdb=" O ARG A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 281 removed outlier: 3.743A pdb=" N CYS A 274 " --> pdb=" O PRO A 270 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET A 275 " --> pdb=" O TRP A 271 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 318 removed outlier: 4.377A pdb=" N TRP A 297 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS A 298 " --> pdb=" O PRO A 294 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Proline residue: A 303 - end of helix removed outlier: 3.687A pdb=" N TRP A 315 " --> pdb=" O ILE A 311 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 349 removed outlier: 3.892A pdb=" N PHE A 339 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 343 " --> pdb=" O PHE A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 375 removed outlier: 4.079A pdb=" N VAL A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 392 removed outlier: 3.666A pdb=" N SER A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N MET A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 409 Processing helix chain 'A' and resid 412 through 433 removed outlier: 3.622A pdb=" N LEU A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 466 removed outlier: 3.916A pdb=" N TYR A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR A 449 " --> pdb=" O TRP A 445 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE A 450 " --> pdb=" O TRP A 446 " (cutoff:3.500A) Proline residue: A 451 - end of helix removed outlier: 3.548A pdb=" N LYS A 461 " --> pdb=" O VAL A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 499 removed outlier: 3.842A pdb=" N ALA A 497 " --> pdb=" O THR A 493 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 499 " --> pdb=" O LEU A 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 191 No H-bonds generated for 'chain 'C' and resid 189 through 191' Processing helix chain 'C' and resid 192 through 212 removed outlier: 4.309A pdb=" N CYS C 196 " --> pdb=" O CYS C 192 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA C 203 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL C 204 " --> pdb=" O SER C 200 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU C 205 " --> pdb=" O SER C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 219 removed outlier: 3.752A pdb=" N LEU C 218 " --> pdb=" O THR C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 250 removed outlier: 3.843A pdb=" N LEU C 226 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 260 removed outlier: 3.756A pdb=" N PHE C 259 " --> pdb=" O LYS C 255 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N HIS C 260 " --> pdb=" O ARG C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 267 removed outlier: 3.527A pdb=" N VAL C 264 " --> pdb=" O PRO C 261 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASN C 265 " --> pdb=" O VAL C 262 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE C 266 " --> pdb=" O ARG C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 281 removed outlier: 3.744A pdb=" N CYS C 274 " --> pdb=" O PRO C 270 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET C 275 " --> pdb=" O TRP C 271 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE C 276 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER C 280 " --> pdb=" O PHE C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 318 removed outlier: 4.377A pdb=" N TRP C 297 " --> pdb=" O HIS C 293 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS C 298 " --> pdb=" O PRO C 294 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE C 300 " --> pdb=" O ILE C 296 " (cutoff:3.500A) Proline residue: C 303 - end of helix removed outlier: 3.687A pdb=" N TRP C 315 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C 316 " --> pdb=" O TYR C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 349 removed outlier: 3.892A pdb=" N PHE C 339 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE C 343 " --> pdb=" O PHE C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 375 removed outlier: 4.079A pdb=" N VAL C 367 " --> pdb=" O ALA C 363 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG C 375 " --> pdb=" O THR C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 392 removed outlier: 3.666A pdb=" N SER C 391 " --> pdb=" O HIS C 387 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N MET C 392 " --> pdb=" O PRO C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 409 Processing helix chain 'C' and resid 412 through 433 removed outlier: 3.622A pdb=" N LEU C 429 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL C 430 " --> pdb=" O TYR C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 466 removed outlier: 3.916A pdb=" N TYR