Starting phenix.real_space_refine on Fri Jul 25 15:01:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gw7_34304/07_2025/8gw7_34304_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gw7_34304/07_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_34304/07_2025/8gw7_34304.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gw7_34304/07_2025/8gw7_34304.map" model { file = "/net/cci-nas-00/data/ceres_data/8gw7_34304/07_2025/8gw7_34304_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gw7_34304/07_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-5711/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: 4.66, per 1000 atoms: 0.62 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: 1.82 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: 0.66 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: 1.97 Time building geometry restraints manager: 2.18 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: 1.030 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.190 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.710 ------------------------------------------------------------------------------- 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 : 0.805 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: 0.1660 time to fit residues: 43.4631 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 : 0.806 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.139879 restraints weight = 12464.040| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.54 r_work: 0.3593 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 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 : 0.836 Fit side-chains REVERT: A 255 LYS cc_start: 0.8072 (tttm) cc_final: 0.7857 (ttpp) REVERT: C 314 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8330 (tm-30) REVERT: B 255 LYS cc_start: 0.8252 (tttm) cc_final: 0.7737 (mttm) outliers start: 22 outliers final: 18 residues processed: 177 average time/residue: 0.1639 time to fit residues: 40.6873 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 : 0.752 ------------------------------------------------------------------------------- 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: 0.0870 chunk 10 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- 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 = 0.3870 r_free = 0.3870 target = 0.156954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.134533 restraints weight = 12618.952| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.57 r_work: 0.3522 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 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 : 0.004 0.050 7818 Z= 0.177 Angle : 0.633 8.335 10749 Z= 0.313 Chirality : 0.043 0.146 1230 Planarity : 0.005 0.039 1269 Dihedral : 7.437 44.419 1212 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.71 % Allowed : 16.21 % Favored : 79.08 % 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: 2.61 (0.28), residues: 933 helix: 2.42 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -0.16 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 446 HIS 0.004 0.001 HIS B 387 PHE 0.022 0.002 PHE B 450 TYR 0.010 0.001 TYR A 258 ARG 0.002 0.000 ARG A 472 Details of bonding type rmsd hydrogen bonds : bond 0.07149 ( 474) hydrogen bonds : angle 4.07553 ( 1404) covalent geometry : bond 0.00390 ( 7818) covalent geometry : angle 0.63292 (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 182 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 0.766 Fit side-chains REVERT: A 255 LYS cc_start: 0.8058 (tttm) cc_final: 0.7850 (ttpp) REVERT: A 392 MET cc_start: 0.8208 (mpp) cc_final: 0.7846 (mpp) REVERT: C 314 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8355 (tm-30) REVERT: C 392 MET cc_start: 0.8301 (mpp) cc_final: 0.7871 (mpp) REVERT: C 411 PHE cc_start: 0.7486 (OUTLIER) cc_final: 0.6735 (m-10) REVERT: B 187 ARG cc_start: 0.8504 (ptp-110) cc_final: 0.8206 (ptp-110) REVERT: B 255 LYS cc_start: 0.8246 (tttm) cc_final: 0.7696 (mttm) REVERT: B 314 GLN cc_start: 0.8589 (mm-40) cc_final: 0.8230 (tm-30) REVERT: B 392 MET cc_start: 0.8390 (mpp) cc_final: 0.7915 (mpp) REVERT: B 426 TYR cc_start: 0.8618 (t80) cc_final: 0.8280 (t80) outliers start: 36 outliers final: 27 residues processed: 173 average time/residue: 0.1713 time to fit residues: 40.9008 Evaluate side-chains 165 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 298 CYS 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 A residue 483 THR Chi-restraints excluded: chain C residue 185 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 368 VAL Chi-restraints excluded: chain C residue 406 THR 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 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 483 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 47 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** 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 = 0.3905 r_free = 0.3905 target = 0.160535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.138763 restraints weight = 12436.957| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.61 r_work: 0.3566 