Starting phenix.real_space_refine on Thu Sep 18 01:02:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ze2_60021/09_2025/8ze2_60021_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ze2_60021/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ze2_60021/09_2025/8ze2_60021_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ze2_60021/09_2025/8ze2_60021_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ze2_60021/09_2025/8ze2_60021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ze2_60021/09_2025/8ze2_60021.map" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: B, C, D, F, G, H Time building chain proxies: 2.37, per 1000 atoms: 0.18 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: 1.04 Conformation dependent library (CDL) restraints added in 448.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.36 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: 2.22 Time building geometry restraints manager: 1.33 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.090 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.670 ------------------------------------------------------------------------------- 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 : 20.97 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.001 ARG D 388 TYR 0.020 0.002 TYR A 356 PHE 0.028 0.002 PHE C 224 TRP 0.028 0.002 TRP D 347 HIS 0.002 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00752 (13296) covalent geometry : angle 0.83797 (18040) hydrogen bonds : bond 0.08326 ( 946) hydrogen bonds : angle 6.39115 ( 2838) Misc. bond : bond 0.61278 ( 1) link_ALPHA1-2 : bond 0.06334 ( 4) link_ALPHA1-2 : angle 3.64292 ( 12) *********************** 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 : 0.486 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: 0.3812 time to fit residues: 151.8161 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 : 0.448 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 ASN A 441 GLN B 261 ASN B 329 ASN B 441 GLN ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN D 118 HIS ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 GLN D 329 ASN D 340 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.176123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.143092 restraints weight = 18067.871| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.14 r_work: 0.3806 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 13301 Z= 0.229 Angle : 0.760 9.446 18052 Z= 0.380 Chirality : 0.046 0.223 2104 Planarity : 0.007 0.079 2184 Dihedral : 7.689 59.901 1938 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.65 % Favored : 96.09 % Rotamer: Outliers : 4.72 % Allowed : 21.90 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.20), residues: 1560 helix: 0.27 (0.14), residues: 1220 sheet: None (None), residues: 0 loop : -2.56 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 392 TYR 0.016 0.002 TYR C 360 PHE 0.025 0.002 PHE A 68 TRP 0.025 0.002 TRP A 347 HIS 0.005 0.001 HIS D 197 Details of bonding type rmsd covalent geometry : bond 0.00497 (13296) covalent geometry : angle 0.74978 (18040) hydrogen bonds : bond 0.06058 ( 946) hydrogen bonds : angle 5.59099 ( 2838) Misc. bond : bond 0.00322 ( 1) link_ALPHA1-2 : bond 0.00501 ( 4) link_ALPHA1-2 : angle 4.84335 ( 12) *********************** 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 391 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 324 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 210 ARG cc_start: 0.8361 (ptp-170) cc_final: 0.7594 (ptp-170) REVERT: B 88 ARG cc_start: 0.7900 (mtp85) cc_final: 0.7430 (ttm-80) REVERT: B 128 ASN cc_start: 0.7707 (m110) cc_final: 0.7484 (m110) REVERT: B 210 ARG cc_start: 0.8277 (ptp-170) cc_final: 0.7396 (ptp-170) REVERT: B 247 VAL cc_start: 0.8670 (t) cc_final: 0.8354 (m) REVERT: B 347 TRP cc_start: 0.7951 (m100) cc_final: 0.7159 (m-10) REVERT: B 369 PHE cc_start: 0.6986 (m-10) cc_final: 0.6743 (m-80) REVERT: C 257 THR cc_start: 0.8247 (OUTLIER) cc_final: 0.7989 (m) REVERT: C 392 ARG cc_start: 0.8271 (mmm-85) cc_final: 0.7993 (mmm-85) REVERT: D 210 ARG cc_start: 0.8378 (ptp-170) cc_final: 0.7375 (ptp-170) REVERT: D 257 THR cc_start: 0.8227 (OUTLIER) cc_final: 0.7958 (m) REVERT: D 347 TRP cc_start: 0.7726 (m100) cc_final: 0.7342 (m-10) REVERT: D 392 ARG cc_start: 0.8332 (mmm-85) cc_final: 0.7980 (mmm-85) outliers start: 67 outliers final: 26 residues processed: 355 average time/residue: 0.4011 time to fit residues: 160.3077 Evaluate side-chains 310 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 282 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 122 ILE 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 B residue 75 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 398 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 125 THR 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 391 SER 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 208 TYR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 354 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 143 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 101 optimal weight: 0.0040 chunk 19 optimal weight: 0.7980 chunk 137 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN A 340 ASN B 118 HIS B 201 GLN C 118 HIS C 329 ASN D 118 HIS ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.179278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.146900 restraints weight = 18156.039| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 2.15 r_work: 0.3857 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13301 Z= 0.157 Angle : 0.691 10.598 18052 Z= 0.344 Chirality : 0.043 0.220 2104 Planarity : 0.006 0.065 2184 Dihedral : 6.270 35.656 1928 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.36 % Favored : 95.38 % Rotamer: Outliers : 4.51 % Allowed : 22.82 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.21), residues: 1560 helix: 0.74 (0.14), residues: 1184 sheet: None (None), residues: 0 loop : -2.51 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 210 TYR 0.015 0.001 TYR B 208 PHE 0.014 0.001 PHE A 64 TRP 0.030 0.002 TRP A 347 HIS 0.002 0.001 HIS D 197 Details of bonding type rmsd covalent geometry : bond 0.00321 (13296) covalent geometry : angle 0.68596 (18040) hydrogen bonds : bond 0.05280 ( 946) hydrogen bonds : angle 5.31265 ( 2838) Misc. bond : bond 0.00066 ( 1) link_ALPHA1-2 : bond 0.00883 ( 4) link_ALPHA1-2 : angle 3.39260 ( 12) *********************** 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 377 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 313 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 67 MET cc_start: 0.8226 (mtp) cc_final: 0.7935 (mtt) REVERT: B 210 ARG cc_start: 0.8252 (ptp-170) cc_final: 0.7219 (ptp-170) REVERT: B 257 THR cc_start: 0.8045 (OUTLIER) cc_final: 0.7693 (m) REVERT: B 347 TRP cc_start: 0.7867 (m100) cc_final: 0.7445 (m-10) REVERT: B 378 GLU cc_start: 0.7417 (tp30) cc_final: 0.7122 (tp30) REVERT: C 257 THR cc_start: 0.8167 (OUTLIER) cc_final: 0.7909 (m) REVERT: C 378 GLU cc_start: 0.7551 (tp30) cc_final: 0.7163 (tp30) REVERT: D 121 LYS cc_start: 0.8913 (tttt) cc_final: 0.8711 (ttmt) REVERT: D 210 ARG cc_start: 0.8261 (ptp-170) cc_final: 0.7102 (ptp-170) REVERT: D 257 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7915 (m) REVERT: D 378 GLU cc_start: 0.7447 (tp30) cc_final: 0.7165 (tp30) REVERT: D 392 ARG cc_start: 0.8268 (mmm-85) cc_final: 0.7959 (mmm-85) outliers start: 64 outliers final: 20 residues processed: 347 average time/residue: 0.3793 time to fit residues: 148.1958 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 : 0.472 ------------------------------------------------------------------------------- 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 105 MET Chi-restraints excluded: chain A residue 127 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 148 LEU 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 148 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain C residue 75 ILE 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 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 