C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR C 449 " --> pdb=" O TRP C 445 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE C 450 " --> pdb=" O TRP C 446 " (cutoff:3.500A) Proline residue: C 451 - end of helix removed outlier: 3.548A pdb=" N LYS C 461 " --> pdb=" O VAL C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 499 removed outlier: 3.842A pdb=" N ALA C 497 " --> pdb=" O THR C 493 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE C 498 " --> pdb=" O LEU C 494 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL C 499 " --> pdb=" O LEU C 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 191 No H-bonds generated for 'chain 'B' and resid 189 through 191' Processing helix chain 'B' and resid 192 through 212 removed outlier: 4.310A pdb=" N CYS B 196 " --> pdb=" O CYS B 192 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL B 204 " --> pdb=" O SER B 200 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B 205 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 219 removed outlier: 3.752A pdb=" N LEU B 218 " --> pdb=" O THR B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 250 removed outlier: 3.842A pdb=" N LEU B 226 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 260 removed outlier: 3.757A pdb=" N PHE B 259 " --> pdb=" O LYS B 255 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N HIS B 260 " --> pdb=" O ARG B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 267 removed outlier: 3.525A pdb=" N VAL B 264 " --> pdb=" O PRO B 261 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASN B 265 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE B 266 " --> pdb=" O ARG B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 281 removed outlier: 3.744A pdb=" N CYS B 274 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET B 275 " --> pdb=" O TRP B 271 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B 280 " --> pdb=" O PHE B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 318 removed outlier: 4.377A pdb=" N TRP B 297 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS B 298 " --> pdb=" O PRO B 294 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B 300 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Proline residue: B 303 - end of helix removed outlier: 3.687A pdb=" N TRP B 315 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 316 " --> pdb=" O TYR B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 349 removed outlier: 3.893A pdb=" N PHE B 339 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 343 " --> pdb=" O PHE B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 375 removed outlier: 4.079A pdb=" N VAL B 367 " --> pdb=" O ALA B 363 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 392 removed outlier: 3.667A pdb=" N SER B 391 " --> pdb=" O HIS B 387 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N MET B 392 " --> pdb=" O PRO B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 409 Processing helix chain 'B' and resid 412 through 433 removed outlier: 3.623A pdb=" N LEU B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL B 430 " --> pdb=" O TYR B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 466 removed outlier: 3.915A pdb=" N TYR B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR B 449 " --> pdb=" O TRP B 445 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE B 450 " --> pdb=" O TRP B 446 " (cutoff:3.500A) Proline residue: B 451 - end of helix removed outlier: 3.547A pdb=" N LYS B 461 " --> pdb=" O VAL B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 499 removed outlier: 3.841A pdb=" N ALA B 497 " --> pdb=" O THR B 493 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) 474 hydrogen bonds defined for protein. 1404 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: 1.87 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1185 1.33 - 1.45: 2368 1.45 - 1.57: 4211 1.57 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 7818 Sorted by residual: bond pdb=" CBD Y01 B 903 " pdb=" CBF Y01 B 903 " ideal model delta sigma weight residual 1.536 1.463 0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" CBD Y01 C 903 " pdb=" CBF Y01 C 903 " ideal model delta sigma weight residual 1.536 1.463 0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" CBD Y01 A 903 " pdb=" CBF Y01 A 903 " ideal model delta sigma weight residual 1.536 1.463 0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" CAK Y01 A 903 " pdb=" CBD Y01 A 903 " ideal model delta sigma weight residual 1.525 1.467 0.058 2.00e-02 2.50e+03 8.47e+00 bond pdb=" CAK Y01 B 903 " pdb=" CBD Y01 B 903 " ideal model delta sigma weight residual 1.525 1.467 0.058 2.00e-02 2.50e+03 8.45e+00 ... (remaining 