Starting phenix.real_space_refine on Mon Dec 30 09:37:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ze2_60021/12_2024/8ze2_60021_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ze2_60021/12_2024/8ze2_60021.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ze2_60021/12_2024/8ze2_60021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ze2_60021/12_2024/8ze2_60021.map" model { file = "/net/cci-nas-00/data/ceres_data/8ze2_60021/12_2024/8ze2_60021_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ze2_60021/12_2024/8ze2_60021_trim.cif" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.083 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 8576 2.51 5 N 2124 2.21 5 O 2180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12972 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3220 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 14, 'TRANS': 377} Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 1, 'Z9N': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, B, D, G, F, H Time building chain proxies: 6.63, per 1000 atoms: 0.51 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: 4.00 Conformation dependent library (CDL) restraints added in 1.9 seconds 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3024 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 0 sheets defined 79.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 58 through 73 Proline residue: A 65 - end of helix removed outlier: 3.899A pdb=" N LEU A 69 " --> pdb=" O PRO A 65 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 123 Processing helix chain 'A' and resid 128 through 164 removed outlier: 4.052A pdb=" N LEU A 132 " --> pdb=" O ASN A 128 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A 151 " --> pdb=" O ARG A 147 " (cutoff:3.500A) Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 165 through 168 removed outlier: 3.638A pdb=" N LYS A 168 " --> pdb=" O PRO A 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 165 through 168' Processing helix chain 'A' and resid 177 through 213 removed outlier: 3.736A pdb=" N ALA A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 242 through 288 removed outlier: 4.294A pdb=" N ASP A 264 " --> pdb=" O TRP A 260 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 288 " --> pdb=" O ARG A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 340 removed outlier: 5.345A pdb=" N SER A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LEU A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 388 removed outlier: 3.612A pdb=" N ILE A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 394 removed outlier: 3.651A pdb=" N SER A 393 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TRP A 394 " --> pdb=" O SER A 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 390 through 394' Processing helix chain 'A' and resid 396 through 408 Processing helix chain 'A' and resid 421 through 443 removed outlier: 4.342A pdb=" N GLN A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 73 Proline residue: B 65 - end of helix removed outlier: 3.899A pdb=" N LEU B 69 " --> pdb=" O PRO B 65 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 123 Processing helix chain 'B' and resid 128 through 164 removed outlier: 4.053A pdb=" N LEU B 132 " --> pdb=" O ASN B 128 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS B 151 " --> pdb=" O ARG B 147 " (cutoff:3.500A) Proline residue: B 153 - end of helix Processing helix chain 'B' and resid 165 through 168 removed outlier: 3.638A pdb=" N LYS B 168 " --> pdb=" O PRO B 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 165 through 168' Processing helix chain 'B' and resid 177 through 213 removed outlier: 3.736A pdb=" N ALA B 185 " --> pdb=" O ARG B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 242 through 288 removed outlier: 4.295A pdb=" N ASP B 264 " --> pdb=" O TRP B 260 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG B 277 " --> pdb=" O GLY B 273 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 288 " --> pdb=" O ARG B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 319 Processing helix chain 'B' and resid 319 through 340 Processing helix chain 'B' and resid 347 through 388 removed outlier: 3.612A pdb=" N ILE B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY B 384 " --> pdb=" O LYS B 380 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL B 385 " --> pdb=" O ARG B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 394 removed outlier: 3.650A pdb=" N SER B 393 " --> pdb=" O SER B 390 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TRP B 394 " --> pdb=" O SER B 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 390 through 394' Processing helix chain 'B' and resid 396 through 408 Processing helix chain 'B' and resid 421 through 443 removed outlier: 4.342A pdb=" N GLN