Starting phenix.real_space_refine on Wed Mar 4 02:08:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s5t_24839/03_2026/7s5t_24839.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s5t_24839/03_2026/7s5t_24839.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7s5t_24839/03_2026/7s5t_24839.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s5t_24839/03_2026/7s5t_24839.map" model { file = "/net/cci-nas-00/data/ceres_data/7s5t_24839/03_2026/7s5t_24839.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s5t_24839/03_2026/7s5t_24839.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.005 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 2 8.98 5 S 64 5.16 5 C 6488 2.51 5 N 1720 2.21 5 O 1804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10078 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2519 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain: "B" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2519 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain: "C" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2519 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain: "D" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2519 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.22, per 1000 atoms: 0.22 Number of scatterers: 10078 At special positions: 0 Unit cell: (91, 89.7, 122.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 2 19.00 S 64 16.00 O 1804 8.00 N 1720 7.00 C 6488 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 110 " - pdb=" SG CYS D 142 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 498.2 milliseconds 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2416 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 20 sheets defined 34.8% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 51 through 57 removed outlier: 3.783A pdb=" N ARG A 54 " --> pdb=" O GLU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 65 removed outlier: 3.670A pdb=" N THR A 62 " --> pdb=" O ASP A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 97 Processing helix chain 'A' and resid 116 through 129 Processing helix chain 'A' and resid 142 through 172 removed outlier: 3.557A pdb=" N ILE A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 removed outlier: 4.042A pdb=" N ARG A 176 " --> pdb=" O GLN A 173 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA A 178 " --> pdb=" O HIS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.809A pdb=" N LEU A 275 " --> pdb=" O PRO A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 333 Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'B' and resid 51 through 57 removed outlier: 3.783A pdb=" N ARG B 54 " --> pdb=" O GLU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 65 removed outlier: 3.670A pdb=" N THR B 62 " --> pdb=" O ASP B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 97 Processing helix chain 'B' and resid 116 through 129 Processing helix chain 'B' and resid 142 through 172 removed outlier: 3.557A pdb=" N ILE B 146 " --> pdb=" O CYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 179 removed outlier: 4.042A pdb=" N ARG B 176 " --> pdb=" O GLN B 173 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA B 178 " --> pdb=" O HIS B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 275 removed outlier: 3.809A pdb=" N LEU B 275 " --> pdb=" O PRO B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 333 Processing helix chain 'B' and resid 346 through 351 Processing helix chain 'C' and resid 51 through 57 removed outlier: 3.784A pdb=" N ARG C 54 " --> pdb=" O GLU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 65 removed outlier: 3.668A pdb=" N THR C 62 " --> pdb=" O ASP C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 97 Processing helix chain 'C' and resid 116 through 129 Processing helix chain 'C' and resid 142 through 172 removed outlier: 3.558A pdb=" N ILE C 146 " --> pdb=" O CYS C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 179 removed outlier: 4.042A pdb=" N ARG C 176 " --> pdb=" O GLN C 173 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA C 178 " --> pdb=" O HIS C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 333 Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'D' and resid 51 through 57 removed outlier: 3.783A pdb=" N ARG D 54 " --> pdb=" O GLU D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 65 removed outlier: 3.669A pdb=" N THR D 62 " --> pdb=" O ASP D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 97 Processing helix chain 'D' and resid 116 through 129 Processing helix chain 'D' and resid 142 through 172 removed outlier: 3.557A pdb=" N ILE D 146 " --> pdb=" O CYS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 179 removed outlier: 4.042A pdb=" N ARG D 176 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA D 178 " --> pdb=" O HIS D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 275 removed outlier: 3.810A pdb=" N LEU D 275 " --> pdb=" O PRO D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 333 Processing helix chain 'D' and resid 346 through 351 Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 183 removed outlier: 6.773A pdb=" N ALA A 187 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 230 through 238 removed outlier: 5.064A pdb=" N THR A 223 " --> pdb=" O PRO A 232 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET A 217 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA A 213 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLU A 288 " --> pdb=" O ALA A 213 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE A 215 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE A 286 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N MET A 217 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE A 284 " --> pdb=" O MET A 217 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N