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3699 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= 0.131 Angle : 0.578 8.618 10749 Z= 0.279 Chirality : 0.041 0.161 1230 Planarity : 0.004 0.033 1269 Dihedral : 7.083 50.096 1212 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.31 % Allowed : 19.87 % Favored : 75.82 % 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: 2.73 (0.29), residues: 933 helix: 2.56 (0.21), residues: 678 sheet: None (None), residues: 0 loop : -0.29 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 206 HIS 0.003 0.001 HIS B 387 PHE 0.021 0.001 PHE C 184 TYR 0.008 0.001 TYR A 258 ARG 0.001 0.000 ARG C 432 Details of bonding type rmsd hydrogen bonds : bond 0.05474 ( 474) hydrogen bonds : angle 3.69986 ( 1404) covalent geometry : bond 0.00268 ( 7818) covalent geometry : angle 0.57769 (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 182 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.836 Fit side-chains REVERT: A 277 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8127 (mp) REVERT: A 375 ARG cc_start: 0.7302 (ptp-170) cc_final: 0.7021 (ptp90) REVERT: C 249 PHE cc_start: 0.7239 (OUTLIER) cc_final: 0.6931 (m-80) REVERT: C 255 LYS cc_start: 0.8018 (tttm) cc_final: 0.7791 (ttpp) REVERT: C 285 PHE cc_start: 0.7809 (m-10) cc_final: 0.7587 (m-80) REVERT: C 314 GLN cc_start: 0.8689 (mm-40) cc_final: 0.8420 (tm-30) REVERT: C 462 TYR cc_start: 0.8780 (t80) cc_final: 0.8568 (t80) REVERT: B 187 ARG cc_start: 0.8465 (ptp-110) cc_final: 0.8137 (ptp-110) REVERT: B 249 PHE cc_start: 0.7026 (OUTLIER) cc_final: 0.6150 (m-80) REVERT: B 255 LYS cc_start: 0.8214 (tttm) cc_final: 0.7670 (mttm) REVERT: B 314 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8231 (tm-30) REVERT: B 375 ARG cc_start: 0.7148 (ptp-170) cc_final: 0.6924 (ptp90) REVERT: B 426 TYR cc_start: 0.8581 (t80) cc_final: 0.8294 (t80) outliers start: 33 outliers final: 21 residues processed: 168 average time/residue: 0.1805 time to fit residues: 41.7979 Evaluate side-chains 163 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 335 VAL 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 195 ILE 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 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 249 PHE 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 372 LEU 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: 4.9990 chunk 69 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 A 260 HIS C 219 HIS C 225 ASN B 219 HIS B 225 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.153901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.131805 restraints weight = 12500.152| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.56 r_work: 0.3478 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 7818 Z= 0.203 Angle : 0.661 8.978 10749 Z= 0.328 Chirality : 0.044 0.162 1230 Planarity : 0.005 0.034 1269 Dihedral : 7.210 50.546 1212 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 7.71 % Allowed : 20.13 % 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: 2.34 (0.21), residues: 684 sheet: None (None), residues: 0 loop : -0.57 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 206 HIS 0.005 0.001 HIS B 387 PHE 0.028 0.002 PHE B 450 TYR 0.011 0.001 TYR B 390 ARG 0.001 0.000 ARG B 432 Details of bonding type rmsd hydrogen bonds : bond 0.07416 ( 474) hydrogen bonds : angle 4.08311 ( 1404) covalent geometry : bond 0.00462 ( 7818) covalent geometry : angle 0.66148 (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 205 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 146 time to evaluate : 0.754 Fit side-chains REVERT: A 249 PHE cc_start: 0.7028 (OUTLIER) cc_final: 0.6330 (m-80) REVERT: A 277 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8252 (mp) REVERT: A 375 ARG cc_start: 0.7515 (ptp-170) cc_final: 0.7178 (ptp90) REVERT: A 392 MET cc_start: 0.8316 (mpp) cc_final: 0.7979 (mpp) REVERT: A 426 TYR cc_start: 0.8675 (t80) cc_final: 0.8447 (t80) REVERT: C 195 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7833 (tt) REVERT: C 249 PHE cc_start: 0.7353 (OUTLIER) cc_final: 0.6493 (m-80) REVERT: C 314 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8384 (tm-30) REVERT: C 426 TYR cc_start: 0.8684 (t80) cc_final: 0.8419 (t80) REVERT: B 249 PHE cc_start: 0.7145 (OUTLIER) cc_final: 0.6300 (m-80) REVERT: B 314 GLN cc_start: 0.8589 (mm-40) cc_final: 0.8334 (tm-30) REVERT: B 426 TYR cc_start: 0.8633 (t80) cc_final: 0.8354 (t80) outliers start: 59 outliers final: 37 residues processed: 187 average time/residue: 0.1756 time to fit residues: 45.3901 Evaluate side-chains 184 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 142 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 298 CYS 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 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 195 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 414 CYS Chi-restraints excluded: chain C residue 430 VAL 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 231 PHE 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 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 