Starting phenix.real_space_refine on Wed Jun 11 11:48:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ze2_60021/06_2025/8ze2_60021_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ze2_60021/06_2025/8ze2_60021.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ze2_60021/06_2025/8ze2_60021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ze2_60021/06_2025/8ze2_60021.map" model { file = "/net/cci-nas-00/data/ceres_data/8ze2_60021/06_2025/8ze2_60021_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ze2_60021/06_2025/8ze2_60021_trim.cif" } resolution = 2.57 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= 0.005 sd= 0.083 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 8576 2.51 5 N 2124 2.21 5 O 2180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12972 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3220 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 14, 'TRANS': 377} Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 1, 'Z9N': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, B, D, G, F, H Time building chain proxies: 6.81, per 1000 atoms: 0.52 Number of scatterers: 12972 At special positions: 0 Unit cell: (112.772, 112.772, 96.928, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 2180 8.00 N 2124 7.00 C 8576 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=1, symmetry=0 Links applied ALPHA1-2 " Z9N E 2 " - " GLC E 1 " " Z9N F 2 " - " GLC F 1 " " Z9N G 2 " - " GLC G 1 " " Z9N H 2 " - " GLC H 1 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 1.6 seconds 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3024 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 0 sheets defined 79.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 58 through 73 Proline residue: A 65 - end of helix removed outlier: 3.899A pdb=" N LEU A 69 " --> pdb=" O PRO A 65 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 123 Processing helix chain 'A' and resid 128 through 164 removed outlier: 4.052A pdb=" N LEU A 132 " --> pdb=" O ASN A 128 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A 151 " --> pdb=" O ARG A 147 " (cutoff:3.500A) Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 165 through 168 removed outlier: 3.638A pdb=" N LYS A 168 " --> pdb=" O PRO A 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 165 through 168' Processing helix chain 'A' and resid 177 through 213 removed outlier: 3.736A pdb=" N ALA A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 242 through 288 removed outlier: 4.294A pdb=" N ASP A 264 " --> pdb=" O TRP A 260 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 288 " --> pdb=" O ARG A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 340 removed outlier: 5.345A pdb=" N SER A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LEU A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 388 removed outlier: 3.612A pdb=" N ILE A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 394 removed outlier: 3.651A pdb=" N SER A 393 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TRP A 394 " --> pdb=" O SER A 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 390 through 394' Processing helix chain 'A' and resid 396 through 408 Processing helix chain 'A' and resid 421 through 443 removed outlier: 4.342A pdb=" N GLN A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 73 Proline residue: B 65 - end of helix removed outlier: 3.899A pdb=" N LEU B 69 " --> pdb=" O PRO B 65 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 123 Processing helix chain 'B' and resid 128 through 164 removed outlier: 4.053A pdb=" N LEU B 132 " --> pdb=" O ASN B 128 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS B 151 " --> pdb=" O ARG B 147 " (cutoff:3.500A) Proline residue: B 153 - end of helix Processing helix chain 'B' and resid 165 through 168 removed outlier: 3.638A pdb=" N LYS B 168 " --> pdb=" O PRO B 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 165 through 168' Processing helix chain 'B' and resid 177 through 213 removed outlier: 3.736A pdb=" N ALA B 185 " --> pdb=" O ARG B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 242 through 288 removed outlier: 4.295A pdb=" N ASP B 264 " --> pdb=" O TRP B 260 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG B 277 " --> pdb=" O GLY B 273 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 288 " --> pdb=" O ARG B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 319 Processing helix chain 'B' and resid 319 through 340 Processing helix chain 'B' and resid 347 through 388 removed outlier: 3.612A pdb=" N ILE B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY B 384 " --> pdb=" O LYS B 380 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL B 385 " --> pdb=" O ARG B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 394 removed outlier: 3.650A pdb=" N SER B 393 " --> pdb=" O SER B 390 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TRP B 394 " --> pdb=" O SER B 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 390 through 394' Processing helix chain 'B' and resid 396 through 408 Processing helix chain 'B' and resid 421 through 443 removed outlier: 4.342A pdb=" N GLN B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 73 Proline residue: C 65 - end of helix removed outlier: 3.898A pdb=" N LEU C 69 " --> pdb=" O PRO C 65 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 123 Processing helix chain 'C' and resid 128 through 164 removed outlier: 4.053A pdb=" N LEU