VAL A 219 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLU A 282 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 313 through 315 Processing sheet with id=AA5, first strand: chain 'A' and resid 319 through 322 Processing sheet with id=AA6, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'B' and resid 181 through 183 removed outlier: 6.773A pdb=" N ALA B 187 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 230 through 238 removed outlier: 5.064A pdb=" N THR B 223 " --> pdb=" O PRO B 232 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET B 217 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA B 213 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLU B 288 " --> pdb=" O ALA B 213 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE B 215 " --> pdb=" O ILE B 286 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE B 286 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N MET B 217 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE B 284 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N VAL B 219 " --> pdb=" O GLU B 282 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLU B 282 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 313 through 315 Processing sheet with id=AB1, first strand: chain 'B' and resid 319 through 322 Processing sheet with id=AB2, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AB3, first strand: chain 'C' and resid 181 through 183 removed outlier: 6.774A pdb=" N ALA C 187 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 230 through 238 removed outlier: 5.064A pdb=" N THR C 223 " --> pdb=" O PRO C 232 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N MET C 217 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA C 213 " --> pdb=" O GLU C 288 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLU C 288 " --> pdb=" O ALA C 213 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE C 215 " --> pdb=" O ILE C 286 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE C 286 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N MET C 217 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE C 284 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N VAL C 219 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU C 282 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 313 through 315 Processing sheet with id=AB6, first strand: chain 'C' and resid 319 through 322 Processing sheet with id=AB7, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AB8, first strand: chain 'D' and resid 181 through 183 removed outlier: 6.773A pdb=" N ALA D 187 " --> pdb=" O LEU D 310 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 230 through 238 removed outlier: 5.064A pdb=" N THR D 223 " --> pdb=" O PRO D 232 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET D 217 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA D 213 " --> pdb=" O GLU D 288 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLU D 288 " --> pdb=" O ALA D 213 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE D 215 " --> pdb=" O ILE D 286 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE D 286 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N MET D 217 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE D 284 " --> pdb=" O MET D 217 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N VAL D 219 " --> pdb=" O GLU D 282 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU D 282 " --> pdb=" O VAL D 219 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 313 through 315 Processing sheet with id=AC2, first strand: chain 'D' and resid 319 through 322 447 hydrogen bonds defined for protein. 1224 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: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3272 1.34 - 1.46: 2071 1.46 - 1.57: 4857 1.57 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 10304 Sorted by residual: bond pdb=" CB GLU D 104 " pdb=" CG GLU D 104 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.05e+00 bond pdb=" CB GLU C 104 " pdb=" CG GLU C 104 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.04e+00 bond pdb=" CB GLU B 104 " pdb=" CG GLU B 104 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.03e+00 bond pdb=" CB GLU A 104 " pdb=" CG GLU A 104 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.98e+00 bond pdb=" CG GLU A 104 " pdb=" CD GLU A 104 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.16e+00 ... (remaining 10299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 13302 1.29 - 2.58: 580 2.58 - 3.88: 62 3.88 - 5.17: 41 5.17 - 6.46: 23 Bond angle restraints: 14008 Sorted by residual: angle pdb=" CB GLU B 104 " pdb=" CG GLU B 104 " pdb=" CD GLU B 104 " ideal model delta sigma weight residual 112.60 118.72 -6.12 1.70e+00 3.46e-01 1.29e+01 angle pdb=" CB GLU C 104 " pdb=" CG GLU C 104 " pdb=" CD GLU C 104 " ideal model delta sigma weight residual 112.60 118.71 -6.11 1.70e+00 3.46e-01 1.29e+01 angle pdb=" CB GLU A 104 " pdb=" CG GLU A 104 " pdb=" CD GLU A 104 " ideal model delta sigma weight residual 112.60 118.71 -6.11 1.70e+00 3.46e-01 1.29e+01 angle pdb=" CB GLU D 104 " pdb=" CG GLU D 104 " pdb=" CD GLU D 104 " ideal model delta sigma weight residual 112.60 118.71 -6.11 1.70e+00 3.46e-01 1.29e+01 angle pdb=" CA GLU C 104 " pdb=" CB GLU C 104 " pdb=" CG GLU C 104 " ideal model delta sigma weight residual 114.10 120.56 -6.46 2.00e+00 2.50e-01 1.04e+01 ... (remaining 14003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 5494 16.98 - 33.95: 446 33.95 - 50.93: 120 50.93 - 67.91: 52 67.91 - 84.88: 16 Dihedral angle restraints: 6128 sinusoidal: 2412 harmonic: 3716 Sorted by residual: dihedral pdb=" CB CYS A 110 " pdb=" SG CYS A 110 " pdb=" SG CYS A 142 " pdb=" CB CYS A 142 " ideal model delta sinusoidal sigma weight residual -86.00 -12.06 -73.94 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CB