Starting phenix.real_space_refine on Thu Jul 2 08:03:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gw7_34304/07_2026/8gw7_34304_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gw7_34304/07_2026/8gw7_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_2026/8gw7_34304.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gw7_34304/07_2026/8gw7_34304.map" model { file = "/net/cci-nas-00/data/ceres_data/8gw7_34304/07_2026/8gw7_34304_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gw7_34304/07_2026/8gw7_34304_trim.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Ad-hoc single atom residues: {' CL': 2} Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Restraints were copied for chains: C, B Time building chain proxies: 1.29, per 1000 atoms: 0.17 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: 0.48 Conformation dependent library (CDL) restraints added in 276.9 milliseconds 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: 0.14 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: 0.93 Time building geometry restraints manager: 0.65 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: 0.02 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: 0.770 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.050 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG B 187 TYR 0.012 0.001 TYR B 390 PHE 0.006 0.001 PHE A 217 TRP 0.008 0.001 TRP B 446 HIS 0.004 0.001 HIS B 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.19 ( 7818) covalent geometry : angle 0.78868 / 0.33 (10749) hydrogen bonds : bond 0.30221 / 19.65 ( 474) hydrogen bonds : angle 6.48778 / 4.62 ( 1404) *********************** 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 : 0.224 Fit side-chains REVERT: A 195 ILE cc_start: 0.8634 (tt) cc_final: 0.8265 (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: 0.0601 time to fit residues: 16.0477 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 : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 HIS ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3935 r_free = 0.3935 target = 0.163730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.143469 restraints weight = 12573.317| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.48 r_work: 0.3620 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2751 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= 0.166 Angle : 0.633 8.974 10749 Z= 0.314 Chirality : 0.043 0.143 1230 Planarity : 0.006 0.044 1269 Dihedral : 7.675 45.292 1212 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.61 % Allowed : 12.29 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.64 (0.28), residues: 933 helix: 2.38 (0.20), residues: 675 sheet: None (None), residues: 0 loop : 0.08 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 472 TYR 0.015 0.002 TYR A 365 PHE 0.020 0.001 PHE B 184 TRP 0.013 0.001 TRP C 206 HIS 0.003 0.001 HIS C 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.17 ( 7818) covalent geometry : angle 0.63338 / 0.31 (10749) hydrogen bonds : bond 0.06872 / 4.54 ( 474) hydrogen bonds : angle 4.16788 / 3.01 ( 1404) *********************** 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 180 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.176 Fit side-chains REVERT: A 255 LYS cc_start: 0.8052 (tttm) cc_final: 0.7840 (ttpp) REVERT: A 314 GLN cc_start: 0.8504 (mm-40) cc_final: 0.8175 (tm-30) REVERT: C 314 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8328 (tm-30) REVERT: B 255 LYS cc_start: 0.8247 (tttm) cc_final: 0.7725 (mttm) outliers start: 20 outliers final: 16 residues processed: 178 average time/residue: 0.0646 time to fit residues: 16.4983 Evaluate side-chains 158 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 32 optimal weight: 0.0060 chunk 5 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 45 optimal weight: 0.2980 chunk 49 optimal weight: 0.1980 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 HIS ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 HIS C 219 HIS B 219 HIS ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.166828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.145608 restraints weight = 12355.365| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.62 r_work: 0.3651 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3541 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= 0.126 Angle : 0.562 8.385 10749 Z= 0.270 Chirality : 0.040 0.161 1230 Planarity : 0.005 0.035 1269 Dihedral : 7.277 42.109 1212 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.09 % Allowed : 15.42 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.69 (0.28), residues: 933 helix: 2.47 (0.20), residues: 675 sheet: None (None), residues: 0 loop : -0.10 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 432 TYR 0.009 0.001 TYR C 365 PHE 0.021 0.001 PHE A 441 TRP 0.016 0.001 TRP C 446 HIS 0.003 0.001 HIS B 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.13 ( 7818) covalent geometry : angle 0.56236 / 0.27 (10749) hydrogen bonds : bond 0.04874 / 3.17 ( 474) hydrogen bonds : angle 3.63395 / 2.63 ( 1404) *********************** 