C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS C 151 " --> pdb=" O ARG C 147 " (cutoff:3.500A) Proline residue: C 153 - end of helix Processing helix chain 'C' and resid 165 through 168 removed outlier: 3.638A pdb=" N LYS C 168 " --> pdb=" O PRO C 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 165 through 168' Processing helix chain 'C' and resid 177 through 213 removed outlier: 3.736A pdb=" N ALA C 185 " --> pdb=" O ARG C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 242 through 288 removed outlier: 4.295A pdb=" N ASP C 264 " --> pdb=" O TRP C 260 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG C 277 " --> pdb=" O GLY C 273 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU C 288 " --> pdb=" O ARG C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 340 removed outlier: 5.344A pdb=" N SER C 321 " --> pdb=" O SER C 317 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LEU C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 388 removed outlier: 3.613A pdb=" N ILE C 375 " --> pdb=" O THR C 371 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY C 384 " --> pdb=" O LYS C 380 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL C 385 " --> pdb=" O ARG C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 394 removed outlier: 3.650A pdb=" N SER C 393 " --> pdb=" O SER C 390 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N TRP C 394 " --> pdb=" O SER C 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 390 through 394' Processing helix chain 'C' and resid 396 through 408 Processing helix chain 'C' and resid 421 through 443 removed outlier: 4.342A pdb=" N GLN C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 73 Proline residue: D 65 - end of helix removed outlier: 3.899A pdb=" N LEU D 69 " --> pdb=" O PRO D 65 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 123 Processing helix chain 'D' and resid 128 through 164 removed outlier: 4.053A pdb=" N LEU D 132 " --> pdb=" O ASN D 128 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS D 151 " --> pdb=" O ARG D 147 " (cutoff:3.500A) Proline residue: D 153 - end of helix Processing helix chain 'D' and resid 165 through 168 removed outlier: 3.637A pdb=" N LYS D 168 " --> pdb=" O PRO D 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 165 through 168' Processing helix chain 'D' and resid 177 through 213 removed outlier: 3.736A pdb=" N ALA D 185 " --> pdb=" O ARG D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 242 through 288 removed outlier: 4.294A pdb=" N ASP D 264 " --> pdb=" O TRP D 260 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG D 277 " --> pdb=" O GLY D 273 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D 288 " --> pdb=" O ARG D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 319 Processing helix chain 'D' and resid 319 through 340 Processing helix chain 'D' and resid 347 through 388 removed outlier: 3.612A pdb=" N ILE D 375 " --> pdb=" O THR D 371 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN D 376 " --> pdb=" O ALA D 372 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU D 383 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL D 385 " --> pdb=" O ARG D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 394 removed outlier: 3.651A pdb=" N SER D 393 " --> pdb=" O SER D 390 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TRP D 394 " --> pdb=" O SER D 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 390 through 394' Processing helix chain 'D' and resid 396 through 408 Processing helix chain 'D' and resid 421 through 443 removed outlier: 4.341A pdb=" N GLN D 441 " --> pdb=" O LEU D 437 " (cutoff:3.500A) 946 hydrogen bonds defined for protein. 2838 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: 3.40 Time building geometry restraints manager: 3.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3898 1.34 - 1.46: 3070 1.46 - 1.58: 6176 1.58 - 1.70: 4 1.70 - 1.81: 148 Bond restraints: 13296 Sorted by residual: bond pdb=" C4 Z9N H 2 " pdb=" C5 Z9N H 2 " ideal model delta sigma weight residual 1.527 1.303 0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C4 Z9N G 2 " pdb=" C5 Z9N G 2 " ideal model delta sigma weight residual 1.527 1.303 0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C4 Z9N E 2 " pdb=" C5 Z9N E 2 " ideal model delta sigma weight residual 1.527 1.303 0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C4 Z9N F 2 " pdb=" C5 Z9N F 2 " ideal model delta sigma weight residual 1.527 1.303 0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C5 Z9N E 2 " pdb=" O5 Z9N E 2 " ideal model delta sigma weight residual 1.421 1.594 -0.173 2.00e-02 2.50e+03 7.48e+01 ... (remaining 13291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 17413 1.92 - 3.84: 487 3.84 - 5.76: 80 5.76 - 7.68: 44 7.68 - 9.60: 16 Bond angle restraints: 18040 Sorted by residual: angle pdb=" C ILE C 205 " pdb=" N LEU C 206 " pdb=" CA LEU C 206 " ideal model delta sigma weight residual 120.65 115.77 4.88 1.32e+00 5.74e-01 1.37e+01 angle pdb=" C ILE D 205 " pdb=" N LEU D 206 " pdb=" CA LEU D 206 " ideal model delta sigma weight residual 120.65 115.79 4.86 1.32e+00 5.74e-01 1.36e+01 angle pdb=" C ILE B 205 " pdb=" N LEU B 206 " pdb=" CA LEU B 206 " ideal model delta sigma weight residual 120.65 115.79 4.86 1.32e+00 5.74e-01 1.36e+01 angle pdb=" C ILE A 205 " pdb=" N LEU A 206 " pdb=" CA LEU A 206 " ideal model delta sigma weight residual 120.65 115.79 4.86 1.32e+00 5.74e-01 1.36e+01 