321 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 83 optimal weight: 0.0060 chunk 114 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 152 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 GLN ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 HIS ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.178577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.146197 restraints weight = 18185.820| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.19 r_work: 0.3810 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13301 Z= 0.154 Angle : 0.689 11.662 18052 Z= 0.340 Chirality : 0.043 0.223 2104 Planarity : 0.006 0.058 2184 Dihedral : 5.693 32.306 1926 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.74 % Favored : 95.00 % Rotamer: Outliers : 4.44 % Allowed : 23.03 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.21), residues: 1560 helix: 0.89 (0.15), residues: 1188 sheet: None (None), residues: 0 loop : -2.59 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 392 TYR 0.017 0.001 TYR C 208 PHE 0.023 0.001 PHE A 224 TRP 0.033 0.002 TRP D 347 HIS 0.005 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00315 (13296) covalent geometry : angle 0.68417 (18040) hydrogen bonds : bond 0.05066 ( 946) hydrogen bonds : angle 5.17309 ( 2838) Misc. bond : bond 0.00061 ( 1) link_ALPHA1-2 : bond 0.00698 ( 4) link_ALPHA1-2 : angle 3.21285 ( 12) *********************** 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 377 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 314 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 THR cc_start: 0.8029 (OUTLIER) cc_final: 0.7714 (m) REVERT: A 339 LEU cc_start: 0.8299 (tm) cc_final: 0.7759 (mp) REVERT: A 374 ASP cc_start: 0.8108 (t0) cc_final: 0.7828 (t0) REVERT: B 115 MET cc_start: 0.6849 (OUTLIER) cc_final: 0.6442 (ptm) REVERT: B 210 ARG cc_start: 0.8290 (ptp-170) cc_final: 0.7528 (ptp-170) REVERT: B 257 THR cc_start: 0.8002 (OUTLIER) cc_final: 0.7632 (m) REVERT: B 347 TRP cc_start: 0.7915 (m100) cc_final: 0.7563 (m100) REVERT: C 257 THR cc_start: 0.8156 (OUTLIER) cc_final: 0.7872 (m) REVERT: C 374 ASP cc_start: 0.8256 (t0) cc_final: 0.7968 (t0) REVERT: D 121 LYS cc_start: 0.8920 (tttt) cc_final: 0.8719 (ttmt) REVERT: D 210 ARG cc_start: 0.8131 (ptp-170) cc_final: 0.7426 (ptp-170) REVERT: D 257 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7718 (m) REVERT: D 339 LEU cc_start: 0.8451 (tt) cc_final: 0.8091 (mt) REVERT: D 347 TRP cc_start: 0.7660 (m100) cc_final: 0.7103 (m-10) outliers start: 63 outliers final: 12 residues processed: 346 average time/residue: 0.3687 time to fit residues: 144.3492 Evaluate side-chains 291 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 274 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 105 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 130 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain C residue 75 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 115 MET Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 257 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 87 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 95 optimal weight: 0.0470 chunk 97 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.0080 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.177766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.145205 restraints weight = 18336.863| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.20 r_work: 0.3806 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13301 Z= 0.165 Angle : 0.716 12.134 18052 Z= 0.351 Chirality : 0.044 0.208 2104 Planarity : 0.006 0.055 2184 Dihedral : 5.481 34.010 1926 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.55 % Favored : 95.19 % Rotamer: Outliers : 4.44 % Allowed : 23.24 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.21), residues: 1560 helix: 1.05 (0.15), residues: 1188 sheet: None (None), residues: 0 loop : -2.58 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 392 TYR 0.015 0.001 TYR C 208 PHE 