CYS D 110 " pdb=" SG CYS D 110 " pdb=" SG CYS D 142 " pdb=" CB CYS D 142 " ideal model delta sinusoidal sigma weight residual -86.00 -12.07 -73.93 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CB CYS C 110 " pdb=" SG CYS C 110 " pdb=" SG CYS C 142 " pdb=" CB CYS C 142 " ideal model delta sinusoidal sigma weight residual -86.00 -12.08 -73.92 1 1.00e+01 1.00e-02 6.94e+01 ... (remaining 6125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 834 0.029 - 0.058: 487 0.058 - 0.086: 148 0.086 - 0.115: 145 0.115 - 0.144: 38 Chirality restraints: 1652 Sorted by residual: chirality pdb=" CB ILE B 210 " pdb=" CA ILE B 210 " pdb=" CG1 ILE B 210 " pdb=" CG2 ILE B 210 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CB ILE A 210 " pdb=" CA ILE A 210 " pdb=" CG1 ILE A 210 " pdb=" CG2 ILE A 210 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CB ILE D 210 " pdb=" CA ILE D 210 " pdb=" CG1 ILE D 210 " pdb=" CG2 ILE D 210 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.98e-01 ... (remaining 1649 not shown) Planarity restraints: 1764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP D 68 " 0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO D 69 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO D 69 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 69 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 68 " -0.026 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO B 69 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 69 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 69 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP C 68 " -0.026 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO C 69 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 69 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 69 " -0.022 5.00e-02 4.00e+02 ... (remaining 1761 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.83: 3141 2.83 - 3.41: 10274 3.41 - 3.98: 19076 3.98 - 4.56: 26741 4.56 - 5.14: 40974 Nonbonded interactions: 100206 Sorted by model distance: nonbonded pdb=" O PRO C 109 " pdb=" OG1 THR C 139 " model vdw 2.252 3.040 nonbonded pdb=" O PRO B 109 " pdb=" OG1 THR B 139 " model vdw 2.252 3.040 nonbonded pdb=" O PRO D 109 " pdb=" OG1 THR D 139 " model vdw 2.252 3.040 nonbonded pdb=" O PRO A 109 " pdb=" OG1 THR A 139 " model vdw 2.253 3.040 nonbonded pdb=" OE2 GLU C 140 " pdb=" OG SER D 119 " model vdw 2.263 3.040 ... (remaining 100201 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 32 through 352) 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: 3.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.340 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 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 : 0.005 0.043 10308 Z= 0.235 Angle : 0.679 6.459 14016 Z= 0.398 Chirality : 0.048 0.144 1652 Planarity : 0.005 0.039 1764 Dihedral : 15.459 84.882 3700 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.68 % Allowed : 16.19 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.19), residues: 1276 helix: -1.26 (0.21), residues: 396 sheet: -1.35 (0.31), residues: 256 loop : -1.87 (0.20), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 177 TYR 0.007 0.001 TYR A 258 PHE 0.015 0.002 PHE B 75 TRP 0.006 0.001 TRP B 311 HIS 0.003 0.001 HIS D 175 Details of bonding type rmsd covalent geometry : bond 0.00514 (10304) covalent geometry : angle 0.67748 (14008) SS BOND : bond 0.00228 ( 4) SS BOND : angle 1.78093 ( 8) hydrogen bonds : bond 0.15100 ( 439) hydrogen bonds : angle 5.16719 ( 1224) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 172 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8968 (mmtm) cc_final: 0.8742 (mtmm) REVERT: A 47 LYS cc_start: 0.8461 (mtpp) cc_final: 0.8228 (mtpp) REVERT: A 332 LYS cc_start: 0.9210 (mttt) cc_final: 0.8944 (mtpp) REVERT: B 110 CYS cc_start: 0.6925 (OUTLIER) cc_final: 0.6448 (m) REVERT: B 137 MET cc_start: 0.9032 (ptt) cc_final: 0.8364 (ptm) REVERT: B 169 MET cc_start: 0.8866 (ttm) cc_final: 0.8451 (ttm) REVERT: B 185 LYS cc_start: 0.8927 (ttpp) cc_final: 0.8659 (ttpt) REVERT: B 222 LYS cc_start: 0.9133 (ttmt) cc_final: 0.8628 (ttpp) REVERT: B 225 SER cc_start: 0.8256 (OUTLIER) cc_final: 0.7555 (p) REVERT: C 67 LYS cc_start: 0.7945 (mttp) cc_final: 0.7209 (mmmt) REVERT: C 88 MET cc_start: 0.7668 (mtt) cc_final: 0.7462 (mtt) REVERT: C 102 PRO cc_start: 0.7896 (Cg_endo) cc_final: 0.7666 (Cg_exo) REVERT: C 185 LYS cc_start: 0.8762 (ttpp) cc_final: 0.8477 (tptt) REVERT: C 240 MET cc_start: 0.9007 (ttp) cc_final: 0.8788 (ttp) REVERT: C 304 TYR cc_start: 0.9174 (m-80) cc_final: 0.8871 (m-80) REVERT: D 47 LYS cc_start: 0.8207 (mtpp) cc_final: 0.7880 (mmtt) REVERT: D 67 LYS cc_start: 0.7763 (mttp) cc_final: 0.7459 (mtmt) REVERT: D 102 PRO cc_start: 0.7467 (Cg_endo) cc_final: 0.7149 (Cg_exo) REVERT: D 199 MET cc_start: 0.9054 (mtm) cc_final: 0.8827 (mtp) REVERT: D 217 MET cc_start: 0.8874 (mtm) cc_final: 0.8635 (mtm) outliers start: 52 outliers final: 27 residues processed: 215 average time/residue: 0.1103 time to fit residues: 32.7237 Evaluate side-chains 161 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 110 CYS Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 337 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.0040 chunk 35 optimal weight: 2.9990 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN A 160 ASN A 218 GLN A 234 HIS A 276 HIS A 277 HIS B 48 ASN B 218 GLN B 276 HIS ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN C 218 GLN C 234 HIS ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN D 218 GLN D 264 ASN D 276 HIS ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.088263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.077786 restraints weight = 16373.461| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.02 r_work: 0.2808 