7813 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 10564 2.36 - 4.73: 119 4.73 - 7.09: 39 7.09 - 9.45: 13 9.45 - 11.81: 14 Bond angle restraints: 10749 Sorted by residual: angle pdb=" CAK Y01 A 903 " pdb=" CAI Y01 A 903 " pdb=" CAZ Y01 A 903 " ideal model delta sigma weight residual 124.96 113.15 11.81 3.00e+00 1.11e-01 1.55e+01 angle pdb=" CAK Y01 C 903 " pdb=" CAI Y01 C 903 " pdb=" CAZ Y01 C 903 " ideal model delta sigma weight residual 124.96 113.21 11.75 3.00e+00 1.11e-01 1.53e+01 angle pdb=" CAK Y01 B 903 " pdb=" CAI Y01 B 903 " pdb=" CAZ Y01 B 903 " ideal model delta sigma weight residual 124.96 113.25 11.71 3.00e+00 1.11e-01 1.52e+01 angle pdb=" CAD Y01 A 903 " pdb=" CBH Y01 A 903 " pdb=" CAZ Y01 A 903 " ideal model delta sigma weight residual 108.53 98.20 10.33 3.00e+00 1.11e-01 1.19e+01 angle pdb=" CAD Y01 B 903 " pdb=" CBH Y01 B 903 " pdb=" CAZ Y01 B 903 " ideal model delta sigma weight residual 108.53 98.23 10.30 3.00e+00 1.11e-01 1.18e+01 ... (remaining 10744 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 4030 17.05 - 34.10: 350 34.10 - 51.16: 87 51.16 - 68.21: 15 68.21 - 85.26: 6 Dihedral angle restraints: 4488 sinusoidal: 1701 harmonic: 2787 Sorted by residual: dihedral pdb=" CB GLU C 308 " pdb=" CG GLU C 308 " pdb=" CD GLU C 308 " pdb=" OE1 GLU C 308 " ideal model delta sinusoidal sigma weight residual 0.00 -85.26 85.26 1 3.00e+01 1.11e-03 9.79e+00 dihedral pdb=" CB GLU B 308 " pdb=" CG GLU B 308 " pdb=" CD GLU B 308 " pdb=" OE1 GLU B 308 " ideal model delta sinusoidal sigma weight residual 0.00 -85.26 85.26 1 3.00e+01 1.11e-03 9.79e+00 dihedral pdb=" CB GLU A 308 " pdb=" CG GLU A 308 " pdb=" CD GLU A 308 " pdb=" OE1 GLU A 308 " ideal model delta sinusoidal sigma weight residual 0.00 -85.24 85.24 1 3.00e+01 1.11e-03 9.78e+00 ... (remaining 4485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 1212 0.144 - 0.288: 6 0.288 - 0.431: 9 0.431 - 0.575: 0 0.575 - 0.719: 3 Chirality restraints: 1230 Sorted by residual: chirality pdb=" CBH Y01 A 903 " pdb=" CAT Y01 A 903 " pdb=" CAZ Y01 A 903 " pdb=" CBF Y01 A 903 " both_signs ideal model delta sigma weight residual False -2.85 -2.13 -0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" CBH Y01 B 903 " pdb=" CAT Y01 B 903 " pdb=" CAZ Y01 B 903 " pdb=" CBF Y01 B 903 " both_signs ideal model delta sigma weight residual False -2.85 -2.13 -0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" CBH Y01 C 903 " pdb=" CAT Y01 C 903 " pdb=" CAZ Y01 C 903 " pdb=" CBF Y01 C 903 " both_signs ideal model delta sigma weight residual False -2.85 -2.14 -0.72 2.00e-01 2.50e+01 1.28e+01 ... (remaining 1227 not shown) Planarity restraints: 1269 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 286 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO B 287 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 287 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 287 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 286 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO A 287 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 287 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 287 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 286 " -0.036 5.00e-02 4.00e+02 5.47e-02 4.79e+00 pdb=" N PRO C 287 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 287 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 287 " -0.030 5.00e-02 4.00e+02 ... (remaining 1266 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 970 2.76 - 3.29: 7878 3.29 - 3.83: 11781 3.83 - 4.36: 13144 4.36 - 4.90: 22551 Nonbonded interactions: 56324 Sorted by model distance: nonbonded pdb=" OE1 GLN B 202 " pdb=" OG1 THR B 453 " model vdw 2.220 3.040 nonbonded pdb=" OE1 GLN A 202 " pdb=" OG1 THR A 453 " model vdw 2.220 3.040 nonbonded pdb=" OE1 GLN C 202 " pdb=" OG1 THR C 453 " model vdw 2.221 3.040 nonbonded pdb=" O PHE A 498 " pdb=" NE2 GLN A 501 " model vdw 2.288 3.120 nonbonded pdb=" O PHE C 498 " pdb=" NE2 GLN C 501 " model vdw 2.288 3.120 ... (remaining 56319 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' 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: 0.720 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.840 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 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 : 0.004 0.073 7818 Z= 0.190 Angle : 0.789 11.813 10749 Z= 0.331 Chirality : 0.060 0.719 1230 Planarity : 0.006 0.055 1269 Dihedral : 13.998 85.261 2682 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.39 % Allowed : 1.96 % Favored : 97.65 % 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: 1.51 (0.25), residues: 933 helix: 1.58 (0.18), residues: 651 sheet: None (None), residues: 