0.018 0.001 PHE B 68 TRP 0.019 0.002 TRP D 347 HIS 0.007 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00344 (13296) covalent geometry : angle 0.71206 (18040) hydrogen bonds : bond 0.05066 ( 946) hydrogen bonds : angle 5.08234 ( 2838) Misc. bond : bond 0.00062 ( 1) link_ALPHA1-2 : bond 0.00502 ( 4) link_ALPHA1-2 : angle 2.96657 ( 12) *********************** 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 360 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 297 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6932 (OUTLIER) cc_final: 0.6555 (ptm) REVERT: A 257 THR cc_start: 0.8049 (OUTLIER) cc_final: 0.7715 (m) REVERT: A 354 PHE cc_start: 0.7915 (t80) cc_final: 0.6975 (m-80) REVERT: B 115 MET cc_start: 0.6913 (OUTLIER) cc_final: 0.6521 (ptm) REVERT: B 210 ARG cc_start: 0.8282 (ptp-170) cc_final: 0.7191 (ptp-170) REVERT: B 257 THR cc_start: 0.8066 (OUTLIER) cc_final: 0.7702 (m) REVERT: B 347 TRP cc_start: 0.7893 (m100) cc_final: 0.7625 (m100) REVERT: B 374 ASP cc_start: 0.8213 (t0) cc_final: 0.7987 (t0) REVERT: C 257 THR cc_start: 0.8231 (OUTLIER) cc_final: 0.7933 (m) REVERT: C 374 ASP cc_start: 0.8270 (t0) cc_final: 0.8033 (t0) REVERT: D 90 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7461 (ptt90) REVERT: D 210 ARG cc_start: 0.8148 (ptp-170) cc_final: 0.7119 (ptp-170) REVERT: D 257 THR cc_start: 0.8106 (OUTLIER) cc_final: 0.7756 (m) REVERT: D 289 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7521 (tm-30) REVERT: D 339 LEU cc_start: 0.8507 (tt) cc_final: 0.8127 (mp) REVERT: D 347 TRP cc_start: 0.7774 (m100) cc_final: 0.7214 (m-10) outliers start: 63 outliers final: 13 residues processed: 332 average time/residue: 0.3550 time to fit residues: 133.9091 Evaluate side-chains 301 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 280 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 105 MET 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 130 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain C residue 75 ILE 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 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 289 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 100 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 0.0010 overall best weight: 0.6786 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.179024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.146598 restraints weight = 18164.803| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 2.21 r_work: 0.3819 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13301 Z= 0.154 Angle : 0.715 13.308 18052 Z= 0.348 Chirality : 0.044 0.208 2104 Planarity : 0.006 0.054 2184 Dihedral : 5.335 35.505 1924 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.38 % Favored : 94.49 % Rotamer: Outliers : 4.51 % Allowed : 23.59 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.21), residues: 1560 helix: 1.13 (0.15), residues: 1188 sheet: None (None), residues: 0 loop : -2.53 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 392 TYR 0.015 0.001 TYR C 208 PHE 0.027 0.001 PHE A 224 TRP 0.016 0.002 TRP B 152 HIS 0.009 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00320 (13296) covalent geometry : angle 0.71130 (18040) hydrogen bonds : bond 0.04846 ( 946) hydrogen bonds : angle 5.01494 ( 2838) Misc. bond : bond 0.00050 ( 1) link_ALPHA1-2 : bond 0.00421 ( 4) link_ALPHA1-2 : angle 2.88606 ( 12) *********************** 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 356 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 292 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6948 (OUTLIER) cc_final: 0.6632 (ptm) REVERT: A 210 ARG cc_start: 0.8276 (ptp-170) cc_final: 0.7387 (ptp-170) REVERT: A 257 THR cc_start: 0.8034 (OUTLIER) cc_final: 0.7712 (m) REVERT: A 289 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7677 (tm-30) REVERT: A 347 TRP cc_start: 0.7752 (m100) cc_final: 0.7489 (m-10) REVERT: A 354 PHE cc_start: 0.8111 (t80) cc_final: 0.6991 (m-80) REVERT: B 115 MET cc_start: 0.6960 (OUTLIER) cc_final: 0.6594 (ptm) REVERT: B 210 ARG cc_start: 0.8378 (ptp-170) cc_final: 0.7310 (ptp-170) REVERT: B 257 THR cc_start: 0.8027 (OUTLIER) cc_final: 0.7665 (m) REVERT: B 347 TRP cc_start: 0.7881 (m100) cc_final: 0.7589 (m100) REVERT: C 122 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8268 (pp) REVERT: C 257 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7871 (m) REVERT: C 374 ASP cc_start: 0.8152 (t0) cc_final: 0.7684 (t0) REVERT: D 210 ARG cc_start: 0.8131 (ptp-170) cc_final: 0.7228 (ptp-170) REVERT: D 257 THR cc_start: 0.8071 (OUTLIER) cc_final: 0.7730 (m) REVERT: D 339 LEU cc_start: 0.8539 (tt) cc_final: 0.8231 (mp) REVERT: D 347 TRP cc_start: 0.7780 (m100) cc_final: 0.7312 (m-10) REVERT: D 374 ASP cc_start: 0.8120 (t0) cc_final: 0.7821 (t0) outliers start: 64 outliers final: 19 residues processed: 328 average time/residue: 0.3579 time to fit residues: 133.8898 Evaluate side-chains 306 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 279 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 105 MET 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 289 GLU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 148 LEU 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 122 ILE 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 42 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 59 optimal weight: 0.1980 chunk 55 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 253 ASN B 253 ASN C 253 ASN D 253 ASN ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.177475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.144968 restraints weight = 18218.021| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.20 r_work: 0.3797 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 13301 Z= 0.172 Angle : 0.757 14.971 18052 Z= 0.365 Chirality : 0.045 0.212 2104 Planarity : 0.006 0.056 2184 Dihedral : 5.360 37.187 1924 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.15 % Allowed : 23.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.21), residues: 1560 helix: 1.17 (0.15), residues: 1188 sheet: None (None), residues: 0 loop : -2.48 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 392 TYR 0.012 0.001 TYR A 208 PHE 0.017 0.001 PHE A 116 TRP 0.023 0.002 TRP A 152 HIS 0.010 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00372 (13296) covalent geometry : angle 0.75409 (18040) hydrogen bonds : bond 0.05008 ( 946) hydrogen bonds : angle 5.03018 ( 2838) Misc. bond : bond 0.00053 ( 1) link_ALPHA1-2 : bond 0.00337 ( 4) link_ALPHA1-2 : angle 2.75906 ( 12) *********************** 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 351 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 292 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6864 (OUTLIER) cc_final: 0.6522 (ptm) REVERT: A 210 ARG cc_start: 0.8312 (ptp-170) cc_final: 0.7415 (ptp-170) REVERT: A 257 THR cc_start: 0.8093 (OUTLIER) cc_final: 0.7750 (m) REVERT: A 289 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7740 (tm-30) REVERT: A 347 TRP cc_start: 0.7768 (m100) cc_final: 0.7519 (m-10) REVERT: A 354 PHE cc_start: 0.8226 (t80) cc_final: 0.6917 (m-80) REVERT: B 115 MET cc_start: 0.6949 (OUTLIER) cc_final: 0.6711 (ptm) REVERT: B 210 ARG cc_start: 0.8347 (ptp-170) cc_final: 0.7389 (ptp-170) REVERT: B 257 THR cc_start: 0.8087 (OUTLIER) cc_final: 0.7725 (m) REVERT: B 347 TRP cc_start: 0.7925 (m100) cc_final: 0.7630 (m100) REVERT: B 374 ASP cc_start: 0.8176 (t0) cc_final: 0.7824 (t0) REVERT: C 152 TRP cc_start: 0.7156 (t-100) cc_final: 0.6687 (t-100) REVERT: C 257 THR cc_start: 0.8173 (OUTLIER) cc_final: 0.7878 (m) REVERT: C 374 ASP cc_start: 0.8169 (t0) cc_final: 0.7813 (t0) REVERT: D 152 TRP cc_start: 0.7177 (t-100) cc_final: 0.6943 (t-100) REVERT: D 210 ARG cc_start: 0.8156 (ptp-170) cc_final: 0.7200 (ptp-170) REVERT: D 257 THR cc_start: 0.8118 (OUTLIER) cc_final: 0.7798 (m) REVERT: D 289 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7523 (tm-30) REVERT: D 347 TRP cc_start: 0.7776 (m100) cc_final: 0.7289 (m-10) outliers start: 59 outliers final: 23 residues