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 10308 Z= 0.248 Angle : 0.563 7.200 14016 Z= 0.303 Chirality : 0.046 0.129 1652 Planarity : 0.004 0.033 1764 Dihedral : 6.899 75.624 1403 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.51 % Allowed : 15.92 % Favored : 80.58 % 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: -0.88 (0.22), residues: 1276 helix: 0.66 (0.25), residues: 400 sheet: -1.14 (0.30), residues: 252 loop : -1.12 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 136 TYR 0.008 0.001 TYR A 268 PHE 0.017 0.002 PHE A 117 TRP 0.009 0.001 TRP C 311 HIS 0.003 0.001 HIS C 193 Details of bonding type rmsd covalent geometry : bond 0.00574 (10304) covalent geometry : angle 0.56165 (14008) SS BOND : bond 0.00544 ( 4) SS BOND : angle 1.75119 ( 8) hydrogen bonds : bond 0.04611 ( 439) hydrogen bonds : angle 4.34459 ( 1224) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 145 time to evaluate : 0.388 Fit side-chains REVERT: A 67 LYS cc_start: 0.8573 (mttp) cc_final: 0.7897 (mmmt) REVERT: A 77 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8537 (mpp) REVERT: A 160 ASN cc_start: 0.8941 (m-40) cc_final: 0.8638 (m110) REVERT: A 247 ASN cc_start: 0.9019 (p0) cc_final: 0.8709 (p0) REVERT: A 332 LYS cc_start: 0.9289 (mttt) cc_final: 0.9063 (mtpp) REVERT: B 47 LYS cc_start: 0.8610 (mtpp) cc_final: 0.8203 (mmmt) REVERT: B 67 LYS cc_start: 0.8418 (mttp) cc_final: 0.8038 (mtpt) REVERT: B 137 MET cc_start: 0.9435 (ptt) cc_final: 0.8933 (ptm) REVERT: B 160 ASN cc_start: 0.8931 (m-40) cc_final: 0.8701 (m-40) REVERT: B 169 MET cc_start: 0.9111 (ttm) cc_final: 0.8717 (ttm) REVERT: B 185 LYS cc_start: 0.9159 (ttpp) cc_final: 0.8832 (ttpt) REVERT: B 222 LYS cc_start: 0.9355 (ttmt) cc_final: 0.9043 (ttpp) REVERT: C 67 LYS cc_start: 0.8480 (mttp) cc_final: 0.7730 (mmmt) REVERT: C 185 LYS cc_start: 0.9072 (ttpp) cc_final: 0.8631 (tptt) REVERT: C 207 LYS cc_start: 0.8989 (tptm) cc_final: 0.8753 (tptt) REVERT: C 251 LEU cc_start: 0.9093 (tp) cc_final: 0.8875 (tp) REVERT: C 304 TYR cc_start: 0.9414 (m-80) cc_final: 0.9105 (m-80) REVERT: C 334 ASP cc_start: 0.9109 (OUTLIER) cc_final: 0.8514 (m-30) REVERT: D 32 ARG cc_start: 0.6630 (mmt90) cc_final: 0.6059 (mmt90) REVERT: D 47 LYS cc_start: 0.8619 (mtpp) cc_final: 0.8246 (mmtm) REVERT: D 57 GLN cc_start: 0.8536 (mt0) cc_final: 0.8108 (mm-40) REVERT: D 67 LYS cc_start: 0.8390 (mttp) cc_final: 0.8029 (mtmt) REVERT: D 93 ILE cc_start: 0.9429 (mm) cc_final: 0.9208 (mt) REVERT: D 199 MET cc_start: 0.9376 (mtm) cc_final: 0.9112 (mtp) REVERT: D 278 HIS cc_start: 0.7711 (OUTLIER) cc_final: 0.7179 (m-70) REVERT: D 305 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8911 (mm) REVERT: D 338 LYS cc_start: 0.8599 (mtpp) cc_final: 0.7925 (tptt) outliers start: 39 outliers final: 21 residues processed: 179 average time/residue: 0.1194 time to fit residues: 28.6329 Evaluate side-chains 159 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 334 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 87 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN C 276 HIS ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 GLN D 348 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.089578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.078773 restraints weight = 16456.402| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.08 r_work: 0.2811 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10308 Z= 0.193 Angle : 0.504 5.867 14016 Z= 0.271 Chirality : 0.045 0.137 1652 Planarity : 0.003 0.035 1764 Dihedral : 6.108 57.797 1385 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.87 % Allowed : 16.73 % Favored : 79.41 % 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: -0.23 (0.23), residues: 1276 helix: 1.39 (0.27), residues: 400 sheet: -0.94 (0.31), residues: 252 loop : -0.79 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 136 TYR 0.008 0.001 TYR A 330 PHE 0.016 0.001 PHE A 75 TRP 0.008 0.001 TRP C 311 HIS 0.003 0.001 HIS D 276 Details of bonding type rmsd covalent geometry : bond 0.00448 (10304) covalent geometry : angle 0.50261 (14008) SS BOND : bond 0.00322 ( 4) SS BOND : angle 1.55411 ( 8) hydrogen bonds : bond 0.04355 ( 439) hydrogen bonds : angle 4.14492 ( 1224) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 144 time to evaluate : 0.276 Fit side-chains REVERT: A 67 LYS cc_start: 0.8626 (mttp) cc_final: 0.7979 (mmmt) REVERT: A 77 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8557 (mpp) REVERT: B 47 LYS cc_start: 0.8638 (mtpp) cc_final: 0.8278 (mmmt) REVERT: B 67 LYS cc_start: 0.8578 (mttp) cc_final: 0.8336 (mtpt) REVERT: B 137 MET cc_start: 0.9442 (ptt) cc_final: 0.8940 (ptm) REVERT: B 185 LYS cc_start: 0.9138 (ttpp) cc_final: 0.8829 (ttpt) REVERT: C 67 LYS cc_start: 0.8586 (mttp) cc_final: 0.7853 (mmmt) REVERT: C 185 LYS cc_start: 0.9051 (ttpp) cc_final: 0.8692 (tptt) REVERT: C 207 LYS cc_start: 0.8938 (tptm) cc_final: 0.8607 (tptt) REVERT: C 304 TYR cc_start: 0.9384 (m-80) cc_final: 0.9176 (m-80) REVERT: C 334 ASP cc_start: 0.9187 (OUTLIER) cc_final: 0.8637 (m-30) REVERT: D 47 LYS cc_start: 0.8628 (mtpp) cc_final: 0.8372 (mmtm) REVERT: D 67 LYS cc_start: 0.8487 (mttp) cc_final: 0.8089 (mtmt) REVERT: D 199 MET cc_start: 0.9385 (mtm) cc_final: 0.9129 (mtp) REVERT: D 235 GLN cc_start: 0.9300 (OUTLIER) cc_final: 0.9025 (mt0) REVERT: D 278 HIS cc_start: 0.7695 (OUTLIER) cc_final: 0.7189 (m-70) REVERT: D 305 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9017 (mm) REVERT: D 338 LYS cc_start: 0.8613 (mtpp) cc_final: 0.7951 (tptt) outliers start: 43 outliers final: 29 residues processed: 176 average time/residue: 0.1174 time to fit residues: 27.6572 Evaluate side-chains 169 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 235 GLN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 339 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 