B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 73 Proline residue: C 65 - end of helix removed outlier: 3.898A pdb=" N LEU C 69 " --> pdb=" O PRO C 65 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 123 Processing helix chain 'C' and resid 128 through 164 removed outlier: 4.053A pdb=" N LEU C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS C 151 " --> pdb=" O ARG C 147 " (cutoff:3.500A) Proline residue: C 153 - end of helix Processing helix chain 'C' and resid 165 through 168 removed outlier: 3.638A pdb=" N LYS C 168 " --> pdb=" O PRO C 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 165 through 168' Processing helix chain 'C' and resid 177 through 213 removed outlier: 3.736A pdb=" N ALA C 185 " --> pdb=" O ARG C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 242 through 288 removed outlier: 4.295A pdb=" N ASP C 264 " --> pdb=" O TRP C 260 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG C 277 " --> pdb=" O GLY C 273 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU C 288 " --> pdb=" O ARG C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 340 removed outlier: 5.344A pdb=" N SER C 321 " --> pdb=" O SER C 317 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LEU C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 388 removed outlier: 3.613A pdb=" N ILE C 375 " --> pdb=" O THR C 371 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY C 384 " --> pdb=" O LYS C 380 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL C 385 " --> pdb=" O ARG C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 394 removed outlier: 3.650A pdb=" N SER C 393 " --> pdb=" O SER C 390 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N TRP C 394 " --> pdb=" O SER C 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 390 through 394' Processing helix chain 'C' and resid 396 through 408 Processing helix chain 'C' and resid 421 through 443 removed outlier: 4.342A pdb=" N GLN C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 73 Proline residue: D 65 - end of helix removed outlier: 3.899A pdb=" N LEU D 69 " --> pdb=" O PRO D 65 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 123 Processing helix chain 'D' and resid 128 through 164 removed outlier: 4.053A pdb=" N LEU D 132 " --> pdb=" O ASN D 128 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS D 151 " --> pdb=" O ARG D 147 " (cutoff:3.500A) Proline residue: D 153 - end of helix Processing helix chain 'D' and resid 165 through 168 removed outlier: 3.637A pdb=" N LYS D 168 " --> pdb=" O PRO D 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 165 through 168' Processing helix chain 'D' and resid 177 through 213 removed outlier: 3.736A pdb=" N ALA D 185 " --> pdb=" O ARG D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 242 through 288 removed outlier: 4.294A pdb=" N ASP D 264 " --> pdb=" O TRP D 260 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG D 277 " --> pdb=" O GLY D 273 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D 288 " --> pdb=" O ARG D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 319 Processing helix chain 'D' and resid 319 through 340 Processing helix chain 'D' and resid 347 through 388 removed outlier: 3.612A pdb=" N ILE D 375 " --> pdb=" O THR D 371 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN D 376 " --> pdb=" O ALA D 372 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU D 383 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL D 385 " --> pdb=" O ARG D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 394 removed outlier: 3.651A pdb=" N SER D 393 " --> pdb=" O SER D 390 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TRP D 394 " --> pdb=" O SER D 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 390 through 394' Processing helix chain 'D' and resid 396 through 408 Processing helix chain 'D' and resid 421 through 443 removed outlier: 4.341A pdb=" N GLN D 441 " --> pdb=" O LEU D 437 " (cutoff:3.500A) 946 hydrogen bonds defined for protein. 2838 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.47 Time building geometry restraints manager: 4.04 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: 0.00 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: 0.620 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: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 28.730 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:16.