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 172 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.211 Fit side-chains REVERT: A 314 GLN cc_start: 0.8468 (mm-40) cc_final: 0.8237 (tm-30) REVERT: A 375 ARG cc_start: 0.7200 (ptp-170) cc_final: 0.6966 (ptp90) REVERT: C 314 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8425 (tm-30) REVERT: B 255 LYS cc_start: 0.8220 (tttm) cc_final: 0.7736 (mttm) REVERT: B 314 GLN cc_start: 0.8562 (mm-40) cc_final: 0.8202 (tm-30) REVERT: B 375 ARG cc_start: 0.7084 (ptp-170) cc_final: 0.6833 (ptp90) outliers start: 16 outliers final: 12 residues processed: 168 average time/residue: 0.0641 time to fit residues: 15.2948 Evaluate side-chains 147 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 411 PHE Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 414 CYS 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 411 PHE Chi-restraints excluded: chain B residue 414 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 40 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 25 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 HIS A 225 ASN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.160639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.138825 restraints weight = 12479.998| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.61 r_work: 0.3567 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3594 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= 0.142 Angle : 0.590 8.111 10749 Z= 0.284 Chirality : 0.041 0.140 1230 Planarity : 0.004 0.033 1269 Dihedral : 7.055 41.436 1212 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.44 % Allowed : 17.52 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.77 (0.29), residues: 933 helix: 2.57 (0.21), residues: 678 sheet: None (None), residues: 0 loop : -0.25 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 472 TYR 0.010 0.001 TYR A 258 PHE 0.020 0.001 PHE C 450 TRP 0.010 0.001 TRP C 206 HIS 0.003 0.001 HIS B 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 7818) covalent geometry : angle 0.59016 / 0.28 (10749) hydrogen bonds : bond 0.05787 / 3.82 ( 474) hydrogen bonds : angle 3.70547 / 2.68 ( 1404) *********************** 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 181 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 0.160 Fit side-chains REVERT: A 285 PHE cc_start: 0.7950 (m-10) cc_final: 0.7643 (m-80) REVERT: A 375 ARG cc_start: 0.7280 (ptp-170) cc_final: 0.7004 (ptp90) REVERT: C 199 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7327 (tt) REVERT: C 314 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8371 (tm-30) REVERT: C 462 TYR cc_start: 0.8706 (t80) cc_final: 0.8503 (t80) REVERT: B 187 ARG cc_start: 0.8479 (ptp-110) cc_final: 0.8177 (ptp-110) REVERT: B 255 LYS cc_start: 0.8276 (tttm) cc_final: 0.7719 (mttm) REVERT: B 314 GLN cc_start: 0.8541 (mm-40) cc_final: 0.8221 (tm-30) REVERT: B 375 ARG cc_start: 0.7190 (ptp-170) cc_final: 0.6902 (ptp90) outliers start: 34 outliers final: 22 residues processed: 168 average time/residue: 0.0694 time to fit residues: 16.3659 Evaluate side-chains 160 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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 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 199 LEU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 414 CYS Chi-restraints excluded: chain C residue 460 ILE 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 264 VAL 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 64 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 0.0770 chunk 24 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 HIS A 260 HIS C 219 HIS C 225 ASN B 219 HIS B 225 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.163239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.141657 restraints weight = 12382.250| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.62 r_work: 0.3600 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3905 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= 0.126 Angle : 0.571 7.974 10749 Z= 0.273 Chirality : 0.040 0.141 1230 Planarity : 0.004 0.030 1269 Dihedral : 6.814 45.268 1212 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.71 % Allowed : 20.26 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.58 (0.29), residues: 933 helix: 2.46 (0.21), residues: 687 sheet: None (None), residues: 0 loop : -0.53 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 472 TYR 0.012 0.001 TYR A 390 PHE 0.023 0.001 PHE B 441 TRP 0.013 0.001 TRP C 206 HIS 0.003 0.001 HIS C 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 ( 7818) covalent geometry : angle 0.57105 / 0.27 (10749) hydrogen bonds : bond 0.05024 / 3.30 ( 474) hydrogen bonds : angle 3.59534 / 2.60 ( 1404) *********************** 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 188 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.257 Fit side-chains REVERT: A 249 PHE cc_start: 0.6760 (OUTLIER) cc_final: 0.6017 (m-80) REVERT: A 285 PHE cc_start: 0.7932 (m-10) cc_final: 0.7724 (m-80) REVERT: A 375 ARG cc_start: 0.7128 (ptp-170) cc_final: 0.6830 (ptp90) REVERT: C 199 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7235 (tt) REVERT: C 249 PHE cc_start: 0.7036 (OUTLIER) cc_final: 0.6278 (m-80) REVERT: B 187 ARG cc_start: 0.8448 (ptp-110) cc_final: 0.8096 (ptp-110) REVERT: B 249 PHE cc_start: 0.6822 (OUTLIER) cc_final: 0.5992 (m-80) REVERT: B 255 LYS cc_start: 0.8263 (tttm) cc_final: 0.7706 (mttm) REVERT: B 314 GLN cc_start: 0.8564 (mm-40) cc_final: 0.8279 (tm-30) REVERT: B 375 ARG cc_start: 0.7052 (ptp-170) cc_final: 0.6736 (ptp90) outliers start: 36 outliers final: 26 residues processed: 174 average time/residue: 0.0674 time to fit residues: 16.4278 Evaluate side-chains 175 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.185 ------------------------------------------------------------------------------- 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 298 CYS Chi-restraints excluded: chain A residue 335 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 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 298 CYS Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 414 CYS Chi-restraints excluded: chain C residue 460 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 25 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 71 optimal weight: 0.0770 chunk 60 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3956 r_free = 0.3956 target = 0.165163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.143817 restraints weight = 12318.583| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.59 r_work: 0.3612 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7818 Z= 0.121 Angle : 0.567 7.746 10749 Z= 0.270 Chirality : 0.040 0.136 1230 Planarity : 0.004 0.028 1269 Dihedral : 6.711 46.829 1212 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 5.36 % Allowed : 20.39 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.29), residues: 933 helix: 2.46 (0.21), residues: 690 sheet: None (None), residues: 0 loop : -0.62 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 432 TYR 0.012 0.001 TYR B 390 PHE 0.014 0.001 PHE A 184 TRP 0.012 0.001 TRP C 206 HIS 0.003 0.001 HIS C 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 ( 7818) covalent geometry : angle 0.56706 / 0.27 (10749) hydrogen bonds : bond 0.04713 / 3.10 ( 474) hydrogen bonds : angle 3.51530 / 2.54 ( 1404) *********************** 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 192 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 0.205 Fit side-chains REVERT: A 249 PHE cc_start: 0.6741 (OUTLIER) cc_final: 0.6033 (m-80) REVERT: A 375 ARG cc_start: 0.7157 (ptp-170) cc_final: 0.6834 (ptp90) REVERT: C 199 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7172 (tt) REVERT: C 249 PHE cc_start: 0.6922 (OUTLIER) cc_final: 0.6203 (m-80) REVERT: B 249 PHE cc_start: 0.6830 (OUTLIER) cc_final: 0.5963 (m-80) REVERT: B 255 LYS cc_start: 0.8250 (tttm) cc_final: 0.7695 (mttm) REVERT: B 285 PHE cc_start: 0.7790 (m-10) cc_final: 0.7576 (m-80) REVERT: B 314 GLN cc_start: 0.8593 (mm-40) cc_final: 0.8292 (tm-30) REVERT: B 375 ARG cc_start: 0.7014 (ptp-170) cc_final: 0.6683 (ptp90) REVERT: B 390 TYR cc_start: 0.7646 (t80) cc_final: 0.7387 (t80) outliers start: 41 outliers final: 30 residues processed: 179 average time/residue: 0.0638 time to fit residues: 16.0348 Evaluate side-chains 184 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 298 CYS Chi-restraints excluded: chain A residue 311 ILE 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 411 PHE 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 298 CYS Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 414 CYS Chi-restraints excluded: chain C residue 460 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 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 412 ASP Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 430 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 65 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3901 r_free = 0.3901 target = 0.159678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.137787 restraints weight = 12458.198| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.62 r_work: 0.3556 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4067 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= 0.148 Angle : 0.615 8.131 10749 Z= 0.294 Chirality : 0.042 0.139 1230 Planarity : 0.004 0.028 1269 Dihedral : 6.836 47.746 1212 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 5.49 % Allowed : 21.