Starting phenix.real_space_refine on Sun May 3 04:01:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nyk_49935/05_2026/9nyk_49935.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nyk_49935/05_2026/9nyk_49935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nyk_49935/05_2026/9nyk_49935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nyk_49935/05_2026/9nyk_49935.map" model { file = "/net/cci-nas-00/data/ceres_data/9nyk_49935/05_2026/9nyk_49935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nyk_49935/05_2026/9nyk_49935.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.052 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 32 5.16 5 C 6800 2.51 5 N 1676 2.21 5 O 1880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10404 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2541 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 13, 'TRANS': 298} Chain: "B" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2541 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 13, 'TRANS': 298} Chain: "C" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2541 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 13, 'TRANS': 298} Chain: "D" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2541 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 13, 'TRANS': 298} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {' MG': 1, '5TR': 1, 'UPG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'5TR:plan-4': 1, '5TR:plan-5': 1, '5TR:plan-6': 1, '5TR:plan-7': 1, '5TR:plan-8': 1, '5TR:plan-9': 1, '5TR:plan-10': 1, '5TR:plan-11': 1} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {' MG': 1, '5TR': 1, 'UPG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'5TR:plan-4': 1, '5TR:plan-5': 1, '5TR:plan-6': 1, '5TR:plan-7': 1, '5TR:plan-8': 1, '5TR:plan-9': 1, '5TR:plan-10': 1, '5TR:plan-11': 1} Unresolved non-hydrogen planarities: 37 Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {' MG': 1, '5TR': 1, 'UPG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'5TR:plan-4': 1, '5TR:plan-5': 1, '5TR:plan-6': 1, '5TR:plan-7': 1, '5TR:plan-8': 1, '5TR:plan-9': 1, '5TR:plan-10': 1, '5TR:plan-11': 1} Unresolved non-hydrogen planarities: 37 Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {' MG': 1, '5TR': 1, 'UPG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'5TR:plan-4': 1, '5TR:plan-5': 1, '5TR:plan-6': 1, '5TR:plan-7': 1, '5TR:plan-8': 1, '5TR:plan-9': 1, '5TR:plan-10': 1, '5TR:plan-11': 1} Unresolved non-hydrogen planarities: 37 Time building chain proxies: 2.73, per 1000 atoms: 0.26 Number of scatterers: 10404 At special positions: 0 Unit cell: (110.39, 112.05, 101.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 32 16.00 P 12 15.00 Mg 4 11.99 O 1880 8.00 N 1676 7.00 C 6800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 385.6 milliseconds 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2328 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 4 sheets defined 54.0% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 17 through 30 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 48 through 60 removed outlier: 3.574A pdb=" N GLN A 52 " --> pdb=" O LYS A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 84 Processing helix chain 'A' and resid 102 through 113 removed outlier: 4.094A pdb=" N GLU A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 147 Processing helix chain 'A' and resid 163 through 171 Processing helix chain 'A' and resid 178 through 186 removed outlier: 3.991A pdb=" N ALA A 184 " --> pdb=" O LYS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.735A pdb=" N GLN A 202 " --> pdb=" O PRO A 199 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY A 203 " --> pdb=" O ARG A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 222 Processing helix chain 'A' and resid 225 through 231 removed outlier: 3.690A pdb=" N TRP A 231 " --> pdb=" O PRO A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 removed outlier: 3.511A pdb=" N SER A 239 " --> pdb=" O GLY A 235 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N TYR A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N PHE A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 297 removed outlier: 3.870A pdb=" N ALA A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 33 removed outlier: 3.768A pdb=" N LEU B 26 " --> pdb=" O PHE B 22 " (cutoff:3.500A) Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 48 through 60 Processing helix chain 'B' and resid 73 through 84 Processing helix chain 'B' and resid 102 through 113 removed outlier: 3.973A pdb=" N GLU B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 147 removed outlier: 3.753A pdb=" N ARG B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET B 146 " --> pdb=" O VAL B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 171 Processing helix chain 'B' and resid 178 through 186 removed outlier: 4.029A pdb=" N ALA B 184 " --> pdb=" O LYS B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 222 Processing helix chain 'B' and resid 225 through 255 Processing helix chain 'B' and resid 264 through 297 removed outlier: 3.696A pdb=" N VAL B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA B 297 " --> pdb=" O GLU B 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 