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.810 ------------------------------------------------------------------------------- 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 : 0.008 0.224 13296 Z= 0.457 Angle : 0.838 9.602 18040 Z= 0.423 Chirality : 0.048 0.275 2104 Planarity : 0.008 0.119 2184 Dihedral : 17.746 83.059 4972 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 21.00 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.58 % Favored : 94.17 % Rotamer: Outliers : 0.56 % Allowed : 24.23 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.20), residues: 1560 helix: -0.27 (0.14), residues: 1172 sheet: None (None), residues: 0 loop : -2.39 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 347 HIS 0.002 0.001 HIS A 197 PHE 0.028 0.002 PHE C 224 TYR 0.020 0.002 TYR A 356 ARG 0.007 0.001 ARG D 388 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 354 time to evaluate : 1.514 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: 0.9893 time to fit residues: 395.0987 Evaluate side-chains 298 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 291 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 354 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 chunk 79 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 340 ASN A 441 GLN B 261 ASN B 441 GLN C 441 GLN D 118 HIS D 300 GLN D 340 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13296 Z= 0.229 Angle : 0.702 8.940 18040 Z= 0.353 Chirality : 0.045 0.228 2104 Planarity : 0.007 0.080 2184 Dihedral : 7.800 59.916 1938 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.36 % Favored : 95.38 % Rotamer: Outliers : 4.37 % Allowed : 22.54 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.20), residues: 1560 helix: 0.37 (0.14), residues: 1184 sheet: None (None), residues: 0 loop : -2.51 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 347 HIS 0.006 0.001 HIS D 197 PHE 0.024 0.002 PHE A 68 TYR 0.017 0.002 TYR B 356 ARG 0.008 0.001 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 324 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 210 ARG cc_start: 0.8343 (ptp-170) cc_final: 0.7424 (ptp-170) REVERT: B 247 VAL cc_start: 0.8399 (t) cc_final: 0.8185 (m) REVERT: B 347 TRP cc_start: 0.7495 (m100) cc_final: 0.6982 (m-10) REVERT: D 210 ARG cc_start: 0.8406 (ptp-170) cc_final: 0.7292 (ptp-170) outliers start: 62 outliers final: 19 residues processed: 353 average time/residue: 0.9221 time to fit residues: 367.8997 Evaluate side-chains 290 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 271 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 208 TYR Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 90 ARG Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 130 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 117 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 141 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 13296 Z= 0.308 Angle : 0.725 10.649 18040 Z= 0.368 Chirality : 0.046 0.221 2104 Planarity : 0.007 0.065 2184 Dihedral : 6.400 32.454 1928 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.85 % Favored : 95.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.21), residues: 1560 helix: 0.56 (0.14), residues: 1220 sheet: None (None), residues: 0 loop : -2.73 (0.29), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 347 HIS 0.002 0.001 HIS A 60 PHE 0.017 0.002 PHE A 64 TYR 0.017 0.002 TYR C 336 ARG 0.009 0.001 ARG C 388 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 312 time to evaluate : 1.494 Fit side-chains revert: symmetry clash REVERT: B 210 ARG cc_start: 0.8436 (ptp-170) cc_final: 0.7551 (ptp-170) REVERT: B 369 PHE cc_start: 0.6690 (m-10) cc_final: 0.6368 (m-80) REVERT: D 67 MET cc_start: 0.8264 (mtp) cc_final: 0.7953 (mtt) REVERT: D 210 ARG cc_start: 0.8489 (ptp-170) cc_final: 0.7457 (ptp-170) REVERT: D 346 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6932 (tpp80) REVERT: D 347 TRP cc_start: 0.7423 (m100) cc_final: 0.6839 (m-10) outliers start: 67 outliers final: 24 residues processed: 347 average time/residue: 0.8649 time to fit residues: 339.4667 Evaluate side-chains 299 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 274 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 122 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 C residue 75 ILE Chi-restraints excluded: chain C residue 90 ARG 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 184 LEU Chi-restraints excluded: chain D residue 75 ILE 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 250 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 346 ARG Chi-restraints excluded: chain D residue 398 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 142 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 GLN D 118 HIS D 201 GLN D 441 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13296 Z= 0.292 Angle : 0.729 11.450 18040 Z= 0.363 Chirality : 0.045 0.195 2104 Planarity : 0.006 0.058 2184 Dihedral : 6.019 32.932 1926 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.49 % Favored : 95.26 % Rotamer: Outliers : 4.51 % Allowed : 23.03 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.21), residues: 1560 helix: 0.70 (0.15), residues: 1212 sheet: None (None), residues: 0 loop : -2.77 (0.29), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 347 HIS 0.003 0.001 HIS C 118 PHE 0.024 0.002 PHE A 224 TYR 0.016 0.002 TYR C 208 ARG 0.010 0.001 ARG A 210 *********************** 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 373 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 309 time to evaluate : 1.386 Fit side-chains revert: symmetry clash REVERT: A 210 ARG cc_start: 0.8355 (ptp-170) cc_final: 0.7418 (ptp-170) REVERT: B 115 MET cc_start: 0.6126 (OUTLIER) cc_final: 0.5885 (ptm) REVERT: B 210 ARG cc_start: 0.8290 (ptp-170) cc_final: 0.7301 (ptp-170) REVERT: B 347 TRP cc_start: 0.7542 (m100) cc_final: 0.6797 (m-10) REVERT: D 210 ARG cc_start: 0.8473 (ptp-170) cc_final: 0.7326 (ptp-170) REVERT: D 346 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.7007 (tpp80) REVERT: D 347 TRP cc_start: 0.7473 (m100) cc_final: 0.7084 (m-10) outliers start: 64 outliers final: 22 residues processed: 346 average time/residue: 0.8633 time to fit residues: 338.0270 Evaluate side-chains 309 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 285 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 398 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 398 VAL 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 398 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 90 ARG Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 346 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 62 optimal weight: 0.0970 chunk 128 optimal weight: 0.0040 chunk 104 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 135 optimal weight: 20.0000 chunk 38 optimal weight: 4.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN B 329 ASN ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 GLN D 329 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 13296 Z= 0.203 Angle : 0.708 12.407 18040 Z= 0.346 Chirality : 0.043 0.206 2104 Planarity : 0.006 0.054 2184 Dihedral : 5.506 33.362 1924 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.00 % Favored : 94.74 % Rotamer: Outliers : 4.01 % Allowed : 24.15 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.21), residues: 1560 helix: 0.94 (0.15), residues: 1188 sheet: None (None), residues: 0 loop : -2.62 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 347 HIS 0.006 0.001 HIS C 118 PHE 0.017 0.001 PHE B 354 TYR 0.015 0.001 TYR B 208 ARG 0.009 0.000 ARG B 392 *********************** 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 378 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 321 time to evaluate : 1.584 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.6033 (OUTLIER) cc_final: 0.5821 (ptm) REVERT: B 210 ARG cc_start: 0.8363 (ptp-170) cc_final: 0.7260 (ptp-170) REVERT: B 347 TRP cc_start: 0.7381 (m100) cc_final: 0.6862 (m-10) REVERT: B 369 PHE cc_start: 0.6679 (m-10) cc_final: 0.6246 (m-80) REVERT: C 332 TYR cc_start: 0.7484 (t80) cc_final: 0.7256 (t80) REVERT: D 67 MET cc_start: 0.8226 (mtp) cc_final: 0.7926 (mtt) REVERT: D 210 ARG cc_start: 0.8454 (ptp-170) cc_final: 0.7248 (ptp-170) outliers start: 57 outliers final: 12 residues processed: 350 average time/residue: 0.8689 time to fit residues: 343.5564 Evaluate side-chains 296 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 283 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 130 VAL 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 268 MET Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 148 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.5980 chunk 135 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 150 optimal weight: 4.9990 chunk 125 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 79 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 201 GLN A 253 ASN B 253 ASN B 350 ASN ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 ASN C 329 ASN C 350 ASN D 201 GLN D 253 ASN D 350 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13296 Z= 0.215 Angle : 0.735 13.641 18040 Z= 0.357 Chirality : 0.045 0.209 2104 Planarity : 0.006 0.056 2184 Dihedral : 5.312 35.956 1924 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.13 % Favored : 94.68 % Rotamer: Outliers : 4.37 % Allowed : 23.