Starting phenix.real_space_refine on Sat Aug 23 01:46:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z9p_39866/08_2025/8z9p_39866.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z9p_39866/08_2025/8z9p_39866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z9p_39866/08_2025/8z9p_39866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z9p_39866/08_2025/8z9p_39866.map" model { file = "/net/cci-nas-00/data/ceres_data/8z9p_39866/08_2025/8z9p_39866.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z9p_39866/08_2025/8z9p_39866.cif" } resolution = 2.5 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= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5828 2.51 5 N 1562 2.21 5 O 1698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9151 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2448 Classifications: {'peptide': 303} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 290} Chain: "C" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1812 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "S" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1784 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "R" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.65, per 1000 atoms: 0.18 Number of scatterers: 9151 At special positions: 0 Unit cell: (89.28, 119.97, 129.27, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1698 8.00 N 1562 7.00 C 5828 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 9 " - pdb=" SG CYS R 258 " distance=2.00 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 168 " distance=2.15 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.02 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.02 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: 0.82 Conformation dependent library (CDL) restraints added in 303.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2166 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 16 sheets defined 40.5% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'B' and resid 2 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 6 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'R' and resid 18 through 48 Proline residue: R 33 - end of helix Processing helix chain 'R' and resid 49 through 52 removed outlier: 6.338A pdb=" N LEU R 52 " --> pdb=" O ARG R 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 49 through 52' Processing helix chain 'R' and resid 53 through 79 Proline residue: R 71 - end of helix Processing helix chain 'R' and resid 87 through 121 removed outlier: 4.544A pdb=" N ILE R 101 " --> pdb=" O PHE R 97 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N TYR R 102 " --> pdb=" O TYR R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 129 Processing helix chain 'R' and resid 130 through 149 Processing helix chain 'R' and resid 150 through 155 Processing helix chain 'R' and resid 175 through 188 removed outlier: 3.631A pdb=" N TRP R 180 " --> pdb=" O GLY R 176 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N MET R 181 " --> pdb=" O TRP R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 210 Processing helix chain 'R' and resid 215 through 254 removed outlier: 3.554A pdb=" N ILE R 230 " --> pdb=" O ALA R 226 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N VAL R 233 " --> pdb=" O LEU R 229 " (cutoff:3.500A) Proline residue: R 239 - end of helix removed outlier: 4.373A pdb=" N LEU R 243 " --> pdb=" O PRO R 239 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 263 Processing helix chain 'R' and resid 264 through 275 Processing helix chain 'R' and resid 277 through 287 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 290 through 310 removed outlier: 4.433A pdb=" N ASP R 296 " --> pdb=" O GLY R 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 33 Processing helix chain 'C' and resid 45 through 53 removed outlier: 4.118A pdb=" N LYS C 51 " --> pdb=" O ASN C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 216 removed outlier: 4.964A pdb=" N ILE C 212 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N HIS C 213 " --> pdb=" O LYS C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 231 removed outlier: 3.578A pdb=" N ASP C 231 " --> pdb=" O SER C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 255 Processing helix chain 'C' and resid 270 through 278 Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 295 through 309 Processing helix chain 'C' and resid 330 through 351 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.732A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 74 through 76 No H-bonds generated for 'chain 'S' and resid 74 through 76' Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'S' and resid 220 through 224 Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.616A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.565A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.954A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.539A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.529A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.579A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.518A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 