30 Processing helix chain 'C' and resid 49 through 60 removed outlier: 3.519A pdb=" N SER C 59 " --> pdb=" O ASP C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 85 Processing helix chain 'C' and resid 102 through 114 removed outlier: 4.002A pdb=" N GLU C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY C 114 " --> pdb=" O LYS C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 147 removed outlier: 3.591A pdb=" N PHE C 134 " --> pdb=" O TRP C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 171 Processing helix chain 'C' and resid 178 through 186 Processing helix chain 'C' and resid 208 through 222 Processing helix chain 'C' and resid 225 through 231 removed outlier: 3.573A pdb=" N TRP C 231 " --> pdb=" O PRO C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 244 Processing helix chain 'C' and resid 246 through 257 Processing helix chain 'C' and resid 264 through 297 removed outlier: 3.716A pdb=" N VAL C 268 " --> pdb=" O ALA C 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 33 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 48 through 60 removed outlier: 3.954A pdb=" N GLN D 52 " --> pdb=" O LYS D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 84 Processing helix chain 'D' and resid 102 through 113 removed outlier: 4.363A pdb=" N GLU D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 132 Processing helix chain 'D' and resid 133 through 147 Processing helix chain 'D' and resid 163 through 171 Processing helix chain 'D' and resid 178 through 186 Processing helix chain 'D' and resid 208 through 222 removed outlier: 3.768A pdb=" N ALA D 216 " --> pdb=" O LEU D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 231 Processing helix chain 'D' and resid 233 through 255 Processing helix chain 'D' and resid 265 through 297 removed outlier: 3.784A pdb=" N ALA D 297 " --> pdb=" O GLU D 293 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 195 removed outlier: 5.672A pdb=" N PHE A 158 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N ARG A 122 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N GLY A 156 " --> pdb=" O ARG A 122 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG A 159 " --> pdb=" O PRO A 92 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE A 65 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU D 306 " --> pdb=" O ILE A 65 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASN A 67 " --> pdb=" O SER D 304 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 303 through 307 removed outlier: 6.831A pdb=" N ASN B 67 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU A 306 " --> pdb=" O ILE B 65 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE B 65 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE B 7 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL B 41 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE B 9 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N SER B 6 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG B 159 " --> pdb=" O PRO B 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 303 through 307 removed outlier: 6.950A pdb=" N ASN C 67 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LEU B 306 " --> pdb=" O ILE C 65 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE C 65 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER C 6 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG C 159 " --> pdb=" O PRO C 92 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N GLY C 156 " --> pdb=" O ARG C 122 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N ARG C 122 " --> pdb=" O GLY C 156 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N PHE C 158 " --> pdb=" O ALA C 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 303 through 307 removed outlier: 6.872A pdb=" N ASN D 67 " --> pdb=" O SER C 304 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LEU C 306 " --> pdb=" O ILE D 65 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE D 65 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU D 5 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE D 39 " --> pdb=" O LEU D 5 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE D 7 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL D 41 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE D 9 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N SER D 6 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG D 159 " --> pdb=" O PRO D 92 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N GLY D 156 " --> pdb=" O ARG D 122 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N ARG D 122 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N PHE D 158 " --> pdb=" O ALA D 120 " (cutoff:3.500A) 534 hydrogen bonds defined for protein. 