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.21), residues: 1560 helix: 1.05 (0.15), residues: 1188 sheet: None (None), residues: 0 loop : -2.54 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 347 HIS 0.009 0.001 HIS C 118 PHE 0.028 0.001 PHE A 224 TYR 0.016 0.001 TYR B 336 ARG 0.010 0.001 ARG D 210 *********************** 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 358 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 296 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6064 (OUTLIER) cc_final: 0.5814 (ptm) REVERT: B 210 ARG cc_start: 0.8400 (ptp-170) cc_final: 0.7227 (ptp-170) REVERT: B 347 TRP cc_start: 0.7355 (m100) cc_final: 0.6979 (m-10) REVERT: D 210 ARG cc_start: 0.8353 (ptp-170) cc_final: 0.7975 (ptp-170) REVERT: D 346 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.7083 (tpp80) REVERT: D 347 TRP cc_start: 0.7185 (m100) cc_final: 0.6896 (m-10) outliers start: 62 outliers final: 20 residues processed: 339 average time/residue: 0.8258 time to fit residues: 318.2583 Evaluate side-chains 305 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 283 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 253 ASN 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 253 ASN 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 253 ASN Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 346 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 chunk 150 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 93 optimal weight: 10.0000 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN B 253 ASN C 253 ASN ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 13296 Z= 0.228 Angle : 0.759 16.201 18040 Z= 0.363 Chirality : 0.044 0.208 2104 Planarity : 0.006 0.055 2184 Dihedral : 5.267 36.011 1924 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.87 % Allowed : 24.01 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.21), residues: 1560 helix: 1.13 (0.15), residues: 1188 sheet: None (None), residues: 0 loop : -2.49 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 347 HIS 0.011 0.001 HIS C 118 PHE 0.029 0.001 PHE B 354 TYR 0.021 0.001 TYR A 336 ARG 0.006 0.000 ARG C 392 *********************** 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 348 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 293 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6024 (OUTLIER) cc_final: 0.5764 (ptm) REVERT: B 115 MET cc_start: 0.5989 (OUTLIER) cc_final: 0.5683 (ptm) REVERT: B 210 ARG cc_start: 0.8463 (ptp-170) cc_final: 0.7377 (ptp-170) REVERT: B 347 TRP cc_start: 0.7343 (m100) cc_final: 0.6983 (m-10) REVERT: D 346 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.7078 (tpt170) outliers start: 55 outliers final: 25 residues processed: 323 average time/residue: 0.8187 time to fit residues: 300.9899 Evaluate side-chains 305 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 277 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 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 148 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 115 MET 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 268 MET Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 268 MET Chi-restraints excluded: chain D residue 346 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 136 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN B 253 ASN ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 ASN ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 13296 Z= 0.401 Angle : 0.875 18.206 18040 Z= 0.426 Chirality : 0.050 0.222 2104 Planarity : 0.007 0.060 2184 Dihedral : 5.774 42.306 1924 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.68 % Favored : 95.26 % Rotamer: Outliers : 4.30 % Allowed : 23.31 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.21), residues: 1560 helix: 0.91 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -2.25 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP B 152 HIS 0.011 0.002 HIS C 118 PHE 0.033 0.002 PHE B 224 TYR 0.018 0.002 TYR C 208 ARG 0.012 0.001 ARG C 392 *********************** 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 361 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 300 time to evaluate : 1.328 Fit side-chains revert: symmetry clash REVERT: B 210 ARG cc_start: 0.8518 (ptp-170) cc_final: 0.7206 (ptp-170) REVERT: B 347 TRP cc_start: 0.7491 (m100) cc_final: 0.7045 (m100) outliers start: 61 outliers final: 26 residues processed: 337 average time/residue: 0.7624 time to fit residues: 295.4077 Evaluate side-chains 309 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 283 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 268 MET Chi-restraints excluded: chain A residue 398 VAL 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 253 ASN Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 253 ASN Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 398 VAL 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 206 LEU Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 268 MET 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 131 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 144 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 253 ASN ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13296 Z= 0.280 Angle : 0.853 17.638 18040 Z= 0.414 Chirality : 0.049 0.293 2104 Planarity : 0.006 0.056 2184 Dihedral : 5.669 36.349 1924 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.17 % Allowed : 25.21 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.21), residues: 