412 ASP Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 460 ILE 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: 1.9990 chunk 56 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 B 219 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.159495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.138008 restraints weight = 12351.367| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.59 r_work: 0.3552 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4028 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= 0.132 Angle : 0.598 8.396 10749 Z= 0.285 Chirality : 0.041 0.167 1230 Planarity : 0.004 0.031 1269 Dihedral : 7.038 56.611 1212 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 6.54 % Allowed : 20.65 % Favored : 72.81 % 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: 2.55 (0.29), residues: 933 helix: 2.46 (0.21), residues: 684 sheet: None (None), residues: 0 loop : -0.56 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 206 HIS 0.004 0.001 HIS A 387 PHE 0.020 0.001 PHE A 184 TYR 0.014 0.001 TYR C 390 ARG 0.004 0.000 ARG B 187 Details of bonding type rmsd hydrogen bonds : bond 0.05508 ( 474) hydrogen bonds : angle 3.67633 ( 1404) covalent geometry : bond 0.00276 ( 7818) covalent geometry : angle 0.59845 (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 196 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 146 time to evaluate : 0.838 Fit side-chains REVERT: A 249 PHE cc_start: 0.6984 (OUTLIER) cc_final: 0.6211 (m-80) REVERT: A 277 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8176 (mp) REVERT: A 375 ARG cc_start: 0.7340 (ptp-170) cc_final: 0.7008 (ptp90) REVERT: A 392 MET cc_start: 0.8248 (mpp) cc_final: 0.7920 (mpp) REVERT: C 249 PHE cc_start: 0.7296 (OUTLIER) cc_final: 0.6488 (m-80) REVERT: C 255 LYS cc_start: 0.8058 (tttm) cc_final: 0.7821 (ttpp) REVERT: B 249 PHE cc_start: 0.7066 (OUTLIER) cc_final: 0.6267 (m-80) REVERT: B 277 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8147 (mp) REVERT: B 314 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8320 (tm-30) REVERT: B 426 TYR cc_start: 0.8614 (t80) cc_final: 0.8215 (t80) outliers start: 50 outliers final: 30 residues processed: 177 average time/residue: 0.1728 time to fit residues: 42.5098 Evaluate side-chains 175 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 140 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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 372 LEU Chi-restraints excluded: chain A residue 406 THR 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 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 449 THR Chi-restraints excluded: chain C residue 460 ILE 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 231 PHE 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 335 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 430 VAL 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: 0.2980 chunk 0 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 24 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 B 219 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.156441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.134664 restraints weight = 12395.555| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.58 r_work: 0.3510 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7818 Z= 0.165 Angle : 0.640 9.002 10749 Z= 0.307 Chirality : 0.042 0.165 1230 Planarity : 0.004 0.031 1269 Dihedral : 7.058 55.286 1212 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 7.32 % Allowed : 20.00 % Favored : 72.68 % 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: 2.43 (0.29), residues: 933 helix: 2.38 (0.21), residues: 684 sheet: None (None), residues: 0 loop : -0.61 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 206 HIS 0.004 0.001 HIS A 387 PHE 0.023 0.001 PHE B 450 TYR 0.017 0.001 TYR B 390 ARG 0.003 0.000 ARG B 187 Details of bonding type rmsd hydrogen bonds : bond 0.06496 ( 474) hydrogen bonds : angle 3.86034 ( 1404) covalent geometry : bond 0.00366 ( 7818) covalent geometry : angle 0.64034 (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 198 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 142 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: A 249 PHE cc_start: 0.6984 (OUTLIER) cc_final: 0.6656 (m-80) REVERT: A 277 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8192 (mp) REVERT: A 375 ARG cc_start: 0.7469 (ptp-170) cc_final: 0.7126 (ptp90) REVERT: A 426 TYR cc_start: 0.8651 (t80) cc_final: 0.8416 (t80) REVERT: C 184 PHE cc_start: 0.8133 (t80) cc_final: 0.7846 (t80) REVERT: C 249 PHE cc_start: 0.7280 (OUTLIER) cc_final: 0.6465 (m-80) REVERT: B 249 PHE cc_start: 0.7052 (OUTLIER) cc_final: 0.6676 (m-80) REVERT: B 277 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8202 (mp) REVERT: B 314 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8343 (tm-30) REVERT: B 426 TYR cc_start: 0.8649 (t80) cc_final: 0.8374 (t80) outliers start: 56 outliers final: 40 residues processed: 183 average time/residue: 0.1696 time to fit residues: 43.1385 Evaluate side-chains 181 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 