1596 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.59 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: 1.16 - 1.29: 1625 1.29 - 1.42: 2764 1.42 - 1.55: 6173 1.55 - 1.68: 26 1.68 - 1.81: 60 Bond restraints: 10648 Sorted by residual: bond pdb=" C4C UPG D 401 " pdb=" O4C UPG D 401 " ideal model delta sigma weight residual 1.431 1.670 -0.239 2.00e-02 2.50e+03 1.42e+02 bond pdb=" C4C UPG C 401 " pdb=" O4C UPG C 401 " ideal model delta sigma weight residual 1.431 1.669 -0.238 2.00e-02 2.50e+03 1.42e+02 bond pdb=" C4C UPG A 401 " pdb=" O4C UPG A 401 " ideal model delta sigma weight residual 1.431 1.668 -0.237 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C4C UPG B 401 " pdb=" O4C UPG B 401 " ideal model delta sigma weight residual 1.431 1.666 -0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" O02 5TR C 402 " pdb=" P01 5TR C 402 " ideal model delta sigma weight residual 1.824 1.622 0.202 2.00e-02 2.50e+03 1.03e+02 ... (remaining 10643 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.88: 14337 3.88 - 7.76: 95 7.76 - 11.64: 9 11.64 - 15.53: 13 15.53 - 19.41: 6 Bond angle restraints: 14460 Sorted by residual: angle pdb=" CA PRO B 261 " pdb=" N PRO B 261 " pdb=" CD PRO B 261 " ideal model delta sigma weight residual 112.00 92.59 19.41 1.40e+00 5.10e-01 1.92e+02 angle pdb=" N PRO B 261 " pdb=" CD PRO B 261 " pdb=" CG PRO B 261 " ideal model delta sigma weight residual 103.20 86.24 16.96 1.50e+00 4.44e-01 1.28e+02 angle pdb=" CA PRO B 261 " pdb=" CB PRO B 261 " pdb=" CG PRO B 261 " ideal model delta sigma weight residual 104.50 92.40 12.10 1.90e+00 2.77e-01 4.06e+01 angle pdb=" O04 5TR B 402 " pdb=" P01 5TR B 402 " pdb=" O05 5TR B 402 " ideal model delta sigma weight residual 129.39 112.62 16.77 3.00e+00 1.11e-01 3.12e+01 angle pdb=" O04 5TR D 402 " pdb=" P01 5TR D 402 " pdb=" O05 5TR D 402 " ideal model delta sigma weight residual 129.39 112.70 16.69 3.00e+00 1.11e-01 3.10e+01 ... (remaining 14455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.80: 5879 30.80 - 61.59: 498 61.59 - 92.39: 52 92.39 - 123.19: 23 123.19 - 153.98: 4 Dihedral angle restraints: 6456 sinusoidal: 2820 harmonic: 3636 Sorted by residual: dihedral pdb=" CA LEU A 243 " pdb=" C LEU A 243 " pdb=" N ALA A 244 " pdb=" CA ALA A 244 " ideal model delta harmonic sigma weight residual 180.00 157.39 22.61 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" C26 5TR B 402 " pdb=" C29 5TR B 402 " pdb=" C34 5TR B 402 " pdb=" C31 5TR B 402 " ideal model delta sinusoidal sigma weight residual 271.18 117.20 153.98 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" C17 5TR D 402 " pdb=" C19 5TR D 402 " pdb=" C27 5TR D 402 " pdb=" C20 5TR D 402 " ideal model delta sinusoidal sigma weight residual 154.17 1.67 152.50 1 3.00e+01 1.11e-03 2.01e+01 ... (remaining 6453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1358 0.059 - 0.118: 236 0.118 - 0.177: 20 0.177 - 0.236: 2 0.236 - 0.294: 4 Chirality restraints: 1620 Sorted by residual: chirality pdb=" C3C UPG B 401 " pdb=" C2C UPG B 401 " pdb=" C4C UPG B 401 " pdb=" O3C UPG B 401 " both_signs ideal model delta sigma weight residual False -2.74 -2.44 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C3C UPG A 401 " pdb=" C2C UPG A 401 " pdb=" C4C UPG A 401 " pdb=" O3C UPG A 401 " both_signs ideal model delta sigma weight residual False -2.74 -2.45 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C3C UPG D 401 " pdb=" C2C UPG D 401 " pdb=" C4C UPG D 401 " pdb=" O3C UPG D 401 " both_signs ideal model delta sigma weight residual False -2.74 -2.47 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 1617 not shown) Planarity restraints: 1772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 260 " -0.128 5.00e-02 4.00e+02 1.73e-01 4.79e+01 pdb=" N PRO B 261 " 0.298 5.00e-02 4.00e+02 pdb=" CA PRO B 261 " -0.087 5.00e-02 4.00e+02 pdb=" CD PRO B 261 " -0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 260 " 0.072 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PRO A 261 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO A 261 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 261 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C31 5TR A 402 " 0.003 2.00e-02 2.50e+03 3.27e-02 1.34e+01 pdb=" C36 5TR A 402 " 0.024 2.00e-02 2.50e+03 pdb=" C45 5TR A 402 " -0.039 2.00e-02 2.50e+03 pdb=" C46 5TR A 402 " 0.046 2.00e-02 2.50e+03 pdb=" C50 5TR A 402 " -0.034 2.00e-02 2.50e+03 ... (remaining 1769 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.32: 26 2.32 - 2.96: 4927 2.96 - 3.61: 15314 3.61 - 4.25: 24376 4.25 - 4.90: 41179 Nonbonded interactions: 85822 Sorted by model distance: nonbonded pdb=" OD2 ASP C 96 " pdb="MG MG C 403 " model vdw 1.675 2.170 nonbonded pdb=" O1B UPG C 401 " pdb="MG MG C 403 " model vdw 1.748 2.170 nonbonded pdb=" OD2 ASP B 96 " pdb="MG MG B 403 " model vdw 1.933 2.170 nonbonded pdb=" O1B UPG B 401 " pdb="MG MG B 403 " model vdw 1.934 2.170 nonbonded pdb=" O1A UPG D 401 " pdb="MG MG D 403 " model vdw 1.934 2.170 ... (remaining 85817 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.840 Find NCS groups from input model: 0.120 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:7.