angle pdb=" CA PRO C 243 " pdb=" N PRO C 243 " pdb=" CD PRO C 243 " ideal model delta sigma weight residual 112.00 107.21 4.79 1.40e+00 5.10e-01 1.17e+01 ... (remaining 18035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.61: 6588 16.61 - 33.22: 1018 33.22 - 49.84: 306 49.84 - 66.45: 72 66.45 - 83.06: 12 Dihedral angle restraints: 7996 sinusoidal: 3328 harmonic: 4668 Sorted by residual: dihedral pdb=" CA TRP D 394 " pdb=" C TRP D 394 " pdb=" N CYS D 395 " pdb=" CA CYS D 395 " ideal model delta harmonic sigma weight residual 180.00 158.04 21.96 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA TRP C 394 " pdb=" C TRP C 394 " pdb=" N CYS C 395 " pdb=" CA CYS C 395 " ideal model delta harmonic sigma weight residual 180.00 158.07 21.93 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA TRP A 394 " pdb=" C TRP A 394 " pdb=" N CYS A 395 " pdb=" CA CYS A 395 " ideal model delta harmonic sigma weight residual 180.00 158.09 21.91 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 7993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1670 0.055 - 0.110: 376 0.110 - 0.165: 42 0.165 - 0.220: 4 0.220 - 0.275: 12 Chirality restraints: 2104 Sorted by residual: chirality pdb=" CG LEU C 440 " pdb=" CB LEU C 440 " pdb=" CD1 LEU C 440 " pdb=" CD2 LEU C 440 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CG LEU B 440 " pdb=" CB LEU B 440 " pdb=" CD1 LEU B 440 " pdb=" CD2 LEU B 440 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CG LEU D 440 " pdb=" CB LEU D 440 " pdb=" CD1 LEU D 440 " pdb=" CD2 LEU D 440 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 2101 not shown) Planarity restraints: 2184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 242 " 0.080 5.00e-02 4.00e+02 1.19e-01 2.28e+01 pdb=" N PRO D 243 " -0.206 5.00e-02 4.00e+02 pdb=" CA PRO D 243 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO D 243 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 242 " -0.080 5.00e-02 4.00e+02 1.19e-01 2.27e+01 pdb=" N PRO B 243 " 0.206 5.00e-02 4.00e+02 pdb=" CA PRO B 243 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO B 243 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 242 " 0.080 5.00e-02 4.00e+02 1.19e-01 2.27e+01 pdb=" N PRO A 243 " -0.206 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " 0.063 5.00e-02 4.00e+02 ... (remaining 2181 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 182 2.61 - 3.18: 11805 3.18 - 3.75: 22103 3.75 - 4.33: 29859 4.33 - 4.90: 48528 Nonbonded interactions: 112477 Sorted by model distance: nonbonded pdb=" CB THR C 257 " pdb=" O3 GLC G 1 " model vdw 2.033 3.470 nonbonded pdb=" CB THR A 257 " pdb=" O3 GLC E 1 " model vdw 2.076 3.470 nonbonded pdb=" CZ3 TRP D 260 " pdb=" O6 GLC H 1 " model vdw 2.090 3.340 nonbonded pdb=" CZ3 TRP A 260 " pdb=" O6 GLC E 1 " model vdw 2.097 3.340 nonbonded pdb=" CZ3 TRP B 260 " pdb=" O6 GLC F 1 " model vdw 2.101 3.340 ... (remaining 112472 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'F' selection = chain 'H' } 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: 0.500 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: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 29.560 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:13.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 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 : 0.009 0.613 13301 Z= 0.650 Angle : 0.843 9.602 18052 Z= 0.424 Chirality : 0.048 0.275 2104 Planarity : 0.008 0.119 2184 Dihedral : 17.746 83.059 4972 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 21.00 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.58 % Favored : 94.17 % Rotamer: Outliers : 0.56 % Allowed : 24.23 % Favored : 75.21 % 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: -1.29 (0.20), residues: 1560 helix: -0.27 (0.14), residues: 1172 sheet: None (None), residues: 0 loop : -2.39 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 347 HIS 0.002 0.001 HIS A 197 PHE 0.028 0.002 PHE C 224 TYR 0.020 0.002 TYR A 356 ARG 0.007 0.001 ARG D 388 Details of bonding type rmsd link_ALPHA1-2 : bond 0.06334 ( 4) link_ALPHA1-2 : angle 3.64292 ( 12) hydrogen bonds : bond 0.08326 ( 946) hydrogen bonds : angle 6.39115 ( 2838) covalent geometry : bond 0.00752 (13296) covalent geometry : angle 0.83797 (18040) Misc. bond : bond 0.61278 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 354 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.7831 (mtp) cc_final: 0.6892 (mtm) REVERT: A 211 ARG cc_start: 0.6891 (tpt170) cc_final: 0.6657 (tpt170) REVERT: D 300 GLN cc_start: 0.7963 (tt0) cc_final: 0.7730 (tt0) outliers start: 8 outliers final: 7 residues processed: 356 average time/residue: 0.9835 time to fit residues: 392.6323 Evaluate side-chains 298 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 291 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 354 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 chunk 79 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 340 ASN A 441 GLN B 261 ASN B 441 GLN C 441 GLN D 118 HIS D 300 GLN D 340 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.182004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.149959 restraints weight = 18098.595| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 2.17 r_work: 0.3905 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13301 Z= 0.171 Angle : 0.712 8.940 18052 Z= 0.355 Chirality : 0.045 0.228 2104 Planarity : 0.007 0.080 2184 Dihedral : 7.800 59.916 1938 