94 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 97 optimal weight: 0.0020 chunk 121 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN C 348 GLN D 43 ASN D 277 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.090551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.080110 restraints weight = 16371.340| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 1.97 r_work: 0.2844 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10308 Z= 0.147 Angle : 0.469 5.202 14016 Z= 0.254 Chirality : 0.045 0.173 1652 Planarity : 0.003 0.036 1764 Dihedral : 5.805 57.294 1385 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.60 % Allowed : 16.73 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.24), residues: 1276 helix: 1.72 (0.27), residues: 400 sheet: -0.42 (0.34), residues: 220 loop : -0.53 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 206 TYR 0.006 0.001 TYR A 330 PHE 0.015 0.001 PHE A 75 TRP 0.006 0.001 TRP B 68 HIS 0.003 0.001 HIS D 276 Details of bonding type rmsd covalent geometry : bond 0.00336 (10304) covalent geometry : angle 0.46820 (14008) SS BOND : bond 0.00259 ( 4) SS BOND : angle 1.19427 ( 8) hydrogen bonds : bond 0.04195 ( 439) hydrogen bonds : angle 4.04038 ( 1224) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 0.389 Fit side-chains REVERT: A 67 LYS cc_start: 0.8647 (mttp) cc_final: 0.7997 (mmmt) REVERT: A 77 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8503 (mpp) REVERT: A 160 ASN cc_start: 0.8710 (m-40) cc_final: 0.8294 (m110) REVERT: A 268 TYR cc_start: 0.9205 (t80) cc_final: 0.8982 (t80) REVERT: B 47 LYS cc_start: 0.8589 (mtpp) cc_final: 0.8266 (mmmt) REVERT: B 67 LYS cc_start: 0.8627 (mttp) cc_final: 0.8037 (mmmt) REVERT: B 137 MET cc_start: 0.9384 (ptt) cc_final: 0.8889 (ptm) REVERT: B 185 LYS cc_start: 0.9107 (ttpp) cc_final: 0.8722 (ttpt) REVERT: B 334 ASP cc_start: 0.8922 (OUTLIER) cc_final: 0.8668 (m-30) REVERT: C 67 LYS cc_start: 0.8620 (mttp) cc_final: 0.7917 (mmmt) REVERT: C 185 LYS cc_start: 0.9025 (ttpp) cc_final: 0.8626 (tptt) REVERT: C 207 LYS cc_start: 0.8911 (tptm) cc_final: 0.8576 (tptt) REVERT: C 268 TYR cc_start: 0.9098 (t80) cc_final: 0.8688 (t80) REVERT: C 334 ASP cc_start: 0.9111 (OUTLIER) cc_final: 0.8636 (m-30) REVERT: D 47 LYS cc_start: 0.8609 (mtpp) cc_final: 0.8342 (mttm) REVERT: D 67 LYS cc_start: 0.8514 (mttp) cc_final: 0.8128 (mtmt) REVERT: D 199 MET cc_start: 0.9367 (mtm) cc_final: 0.9109 (mtp) REVERT: D 278 HIS cc_start: 0.7692 (OUTLIER) cc_final: 0.7198 (m-70) REVERT: D 305 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9108 (mm) REVERT: D 338 LYS cc_start: 0.8608 (mtpp) cc_final: 0.7924 (tptt) outliers start: 40 outliers final: 22 residues processed: 170 average time/residue: 0.1195 time to fit residues: 27.0716 Evaluate side-chains 166 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 235 GLN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 334 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 99 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 36 optimal weight: 0.0470 chunk 61 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 77 optimal weight: 0.0470 overall best weight: 0.5776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN B 277 HIS B 348 GLN C 41 ASN D 43 ASN D 277 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.091940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.081185 restraints weight = 16303.787| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.08 r_work: 0.2862 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10308 Z= 0.127 Angle : 0.451 5.249 14016 Z= 0.243 Chirality : 0.044 0.148 1652 Planarity : 0.003 0.036 1764 Dihedral : 5.358 54.220 1383 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.15 % Allowed : 17.63 % Favored : 79.23 % 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: 0.46 (0.24), residues: 1276 helix: 1.88 (0.27), residues: 400 sheet: -0.21 (0.35), residues: 216 loop : -0.47 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 206 TYR 0.007 0.001 TYR A 330 PHE 0.014 0.001 PHE D 75 TRP 0.005 0.001 TRP B 68 HIS 0.003 0.000 HIS D 276 Details of bonding type rmsd covalent geometry : bond 0.00289 (10304) covalent geometry : angle 0.45005 (14008) SS BOND : bond 0.00232 ( 4) SS BOND : angle 1.07293 ( 8) hydrogen bonds : bond 0.04047 ( 439) hydrogen bonds : angle 3.90051 ( 1224) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 0.297 Fit side-chains REVERT: A 67 LYS cc_start: 0.8621 (mttp) cc_final: 0.7978 (mmmt) REVERT: A 77 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8497 (mpp) REVERT: A 160 ASN cc_start: 0.8750 (m-40) cc_final: 0.8409 (m110) REVERT: A 268 TYR cc_start: 0.9182 (t80) cc_final: 0.8937 (t80) REVERT: B 47 LYS cc_start: 0.8576 (mtpp) cc_final: 0.8231 (mmmt) REVERT: B 67 LYS cc_start: 0.8507 (mttp) cc_final: 0.8250 (mtpt) REVERT: B 137 MET cc_start: 0.9350 (ptt) cc_final: 0.8841 (ptm) REVERT: B 185 LYS cc_start: 0.9129 (ttpp) cc_final: 0.8727 (ttpt) REVERT: B 277 HIS cc_start: 0.7649 (OUTLIER) cc_final: 0.7423 (t70) REVERT: C 67 LYS cc_start: 0.8607 (mttp) cc_final: 0.7882 (mmmt) REVERT: C 185 LYS cc_start: 0.9025 (ttpp) cc_final: 0.8687 (tptt) REVERT: C 207 LYS cc_start: 0.8957 (tptm) cc_final: 0.8593 (mptt) REVERT: C 304 TYR cc_start: 0.9383 (m-80) cc_final: 0.9056 (m-80) REVERT: C 334 ASP cc_start: 0.8963 (OUTLIER) cc_final: 0.8518 (m-30) REVERT: D 47 LYS cc_start: 0.8619 (mtpp) cc_final: 0.8327 (mmtm) REVERT: D 67 LYS cc_start: 0.8397 (mttp) cc_final: 0.8057 (mtmt) REVERT: D 93 ILE cc_start: 0.9386 (mm) cc_final: 0.9185 (mt) REVERT: D 199 MET cc_start: 0.9365 (mtm) cc_final: 0.9111 (mtp) REVERT: D 278 HIS cc_start: 0.7676 (OUTLIER) cc_final: 0.7327 (m-70) REVERT: D 305 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9091 (mm) REVERT: D 338 LYS cc_start: 0.8647 (mtpp) cc_final: 0.7918 (tptt) outliers