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 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 : 0.012 0.340 10648 Z= 0.583 Angle : 0.904 19.408 14460 Z= 0.418 Chirality : 0.045 0.294 1620 Planarity : 0.007 0.173 1772 Dihedral : 22.546 153.983 4128 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.48 % Favored : 94.35 % Rotamer: Outliers : 3.00 % Allowed : 30.64 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.25), residues: 1240 helix: 0.98 (0.20), residues: 652 sheet: -1.51 (0.37), residues: 188 loop : -1.21 (0.35), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 189 TYR 0.016 0.001 TYR A 292 PHE 0.021 0.001 PHE D 192 TRP 0.019 0.001 TRP B 231 HIS 0.003 0.001 HIS D 20 Details of bonding type rmsd covalent geometry : bond 0.01208 (10648) covalent geometry : angle 0.90383 (14460) hydrogen bonds : bond 0.10742 ( 534) hydrogen bonds : angle 5.58755 ( 1596) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: B 79 SER cc_start: 0.8442 (m) cc_final: 0.8208 (p) REVERT: C 61 ARG cc_start: 0.6456 (mpt180) cc_final: 0.6243 (mpt180) REVERT: D 19 GLU cc_start: 0.7730 (tp30) cc_final: 0.7314 (pp20) outliers start: 33 outliers final: 27 residues processed: 163 average time/residue: 0.4570 time to fit residues: 81.6022 Evaluate side-chains 153 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 263 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.0060 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 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 = 0.3715 r_free = 0.3715 target = 0.152612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.121028 restraints weight = 12534.712| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.88 r_work: 0.3220 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.0577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 10648 Z= 0.136 Angle : 0.574 8.691 14460 Z= 0.289 Chirality : 0.044 0.252 1620 Planarity : 0.005 0.109 1772 Dihedral : 17.774 144.068 1706 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.40 % Favored : 94.44 % Rotamer: Outliers : 6.00 % Allowed : 26.18 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.26), residues: 1240 helix: 1.34 (0.20), residues: 660 sheet: -1.48 (0.38), residues: 188 loop : -1.02 (0.36), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 189 TYR 0.017 0.001 TYR A 292 PHE 0.014 0.001 PHE A 215 TRP 0.018 0.001 TRP B 231 HIS 0.001 0.000 HIS C 20 Details of bonding type rmsd covalent geometry : bond 0.00319 (10648) covalent geometry : angle 0.57386 (14460) hydrogen bonds : bond 0.03569 ( 534) hydrogen bonds : angle 4.48517 ( 1596) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 144 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8344 (t0) cc_final: 0.8116 (t0) REVERT: A 83 ASP cc_start: 0.8453 (m-30) cc_final: 0.8147 (m-30) REVERT: A 146 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7532 (mtp) REVERT: B 79 SER cc_start: 0.8327 (m) cc_final: 0.8125 (p) REVERT: B 294 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8049 (mm-30) REVERT: C 19 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.6339 (mm-30) REVERT: C 112 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.7031 (mpt-90) REVERT: D 33 LYS cc_start: 0.8515 (ttmm) cc_final: 0.8200 (tttp) REVERT: D 141 LYS cc_start: 0.7621 (mtpt) cc_final: 0.6916 (mmpt) outliers start: 66 outliers final: 24 residues processed: 190 average time/residue: 0.5116 time to fit residues: 105.4276 Evaluate side-chains 163 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 112 ARG Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 263 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 43 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 5 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.150645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.118019 restraints weight = 12656.946| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.93 r_work: 0.3160 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10648 Z= 0.208 Angle : 0.622 10.076 14460 Z= 0.306 Chirality : 0.047 0.307 1620 Planarity : 0.005 0.136 1772 Dihedral : 16.078 134.344 1681 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.56 % Favored : 94.27 % Rotamer: Outliers : 6.00 % Allowed : 26.91 % Favored : 67.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.26), residues: 1240 helix: 1.31 (0.20), residues: 656 sheet: -1.12 (0.41), residues: 176 loop : -1.21 (0.35), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 189 TYR 0.018 0.001 TYR A 292 PHE 0.008 0.001 PHE D 195 TRP 0.019 0.001 TRP B 231 HIS 0.003 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00500 (10648) covalent geometry : angle 0.62200 (14460) hydrogen bonds : bond 0.03729 ( 534) hydrogen bonds : angle 4.46786 ( 1596) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 143 time to evaluate : 0.378 Fit side-chains REVERT: A 47 ASP cc_start: 0.8288 (t0) cc_final: 0.7946 (t0) REVERT: A 83 ASP cc_start: 0.8508 (m-30) cc_final: 0.8236 (m-30) REVERT: A 146 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7545 (mtp) REVERT: A 294 GLU cc_start: 0.8614 (tp30) cc_final: 0.8019 (tp30) REVERT: B 226 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7838 (tp) REVERT: B 237 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8540 (mp) REVERT: C 15 GLU cc_start: 0.7499 (pt0) cc_final: 0.7249 (pt0) REVERT: C 47 ASP cc_start: 0.7860 (t0) cc_final: 0.7169 (t0) REVERT: C 112 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.6865 (mpt-90) REVERT: C 175 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.7070 (mmp80) REVERT: C 218 ASP cc_start: 0.7238 (m-30) cc_final: 0.6802 (m-30) REVERT: D 33 LYS cc_start: 0.8506 (ttmm) cc_final: 0.8185 (tttp) REVERT: D 47 ASP cc_start: 0.8506 (t70) cc_final: 0.8129 (t0) outliers start: 66 outliers final: 26 residues processed: 191 average time/residue: 0.5012 time to fit residues: 103.9369 Evaluate side-chains 162 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 112 ARG Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 263 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 14 optimal weight: 8.9990 chunk 99 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.151636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.119716 restraints weight = 12687.874| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.90 r_work: 0.3206 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10648 Z= 0.156 Angle : 0.596 11.050 14460 Z= 0.290 Chirality : 0.046 0.365 1620 Planarity : 0.005 0.139 1772 Dihedral : 14.947 127.380 1675 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.40 % Favored : 94.52 % Rotamer: Outliers : 5.64 % Allowed : 27.36 % Favored : 67.