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.36 % Favored : 95.38 % Rotamer: Outliers : 4.37 % Allowed : 22.54 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.20), residues: 1560 helix: 0.37 (0.14), residues: 1184 sheet: None (None), residues: 0 loop : -2.51 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 347 HIS 0.006 0.001 HIS D 197 PHE 0.024 0.002 PHE A 68 TYR 0.017 0.002 TYR B 356 ARG 0.008 0.001 ARG A 392 Details of bonding type rmsd link_ALPHA1-2 : bond 0.00674 ( 4) link_ALPHA1-2 : angle 4.47499 ( 12) hydrogen bonds : bond 0.05497 ( 946) hydrogen bonds : angle 5.53403 ( 2838) covalent geometry : bond 0.00354 (13296) covalent geometry : angle 0.70249 (18040) Misc. bond : bond 0.00392 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 324 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7035 (mt-10) REVERT: A 339 LEU cc_start: 0.7801 (tm) cc_final: 0.7326 (mm) REVERT: B 128 ASN cc_start: 0.7653 (m110) cc_final: 0.7421 (m110) REVERT: B 210 ARG cc_start: 0.8273 (ptp-170) cc_final: 0.7479 (ptp-170) REVERT: B 247 VAL cc_start: 0.8686 (t) cc_final: 0.8371 (m) REVERT: B 347 TRP cc_start: 0.7916 (m100) cc_final: 0.7140 (m-10) REVERT: C 257 THR cc_start: 0.8275 (OUTLIER) cc_final: 0.7984 (m) REVERT: C 310 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.7031 (mt-10) REVERT: C 378 GLU cc_start: 0.7355 (tp30) cc_final: 0.7036 (tp30) REVERT: C 392 ARG cc_start: 0.8225 (mmm-85) cc_final: 0.7987 (mmm-85) REVERT: D 210 ARG cc_start: 0.8314 (ptp-170) cc_final: 0.7333 (ptp-170) REVERT: D 257 THR cc_start: 0.8140 (OUTLIER) cc_final: 0.7904 (m) REVERT: D 339 LEU cc_start: 0.7884 (tm) cc_final: 0.7431 (mm) REVERT: D 347 TRP cc_start: 0.7692 (m100) cc_final: 0.7337 (m-10) REVERT: D 392 ARG cc_start: 0.8292 (mmm-85) cc_final: 0.7940 (mmm-85) outliers start: 62 outliers final: 19 residues processed: 353 average time/residue: 1.0259 time to fit residues: 410.8268 Evaluate side-chains 296 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 274 time to evaluate : 2.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 208 TYR Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 90 ARG Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 257 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 65 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 140 optimal weight: 0.3980 chunk 119 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 128 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.180545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.148023 restraints weight = 18191.787| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 2.18 r_work: 0.3881 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 13301 Z= 0.166 Angle : 0.684 10.403 18052 Z= 0.344 Chirality : 0.044 0.215 2104 Planarity : 0.006 0.065 2184 Dihedral : 6.298 33.909 1928 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.81 % Favored : 94.94 % Rotamer: Outliers : 4.79 % Allowed : 22.32 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.21), residues: 1560 helix: 0.74 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -2.68 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 347 HIS 0.003 0.001 HIS D 197 PHE 0.015 0.001 PHE A 64 TYR 0.015 0.001 TYR C 208 ARG 0.007 0.000 ARG A 392 Details of bonding type rmsd link_ALPHA1-2 : bond 0.01200 ( 4) link_ALPHA1-2 : angle 3.37169 ( 12) hydrogen bonds : bond 0.05262 ( 946) hydrogen bonds : angle 5.29431 ( 2838) covalent geometry : bond 0.00344 (13296) covalent geometry : angle 0.67839 (18040) Misc. bond : bond 0.00057 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 311 time to evaluate : 1.938 Fit side-chains revert: symmetry clash REVERT: A 378 GLU cc_start: 0.7528 (tp30) cc_final: 0.7205 (tp30) REVERT: B 88 ARG cc_start: 0.7842 (mtp85) cc_final: 0.7414 (ttm-80) REVERT: B 128 ASN cc_start: 0.7655 (m110) cc_final: 0.7415 (m110) REVERT: B 164 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7671 (mp) REVERT: B 210 ARG cc_start: 0.8250 (ptp-170) cc_final: 0.7227 (ptp-170) REVERT: B 257 THR cc_start: 0.7999 (OUTLIER) cc_final: 0.7648 (m) REVERT: B 347 TRP cc_start: 0.7849 (m100) cc_final: 0.7351 (m-10) REVERT: C 257 THR cc_start: 0.8212 (OUTLIER) cc_final: 0.7994 (m) REVERT: D 210 ARG cc_start: 0.8365 (ptp-170) cc_final: 0.7293 (ptp-170) REVERT: D 257 THR cc_start: 0.8137 (OUTLIER) cc_final: 0.7815 (m) REVERT: D 340 ASN cc_start: 0.7742 (m-40) cc_final: 0.7538 (m110) REVERT: D 346 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.6801 (tpp80) REVERT: D 347 TRP cc_start: 0.7795 (m100) cc_final: 0.7488 (m-10) outliers start: 68 outliers final: 18 residues processed: 348 average time/residue: 1.3048 time to fit residues: 513.5301 Evaluate side-chains 302 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 279 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 90 ARG Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 346 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 152 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 117 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN C 118 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.177021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.144448 restraints weight = 18074.136| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.18 r_work: 0.3796 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13301 Z= 0.177 Angle : 0.710 11.738 18052 Z= 0.349 Chirality : 0.045 0.227 2104 Planarity : 0.006 0.057 2184 Dihedral : 5.732 