start: 35 outliers final: 19 residues processed: 171 average time/residue: 0.1184 time to fit residues: 27.4183 Evaluate side-chains 169 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 235 GLN Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 277 HIS Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 337 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 75 optimal weight: 0.7980 chunk 115 optimal weight: 0.5980 chunk 32 optimal weight: 0.0570 chunk 9 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 116 optimal weight: 0.6980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN B 160 ASN B 277 HIS C 41 ASN D 216 HIS D 235 GLN D 277 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.091603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.080781 restraints weight = 16258.938| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.08 r_work: 0.2843 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10308 Z= 0.129 Angle : 0.447 5.201 14016 Z= 0.242 Chirality : 0.044 0.135 1652 Planarity : 0.003 0.039 1764 Dihedral : 4.857 52.315 1375 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.97 % Allowed : 18.35 % Favored : 78.69 % 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: 0.56 (0.24), residues: 1276 helix: 1.95 (0.27), residues: 400 sheet: -0.25 (0.35), residues: 220 loop : -0.35 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 206 TYR 0.018 0.001 TYR C 268 PHE 0.014 0.001 PHE D 75 TRP 0.005 0.001 TRP B 68 HIS 0.007 0.001 HIS B 277 Details of bonding type rmsd covalent geometry : bond 0.00293 (10304) covalent geometry : angle 0.44671 (14008) SS BOND : bond 0.00237 ( 4) SS BOND : angle 0.96862 ( 8) hydrogen bonds : bond 0.04034 ( 439) hydrogen bonds : angle 3.86512 ( 1224) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 0.365 Fit side-chains REVERT: A 67 LYS cc_start: 0.8440 (mttp) cc_final: 0.7785 (mmmt) REVERT: A 77 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8439 (mpp) REVERT: A 160 ASN cc_start: 0.8754 (m-40) cc_final: 0.8365 (m110) REVERT: A 268 TYR cc_start: 0.9223 (t80) cc_final: 0.8845 (t80) REVERT: B 47 LYS cc_start: 0.8484 (mtpp) cc_final: 0.8078 (mmmt) REVERT: B 67 LYS cc_start: 0.8401 (mttp) cc_final: 0.8127 (mtpt) REVERT: B 137 MET cc_start: 0.9321 (ptt) cc_final: 0.8774 (ptm) REVERT: B 185 LYS cc_start: 0.9054 (ttpp) cc_final: 0.8654 (ttpt) REVERT: C 39 LYS cc_start: 0.9208 (mtmm) cc_final: 0.8969 (mtmm) REVERT: C 67 LYS cc_start: 0.8462 (mttp) cc_final: 0.7684 (mmmt) REVERT: C 185 LYS cc_start: 0.9024 (ttpp) cc_final: 0.8572 (tptt) REVERT: C 207 LYS cc_start: 0.8985 (tptm) cc_final: 0.8591 (tptt) REVERT: C 304 TYR cc_start: 0.9377 (m-80) cc_final: 0.9063 (m-80) REVERT: C 334 ASP cc_start: 0.8907 (OUTLIER) cc_final: 0.8441 (m-30) REVERT: D 47 LYS cc_start: 0.8553 (mtpp) cc_final: 0.8183 (mmtm) REVERT: D 57 GLN cc_start: 0.8426 (mt0) cc_final: 0.8001 (mm-40) REVERT: D 67 LYS cc_start: 0.8226 (mttp) cc_final: 0.7482 (tptt) REVERT: D 199 MET cc_start: 0.9340 (mtm) cc_final: 0.9078 (mtp) REVERT: D 247 ASN cc_start: 0.9080 (p0) cc_final: 0.8816 (p0) REVERT: D 278 HIS cc_start: 0.7709 (OUTLIER) cc_final: 0.7357 (m-70) REVERT: D 305 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8960 (mm) REVERT: D 338 LYS cc_start: 0.8687 (mtpp) cc_final: 0.7900 (tptt) outliers start: 33 outliers final: 22 residues processed: 175 average time/residue: 0.1097 time to fit residues: 25.9148 Evaluate side-chains 173 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 235 GLN Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 277 HIS Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 337 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 94 optimal weight: 0.0470 chunk 51 optimal weight: 0.0000 chunk 76 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 overall best weight: 0.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN C 41 ASN D 43 ASN D 216 HIS D 235 GLN D 277 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.092811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.082362 restraints weight = 15874.097| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.99 r_work: 0.2868 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10308 Z= 0.110 Angle : 0.442 5.180 14016 Z= 0.240 Chirality : 0.044 0.133 1652 Planarity : 0.003 0.036 1764 Dihedral : 4.731 49.735 1374 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.15 % Allowed : 17.72 % Favored : 79.14 % 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: 0.65 (0.24), residues: 1276 helix: 2.01 (0.27), residues: 400 sheet: -0.05 (0.35), residues: 216 loop : -0.34 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 206 TYR 0.012 0.001 TYR C 268 PHE 0.014 0.001 PHE A 75 TRP 0.004 0.001 TRP B 68 HIS 0.003 0.000 HIS B 276 Details of bonding type rmsd covalent geometry : bond 0.00242 (10304) covalent geometry : angle 0.44188 (14008) SS BOND : bond 0.00213 ( 4) SS BOND : angle 0.91792 ( 8) hydrogen bonds : bond 0.03966 ( 439) hydrogen bonds : angle 3.80258 ( 1224) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.387 Fit side-chains REVERT: A 67 LYS cc_start: 0.8499 (mttp) cc_final: 0.8292 (mtpt) REVERT: A 77 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8426 (mpp) REVERT: A 140 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8497 (mp0) REVERT: A 160 ASN cc_start: 0.8733 (m-40) cc_final: 0.8352 (m110) REVERT: A 258 TYR cc_start: 0.9136 (p90) cc_final: 0.8545 (p90) REVERT: A 268 TYR cc_start: 0.9205 (t80) cc_final: 0.8811 (t80) REVERT: B 47 LYS cc_start: 0.8453 (mtpp) cc_final: 0.8071 (mmmt) REVERT: B 67 LYS cc_start: 0.8417 (mttp) cc_final: 0.8151 (mtpt) REVERT: B 137 MET cc_start: 0.9305 (ptt) cc_final: 0.8767 (ptm) REVERT: B 185 LYS cc_start: 0.9031 (ttpp) cc_final: 0.8658 (ttpt) REVERT: B 247 ASN cc_start: 0.9214 (p0) cc_final: 0.8698 (p0) REVERT: C 67 LYS cc_start: 