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.26), residues: 1240 helix: 1.40 (0.21), residues: 656 sheet: -1.12 (0.41), residues: 176 loop : -1.17 (0.35), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 189 TYR 0.018 0.001 TYR A 292 PHE 0.007 0.001 PHE B 195 TRP 0.019 0.001 TRP B 231 HIS 0.001 0.000 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00366 (10648) covalent geometry : angle 0.59608 (14460) hydrogen bonds : bond 0.03429 ( 534) hydrogen bonds : angle 4.37468 ( 1596) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 145 time to evaluate : 0.410 Fit side-chains REVERT: A 47 ASP cc_start: 0.8297 (t0) cc_final: 0.7927 (t0) REVERT: A 83 ASP cc_start: 0.8486 (m-30) cc_final: 0.8207 (m-30) REVERT: A 146 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7570 (mtp) REVERT: A 294 GLU cc_start: 0.8585 (tp30) cc_final: 0.8019 (tp30) REVERT: B 26 LEU cc_start: 0.7688 (mt) cc_final: 0.7224 (mt) REVERT: B 200 ARG cc_start: 0.6032 (OUTLIER) cc_final: 0.5426 (mmm-85) REVERT: B 226 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7807 (tp) REVERT: B 237 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8613 (mp) REVERT: C 15 GLU cc_start: 0.7555 (pt0) cc_final: 0.7275 (pt0) REVERT: C 47 ASP cc_start: 0.7856 (t0) cc_final: 0.7116 (t0) REVERT: C 112 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.6953 (mpt-90) REVERT: C 175 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7056 (mmp80) REVERT: C 218 ASP cc_start: 0.7204 (m-30) cc_final: 0.6768 (m-30) REVERT: D 33 LYS cc_start: 0.8489 (ttmm) cc_final: 0.8172 (tttp) REVERT: D 47 ASP cc_start: 0.8502 (t70) cc_final: 0.8138 (t0) REVERT: D 48 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8517 (ttpt) outliers start: 62 outliers final: 29 residues processed: 190 average time/residue: 0.5148 time to fit residues: 106.4361 Evaluate side-chains 171 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 261 PRO Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 200 ARG Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain C residue 61 ARG Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 112 ARG Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 263 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 46 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 34 optimal weight: 0.0770 chunk 54 optimal weight: 3.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.152613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.120531 restraints weight = 12508.438| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.90 r_work: 0.3212 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10648 Z= 0.142 Angle : 0.567 9.010 14460 Z= 0.281 Chirality : 0.046 0.390 1620 Planarity : 0.005 0.130 1772 Dihedral : 13.835 115.116 1674 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.48 % Favored : 94.44 % Rotamer: Outliers : 5.73 % Allowed : 27.27 % Favored : 67.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.26), residues: 1240 helix: 1.45 (0.20), residues: 660 sheet: -1.09 (0.41), residues: 176 loop : -1.14 (0.35), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 189 TYR 0.017 0.001 TYR A 292 PHE 0.014 0.001 PHE A 215 TRP 0.017 0.001 TRP B 231 HIS 0.001 0.000 HIS D 20 Details of bonding type rmsd covalent geometry : bond 0.00330 (10648) covalent geometry : angle 0.56696 (14460) hydrogen bonds : bond 0.03286 ( 534) hydrogen bonds : angle 4.26242 ( 1596) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 143 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8293 (t0) cc_final: 0.7907 (t0) REVERT: A 83 ASP cc_start: 0.8495 (m-30) cc_final: 0.8275 (m-30) REVERT: A 294 GLU cc_start: 0.8572 (tp30) cc_final: 0.8032 (tp30) REVERT: B 26 LEU cc_start: 0.7706 (mt) cc_final: 0.7220 (mt) REVERT: B 61 ARG cc_start: 0.6886 (OUTLIER) cc_final: 0.5787 (ttt180) REVERT: B 200 ARG cc_start: 0.5949 (OUTLIER) cc_final: 0.5419 (mmm-85) REVERT: B 237 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8572 (mp) REVERT: C 15 GLU cc_start: 0.7455 (pt0) cc_final: 0.7183 (pt0) REVERT: C 47 ASP cc_start: 0.7850 (t0) cc_final: 0.7012 (t0) REVERT: C 112 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6892 (mpt-90) REVERT: C 175 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.6989 (mmp80) REVERT: C 218 ASP cc_start: 0.7217 (m-30) cc_final: 0.6786 (m-30) REVERT: C 237 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7571 (mt) REVERT: D 19 GLU cc_start: 0.7989 (tp30) cc_final: 0.7473 (pp20) REVERT: D 33 LYS cc_start: 0.8460 (ttmm) cc_final: 0.8149 (tttp) REVERT: D 47 ASP cc_start: 0.8483 (t70) cc_final: 0.8140 (t0) REVERT: D 48 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8504 (ttpt) REVERT: D 141 LYS cc_start: 0.7603 (mtpt) cc_final: 0.6898 (mmpt) outliers start: 63 outliers final: 27 residues processed: 189 average time/residue: 0.5354 time to fit residues: 109.5211 Evaluate side-chains 168 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain B residue 61 ARG Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 200 ARG Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 61 ARG Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 112 ARG Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 263 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 9 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 117 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.154046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.122185 restraints weight = 12581.755| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.88 r_work: 0.3233 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10648 Z= 0.128 Angle : 0.560 11.956 14460 Z= 0.275 Chirality : 0.045 0.341 1620 Planarity : 0.005 0.141 1772 Dihedral : 12.894 92.506 1671 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.56 % Favored : 94.35 % Rotamer: Outliers : 5.64 % Allowed : 27.27 % Favored : 67.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.26), residues: 1240 helix: 1.53 (0.21), residues: 660 sheet: -1.05 (0.41), residues: 176 loop : -1.11 (0.35), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 189 TYR 0.015 0.001 TYR A 292 PHE 0.007 0.001 PHE B 223 TRP 0.017 0.001 TRP B 231 HIS 0.001 0.000 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00291 (10648) covalent geometry : angle 0.56049 (14460) hydrogen bonds : bond 0.03174 ( 534) hydrogen bonds : angle 4.17175 ( 1596) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 148 time to evaluate : 0.332 Fit side-chains REVERT: A 47 ASP cc_start: 0.8300 (t0) cc_final: 0.7887 (t0) REVERT: A 83 ASP cc_start: 0.8487 (m-30) cc_final: 0.8279 (m-30) REVERT: A 294 GLU cc_start: 0.8569 (tp30) cc_final: 0.8029 (tp30) REVERT: B 4 GLU cc_start: 0.7933 (tp30) cc_final: 0.7317 (tp30) REVERT: B 43 ASP cc_start: 0.8951 (t70) cc_final: 0.8555 (t0) REVERT: B 79 SER cc_start: 0.8386 (m) cc_final: 0.8141 (p) REVERT: B 218 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.7058 (t0) REVERT: B 233 TYR cc_start: 0.7548 (m-80) cc_final: 0.7209 (m-80) REVERT: B 237 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8554 (mp) REVERT: C 14 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7315 (mm-30) REVERT: C 15 GLU cc_start: 0.7359 (pt0) cc_final: 0.7122 (pt0) REVERT: C 47 ASP cc_start: 0.7834 (t70) cc_final: 0.6931 (t0) REVERT: C 61 ARG cc_start: 0.6441 (OUTLIER) cc_final: 0.6177 (mpt180) REVERT: C 112 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6996 (mpt-90) REVERT: C 175 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.6825 (mmp80) REVERT: C 218 ASP cc_start: 0.7171 (m-30) cc_final: 0.6721 (m-30) REVERT: D 33 LYS cc_start: 0.8454 (ttmm) cc_final: 0.7968 (mttt) REVERT: D 47 ASP cc_start: 0.8441 (t70) cc_final: 0.8120 (t0) REVERT: D 48 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8510 (ttpt) REVERT: D 141 LYS cc_start: 0.7609 (mtpt) cc_final: 0.6898 (mmpt) outliers start: 62 outliers final: 25 residues processed: 196 average time/residue: 0.5338 time to fit residues: 113.4188 Evaluate side-chains 173 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain C residue 61 ARG Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 112 ARG Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 263 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 30 optimal weight: 0.5980 chunk 97 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.154196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.122021 restraints weight = 12346.310| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.89 r_work: 0.3243 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10648 Z= 0.119 Angle : 0.531 9.423 14460 Z= 0.268 Chirality : 0.044 0.339 1620 Planarity : 0.004 0.057 1772 Dihedral : 12.283 87.658 1671 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.73 % Allowed : 28.09 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.26), residues: 1240 helix: 1.59 (0.20), residues: 660 sheet: -0.98 (0.41), residues: 176 loop : -1.08 (0.35), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 189 TYR 0.014 0.001 TYR A 292 PHE 0.017 0.001 PHE A 215 TRP 0.016 0.001 TRP B 231 HIS 0.001 0.000 HIS D 20 Details of bonding type rmsd covalent geometry : bond 0.00274 (10648) covalent geometry : angle 0.53136 (14460) hydrogen bonds : bond 0.03132 ( 534) hydrogen bonds : angle 4.11387 ( 1596) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 150 time to evaluate : 0.455 Fit side-chains REVERT: A 47 ASP cc_start: 0.8176 (t0) cc_final: 0.7759 (t0) REVERT: A 83 ASP cc_start: 0.8480 (m-30) cc_final: 0.8257 (m-30) REVERT: A 294 GLU cc_start: 0.8585 (tp30) cc_final: 0.8013 (tp30) REVERT: B 4 GLU cc_start: 0.7979 (tp30) cc_final: 0.7363 (tp30) REVERT: B 233 TYR cc_start: 0.7555 (m-80) cc_final: 0.7191 (m-80) REVERT: B 237 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8494 (mp) REVERT: C 14 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7247 (mm-30) REVERT: C 15 GLU cc_start: 0.7306 (pt0) cc_final: 0.7072 (pt0) REVERT: C 19 GLU cc_start: 0.6648 (OUTLIER) cc_final: 0.6303 (mm-30) REVERT: C 47 ASP cc_start: 0.7814 (t70) cc_final: 0.6864 (t0) REVERT: C 61 ARG cc_start: 0.6378 (OUTLIER) cc_final: 0.6127 (mpt180) REVERT: C 112 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6978 (mpt-90) REVERT: C 175 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.7007 (mmp80) REVERT: C 218 ASP cc_start: 0.7159 (m-30) cc_final: 0.6735 (m-30) REVERT: D 19 GLU cc_start: 0.7917 (tp30) cc_final: 0.7394 (pp20) REVERT: D 33 LYS cc_start: 0.8461 (ttmm) cc_final: 0.7982 (mttt) REVERT: D 47 ASP cc_start: 0.8416 (t70) cc_final: 0.8134 (t0) REVERT: D 48 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8498 (ttpt) REVERT: D 141 LYS cc_start: 0.7569 (mtpt) cc_final: 0.6863 (mmpt) outliers start: 52 outliers final: 27 residues processed: 187 average time/residue: 0.5727 time to fit residues: 115.3485 Evaluate side-chains 175 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 61 ARG Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 112 ARG Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 263 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 30 optimal weight: 0.0370 chunk 32 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 122 optimal weight: 0.3980 chunk 57 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 overall best weight: 1.2662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.153411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.122591 restraints weight = 12467.973| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.82 r_work: 0.3232 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10648 Z= 0.132 Angle : 0.535 9.118 14460 Z= 0.271 Chirality : 0.043 0.309 1620 Planarity : 0.004 0.060 1772 Dihedral : 11.919 85.489 1670 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.45 % Allowed : 28.55 % Favored : 67.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.26), residues: 1240 helix: 1.60 (0.21), residues: 660 sheet: -0.96 (0.42), residues: 176 loop : -1.09 (0.35), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 189 TYR 0.013 0.001 TYR A 292 PHE 0.007 0.001 PHE B 223 TRP 0.016 0.001 TRP B 231 HIS 0.001 0.000 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00310 (10648) covalent geometry : angle 0.53527 (14460) hydrogen bonds : bond 0.03156 ( 534) hydrogen bonds : angle 4.12435 ( 1596) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 142 time to evaluate : 0.405 Fit side-chains REVERT: A 47 ASP cc_start: 0.8202 (t0) cc_final: 0.7827 (t0) REVERT: A 294 GLU cc_start: 0.8585 (tp30) cc_final: 0.8087 (tp30) REVERT: B 4 GLU cc_start: 0.8098 (tp30) cc_final: 0.7537 (tp30) REVERT: B 43 ASP cc_start: 0.8873 (t70) cc_final: 0.8573 (t0) REVERT: B 218 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7175 (t0) REVERT: B 237 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8636 (mp) REVERT: C 47 ASP cc_start: 0.7845 (t70) cc_final: 0.6922 (t0) REVERT: C 61 ARG cc_start: 0.6567 (OUTLIER) cc_final: 0.6299 (mpt180) REVERT: C 112 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7208 (mpt-90) REVERT: C 175 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7112 (mmp80) REVERT: C 218 ASP cc_start: 0.7376 (m-30) cc_final: 0.6901 (m-30) REVERT: D 33 LYS cc_start: 0.8553 (ttmm) cc_final: 0.8077 (mttt) REVERT: D 48 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8610 (ttpt) REVERT: D 141 LYS cc_start: 0.7662 (mtpt) cc_final: 0.6938 (mmpt) REVERT: D 150 LYS cc_start: 0.8236 (mptt) cc_final: 0.7884 (mmtt) outliers start: 49 outliers final: 24 residues processed: 179 average time/residue: 0.5414 time to fit residues: 104.8078 Evaluate side-chains 165 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 61 ARG Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 112 ARG Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 263 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 50 optimal weight: 0.0670 chunk 39 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 34 optimal weight: 0.5980 chunk 81 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 overall best weight: 1.5122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.153079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.121374 restraints weight = 12554.593| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.91 r_work: 0.3219 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10648 Z= 0.146 Angle : 0.555 8.859 14460 Z= 0.283 Chirality : 0.043 0.309 1620 Planarity : 0.004 0.056 1772 Dihedral : 11.666 84.965 1670 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.91 % Allowed : 29.64 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.26), residues: 1240 helix: 1.58 (0.21), residues: 660 sheet: -0.92 (0.42), residues: 176 loop : -1.11 (0.35), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 189 TYR 0.014 0.001 TYR C 287 PHE 0.022 0.001 PHE D 192 TRP 0.016 0.001 TRP B 231 HIS 0.001 0.000 HIS C 20 Details of bonding type rmsd covalent geometry : bond 0.00346 (10648) covalent geometry : angle 0.55538 (14460) hydrogen bonds : bond 0.03236 ( 534) hydrogen bonds : angle 4.14364 ( 