0 loop : -0.26 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 446 HIS 0.004 0.001 HIS B 387 PHE 0.006 0.001 PHE A 217 TYR 0.012 0.001 TYR B 390 ARG 0.002 0.000 ARG B 187 Details of bonding type rmsd hydrogen bonds : bond 0.30221 ( 474) hydrogen bonds : angle 6.48778 ( 1404) covalent geometry : bond 0.00385 ( 7818) covalent geometry : angle 0.78868 (10749) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 185 time to evaluate : 0.696 Fit side-chains REVERT: A 195 ILE cc_start: 0.8634 (tt) cc_final: 0.8266 (pt) REVERT: A 255 LYS cc_start: 0.8077 (tttm) cc_final: 0.7750 (ttpp) REVERT: A 469 TYR cc_start: 0.7262 (m-80) cc_final: 0.6965 (m-80) REVERT: C 195 ILE cc_start: 0.8831 (tt) cc_final: 0.8412 (pt) REVERT: C 469 TYR cc_start: 0.7321 (m-80) cc_final: 0.7109 (m-80) REVERT: B 195 ILE cc_start: 0.8778 (tt) cc_final: 0.8445 (pt) REVERT: B 469 TYR cc_start: 0.7266 (m-80) cc_final: 0.6989 (m-80) outliers start: 3 outliers final: 0 residues processed: 188 average time/residue: 0.1613 time to fit residues: 42.3277 Evaluate side-chains 149 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS A 265 ASN A 405 ASN C 219 HIS C 405 ASN B 219 HIS B 405 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.161294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.139876 restraints weight = 12464.040| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.54 r_work: 0.3591 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7818 Z= 0.171 Angle : 0.637 9.037 10749 Z= 0.317 Chirality : 0.043 0.145 1230 Planarity : 0.006 0.044 1269 Dihedral : 7.711 47.824 1212 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.88 % Allowed : 11.76 % Favored : 85.36 % 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: 2.72 (0.28), residues: 933 helix: 2.43 (0.20), residues: 675 sheet: None (None), residues: 0 loop : 0.11 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 206 HIS 0.003 0.001 HIS B 387 PHE 0.017 0.001 PHE B 184 TYR 0.013 0.001 TYR C 250 ARG 0.002 0.000 ARG A 472 Details of bonding type rmsd hydrogen bonds : bond 0.07686 ( 474) hydrogen bonds : angle 4.29917 ( 1404) covalent geometry : bond 0.00347 ( 7818) covalent geometry : angle 0.63729 (10749) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.752 Fit side-chains REVERT: A 255 LYS cc_start: 0.8065 (tttm) cc_final: 0.7850 (ttpp) REVERT: C 314 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8319 (tm-30) REVERT: B 255 LYS cc_start: 0.8242 (tttm) cc_final: 0.7720 (mttm) outliers start: 22 outliers final: 18 residues processed: 177 average time/residue: 0.1679 time to fit residues: 41.4903 Evaluate side-chains 157 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 298 CYS Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 393 PHE Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 483 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 84 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 76 optimal weight: 0.2980 chunk 10 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 HIS C 219 HIS B 219 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.158949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.136797 restraints weight = 12534.357| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.60 r_work: 0.3550 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7818 Z= 0.154 Angle : 0.603 8.289 10749 Z= 0.296 Chirality : 0.042 0.142 1230 Planarity : 0.005 0.039 1269 Dihedral : 7.371 43.713 1212 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.53 % Allowed : 15.82 % Favored : 80.65 % 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: 2.71 (0.29), residues: 933 helix: 2.49 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -0.11 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 446 HIS 0.003 0.001 HIS B 387 PHE 0.018 0.001 PHE C 450 TYR 0.009 0.001 TYR C 365 ARG 0.002 0.000 ARG A 472 Details of bonding type rmsd hydrogen bonds : bond 0.06456 ( 474) hydrogen bonds : angle 3.92114 ( 1404) covalent geometry : bond 0.00324 ( 7818) covalent geometry : angle 0.60320 (10749) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.721 Fit side-chains REVERT: A 375 ARG cc_start: 0.7359 (ptp-170) cc_final: 0.7110 (ptp90) REVERT: C 195 ILE cc_start: 0.7445 (pt) cc_final: 0.7133 (mt) REVERT: C 255 LYS cc_start: 0.8040 (tttm) cc_final: 0.7829 (ttpp) REVERT: C 411 PHE cc_start: 0.7405 (OUTLIER) cc_final: 0.6572 (m-10) REVERT: B 187 ARG cc_start: 0.8438 (ptp-110) cc_final: 0.8183 (ptp-110) REVERT: B 255 LYS cc_start: 0.8251 (tttm) cc_final: 0.7703 (mttm) REVERT: B 314 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8212 (tm-30) REVERT: B 426 TYR cc_start: 0.8544 (t80) cc_final: 0.8293 (t80) outliers start: 