0.8434 (mttp) cc_final: 0.7697 (mmmt) REVERT: C 185 LYS cc_start: 0.9009 (ttpp) cc_final: 0.8606 (tptt) REVERT: C 207 LYS cc_start: 0.8962 (tptm) cc_final: 0.8584 (tptt) REVERT: C 304 TYR cc_start: 0.9360 (m-80) cc_final: 0.9142 (m-80) REVERT: C 334 ASP cc_start: 0.8887 (OUTLIER) cc_final: 0.8503 (m-30) REVERT: D 47 LYS cc_start: 0.8542 (mtpp) cc_final: 0.8184 (mmtm) REVERT: D 57 GLN cc_start: 0.8387 (mt0) cc_final: 0.7977 (mm-40) REVERT: D 67 LYS cc_start: 0.8268 (mttp) cc_final: 0.7538 (tptt) REVERT: D 199 MET cc_start: 0.9325 (mtm) cc_final: 0.9074 (mtp) REVERT: D 247 ASN cc_start: 0.9094 (p0) cc_final: 0.8861 (p0) REVERT: D 278 HIS cc_start: 0.7757 (OUTLIER) cc_final: 0.7419 (m-70) REVERT: D 305 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.9009 (mm) REVERT: D 338 LYS cc_start: 0.8639 (mtpp) cc_final: 0.7905 (tptt) outliers start: 35 outliers final: 23 residues processed: 172 average time/residue: 0.1233 time to fit residues: 28.7051 Evaluate side-chains 173 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 235 GLN Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 337 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 106 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 0.2980 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 0.1980 chunk 24 optimal weight: 4.9990 chunk 2 optimal weight: 0.3980 chunk 15 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN C 41 ASN D 216 HIS D 235 GLN D 277 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.091953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.080946 restraints weight = 16110.304| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.13 r_work: 0.2890 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10308 Z= 0.108 Angle : 0.440 5.181 14016 Z= 0.238 Chirality : 0.043 0.132 1652 Planarity : 0.003 0.036 1764 Dihedral : 4.640 46.314 1374 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.79 % Allowed : 18.17 % Favored : 79.05 % 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: 0.71 (0.24), residues: 1276 helix: 2.06 (0.27), residues: 400 sheet: -0.05 (0.35), residues: 216 loop : -0.30 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 206 TYR 0.011 0.001 TYR A 330 PHE 0.013 0.001 PHE D 75 TRP 0.004 0.001 TRP B 68 HIS 0.003 0.000 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.00237 (10304) covalent geometry : angle 0.43965 (14008) SS BOND : bond 0.00207 ( 4) SS BOND : angle 0.89336 ( 8) hydrogen bonds : bond 0.03933 ( 439) hydrogen bonds : angle 3.76925 ( 1224) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.412 Fit side-chains REVERT: A 77 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8546 (mmm) REVERT: A 140 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8517 (mp0) REVERT: A 160 ASN cc_start: 0.8727 (m-40) cc_final: 0.8343 (m110) REVERT: A 258 TYR cc_start: 0.9155 (p90) cc_final: 0.8592 (p90) REVERT: A 268 TYR cc_start: 0.9240 (t80) cc_final: 0.8848 (t80) REVERT: B 47 LYS cc_start: 0.8464 (mtpp) cc_final: 0.8078 (mmmt) REVERT: B 67 LYS cc_start: 0.8436 (mttp) cc_final: 0.8181 (mtpt) REVERT: B 137 MET cc_start: 0.9278 (ptt) cc_final: 0.8750 (ptm) REVERT: B 185 LYS cc_start: 0.9039 (ttpp) cc_final: 0.8675 (ttpt) REVERT: C 39 LYS cc_start: 0.9200 (mtmm) cc_final: 0.8955 (mtmm) REVERT: C 67 LYS cc_start: 0.8461 (mttp) cc_final: 0.7575 (tptp) REVERT: C 185 LYS cc_start: 0.9024 (ttpp) cc_final: 0.8691 (tptt) REVERT: C 207 LYS cc_start: 0.9019 (tptm) cc_final: 0.8584 (mptt) REVERT: D 47 LYS cc_start: 0.8573 (mtpp) cc_final: 0.8175 (mtpp) REVERT: D 67 LYS cc_start: 0.8297 (mttp) cc_final: 0.7571 (tptt) REVERT: D 199 MET cc_start: 0.9333 (mtm) cc_final: 0.9086 (mtp) REVERT: D 278 HIS cc_start: 0.7804 (OUTLIER) cc_final: 0.7481 (m-70) REVERT: D 305 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9025 (mm) outliers start: 31 outliers final: 22 residues processed: 169 average time/residue: 0.1170 time to fit residues: 26.6899 Evaluate side-chains 169 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 235 GLN Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 337 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 11 optimal weight: 0.1980 chunk 106 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 107 optimal weight: 1.9990 chunk 51 optimal weight: 0.0010 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN C 41 ASN D 235 GLN D 277 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.092006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.081087 restraints weight = 16184.805| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.12 r_work: 0.2893 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10308 Z= 0.105 Angle : 0.441 5.172 14016 Z= 0.238 Chirality : 0.044 0.137 1652 Planarity : 0.003 0.036 1764 Dihedral : 4.538 43.299 1372 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.79 % Allowed : 18.79 % Favored : 78.42 % 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: 0.76 (0.24), residues: 1276 helix: 2.10 (0.27), residues: 400 sheet: -0.02 (0.35), residues: 216 loop : -0.27 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 206 TYR 0.010 0.001 TYR A 330 PHE 0.013 0.001 PHE D 75 TRP 0.004 0.001 TRP C 68 HIS 0.003 0.000 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.00230 (10304) covalent geometry : angle 0.44024 (14008) SS BOND : bond 0.00202 ( 4) SS BOND : angle 0.86817 ( 8) hydrogen bonds : bond 0.03885 ( 439) hydrogen bonds : angle 3.74476 ( 1224) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.401 Fit side-chains REVERT: A 77 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8539 (mmm) REVERT: A 140 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8510 (mp0) REVERT: A 160 ASN cc_start: 0.8707 (m-40) cc_final: 0.8321 (m110) REVERT: A 258 TYR cc_start: 0.9155 (p90) cc_final: 0.8599 (p90) REVERT: A 268 TYR cc_start: 0.9231 (t80) cc_final: 0.8859 (t80) REVERT: B 47 LYS cc_start: 0.8404 (mtpp) cc_final: 0.8004 (mmmt) REVERT: B 50 ARG cc_start: 0.6812 (mmt-90) cc_final: 0.6534 (mmp80) REVERT: B 67 LYS cc_start: 0.8464 (mttp) cc_final: 0.8228 (mtpt) REVERT: B 93 ILE cc_start: 0.9204 (mm) cc_final: 0.8991 (mt) REVERT: B 137 MET cc_start: 0.9260 (ptt) cc_final: 0.8799 (ptm) REVERT: B 185 LYS cc_start: 0.9038 (ttpp) cc_final: 0.8681 (ttpt) REVERT: C 39 LYS cc_start: 0.9219 (mtmm) cc_final: 0.8978 (mtmm) REVERT: C 67 LYS cc_start: 0.8475 (mttp) cc_final: 0.7564 (tptp) REVERT: C 185 LYS cc_start: 0.9011 (ttpp) cc_final: 0.8745 (tptt) REVERT: C 207 LYS cc_start: 0.9052 (tptm) cc_final: 0.8585 (mptt) REVERT: C 304 TYR cc_start: 0.9317 (m-80) cc_final: 0.9059 (m-80) REVERT: D 47 LYS cc_start: 0.8461 (mtpp) cc_final: 0.8040 (mtpp) REVERT: D 67 LYS cc_start: 0.8311 (mttp) cc_final: 0.7583 (tptt) REVERT: D 199 MET cc_start: 0.9333 (mtm) cc_final: 0.9089 (mtp) REVERT: D 247 ASN cc_start: 0.9114 (p0) cc_final: 0.8783 (p0) REVERT: D 278 HIS cc_start: 0.7800 (OUTLIER) cc_final: 0.7477 (m-70) REVERT: D 305 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.9040 (mm) outliers start: 31 outliers final: 22 residues processed: 171 average time/residue: 0.1230 time to fit residues: 28.2220 Evaluate side-chains 171 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 235 GLN Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 337 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 60 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 79 optimal weight: 0.0870 chunk 19 optimal weight: 0.0870 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 ASN D 235 GLN D 264 ASN D 277 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.091752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.080756 restraints weight = 16058.032| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.12 r_work: 0.2890 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10308 Z= 0.115 Angle : 0.450 6.413 14016 Z= 0.242 Chirality : 0.044 0.130 1652 Planarity : 0.003 0.035 1764 Dihedral : 4.511 40.405 1372 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.79 % Allowed : 18.97 % Favored : 78.24 % 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: 0.78 (0.24), residues: 1276 helix: 2.12 (0.27), residues: 400 sheet: -0.03 (0.35), residues: 216 loop : -0.25 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 206 TYR 0.010 0.001 TYR A 330 PHE 0.014 0.001 PHE D 75 TRP 0.004 0.001 TRP B 68 HIS 0.003 0.000 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.00259 (10304) covalent geometry : angle 0.44933 (14008) SS BOND : bond 0.00220 ( 4) SS BOND : angle 0.88212 ( 8) hydrogen bonds : bond 0.03893 ( 439) hydrogen bonds : angle 3.74369 ( 1224) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.376 Fit side-chains REVERT: A 77 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8541 (mmm) REVERT: A 140 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8549 (mp0) REVERT: A 160 ASN cc_start: 0.8712 (m-40) cc_final: 0.8323 (m110) REVERT: A 258 TYR cc_start: 0.9158 (p90) cc_final: 0.8598 (p90) REVERT: A 268 TYR cc_start: 0.9233 (t80) cc_final: 0.8861 (t80) REVERT: B 47 LYS cc_start: 0.8462 (mtpp) cc_final: 0.8141 (mmmt) REVERT: B 50 ARG cc_start: 0.6820 (mmt-90) cc_final: 0.6544 (mmp80) REVERT: B 67 LYS cc_start: 0.8451 (mttp) cc_final: 0.8198 (mtpt) REVERT: B 93 ILE cc_start: 0.9203 (mm) cc_final: 0.8988 (mt) REVERT: B 137 MET cc_start: 0.9262 (ptt) cc_final: 0.8796 (ptm) REVERT: B 185 LYS cc_start: 0.9054 (ttpp) cc_final: 0.8690 (ttpt) REVERT: C 39 LYS cc_start: 0.9237 (mtmm) cc_final: 0.8958 (mtmm) REVERT: C 67 LYS cc_start: 0.8473 (mttp) cc_final: 0.7529 (tptp) REVERT: C 185 LYS cc_start: 0.9028 (ttpp) cc_final: 0.8759 (tptt) REVERT: C 207 LYS cc_start: 0.9045 (tptm) cc_final: 0.8580 (mptt) REVERT: C 304 TYR cc_start: 0.9367 (m-80) cc_final: 0.9045 (m-80) REVERT: D 47 LYS cc_start: 0.8467 (mtpp) cc_final: 0.8043 (mtpp) REVERT: D 67 LYS cc_start: 0.8295 (mttp) cc_final: 0.7564 (tptt) REVERT: D 199 MET cc_start: 0.9337 (mtm) cc_final: 0.9088 (mtp) REVERT: D 278 HIS cc_start: 0.7755 (OUTLIER) cc_final: 0.7381 (m-70) REVERT: D 305 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.9028 (mm) outliers start: 31 outliers final: 24 residues processed: 167 average time/residue: 0.1102 time to fit residues: 25.0239 Evaluate side-chains 169 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 337 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 75 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 ASN D 235 GLN ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 ASN D 277 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.091811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.081773 restraints weight = 16207.297| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.88 r_work: 0.2852 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10308 Z= 0.171 Angle : 0.481 5.882 14016 Z= 0.259 Chirality : 0.044 0.134 1652 Planarity : 0.003 0.035 1764 Dihedral : 4.629 40.443 1372 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.97 % Allowed : 18.88 % Favored : 78.15 % 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: 0.73 (0.24), residues: 1276 helix: 2.06 (0.27), residues: 400 sheet: -0.04 (0.35), residues: 216 loop : -0.27 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 206 TYR 0.011 0.001 TYR A 330 PHE 0.014 0.001 PHE A 75 TRP 0.006 0.001 TRP C 311 HIS 0.003 0.001 HIS D 276 Details of bonding type rmsd covalent geometry : bond 0.00396 (10304) covalent geometry : angle 0.48072 (14008) SS BOND : bond 0.00291 ( 4) SS BOND : angle 0.95231 ( 8) hydrogen bonds : bond 0.04091 ( 439) hydrogen bonds : angle 3.85069 ( 1224) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2271.36 seconds wall clock time: 39 minutes 44.14 seconds (2384.14 seconds total)