136 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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 298 CYS 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 371 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 406 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 195 ILE Chi-restraints excluded: chain C residue 197 LEU 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 449 THR Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 231 PHE 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 277 LEU 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 414 CYS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 460 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 76 optimal weight: 4.9990 chunk 34 optimal weight: 0.0030 chunk 67 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 44 optimal weight: 0.4980 chunk 32 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 3 optimal weight: 0.0670 overall best weight: 0.2928 ------------------------------------------------------------------------------- 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 B 219 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.164458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.143322 restraints weight = 12422.913| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.62 r_work: 0.3623 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4427 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= 0.121 Angle : 0.595 8.048 10749 Z= 0.279 Chirality : 0.040 0.161 1230 Planarity : 0.004 0.029 1269 Dihedral : 6.947 59.883 1212 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.31 % Allowed : 22.61 % Favored : 73.07 % 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: 2.44 (0.29), residues: 933 helix: 2.37 (0.21), residues: 690 sheet: None (None), residues: 0 loop : -0.67 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 206 HIS 0.003 0.001 HIS A 387 PHE 0.013 0.001 PHE C 411 TYR 0.016 0.001 TYR C 390 ARG 0.002 0.000 ARG B 187 Details of bonding type rmsd hydrogen bonds : bond 0.04260 ( 474) hydrogen bonds : angle 3.50168 ( 1404) covalent geometry : bond 0.00241 ( 7818) covalent geometry : angle 0.59512 (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 193 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.843 Fit side-chains REVERT: A 249 PHE cc_start: 0.6937 (OUTLIER) cc_final: 0.6128 (m-80) REVERT: A 277 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8180 (mp) REVERT: A 375 ARG cc_start: 0.7113 (ptp-170) cc_final: 0.6823 (ptp90) REVERT: A 392 MET cc_start: 0.8209 (mpp) cc_final: 0.7981 (mpp) REVERT: C 184 PHE cc_start: 0.7991 (t80) cc_final: 0.7791 (t80) REVERT: C 249 PHE cc_start: 0.7106 (OUTLIER) cc_final: 0.6340 (m-80) REVERT: C 255 LYS cc_start: 0.8041 (tttm) cc_final: 0.7815 (ttpp) REVERT: B 249 PHE cc_start: 0.6917 (OUTLIER) cc_final: 0.6067 (m-80) REVERT: B 277 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8135 (mp) REVERT: B 390 TYR cc_start: 0.7442 (t80) cc_final: 0.7122 (t80) outliers start: 33 outliers final: 22 residues processed: 180 average time/residue: 0.1762 time to fit residues: 43.8052 Evaluate side-chains 182 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 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 414 CYS Chi-restraints excluded: chain C residue 195 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 335 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 411 PHE Chi-restraints excluded: chain C residue 414 CYS Chi-restraints excluded: chain C residue 449 THR 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 414 CYS Chi-restraints excluded: chain B residue 430 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 5 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 88 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 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 219 HIS C 219 HIS B 219 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.162565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.141355 restraints weight = 12483.515| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.62 r_work: 0.3588 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4416 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= 0.127 Angle : 0.606 8.055 10749 Z= 0.284 Chirality : 0.041 0.154 1230 Planarity : 0.004 0.029 1269 Dihedral : 6.910 56.556 1212 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.05 % Allowed : 23.79 % 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: 2.46 (0.29), residues: 933 helix: 2.40 (0.21), residues: 690 sheet: None (None), residues: 0 loop : -0.70 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 206 HIS 0.004 0.001 HIS A 387 PHE 0.023 0.001 PHE A 184 TYR 0.006 0.001 TYR A 258 ARG 0.004 0.000 ARG B 187 Details of bonding type rmsd hydrogen bonds : bond 0.04781 ( 474) hydrogen bonds : angle 3.53350 ( 1404) covalent geometry : bond 0.00271 ( 7818) covalent geometry : angle 0.60597 (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 183 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 1.270 Fit side-chains REVERT: A 249 PHE cc_start: 0.6877 (OUTLIER) cc_final: 0.6105 (m-80) REVERT: A 277 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8158 (mp) REVERT: A 375 ARG cc_start: 0.7170 (ptp-170) cc_final: 0.6878 (ptp90) REVERT: A 392 MET cc_start: 0.8201 (mpp) cc_final: 0.7973 (mpp) REVERT: C 249 PHE cc_start: 0.7047 (OUTLIER) cc_final: 0.6271 (m-80) REVERT: B 249 PHE cc_start: 0.6807 (OUTLIER) cc_final: 0.6020 (m-80) REVERT: B 277 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8170 (mp) outliers start: 31 outliers final: 21 residues processed: 172 average time/residue: 0.2601 time to fit residues: 61.5762 Evaluate side-chains 175 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 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 414 CYS Chi-restraints excluded: chain C residue 197 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 335 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 406 THR 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 449 THR Chi-restraints excluded: chain B residue 197 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 277 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 430 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 4 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 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 219 HIS C 219 HIS B 219 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.161653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.140285 restraints weight = 12368.840| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.61 r_work: 0.3578 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4461 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= 0.132 Angle : 0.613 7.966 10749 Z= 0.289 Chirality : 0.041 0.151 1230 Planarity : 0.004 0.029 1269 Dihedral : 6.965 57.035 1212 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.66 % Allowed : 23.53 % Favored : 72.81 % 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: 2.41 (0.29), residues: 933 helix: 2.38 (0.21), residues: 690 sheet: None (None), residues: 0 loop : -0.77 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 206 HIS 0.004 0.001 HIS C 219 PHE 0.016 0.001 PHE B 450 TYR 0.020 0.001 TYR C 390 ARG 0.004 0.000 ARG B 187 Details of bonding type rmsd hydrogen bonds : bond 0.05036 ( 474) hydrogen bonds : angle 3.57602 ( 1404) covalent geometry : bond 0.00284 ( 7818) covalent geometry : angle 0.61283 (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 178 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.785 Fit side-chains REVERT: A 249 PHE cc_start: 0.6897 (OUTLIER) cc_final: 0.6126 (m-80) REVERT: A 277 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8167 (mp) REVERT: A 375 ARG cc_start: 0.7226 (ptp-170) cc_final: 0.6920 (ptp90) REVERT: A 392 MET cc_start: 0.8220 (mpp) cc_final: 0.7938 (mpp) REVERT: C 249 PHE cc_start: 0.7078 (OUTLIER) cc_final: 0.6315 (m-80) REVERT: C 285 PHE cc_start: 0.7972 (m-80) cc_final: 0.7638 (m-80) REVERT: B 249 PHE cc_start: 0.6842 (OUTLIER) cc_final: 0.6045 (m-80) REVERT: B 277 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8143 (mp) outliers start: 28 outliers final: 22 residues processed: 167 average time/residue: 0.3362 time to fit residues: 79.4285 Evaluate side-chains 175 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 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 372 LEU Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain C residue 197 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 335 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 406 THR 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 449 THR Chi-restraints excluded: chain B residue 197 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 277 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 430 VAL 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: 0.0370 chunk 51 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 56 optimal weight: 0.2980 chunk 55 optimal weight: 0.0060 chunk 59 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.165767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.144279 restraints weight = 12238.951| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.60 r_work: 0.3634 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.4665 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= 0.120 Angle : 0.595 7.581 10749 Z= 0.279 Chirality : 0.040 0.143 1230 Planarity : 0.004 0.028 1269 Dihedral : 6.913 59.149 1212 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.14 % Allowed : 23.79 % Favored : 73.07 % 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: 2.36 (0.21), residues: 690 sheet: None (None), residues: 0 loop : -0.74 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 206 HIS 0.004 0.001 HIS C 219 PHE 0.014 0.001 PHE C 411 TYR 0.010 0.001 TYR B 390 ARG 0.004 0.000 ARG B 187 Details of bonding type rmsd hydrogen bonds : bond 0.04164 ( 474) hydrogen bonds : angle 3.43947 ( 1404) covalent geometry : bond 0.00249 ( 7818) covalent geometry : angle 0.59478 (10749) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3481.82 seconds wall clock time: 62 minutes 23.08 seconds (3743.08 seconds total)