27 outliers final: 17 residues processed: 168 average time/residue: 0.1798 time to fit residues: 41.5844 Evaluate side-chains 155 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 411 PHE Chi-restraints excluded: chain C residue 414 CYS Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 483 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 47 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 0.3980 chunk 29 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 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 219 HIS C 219 HIS ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 HIS ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.163420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.142949 restraints weight = 12344.057| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.47 r_work: 0.3602 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7818 Z= 0.127 Angle : 0.576 8.428 10749 Z= 0.277 Chirality : 0.041 0.161 1230 Planarity : 0.004 0.032 1269 Dihedral : 6.998 48.039 1212 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.79 % Allowed : 19.22 % Favored : 76.99 % 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: 2.76 (0.29), residues: 933 helix: 2.59 (0.21), residues: 678 sheet: None (None), residues: 0 loop : -0.31 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 206 HIS 0.003 0.001 HIS A 387 PHE 0.013 0.001 PHE A 184 TYR 0.007 0.001 TYR A 258 ARG 0.001 0.000 ARG C 432 Details of bonding type rmsd hydrogen bonds : bond 0.05120 ( 474) hydrogen bonds : angle 3.63423 ( 1404) covalent geometry : bond 0.00256 ( 7818) covalent geometry : angle 0.57603 (10749) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.743 Fit side-chains REVERT: A 277 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8147 (mp) REVERT: A 375 ARG cc_start: 0.7234 (ptp-170) cc_final: 0.6952 (ptp90) REVERT: C 255 LYS cc_start: 0.8017 (tttm) cc_final: 0.7787 (ttpp) REVERT: B 187 ARG cc_start: 0.8442 (ptp-110) cc_final: 0.8141 (ptp-110) REVERT: B 255 LYS cc_start: 0.8221 (tttm) cc_final: 0.7673 (mttm) REVERT: B 314 GLN cc_start: 0.8630 (mm-40) cc_final: 0.8204 (tm-30) REVERT: B 375 ARG cc_start: 0.7082 (ptp-170) cc_final: 0.6871 (ptp90) REVERT: B 426 TYR cc_start: 0.8550 (t80) cc_final: 0.8296 (t80) outliers start: 29 outliers final: 21 residues processed: 176 average time/residue: 0.1665 time to fit residues: 40.3529 Evaluate side-chains 166 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 298 CYS Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 414 CYS Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 414 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 31 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 HIS C 219 HIS C 225 ASN B 219 HIS ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.152749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.130404 restraints weight = 12564.008| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.57 r_work: 0.3453 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 7818 Z= 0.226 Angle : 0.704 9.176 10749 Z= 0.349 Chirality : 0.045 0.167 1230 Planarity : 0.005 0.034 1269 Dihedral : 7.304 49.134 1212 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 7.32 % Allowed : 20.92 % Favored : 71.76 % 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: 2.29 (0.29), residues: 933 helix: 2.25 (0.21), residues: 684 sheet: None (None), residues: 0 loop : -0.59 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 206 HIS 0.004 0.001 HIS C 387 PHE 0.033 0.002 PHE B 450 TYR 0.010 0.002 TYR A 258 ARG 0.002 0.000 ARG A 432 Details of bonding type rmsd hydrogen bonds : bond 0.08169 ( 474) hydrogen bonds : angle 4.25668 ( 1404) covalent geometry : bond 0.00515 ( 7818) covalent geometry : angle 0.70426 (10749) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 153 time to evaluate : 0.796 Fit side-chains REVERT: A 249 PHE cc_start: 0.7046 (OUTLIER) cc_final: 0.6211 (m-10) REVERT: A 277 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8262 (mp) REVERT: A 375 ARG cc_start: 0.7565 (ptp-170) cc_final: 0.7326 (ptp90) REVERT: A 426 TYR cc_start: 0.8701 (t80) cc_final: 0.8469 (t80) REVERT: C 249 PHE cc_start: 0.7337 (OUTLIER) cc_final: 0.6517 (m-80) REVERT: C 426 TYR cc_start: 0.8692 (t80) cc_final: 0.8444 (t80) REVERT: C 489 LEU cc_start: 0.7996 (tt) cc_final: 0.7775 (tp) REVERT: B 249 PHE cc_start: 0.7181 (OUTLIER) cc_final: 0.6321 (m-80) REVERT: B 255 LYS cc_start: 0.8229 (tttm) cc_final: 0.7992 (ttpp) REVERT: B 314 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8308 (tm-30) REVERT: B 426 TYR cc_start: 0.8692 (t80) cc_final: 0.8425 (t80) outliers start: 56 outliers final: 34 residues processed: 191 