32.790 1926 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.68 % Favored : 95.06 % Rotamer: Outliers : 4.44 % Allowed : 22.39 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.21), residues: 1560 helix: 0.91 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -2.60 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 347 HIS 0.003 0.001 HIS C 197 PHE 0.023 0.002 PHE A 224 TYR 0.016 0.001 TYR C 208 ARG 0.008 0.000 ARG A 392 Details of bonding type rmsd link_ALPHA1-2 : bond 0.00851 ( 4) link_ALPHA1-2 : angle 3.22912 ( 12) hydrogen bonds : bond 0.05267 ( 946) hydrogen bonds : angle 5.14846 ( 2838) covalent geometry : bond 0.00370 (13296) covalent geometry : angle 0.70546 (18040) Misc. bond : bond 0.00079 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 307 time to evaluate : 1.511 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.6998 (OUTLIER) cc_final: 0.6750 (ttm) REVERT: A 210 ARG cc_start: 0.8286 (ptp-170) cc_final: 0.7468 (ptp-170) REVERT: A 257 THR cc_start: 0.8029 (OUTLIER) cc_final: 0.7674 (m) REVERT: A 339 LEU cc_start: 0.8373 (tt) cc_final: 0.7896 (mp) REVERT: A 347 TRP cc_start: 0.7625 (m100) cc_final: 0.7243 (m-10) REVERT: B 115 MET cc_start: 0.6882 (OUTLIER) cc_final: 0.6462 (ptm) REVERT: B 128 ASN cc_start: 0.7561 (m110) cc_final: 0.7328 (m110) REVERT: B 210 ARG cc_start: 0.8279 (ptp-170) cc_final: 0.7384 (ptp-170) REVERT: B 257 THR cc_start: 0.8048 (OUTLIER) cc_final: 0.7658 (m) REVERT: B 347 TRP cc_start: 0.7884 (m100) cc_final: 0.7481 (m100) REVERT: C 98 MET cc_start: 0.6657 (mpp) cc_final: 0.5038 (pmm) REVERT: C 257 THR cc_start: 0.8199 (OUTLIER) cc_final: 0.7916 (m) REVERT: C 374 ASP cc_start: 0.8218 (t0) cc_final: 0.7979 (t0) REVERT: D 210 ARG cc_start: 0.8294 (ptp-170) cc_final: 0.7103 (ptp-170) REVERT: D 257 THR cc_start: 0.8109 (OUTLIER) cc_final: 0.7752 (m) REVERT: D 336 TYR cc_start: 0.5934 (t80) cc_final: 0.5614 (t80) REVERT: D 339 LEU cc_start: 0.8442 (tt) cc_final: 0.7949 (mp) REVERT: D 340 ASN cc_start: 0.7722 (m-40) cc_final: 0.7514 (m110) REVERT: D 374 ASP cc_start: 0.8112 (t0) cc_final: 0.7888 (t0) REVERT: D 392 ARG cc_start: 0.8298 (mmm-85) cc_final: 0.8057 (mmm-85) outliers start: 63 outliers final: 20 residues processed: 336 average time/residue: 0.8512 time to fit residues: 323.8239 Evaluate side-chains 309 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 283 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 268 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 147 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 34 optimal weight: 0.2980 chunk 122 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 57 optimal weight: 20.0000 chunk 93 optimal weight: 0.7980 chunk 117 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 ASN A 340 ASN ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN D 118 HIS D 329 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.178981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.146450 restraints weight = 18302.770| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 2.22 r_work: 0.3823 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 13301 Z= 0.154 Angle : 0.710 12.141 18052 Z= 0.345 Chirality : 0.043 0.207 2104 Planarity : 0.006 0.054 2184 Dihedral : 5.454 32.715 1926 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.42 % Favored : 95.32 % Rotamer: Outliers : 3.80 % Allowed : 23.94 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.21), residues: 1560 helix: 1.02 (0.15), residues: 1188 sheet: None (None), residues: 0 loop : -2.65 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 347 HIS 0.006 0.001 HIS C 118 PHE 0.013 0.001 PHE A 64 TYR 0.016 0.001 TYR C 208 ARG 0.008 0.000 ARG A 392 Details of bonding type rmsd link_ALPHA1-2 : bond 0.00438 ( 4) link_ALPHA1-2 : angle 3.02670 ( 12) hydrogen bonds : bond 0.04936 ( 946) hydrogen bonds : angle 5.06022 ( 2838) covalent geometry : bond 0.00323 (13296) covalent geometry : angle 0.70613 (18040) Misc. bond : bond 0.00053 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 302 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 THR cc_start: 0.7989 (OUTLIER) cc_final: 0.7662 (m) REVERT: A 374 ASP cc_start: 0.8126 (t0) cc_final: 0.7437 (t0) REVERT: A 378 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7506 (mm-30) REVERT: B 115 MET cc_start: 0.6845 (OUTLIER) cc_final: 0.6448 (ptm) REVERT: B 122 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8116 (pp) REVERT: B 128 ASN cc_start: 0.7425 (m110) cc_final: 0.7217 (m110) REVERT: B 210 ARG cc_start: 0.8237 (ptp-170) cc_final: 0.7154 (ptp-170) REVERT: B 257 THR cc_start: 0.8004 (OUTLIER) cc_final: 0.7633 (m) REVERT: B 347 TRP cc_start: 0.7871 (m100) cc_final: 0.7621 (m-10) REVERT: B 374 ASP cc_start: 0.8168 (t0) cc_final: 0.7912 (t0) REVERT: C 257 THR cc_start: 0.8211 (OUTLIER) cc_final: 0.7897 (m) REVERT: C 374 ASP cc_start: 0.8158 (t0) cc_final: 0.7912 (t0) REVERT: D 210 ARG cc_start: 0.8159 (ptp-170) cc_final: 0.7318 (ptp-170) REVERT: D 257 THR cc_start: 0.8071 (OUTLIER) cc_final: 0.7735 (m) REVERT: D 346 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.6954 (tpp80) REVERT: D 347 TRP cc_start: 0.7655 (m100) cc_final: 0.7131 (m-10) REVERT: D 354 PHE cc_start: 0.8277 (t80) cc_final: 0.7040 (m-80) REVERT: D 392 ARG cc_start: 0.8311 (mmm-85) cc_final: 0.8050 (mmm-85) outliers start: 54 outliers final: 15 residues processed: 328 average time/residue: 0.8143 time to fit residues: 302.1349 Evaluate side-chains 305 