1560 helix: 0.89 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -2.23 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.100 0.005 TRP A 152 HIS 0.012 0.002 HIS C 118 PHE 0.035 0.002 PHE B 354 TYR 0.018 0.002 TYR C 208 ARG 0.008 0.000 ARG C 392 *********************** 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 344 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 299 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 374 ASP cc_start: 0.7217 (t0) cc_final: 0.6966 (t0) REVERT: B 210 ARG cc_start: 0.8458 (ptp-170) cc_final: 0.7180 (ptp-170) REVERT: B 347 TRP cc_start: 0.7484 (m100) cc_final: 0.7227 (m100) REVERT: B 374 ASP cc_start: 0.7203 (t0) cc_final: 0.6838 (t0) REVERT: C 69 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7402 (tp) REVERT: D 374 ASP cc_start: 0.7212 (t0) cc_final: 0.6830 (t0) outliers start: 45 outliers final: 24 residues processed: 323 average time/residue: 0.7895 time to fit residues: 291.4118 Evaluate side-chains 312 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 287 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 268 MET Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 253 ASN Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 69 LEU 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 253 ASN Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain D residue 75 ILE 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 206 LEU Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 268 MET 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 148 optimal weight: 0.9980 chunk 90 optimal weight: 0.0050 chunk 70 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 123 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.7194 ------------------------------------------------------------------------------- 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 253 ASN ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13296 Z= 0.243 Angle : 0.851 18.436 18040 Z= 0.411 Chirality : 0.048 0.298 2104 Planarity : 0.006 0.053 2184 Dihedral : 5.480 32.118 1924 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.61 % Allowed : 26.48 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.21), residues: 1560 helix: 0.89 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -2.19 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.005 TRP C 152 HIS 0.012 0.002 HIS C 118 PHE 0.038 0.001 PHE B 354 TYR 0.024 0.002 TYR A 232 ARG 0.007 0.000 ARG B 392 ********************** 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 323 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 286 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 ASP cc_start: 0.7048 (t0) cc_final: 0.6819 (t0) REVERT: B 210 ARG cc_start: 0.8429 (ptp-170) cc_final: 0.7311 (ptp-170) REVERT: B 347 TRP cc_start: 0.7405 (m100) cc_final: 0.7168 (m100) REVERT: C 69 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7327 (tp) REVERT: C 210 ARG cc_start: 0.8324 (ptp-170) cc_final: 0.7458 (ptp-170) outliers start: 37 outliers final: 22 residues processed: 307 average time/residue: 0.7831 time to fit residues: 274.4711 Evaluate side-chains 298 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 275 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 268 MET Chi-restraints excluded: chain A residue 398 VAL 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 253 ASN Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 69 LEU 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 253 ASN Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 321 SER 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 206 LEU 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 131 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 18 optimal weight: 20.0000 chunk 34 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 ASN ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 ASN ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.173663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.139906 restraints weight = 18020.690| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.19 r_work: 0.3732 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 13296 Z= 0.334 Angle : 0.895 19.863 18040 Z= 0.435 Chirality : 0.051 0.304 2104 Planarity : 0.006 0.052 2184 Dihedral : 5.541 31.792 1924 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.54 % Allowed : 26.83 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.21), residues: 1560 helix: 0.84 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -2.21 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.092 0.006 TRP C 152 HIS 0.013 0.002 HIS C 118 PHE 0.034 0.002 PHE B 354 TYR 0.024 0.002 TYR A 336 ARG 0.007 0.001 ARG C 392 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5126.79 seconds wall clock time: 93 minutes 25.66 seconds (5605.66 seconds total)