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.29), residues: 933 helix: 2.40 (0.21), residues: 687 sheet: None (None), residues: 0 loop : -0.54 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 187 TYR 0.009 0.001 TYR B 390 PHE 0.030 0.001 PHE A 441 TRP 0.009 0.001 TRP A 206 HIS 0.004 0.001 HIS C 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 7818) covalent geometry : angle 0.61525 / 0.29 (10749) hydrogen bonds : bond 0.05748 / 3.81 ( 474) hydrogen bonds : angle 3.70430 / 2.68 ( 1404) *********************** 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 191 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 149 time to evaluate : 0.232 Fit side-chains REVERT: A 249 PHE cc_start: 0.6837 (OUTLIER) cc_final: 0.6060 (m-80) REVERT: A 285 PHE cc_start: 0.8047 (m-80) cc_final: 0.7844 (m-80) REVERT: A 375 ARG cc_start: 0.7296 (ptp-170) cc_final: 0.6964 (ptp90) REVERT: C 199 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7348 (tt) REVERT: C 249 PHE cc_start: 0.7077 (OUTLIER) cc_final: 0.6326 (m-80) REVERT: C 285 PHE cc_start: 0.8035 (m-80) cc_final: 0.7556 (m-80) REVERT: C 462 TYR cc_start: 0.8833 (t80) cc_final: 0.8434 (t80) REVERT: B 249 PHE cc_start: 0.6901 (OUTLIER) cc_final: 0.6103 (m-80) REVERT: B 314 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8304 (tm-30) REVERT: B 375 ARG cc_start: 0.7088 (ptp-170) cc_final: 0.6755 (ptp90) outliers start: 42 outliers final: 31 residues processed: 176 average time/residue: 0.0604 time to fit residues: 15.2520 Evaluate side-chains 181 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 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 372 LEU Chi-restraints excluded: chain A residue 411 PHE 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 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 371 THR Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 414 CYS 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 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 371 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 3 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3874 r_free = 0.3874 target = 0.157157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.135367 restraints weight = 12619.115| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.57 r_work: 0.3516 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7818 Z= 0.177 Angle : 0.668 9.616 10749 Z= 0.318 Chirality : 0.043 0.149 1230 Planarity : 0.004 0.028 1269 Dihedral : 6.987 51.567 1212 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 5.75 % Allowed : 21.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.29), residues: 933 helix: 2.28 (0.21), residues: 681 sheet: None (None), residues: 0 loop : -0.59 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 187 TYR 0.015 0.001 TYR A 390 PHE 0.025 0.002 PHE B 450 TRP 0.009 0.001 TRP A 206 HIS 0.004 0.001 HIS A 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 ( 7818) covalent geometry : angle 0.66778 / 0.32 (10749) hydrogen bonds : bond 0.06701 / 4.45 ( 474) hydrogen bonds : angle 3.89808 / 2.84 ( 1404) *********************** 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 188 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 144 time to evaluate : 0.329 Fit side-chains REVERT: A 249 PHE cc_start: 0.7018 (OUTLIER) cc_final: 0.6158 (m-80) REVERT: A 375 ARG cc_start: 0.7448 (ptp-170) cc_final: 0.7100 (ptp90) REVERT: A 426 TYR cc_start: 0.8672 (t80) cc_final: 0.8391 (t80) REVERT: C 184 PHE cc_start: 0.7923 (t80) cc_final: 0.7626 (t80) REVERT: C 249 PHE cc_start: 0.7232 (OUTLIER) cc_final: 0.6445 (m-80) REVERT: C 390 TYR cc_start: 0.7608 (t80) cc_final: 0.7345 (t80) REVERT: B 249 PHE cc_start: 0.7039 (OUTLIER) cc_final: 0.6290 (m-80) REVERT: B 277 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8146 (mp) REVERT: B 375 ARG cc_start: 0.7336 (ptp-170) cc_final: 0.6981 (ptp90) outliers start: 44 outliers final: 32 residues processed: 175 average time/residue: 0.0641 time to fit residues: 15.7219 Evaluate side-chains 176 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 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 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 371 THR Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 414 CYS 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 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 298 CYS 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 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 16 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3914 r_free = 0.3914 target = 0.161069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.139674 restraints weight = 12329.383| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.60 r_work: 0.3576 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4299 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= 0.133 Angle : 0.626 8.171 10749 Z= 0.293 Chirality : 0.041 0.152 1230 Planarity : 0.004 0.027 1269 Dihedral : 6.914 56.055 1212 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.05 % Allowed : 23.01 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.29), residues: 933 helix: 2.33 (0.21), residues: 687 sheet: None (None), residues: 0 loop : -0.65 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 187 TYR 0.027 0.001 TYR B 390 PHE 0.015 0.001 PHE B 450 TRP 0.015 0.001 TRP C 206 HIS 0.003 0.001 HIS A 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 7818) covalent geometry : angle 0.62575 / 0.29 (10749) hydrogen bonds : bond 0.05257 / 3.47 ( 474) hydrogen bonds : angle 3.65649 / 2.66 ( 1404) *********************** 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 179 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.274 Fit