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 283 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 268 MET Chi-restraints excluded: chain D residue 346 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 69 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 33 optimal weight: 0.1980 chunk 56 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 129 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.179124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.146534 restraints weight = 18434.938| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 2.22 r_work: 0.3816 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13301 Z= 0.155 Angle : 0.717 13.815 18052 Z= 0.346 Chirality : 0.044 0.210 2104 Planarity : 0.006 0.054 2184 Dihedral : 5.365 35.281 1926 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.32 % Favored : 94.62 % Rotamer: Outliers : 3.94 % Allowed : 23.66 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.21), residues: 1560 helix: 1.10 (0.15), residues: 1188 sheet: None (None), residues: 0 loop : -2.62 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 347 HIS 0.008 0.001 HIS C 118 PHE 0.027 0.001 PHE A 224 TYR 0.018 0.001 TYR C 208 ARG 0.008 0.000 ARG A 392 Details of bonding type rmsd link_ALPHA1-2 : bond 0.00369 ( 4) link_ALPHA1-2 : angle 2.86639 ( 12) hydrogen bonds : bond 0.04835 ( 946) hydrogen bonds : angle 4.98543 ( 2838) covalent geometry : bond 0.00324 (13296) covalent geometry : angle 0.71379 (18040) Misc. bond : bond 0.00052 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 290 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6865 (OUTLIER) cc_final: 0.6501 (ptm) REVERT: A 257 THR cc_start: 0.7988 (OUTLIER) cc_final: 0.7662 (m) REVERT: A 378 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7397 (mm-30) REVERT: B 115 MET cc_start: 0.6968 (OUTLIER) cc_final: 0.6612 (ptm) REVERT: B 122 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8177 (pp) REVERT: B 210 ARG cc_start: 0.8290 (ptp-170) cc_final: 0.7193 (ptp-170) REVERT: B 257 THR cc_start: 0.8048 (OUTLIER) cc_final: 0.7696 (m) REVERT: B 347 TRP cc_start: 0.7857 (m100) cc_final: 0.7600 (m100) REVERT: C 122 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8204 (pp) REVERT: C 257 THR cc_start: 0.8160 (OUTLIER) cc_final: 0.7833 (m) REVERT: C 374 ASP cc_start: 0.8149 (t0) cc_final: 0.7772 (t0) REVERT: D 257 THR cc_start: 0.8077 (OUTLIER) cc_final: 0.7727 (m) REVERT: D 346 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.6949 (tpp80) REVERT: D 374 ASP cc_start: 0.8091 (t0) cc_final: 0.7826 (t0) REVERT: D 392 ARG cc_start: 0.8325 (mmm-85) cc_final: 0.8066 (mmm-85) outliers start: 56 outliers final: 16 residues processed: 319 average time/residue: 0.7982 time to fit residues: 290.3715 Evaluate side-chains 307 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 282 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 268 MET Chi-restraints excluded: chain D residue 346 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 100 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 80 optimal weight: 0.0270 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 overall best weight: 1.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.176376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.143364 restraints weight = 18144.749| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.21 r_work: 0.3774 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 13301 Z= 0.182 Angle : 0.764 13.704 18052 Z= 0.368 Chirality : 0.045 0.212 2104 Planarity : 0.006 0.057 2184 Dihedral : 5.458 37.515 1926 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.94 % Allowed : 23.94 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.21), residues: 1560 helix: 1.14 (0.15), residues: 1188 sheet: None (None), residues: 0 loop : -2.55 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 152 HIS 0.010 0.001 HIS C 118 PHE 0.016 0.002 PHE A 116 TYR 0.017 0.001 TYR C 208 ARG 0.009 0.000 ARG A 392 Details of bonding type rmsd link_ALPHA1-2 : bond 0.00384 ( 4) link_ALPHA1-2 : angle 2.80092 ( 12) hydrogen bonds : bond 0.05063 ( 946) hydrogen bonds : angle 4.98869 ( 2838) covalent geometry : bond 0.00392 (13296) covalent geometry : angle 0.76062 (18040) Misc. bond : bond 0.00059 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 284 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6834 (OUTLIER) cc_final: 0.6475 (ptm) REVERT: A 257 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7705 (m) REVERT: A 374 ASP cc_start: 0.8209 (t0) cc_final: 0.7444 (t0) REVERT: A 378 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7504 (mm-30) REVERT: B 115 MET cc_start: 0.7004 (OUTLIER) cc_final: 0.6715 (ptm) REVERT: B 210 ARG cc_start: 0.8324 (ptp-170) cc_final: 0.7241 (ptp-170) REVERT: B 257 THR cc_start: 0.8102 (OUTLIER) cc_final: 0.7742 (m) REVERT: B 347 TRP cc_start: 0.7896 (m100) cc_final: 0.7602 (m100) REVERT: B 374 ASP cc_start: 0.8271 (t0) cc_final: 0.7972 (t0) REVERT: C 152 TRP cc_start: 0.7115 (t-100) cc_final: 0.6739 (t-100) REVERT: C 257 THR cc_start: 0.8195 (OUTLIER) cc_final: 0.7905 (m) REVERT: C 374 ASP cc_start: 0.8217 (t0) cc_final: 0.7839 (t0) REVERT: D 152 TRP cc_start: 0.7248 (t-100) cc_final: 0.6821 (t-100) REVERT: D 257 THR cc_start: 0.8070 (OUTLIER) cc_final: 0.7760 (m) REVERT: D 346 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.7071 (tpt170) REVERT: D 374 ASP cc_start: 0.8136 (t0) cc_final: 0.7883 (t0) REVERT: D 392 