processed: 325 average time/residue: 0.3728 time to fit residues: 137.0884 Evaluate side-chains 309 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 278 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 122 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 289 GLU 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 148 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 253 ASN Chi-restraints excluded: chain B residue 257 THR 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 253 ASN 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 106 optimal weight: 0.9990 chunk 143 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 253 ASN B 253 ASN C 253 ASN D 253 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.177949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.145439 restraints weight = 18003.582| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.19 r_work: 0.3807 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13301 Z= 0.165 Angle : 0.772 14.229 18052 Z= 0.372 Chirality : 0.045 0.260 2104 Planarity : 0.006 0.055 2184 Dihedral : 5.346 36.984 1924 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.66 % Allowed : 25.63 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.21), residues: 1560 helix: 1.15 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -2.37 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 392 TYR 0.019 0.002 TYR A 336 PHE 0.029 0.001 PHE B 224 TRP 0.081 0.003 TRP A 152 HIS 0.011 0.002 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00349 (13296) covalent geometry : angle 0.76848 (18040) hydrogen bonds : bond 0.04892 ( 946) hydrogen bonds : angle 5.01486 ( 2838) Misc. bond : bond 0.00049 ( 1) link_ALPHA1-2 : bond 0.00391 ( 4) link_ALPHA1-2 : angle 2.79081 ( 12) *********************** 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 337 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 285 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6884 (OUTLIER) cc_final: 0.6547 (ptm) REVERT: A 122 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8320 (pp) REVERT: A 210 ARG cc_start: 0.8400 (ptp-170) cc_final: 0.7301 (ptp-170) REVERT: A 253 ASN cc_start: 0.7485 (OUTLIER) cc_final: 0.7268 (m110) REVERT: A 257 THR cc_start: 0.8138 (OUTLIER) cc_final: 0.7785 (m) REVERT: A 289 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7693 (tm-30) REVERT: A 347 TRP cc_start: 0.7751 (m100) cc_final: 0.7475 (m-10) REVERT: A 374 ASP cc_start: 0.8150 (t0) cc_final: 0.7899 (t0) REVERT: B 210 ARG cc_start: 0.8250 (ptp-170) cc_final: 0.7282 (ptp-170) REVERT: B 257 THR cc_start: 0.8107 (OUTLIER) cc_final: 0.7740 (m) REVERT: B 289 GLU cc_start: 0.7948 (tp30) cc_final: 0.7569 (tm-30) REVERT: B 347 TRP cc_start: 0.7897 (m100) cc_final: 0.7603 (m100) REVERT: B 374 ASP cc_start: 0.8164 (t0) cc_final: 0.7874 (t0) REVERT: C 152 TRP cc_start: 0.7113 (t-100) cc_final: 0.6752 (t-100) REVERT: C 257 THR cc_start: 0.8160 (OUTLIER) cc_final: 0.7866 (m) REVERT: C 374 ASP cc_start: 0.8150 (t0) cc_final: 0.7819 (t0) REVERT: D 210 ARG cc_start: 0.8202 (ptp-170) cc_final: 0.7220 (ptp-170) REVERT: D 257 THR cc_start: 0.8114 (OUTLIER) cc_final: 0.7796 (m) REVERT: D 289 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7519 (tm-30) REVERT: D 347 TRP cc_start: 0.7741 (m100) cc_final: 0.7316 (m-10) outliers start: 52 outliers final: 20 residues processed: 316 average time/residue: 0.3464 time to fit residues: 125.2835 Evaluate side-chains 303 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 274 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 122 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 148 LEU 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 148 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 130 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 94 optimal weight: 10.0000 chunk 115 optimal weight: 0.8980 chunk 145 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 chunk 151 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN C 253 ASN ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.178549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.145916 restraints weight = 18185.554| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 2.20 r_work: 0.3812 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13301 Z= 0.165 Angle : 0.793 15.379 18052 Z= 0.382 Chirality : 0.046 0.261 2104 Planarity : 0.006 0.054 2184 Dihedral : 5.348 36.538 1924 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.45 % Allowed : 26.62 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.21), residues: 1560 helix: 1.18 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -2.32 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 392 TYR 0.014 0.001 TYR A 232 PHE 0.027 0.001 PHE A 354 TRP 0.072 0.003 TRP A 152 HIS 0.012 0.002 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00356 (13296) covalent geometry : angle 0.78973 (18040) hydrogen bonds : bond 0.04837 ( 946) hydrogen bonds : angle 4.98083 ( 2838) Misc. bond : bond 0.00049 ( 1) link_ALPHA1-2 : bond 0.00230 ( 4) link_ALPHA1-2 : angle 2.68696 ( 12) *********************** 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 335 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 286 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6906 (OUTLIER) cc_final: 0.6534 (ptm) REVERT: A 122 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8336 (pp) REVERT: A 257 THR cc_start: 0.8133 (OUTLIER) cc_final: 0.7795 (m) REVERT: A 289 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7638 (tm-30) REVERT: A 354 PHE cc_start: 0.8017 (t80) cc_final: 0.6939 (m-80) REVERT: B 210 ARG cc_start: 0.8261 (ptp-170) cc_final: 0.7258 (ptp-170) REVERT: B 257 THR cc_start: 0.8108 (OUTLIER) cc_final: 0.7775 (m) REVERT: B 347 TRP cc_start: 0.7837 (m100) cc_final: 0.7571 (m100) REVERT: B 374 ASP cc_start: 0.8229 (t0) cc_final: 0.7992 (t0) REVERT: C 152 TRP cc_start: 0.7176 (t-100) cc_final: 0.6782 (t-100) REVERT: C 257 THR cc_start: 0.8131 (OUTLIER) cc_final: 0.7833 (m) REVERT: C 374 ASP cc_start: 0.8168 (t0) cc_final: 0.7847 (t0) REVERT: D 210 ARG cc_start: 0.8211 (ptp-170) cc_final: 0.7266 (ptp-170) REVERT: D 257 THR cc_start: 0.8078 (OUTLIER) cc_final: 0.7776 (m) REVERT: D 289 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7532 (tm-30) REVERT: D 347 TRP cc_start: 0.7764 (m100) cc_final: 0.7343 (m-10) REVERT: D 374 ASP cc_start: 0.8171 (t0) cc_final: 0.7725 (t0) REVERT: D 378 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7819 (mm-30) outliers start: 49 outliers final: 18 residues processed: 314 average time/residue: 0.3608 time to fit residues: 128.8276 Evaluate side-chains 304 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 278 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 122 ILE 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 289 GLU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 124 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 124 ILE 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 253 ASN Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 341 VAL 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 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 80 optimal weight: 0.0040 chunk 72 optimal weight: 0.0370 chunk 38 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 57 optimal weight: 0.0870 chunk 85 optimal weight: 1.9990 chunk 67 optimal weight: 0.0060 chunk 108 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 ASN ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 ASN D 253 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.182502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.150164 restraints weight = 18261.048| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 2.23 r_work: 0.3865 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13301 Z= 0.153 Angle : 0.793 15.058 18052 Z= 0.383 Chirality : 0.045 0.268 2104 Planarity : 0.006 0.052 2184 Dihedral : 5.320 34.411 1924 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.39 % Allowed : 27.54 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.21), residues: 