1596) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 140 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8426 (m-30) cc_final: 0.8210 (m-30) REVERT: A 294 GLU cc_start: 0.8602 (tp30) cc_final: 0.8080 (tp30) REVERT: B 4 GLU cc_start: 0.8115 (tp30) cc_final: 0.7528 (tp30) REVERT: B 43 ASP cc_start: 0.8889 (t70) cc_final: 0.8581 (t0) REVERT: B 200 ARG cc_start: 0.6013 (OUTLIER) cc_final: 0.5502 (mmm-85) REVERT: B 218 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.7141 (t0) REVERT: B 237 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8661 (mp) REVERT: C 19 GLU cc_start: 0.6689 (OUTLIER) cc_final: 0.6341 (mm-30) REVERT: C 61 ARG cc_start: 0.6510 (OUTLIER) cc_final: 0.6243 (mpt180) REVERT: C 112 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7100 (mpt-90) REVERT: C 218 ASP cc_start: 0.7331 (m-30) cc_final: 0.6853 (m-30) REVERT: D 19 GLU cc_start: 0.8037 (tp30) cc_final: 0.7558 (pp20) REVERT: D 33 LYS cc_start: 0.8532 (ttmm) cc_final: 0.8054 (mttt) REVERT: D 48 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8580 (ttpt) REVERT: D 138 MET cc_start: 0.7592 (mmm) cc_final: 0.7056 (mmp) REVERT: D 141 LYS cc_start: 0.7677 (mtpt) cc_final: 0.6956 (mmpt) REVERT: D 150 LYS cc_start: 0.8161 (mptt) cc_final: 0.7811 (mmtt) outliers start: 43 outliers final: 25 residues processed: 173 average time/residue: 0.5677 time to fit residues: 105.9333 Evaluate side-chains 167 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 200 ARG Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 61 ARG Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 112 ARG Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 263 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 51 optimal weight: 20.0000 chunk 77 optimal weight: 0.0670 chunk 24 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.153833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.122211 restraints weight = 12470.284| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.90 r_work: 0.3226 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10648 Z= 0.123 Angle : 0.543 8.881 14460 Z= 0.276 Chirality : 0.043 0.306 1620 Planarity : 0.004 0.057 1772 Dihedral : 11.461 84.053 1670 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.09 % Allowed : 30.55 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.26), residues: 1240 helix: 1.63 (0.21), residues: 660 sheet: -1.01 (0.41), residues: 176 loop : -1.08 (0.35), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 189 TYR 0.013 0.001 TYR C 287 PHE 0.023 0.001 PHE D 192 TRP 0.017 0.001 TRP B 231 HIS 0.001 0.000 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00285 (10648) covalent geometry : angle 0.54308 (14460) hydrogen bonds : bond 0.03150 ( 534) hydrogen bonds : angle 4.10183 ( 1596) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8576 (tp30) cc_final: 0.8079 (tp30) REVERT: B 4 GLU cc_start: 0.8117 (tp30) cc_final: 0.7507 (tp30) REVERT: B 43 ASP cc_start: 0.8880 (t70) cc_final: 0.8562 (t0) REVERT: B 237 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8641 (mp) REVERT: C 61 ARG cc_start: 0.6505 (OUTLIER) cc_final: 0.6233 (mpt180) REVERT: C 112 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.7105 (mpt-90) REVERT: C 218 ASP cc_start: 0.7318 (m-30) cc_final: 0.6844 (m-30) REVERT: D 19 GLU cc_start: 0.8055 (tp30) cc_final: 0.7569 (pp20) REVERT: D 33 LYS cc_start: 0.8540 (ttmm) cc_final: 0.8067 (mttt) REVERT: D 48 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8552 (ttpt) REVERT: D 138 MET cc_start: 0.7544 (mmm) cc_final: 0.6995 (mmp) REVERT: D 141 LYS cc_start: 0.7642 (mtpt) cc_final: 0.6923 (mmpt) REVERT: D 150 LYS cc_start: 0.8157 (mptt) cc_final: 0.7795 (mmtt) outliers start: 34 outliers final: 27 residues processed: 161 average time/residue: 0.5433 time to fit residues: 94.5248 Evaluate side-chains 161 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 61 ARG Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 112 ARG Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 263 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 56 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 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 = 0.3716 r_free = 0.3716 target = 0.153580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.121982 restraints weight = 12542.186| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.90 r_work: 0.3214 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10648 Z= 0.136 Angle : 0.540 8.708 14460 Z= 0.275 Chirality : 0.043 0.308 1620 Planarity : 0.004 0.055 1772 Dihedral : 11.218 84.246 1670 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.45 % Allowed : 30.18 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.26), residues: 1240 helix: 1.62 (0.20), residues: 660 sheet: -0.98 (0.42), residues: 168 loop : -1.09 (0.34), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 189 TYR 0.013 0.001 TYR C 287 PHE 0.022 0.001 PHE D 192 TRP 0.016 0.001 TRP B 231 HIS 0.001 0.000 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00319 (10648) covalent geometry : angle 0.54043 (14460) hydrogen bonds : bond 0.03196 ( 534) hydrogen bonds : angle 4.10504 ( 1596) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3552.90 seconds wall clock time: 61 minutes 25.74 seconds (3685.74 seconds total)