side-chains REVERT: A 249 PHE cc_start: 0.6972 (OUTLIER) cc_final: 0.6143 (m-80) REVERT: A 375 ARG cc_start: 0.7274 (ptp-170) cc_final: 0.6950 (ptp90) REVERT: C 184 PHE cc_start: 0.7930 (t80) cc_final: 0.7678 (t80) REVERT: C 249 PHE cc_start: 0.7197 (OUTLIER) cc_final: 0.6403 (m-80) REVERT: C 462 TYR cc_start: 0.8834 (t80) cc_final: 0.8540 (t80) REVERT: B 249 PHE cc_start: 0.7054 (OUTLIER) cc_final: 0.6200 (m-80) REVERT: B 277 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8099 (mp) REVERT: B 285 PHE cc_start: 0.7886 (m-10) cc_final: 0.7608 (m-80) REVERT: B 375 ARG cc_start: 0.7109 (ptp-170) cc_final: 0.6772 (ptp90) outliers start: 31 outliers final: 25 residues processed: 165 average time/residue: 0.0696 time to fit residues: 16.0527 Evaluate side-chains 175 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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 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 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 371 THR Chi-restraints excluded: chain C residue 411 PHE Chi-restraints excluded: chain C residue 414 CYS Chi-restraints excluded: chain C residue 460 ILE 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 414 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 34 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 81 optimal weight: 0.0050 chunk 12 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 219 HIS B 219 HIS ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.164854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.143664 restraints weight = 12268.844| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.59 r_work: 0.3609 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.4484 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= 0.126 Angle : 0.624 7.856 10749 Z= 0.289 Chirality : 0.041 0.146 1230 Planarity : 0.004 0.027 1269 Dihedral : 6.796 55.853 1212 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.29), residues: 933 helix: 2.29 (0.21), residues: 690 sheet: None (None), residues: 0 loop : -0.75 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 187 TYR 0.015 0.001 TYR A 390 PHE 0.026 0.001 PHE A 184 TRP 0.014 0.001 TRP C 206 HIS 0.003 0.001 HIS A 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 ( 7818) covalent geometry : angle 0.62371 / 0.29 (10749) hydrogen bonds : bond 0.04663 / 3.07 ( 474) hydrogen bonds : angle 3.55598 / 2.59 ( 1404) ********************** 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 : 0.331 Fit side-chains REVERT: A 249 PHE cc_start: 0.6942 (OUTLIER) cc_final: 0.6178 (m-80) REVERT: A 375 ARG cc_start: 0.7123 (ptp-170) cc_final: 0.6823 (ptp90) REVERT: C 184 PHE cc_start: 0.7966 (t80) cc_final: 0.7750 (t80) REVERT: C 249 PHE cc_start: 0.7086 (OUTLIER) cc_final: 0.6306 (m-80) REVERT: C 362 PHE cc_start: 0.8305 (t80) cc_final: 0.8050 (t80) REVERT: C 462 TYR cc_start: 0.8784 (t80) cc_final: 0.8574 (t80) REVERT: B 249 PHE cc_start: 0.6898 (OUTLIER) cc_final: 0.6098 (m-80) REVERT: B 277 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8064 (mp) REVERT: B 362 PHE cc_start: 0.8310 (t80) cc_final: 0.8084 (t80) REVERT: B 375 ARG cc_start: 0.7066 (ptp-170) cc_final: 0.6763 (ptp90) outliers start: 28 outliers final: 24 residues processed: 166 average time/residue: 0.0701 time to fit residues: 16.3334 Evaluate side-chains 176 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 298 CYS Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 353 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 249 PHE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 371 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 460 ILE 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 414 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 66 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 82 optimal weight: 0.0040 chunk 43 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 219 HIS B 219 HIS ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.163113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.141481 restraints weight = 12371.832| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.61 r_work: 0.3592 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4495 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 : 0.620 7.905 10749 Z= 0.287 Chirality : 0.041 0.145 1230 Planarity : 0.004 0.026 1269 Dihedral : 6.834 55.156 1212 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.18 % Allowed : 22.88 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.29), residues: 933 helix: 2.29 (0.21), residues: 690 sheet: None (None), residues: 0 loop : -0.79 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 187 TYR 0.012 0.001 TYR B 390 PHE 0.015 0.001 PHE C 450 TRP 0.013 0.001 TRP C 206 HIS 0.004 0.001 HIS C 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 ( 7818) covalent geometry : angle 0.62035 / 0.29 (10749) hydrogen bonds : bond 0.04845 / 3.20 ( 474) hydrogen bonds : angle 3.55063 / 2.59 ( 1404) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1359.67 seconds wall clock time: 24 minutes 1.79 seconds (1441.79 seconds total)