average time/residue: 0.1679 time to fit residues: 44.1477 Evaluate side-chains 185 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 249 PHE Chi-restraints excluded: chain C residue 298 CYS Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 414 CYS Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 478 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS A 225 ASN C 219 HIS B 219 HIS B 225 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.158468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.136703 restraints weight = 12436.150| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.60 r_work: 0.3536 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7818 Z= 0.142 Angle : 0.609 8.440 10749 Z= 0.292 Chirality : 0.042 0.166 1230 Planarity : 0.004 0.032 1269 Dihedral : 7.092 56.842 1212 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 6.54 % Allowed : 21.70 % Favored : 71.76 % 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: 2.47 (0.29), residues: 933 helix: 2.41 (0.21), residues: 684 sheet: None (None), residues: 0 loop : -0.63 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 206 HIS 0.004 0.001 HIS A 387 PHE 0.019 0.001 PHE A 184 TYR 0.015 0.001 TYR C 390 ARG 0.003 0.000 ARG B 187 Details of bonding type rmsd hydrogen bonds : bond 0.05870 ( 474) hydrogen bonds : angle 3.77422 ( 1404) covalent geometry : bond 0.00303 ( 7818) covalent geometry : angle 0.60923 (10749) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 147 time to evaluate : 0.828 Fit side-chains REVERT: A 249 PHE cc_start: 0.7064 (OUTLIER) cc_final: 0.6284 (m-80) REVERT: A 277 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8160 (mp) REVERT: A 375 ARG cc_start: 0.7398 (ptp-170) cc_final: 0.7077 (ptp90) REVERT: A 426 TYR cc_start: 0.8680 (t80) cc_final: 0.8407 (t80) REVERT: C 249 PHE cc_start: 0.7235 (OUTLIER) cc_final: 0.6419 (m-80) REVERT: C 255 LYS cc_start: 0.8071 (tttm) cc_final: 0.7837 (ttpp) REVERT: C 277 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8273 (mp) REVERT: C 301 MET cc_start: 0.7319 (tpt) cc_final: 0.6696 (tpp) REVERT: B 249 PHE cc_start: 0.7113 (OUTLIER) cc_final: 0.6281 (m-80) REVERT: B 255 LYS cc_start: 0.8214 (tttm) cc_final: 0.7992 (ttpp) REVERT: B 314 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8297 (tm-30) REVERT: B 426 TYR cc_start: 0.8656 (t80) cc_final: 0.8365 (t80) outliers start: 50 outliers final: 32 residues processed: 180 average time/residue: 0.1700 time to fit residues: 42.3026 Evaluate side-chains 175 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 249 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 298 CYS Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 414 CYS Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 460 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 34 optimal weight: 0.0870 chunk 24 optimal weight: 0.0670 chunk 15 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 72 optimal weight: 0.0000 chunk 31 optimal weight: 5.9990 overall best weight: 0.3700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 HIS B 219 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.164932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.144662 restraints weight = 12312.670| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.50 r_work: 0.3624 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7818 Z= 0.118 Angle : 0.584 8.141 10749 Z= 0.274 Chirality : 0.041 0.160 1230 Planarity : 0.004 0.028 1269 Dihedral : 6.843 57.599 1212 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.92 % Allowed : 24.31 % Favored : 71.76 % 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: 2.38 (0.29), residues: 933 helix: 2.38 (0.21), residues: 687 sheet: None (None), residues: 0 loop : -0.81 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 206 HIS 0.003 0.001 HIS C 387 PHE 0.014 0.001 PHE C 411 TYR 0.005 0.001 TYR A 250 ARG 0.003 0.000 ARG B 187 Details of bonding type rmsd hydrogen bonds : bond 0.04324 ( 474) hydrogen bonds : angle 3.51098 ( 1404) covalent geometry : bond 0.00239 ( 7818) covalent geometry : angle 0.58364 (10749) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.785 Fit side-chains REVERT: A 249 PHE cc_start: 0.6899 (OUTLIER) cc_final: 0.6092 (m-80) REVERT: A 277 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8153 (mp) REVERT: A 375 ARG cc_start: 0.7164 (ptp-170) cc_final: 0.6859 (ptp90) REVERT: C 199 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7174 (tt) REVERT: C 249 PHE cc_start: 0.7097 (OUTLIER) cc_final: 0.6322 (m-80) REVERT: C 255 LYS cc_start: 0.8034 (tttm) cc_final: 0.7793 (ttpp) REVERT: C 426 TYR cc_start: 0.8608 (t80) cc_final: 0.8275 (t80) REVERT: B 249 PHE