ARG cc_start: 0.8325 (mmm-85) cc_final: 0.8063 (mmm-85) outliers start: 56 outliers final: 18 residues processed: 312 average time/residue: 0.7192 time to fit residues: 257.2543 Evaluate side-chains 299 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 274 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 268 MET Chi-restraints excluded: chain D residue 346 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 95 optimal weight: 0.0470 chunk 54 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 143 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.178504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.145753 restraints weight = 18100.026| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.21 r_work: 0.3811 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13301 Z= 0.158 Angle : 0.760 16.321 18052 Z= 0.365 Chirality : 0.045 0.219 2104 Planarity : 0.006 0.055 2184 Dihedral : 5.359 36.736 1924 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.10 % Allowed : 25.35 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.21), residues: 1560 helix: 1.15 (0.15), residues: 1188 sheet: None (None), residues: 0 loop : -2.49 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP D 347 HIS 0.011 0.001 HIS C 118 PHE 0.029 0.001 PHE B 224 TYR 0.020 0.001 TYR C 208 ARG 0.011 0.000 ARG B 392 Details of bonding type rmsd link_ALPHA1-2 : bond 0.00324 ( 4) link_ALPHA1-2 : angle 2.81490 ( 12) hydrogen bonds : bond 0.04819 ( 946) hydrogen bonds : angle 4.94889 ( 2838) covalent geometry : bond 0.00333 (13296) covalent geometry : angle 0.75704 (18040) Misc. bond : bond 0.00046 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 285 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6878 (OUTLIER) cc_final: 0.6561 (ptm) REVERT: A 257 THR cc_start: 0.8028 (OUTLIER) cc_final: 0.7706 (m) REVERT: A 347 TRP cc_start: 0.7655 (m100) cc_final: 0.7423 (m-10) REVERT: A 374 ASP cc_start: 0.8136 (t0) cc_final: 0.7371 (t0) REVERT: A 378 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7468 (mm-30) REVERT: B 115 MET cc_start: 0.6964 (OUTLIER) cc_final: 0.6742 (ptm) REVERT: B 210 ARG cc_start: 0.8304 (ptp-170) cc_final: 0.7229 (ptp-170) REVERT: B 257 THR cc_start: 0.8091 (OUTLIER) cc_final: 0.7748 (m) REVERT: B 289 GLU cc_start: 0.7948 (tp30) cc_final: 0.7566 (tm-30) REVERT: B 347 TRP cc_start: 0.7902 (m100) cc_final: 0.7620 (m100) REVERT: B 374 ASP cc_start: 0.8236 (t0) cc_final: 0.7903 (t0) REVERT: C 152 TRP cc_start: 0.7086 (t-100) cc_final: 0.6701 (t-100) REVERT: C 257 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7843 (m) REVERT: C 374 ASP cc_start: 0.8198 (t0) cc_final: 0.7836 (t0) REVERT: D 152 TRP cc_start: 0.7184 (t-100) cc_final: 0.6856 (t-100) REVERT: D 257 THR cc_start: 0.8121 (OUTLIER) cc_final: 0.7811 (m) REVERT: D 374 ASP cc_start: 0.8184 (t0) cc_final: 0.7690 (t0) REVERT: D 378 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7719 (mm-30) REVERT: D 392 ARG cc_start: 0.8320 (mmm-85) cc_final: 0.8069 (mmm-85) outliers start: 44 outliers final: 19 residues processed: 309 average time/residue: 0.8010 time to fit residues: 281.8701 Evaluate side-chains 301 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 276 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 257 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 113 optimal weight: 0.4980 chunk 89 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 chunk 2 optimal weight: 0.0970 chunk 84 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 ASN C 329 ASN D 253 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.179213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.146302 restraints weight = 18049.702| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 2.21 r_work: 0.3816 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13301 Z= 0.157 Angle : 0.787 16.820 18052 Z= 0.377 Chirality : 0.045 0.219 2104 Planarity : 0.006 0.055 2184 Dihedral : 5.349 36.299 1924 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.10 % Allowed : 26.48 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.21), residues: 1560 helix: 1.16 (0.15), residues: 1188 sheet: None (None), residues: 0 loop : -2.48 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP B 152 HIS 0.012 0.001 HIS C 118 PHE 0.014 0.001 PHE B 116 TYR 0.021 0.001 TYR C 208 ARG 0.010 0.000 ARG C 392 Details of bonding type rmsd link_ALPHA1-2 : bond 0.00217 ( 4) link_ALPHA1-2 : angle 2.70053 ( 12) hydrogen bonds : bond 0.04756 ( 946) hydrogen bonds : angle 4.93506 ( 2838) covalent geometry : bond 0.00329 (13296) covalent geometry : angle 0.78394 (18040) Misc. bond : bond 0.00045 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 285 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6890 (OUTLIER) cc_final: 0.6506 (ptm) REVERT: A 257 THR cc_start: 0.7996 (OUTLIER) cc_final: 0.7684 (m) REVERT: A 378 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7457 (mm-30) REVERT: B 115 MET cc_start: 0.6953 (OUTLIER) cc_final: 0.6719 (ptm) REVERT: B 210 ARG cc_start: 0.8273 (ptp-170) cc_final: 0.7189 (ptp-170) REVERT: B 257 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7730 (m) REVERT: B 289 GLU cc_start: 0.7923 (tp30) cc_final: 0.7563 (tm-30) REVERT: B 347 TRP cc_start: 0.7837 (m100) cc_final: 0.7603 (m100) REVERT: B 374 ASP cc_start: 0.8241 (t0) cc_final: 0.8011 (t0) REVERT: C 152 TRP cc_start: 0.7162 (t-100) cc_final: 0.6760 (t-100) REVERT: C 257 THR cc_start: 0.8132 (OUTLIER) cc_final: 0.7826 (m) REVERT: C 374 ASP cc_start: 0.8169 (t0) cc_final: 0.7827 (t0) REVERT: D 152 TRP cc_start: 0.7133 (t-100) cc_final: 0.6858 (t-100) REVERT: D 257 THR cc_start: 0.8092 (OUTLIER) cc_final: 0.7778 (m) REVERT: D 289 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7522 (tm-30) REVERT: D 354 PHE cc_start: 0.8187 (t80) cc_final: 0.7845 (t80) REVERT: D 374 ASP cc_start: 0.8164 (t0) cc_final: 0.7688 (t0) REVERT: D 378 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7729 (mm-30) REVERT: D 392 ARG cc_start: 0.8326 (mmm-85) cc_final: 0.8068 (mmm-85) outliers start: 44 outliers final: 17 residues processed: 313 average time/residue: 0.7394 time to fit residues: 265.5746 Evaluate side-chains 298 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 274 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 398 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 127 optimal weight: 8.9990 chunk 102 optimal weight: 0.7980 chunk 67 optimal weight: 0.2980 chunk 101 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 143 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.180102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.147398 restraints weight = 18166.795| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 2.21 r_work: 0.3833 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13301 Z= 0.161 Angle : 0.798 16.746 18052 Z= 0.384 Chirality : 0.045 0.220 2104 Planarity : 0.006 0.055 2184 Dihedral : 5.328 35.158 1924 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.18 % Allowed : 27.82 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.21), residues: 1560 helix: 1.17 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -2.44 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP B 152 HIS 0.012 0.001 HIS C 118 PHE 0.030 0.001 PHE B 224 TYR 0.026 0.001 TYR C 208 ARG 0.012 0.000 ARG C 392 Details of bonding type rmsd link_ALPHA1-2 : bond 0.00250 ( 4) link_ALPHA1-2 : angle 2.61088 ( 12) hydrogen bonds : bond 0.04714 ( 946) hydrogen bonds : angle 4.93144 ( 2838) covalent geometry : bond 0.00343 (13296) covalent geometry : angle 0.79499 (18040) Misc. bond : bond 0.00046 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 282 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6875 (OUTLIER) cc_final: 0.6496 (ptm) REVERT: A 257 THR cc_start: 0.7982 (OUTLIER) cc_final: 0.7689 (m) REVERT: A 378 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7450 (mm-30) REVERT: B 115 MET cc_start: 0.6918 (OUTLIER) cc_final: 0.6676 (ptm) REVERT: B 184 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7228 (mm) REVERT: B 210 ARG cc_start: 0.8290 (ptp-170) cc_final: 0.7160 (ptp-170) REVERT: B 257 THR cc_start: 0.8067 (OUTLIER) cc_final: 0.7749 (m) REVERT: B 289 GLU cc_start: 0.7830 (tp30) cc_final: 0.7520 (tm-30) REVERT: B 347 TRP cc_start: 0.7821 (m100) cc_final: 0.7613 (m100) REVERT: B 369 PHE cc_start: 0.6868 (m-10) cc_final: 0.6488 (m-80) REVERT: B 374 ASP cc_start: 0.8255 (t0) cc_final: 0.8025 (t0) REVERT: C 152 TRP cc_start: 0.7021 (t-100) cc_final: 0.6666 (t-100) REVERT: C 257 THR cc_start: 0.8071 (OUTLIER) cc_final: 0.7767 (m) REVERT: C 374 ASP cc_start: 0.8210 (t0) cc_final: 0.7889 (t0) REVERT: D 257 THR cc_start: 0.8009 (OUTLIER) cc_final: 0.7718 (m) REVERT: D 289 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7581 (tm-30) REVERT: D 354 PHE cc_start: 0.8187 (t80) cc_final: 0.7901 (t80) REVERT: D 374 ASP cc_start: 0.8119 (t0) cc_final: 0.7677 (t0) REVERT: D 378 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7737 (mm-30) REVERT: D 392 ARG cc_start: 0.8316 (mmm-85) cc_final: 0.8058 (mmm-85) outliers start: 31 outliers final: 17 residues processed: 300 average time/residue: 0.7869 time to fit residues: 271.7200 Evaluate side-chains 299 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 274 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 289 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 94 optimal weight: 20.0000 chunk 28 optimal weight: 0.7980 chunk 133 optimal weight: 20.0000 chunk 145 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 135 optimal weight: 40.0000 chunk 1 optimal weight: 0.0000 chunk 128 optimal weight: 8.9990 chunk 114 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 ASN D 253 ASN D 408 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.179223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.146341 restraints weight = 18159.007| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.22 r_work: 0.3811 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13301 Z= 0.170 Angle : 0.814 16.032 18052 Z= 0.391 Chirality : 0.047 0.253 2104 Planarity : 0.006 0.056 2184 Dihedral : 5.347 34.729 1924 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.54 % Allowed : 27.54 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.21), residues: 1560 helix: 1.19 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -2.42 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP B 152 HIS 0.013 0.001 HIS C 118 PHE 0.014 0.001 PHE B 116 TYR 0.026 0.001 TYR C 208 ARG 0.008 0.000 ARG C 392 Details of bonding type rmsd link_ALPHA1-2 : bond 0.00181 ( 4) link_ALPHA1-2 : angle 2.55335 ( 12) hydrogen bonds : bond 0.04762 ( 946) hydrogen bonds : angle 4.94212 ( 2838) covalent geometry : bond 0.00365 (13296) covalent geometry : angle 0.81150 (18040) Misc. bond : bond 0.00055 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11630.38 seconds wall clock time: 203 minutes 9.32 seconds (12189.32 seconds total)