1560 helix: 1.21 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -2.38 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 392 TYR 0.036 0.001 TYR C 232 PHE 0.032 0.001 PHE B 224 TRP 0.069 0.003 TRP A 152 HIS 0.012 0.002 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00323 (13296) covalent geometry : angle 0.79092 (18040) hydrogen bonds : bond 0.04553 ( 946) hydrogen bonds : angle 4.93002 ( 2838) Misc. bond : bond 0.00049 ( 1) link_ALPHA1-2 : bond 0.00185 ( 4) link_ALPHA1-2 : angle 2.59127 ( 12) ********************** 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 327 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 293 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.6902 (OUTLIER) cc_final: 0.6530 (ptm) REVERT: A 122 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8376 (pp) REVERT: A 161 ARG cc_start: 0.7818 (ttp-110) cc_final: 0.7253 (ttm110) REVERT: A 210 ARG cc_start: 0.8561 (ptp-170) cc_final: 0.7198 (ptp-170) REVERT: A 257 THR cc_start: 0.7967 (OUTLIER) cc_final: 0.7691 (m) REVERT: B 163 GLU cc_start: 0.7174 (pt0) cc_final: 0.6923 (mp0) REVERT: B 184 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7129 (mm) REVERT: B 210 ARG cc_start: 0.8209 (ptp-170) cc_final: 0.7201 (ptp-170) REVERT: B 257 THR cc_start: 0.8035 (OUTLIER) cc_final: 0.7723 (m) REVERT: B 347 TRP cc_start: 0.7792 (m100) cc_final: 0.7566 (m100) REVERT: B 374 ASP cc_start: 0.8120 (t0) cc_final: 0.7910 (t0) REVERT: C 152 TRP cc_start: 0.7000 (t-100) cc_final: 0.6712 (t-100) REVERT: C 251 LEU cc_start: 0.8176 (mm) cc_final: 0.7871 (tm) REVERT: C 257 THR cc_start: 0.8001 (OUTLIER) cc_final: 0.7705 (m) REVERT: C 360 TYR cc_start: 0.7350 (t80) cc_final: 0.6692 (t80) REVERT: C 374 ASP cc_start: 0.8148 (t0) cc_final: 0.7852 (t0) REVERT: D 210 ARG cc_start: 0.8206 (ptp-170) cc_final: 0.7278 (ptp-170) REVERT: D 257 THR cc_start: 0.8030 (OUTLIER) cc_final: 0.7745 (m) REVERT: D 289 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7518 (tm-30) REVERT: D 347 TRP cc_start: 0.7724 (m100) cc_final: 0.7367 (m-10) outliers start: 34 outliers final: 18 residues processed: 313 average time/residue: 0.3713 time to fit residues: 132.0721 Evaluate side-chains 298 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 272 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 122 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain B residue 75 ILE 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 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 253 ASN Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 250 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 46 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 ASN ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 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 = 0.4327 r_free = 0.4327 target = 0.178456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.145467 restraints weight = 17973.676| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.19 r_work: 0.3804 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.3486 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= 0.202 Angle : 0.838 14.171 18052 Z= 0.408 Chirality : 0.049 0.284 2104 Planarity : 0.006 0.056 2184 Dihedral : 5.326 34.720 1924 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.82 % Allowed : 27.96 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.21), residues: 1560 helix: 1.14 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -2.42 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 392 TYR 0.020 0.002 TYR A 336 PHE 0.039 0.002 PHE A 354 TRP 0.079 0.005 TRP A 152 HIS 0.012 0.002 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00449 (13296) covalent geometry : angle 0.83589 (18040) hydrogen bonds : bond 0.05009 ( 946) hydrogen bonds : angle 5.00918 ( 2838) Misc. bond : bond 0.00070 ( 1) link_ALPHA1-2 : bond 0.00253 ( 4) link_ALPHA1-2 : angle 2.45249 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4925.03 seconds wall clock time: 84 minutes 51.96 seconds (5091.96 seconds total)