cc_start: 0.6959 (OUTLIER) cc_final: 0.6115 (m-80) REVERT: B 255 LYS cc_start: 0.8216 (tttm) cc_final: 0.7646 (mttm) REVERT: B 314 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8370 (tm-30) REVERT: B 426 TYR cc_start: 0.8640 (t80) cc_final: 0.8378 (t80) outliers start: 30 outliers final: 16 residues processed: 177 average time/residue: 0.1725 time to fit residues: 41.7195 Evaluate side-chains 176 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 249 PHE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 414 CYS Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 414 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 76 optimal weight: 0.7980 chunk 34 optimal weight: 0.0970 chunk 67 optimal weight: 0.9990 chunk 54 optimal weight: 0.1980 chunk 44 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 HIS B 219 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.163576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.141980 restraints weight = 12467.029| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.65 r_work: 0.3600 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7818 Z= 0.123 Angle : 0.597 7.930 10749 Z= 0.279 Chirality : 0.041 0.154 1230 Planarity : 0.004 0.027 1269 Dihedral : 6.818 55.481 1212 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.66 % Allowed : 24.18 % Favored : 72.16 % 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: 2.40 (0.29), residues: 933 helix: 2.37 (0.21), residues: 690 sheet: None (None), residues: 0 loop : -0.77 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 206 HIS 0.004 0.001 HIS A 387 PHE 0.026 0.001 PHE A 184 TYR 0.010 0.001 TYR B 390 ARG 0.002 0.000 ARG B 187 Details of bonding type rmsd hydrogen bonds : bond 0.04621 ( 474) hydrogen bonds : angle 3.50972 ( 1404) covalent geometry : bond 0.00258 ( 7818) covalent geometry : angle 0.59651 (10749) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 0.802 Fit side-chains REVERT: A 187 ARG cc_start: 0.8701 (ptp-110) cc_final: 0.8458 (ptp-110) REVERT: A 249 PHE cc_start: 0.6842 (OUTLIER) cc_final: 0.6086 (m-80) REVERT: A 277 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8170 (mp) REVERT: A 375 ARG cc_start: 0.7189 (ptp-170) cc_final: 0.6888 (ptp90) REVERT: C 199 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7256 (tt) REVERT: C 249 PHE cc_start: 0.7025 (OUTLIER) cc_final: 0.6270 (m-80) REVERT: C 255 LYS cc_start: 0.8038 (tttm) cc_final: 0.7815 (ttpp) REVERT: B 249 PHE cc_start: 0.6916 (OUTLIER) cc_final: 0.6117 (m-80) REVERT: B 277 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8108 (mp) REVERT: B 314 GLN cc_start: 0.8593 (mm-40) cc_final: 0.8345 (tm-30) REVERT: B 426 TYR cc_start: 0.8610 (t80) cc_final: 0.8296 (t80) outliers start: 28 outliers final: 21 residues processed: 174 average time/residue: 0.1844 time to fit residues: 44.7197 Evaluate side-chains 179 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 249 PHE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 411 PHE Chi-restraints excluded: chain C residue 414 CYS Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 414 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 5 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 HIS B 219 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.162745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.141053 restraints weight = 12595.014| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.60 r_work: 0.3579 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7818 Z= 0.129 Angle : 0.610 8.040 10749 Z= 0.285 Chirality : 0.041 0.150 1230 Planarity : 0.004 0.027 1269 Dihedral : 6.895 55.558 1212 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.66 % Allowed : 24.71 % Favored : 71.63 % 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: 2.38 (0.29), residues: 933 helix: 2.34 (0.21), residues: 690 sheet: None (None), residues: 0 loop : -0.74 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 206 HIS 0.004 0.001 HIS A 387 PHE 0.016 0.001 PHE B 450 TYR 0.008 0.001 TYR B 390 ARG 0.002 0.000 ARG B 187 Details of bonding type rmsd hydrogen bonds : bond 0.04999 ( 474) hydrogen bonds : angle 3.54344 ( 1404) covalent geometry : bond 0.00278 ( 7818) covalent geometry : angle 0.60993 (10749) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.728 Fit side-chains REVERT: A 187 ARG cc_start: 0.8729 (ptp-110) cc_final: 0.8452 (ptp-110) REVERT: A 249 PHE cc_start: 0.6886 (OUTLIER) cc_final: 0.6133 (m-80) REVERT: A 277 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8186 (mp) REVERT: A 375 ARG cc_start: 0.7180 (ptp-170) cc_final: 0.6884 (ptp90) REVERT: C 199 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7318 (tt) REVERT: C 249 PHE cc_start: 0.7033 (OUTLIER) cc_final: 0.6309 (m-80) REVERT: C 255 LYS cc_start: 0.8037 (tttm) cc_final: 0.7814 (ttpp) REVERT: C 285 PHE cc_start: 0.8055 (m-80) cc_final: 0.7532 (m-80) REVERT: C 390 TYR cc_start: 0.7434 (t80) cc_final: 0.7187 (t80) REVERT: C 426 TYR cc_start: 0.8587 (t80) cc_final: 0.8263 (t80) REVERT: B 249 PHE cc_start: 0.6861 (OUTLIER) cc_final: 0.6074 (m-80) REVERT: B 277 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8056 (mp) REVERT: B 314 GLN cc_start: 0.8557 (mm-40) cc_final: 0.8339 (tm-30) REVERT: B 426 TYR cc_start: 0.8621 (t80) cc_final: 0.8315 (t80) outliers start: 28 outliers final: 22 residues processed: 168 average time/residue: 0.1725 time to fit residues: 39.7633 Evaluate side-chains 179 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 249 PHE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 411 PHE Chi-restraints excluded: chain C residue 414 CYS Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 414 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 32 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 HIS B 219 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.162855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.141209 restraints weight = 12487.894| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.62 r_work: 0.3584 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7818 Z= 0.130 Angle : 0.616 7.903 10749 Z= 0.290 Chirality : 0.041 0.149 1230 Planarity : 0.004 0.027 1269 Dihedral : 6.944 57.025 1212 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.92 % Allowed : 24.71 % Favored : 71.37 % 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: 2.36 (0.29), residues: 933 helix: 2.35 (0.21), residues: 690 sheet: None (None), residues: 0 loop : -0.79 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 206 HIS 0.004 0.001 HIS C 387 PHE 0.015 0.001 PHE B 450 TYR 0.014 0.001 TYR A 390 ARG 0.002 0.000 ARG B 187 Details of bonding type rmsd hydrogen bonds : bond 0.04907 ( 474) hydrogen bonds : angle 3.52444 ( 1404) covalent geometry : bond 0.00279 ( 7818) covalent geometry : angle 0.61555 (10749) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.806 Fit side-chains REVERT: A 249 PHE cc_start: 0.6921 (OUTLIER) cc_final: 0.6184 (m-80) REVERT: A 277 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8174 (mp) REVERT: A 375 ARG cc_start: 0.7205 (ptp-170) cc_final: 0.6895 (ptp90) REVERT: C 199 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7290 (tt) REVERT: C 249 PHE cc_start: 0.7037 (OUTLIER) cc_final: 0.6294 (m-80) REVERT: C 255 LYS cc_start: 0.8014 (tttm) cc_final: 0.7793 (ttpp) REVERT: C 426 TYR cc_start: 0.8587 (t80) cc_final: 0.8279 (t80) REVERT: B 249 PHE cc_start: 0.6907 (OUTLIER) cc_final: 0.6068 (m-80) REVERT: B 277 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8025 (mp) REVERT: B 314 GLN cc_start: 0.8548 (mm-40) cc_final: 0.8307 (tm-30) REVERT: B 426 TYR cc_start: 0.8635 (t80) cc_final: 0.8332 (t80) outliers start: 30 outliers final: 23 residues processed: 167 average time/residue: 0.1797 time to fit residues: 40.8024 Evaluate side-chains 180 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 249 PHE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 411 PHE Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 414 CYS Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 414 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 4.9990 chunk 34 optimal weight: 0.0570 chunk 51 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 HIS B 219 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.162992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.141401 restraints weight = 12362.891| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.63 r_work: 0.3592 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7818 Z= 0.127 Angle : 0.607 7.860 10749 Z= 0.285 Chirality : 0.041 0.146 1230 Planarity : 0.004 0.027 1269 Dihedral : 6.959 57.669 1212 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.18 % Allowed : 24.05 % Favored : 71.76 % 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: 2.36 (0.29), residues: 933 helix: 2.35 (0.21), residues: 690 sheet: None (None), residues: 0 loop : -0.80 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 206 HIS 0.004 0.001 HIS C 387 PHE 0.026 0.001 PHE A 184 TYR 0.007 0.001 TYR C 258 ARG 0.004 0.000 ARG B 187 Details of bonding type rmsd hydrogen bonds : bond 0.04824 ( 474) hydrogen bonds : angle 3.50000 ( 1404) covalent geometry : bond 0.00270 ( 7818) covalent geometry : angle 0.60678 (10749) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3094.93 seconds wall clock time: 54 minutes 30.95 seconds (3270.95 seconds total)