158 through 160 Processing sheet with id=AA9, first strand: chain 'C' and resid 185 through 191 removed outlier: 6.159A pdb=" N VAL C 34 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N PHE C 199 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU C 36 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LYS C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE C 222 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N LEU C 39 " --> pdb=" O CYS C 224 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 233 through 234 removed outlier: 5.796A pdb=" N MET C 240 " --> pdb=" O LEU C 234 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.697A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 10 through 12 removed outlier: 4.198A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB6, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.381A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.683A pdb=" N THR S 238 " --> pdb=" O GLN S 231 " (cutoff:3.500A) 484 hydrogen bonds defined for protein. 1305 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: 1.38 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 1946 1.32 - 1.46: 3302 1.46 - 1.59: 4014 1.59 - 1.73: 26 1.73 - 1.87: 70 Bond restraints: 9358 Sorted by residual: bond pdb=" CB LEU S 79 " pdb=" CG LEU S 79 " ideal model delta sigma weight residual 1.530 1.354 0.176 2.00e-02 2.50e+03 7.73e+01 bond pdb=" CB HIS R 121 " pdb=" CG HIS R 121 " ideal model delta sigma weight residual 1.497 1.375 0.122 1.40e-02 5.10e+03 7.59e+01 bond pdb=" CA ALA B 242 " pdb=" C ALA B 242 " ideal model delta sigma weight residual 1.522 1.430 0.092 1.20e-02 6.94e+03 5.93e+01 bond pdb=" NE ARG G 62 " pdb=" CZ ARG G 62 " ideal model delta sigma weight residual 1.326 1.400 -0.074 1.10e-02 8.26e+03 4.47e+01 bond pdb=" C TYR R 184 " pdb=" N ARG R 185 " ideal model delta sigma weight residual 1.334 1.417 -0.083 1.38e-02 5.25e+03 3.61e+01 ... (remaining 9353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.35: 12316 4.35 - 8.71: 364 8.71 - 13.06: 9 13.06 - 17.41: 0 17.41 - 21.76: 1 Bond angle restraints: 12690 Sorted by residual: angle pdb=" N HIS R 85 " pdb=" CA HIS R 85 " pdb=" C HIS R 85 " ideal model delta sigma weight residual 110.80 89.04 21.76 2.13e+00 2.20e-01 1.04e+02 angle pdb=" CA PRO S 107 " pdb=" C PRO S 107 " pdb=" O PRO S 107 " ideal model delta sigma weight residual 121.86 111.37 10.49 1.22e+00 6.72e-01 7.40e+01 angle pdb=" CA ALA C 226 " pdb=" C ALA C 226 " pdb=" O ALA C 226 " ideal model delta sigma weight residual 120.32 111.00 9.32 1.10e+00 8.26e-01 7.17e+01 angle pdb=" N TRP R 194 " pdb=" CA TRP R 194 " pdb=" C TRP R 194 " ideal model delta sigma weight residual 112.23 101.87 10.36 1.26e+00 6.30e-01 6.76e+01 angle pdb=" CA PHE C 274 " pdb=" C PHE C 274 " pdb=" O PHE C 274 " ideal model delta sigma weight residual 120.82 113.03 7.79 1.05e+00 9.07e-01 5.50e+01 ... (remaining 12685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.76: 5427 16.76 - 33.52: 165 33.52 - 50.27: 23 50.27 - 67.03: 11 67.03 - 83.79: 8 Dihedral angle restraints: 5634 sinusoidal: 2272 harmonic: 3362 Sorted by residual: dihedral pdb=" CB CYS S 22 " pdb=" SG CYS S 22 " pdb=" SG CYS S 96 " pdb=" CB CYS S 96 " ideal model delta sinusoidal sigma weight residual 93.00 160.61 -67.61 1 1.00e+01 1.00e-02 5.94e+01 dihedral pdb=" C HIS R 85 " pdb=" N HIS R 85 " pdb=" CA HIS R 85 " pdb=" CB HIS R 85 " ideal model delta harmonic sigma weight residual -122.60 -108.11 -14.49 0 2.50e+00 1.60e-01 3.36e+01 dihedral pdb=" CA ALA R 293 " pdb=" C ALA R 293 " pdb=" N ARG R 294 " pdb=" CA ARG R 294 " ideal model delta harmonic sigma weight residual -180.00 -155.89 -24.11 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 5631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 989 0.105 - 0.209: 359 0.209 - 0.314: 59 0.314 - 0.418: 10 0.418 - 0.523: 3 Chirality restraints: 1420 Sorted by residual: chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.84 0.52 2.00e-01 2.50e+01 6.83e+00 chirality pdb=" C14 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C15 CLR R 402 " pdb=" C8 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.84 0.52 2.00e-01 2.50e+01 6.81e+00 chirality pdb=" CG LEU S 247 " pdb=" CB LEU S 247 " pdb=" CD1 LEU S 247 " pdb=" CD2 LEU S 247 " both_signs ideal model delta sigma weight residual False -2.59 -3.04 0.45 2.00e-01 2.50e+01 4.97e+00 ... (remaining 1417 not shown) Planarity restraints: 1605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 226 " -0.077 2.00e-02 2.50e+03 1.61e-01 2.58e+02 pdb=" C ALA C 226 " 0.278 2.00e-02 2.50e+03 pdb=" O ALA C 226 " -0.105 2.00e-02 2.50e+03 pdb=" N LEU C 227 " -0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 30 " -0.071 2.00e-02 2.50e+03 1.49e-01 2.21e+02 pdb=" C LEU B 30 " 0.257 2.00e-02 2.50e+03 pdb=" O LEU B 30 " -0.099 2.00e-02 2.50e+03 pdb=" N SER B 31 " -0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO S 107 " 0.069 2.00e-02 2.50e+03 1.48e-01 2.18e+02 pdb=" C PRO S 107 " -0.255 2.00e-02 2.50e+03 pdb=" O PRO S 107 " 0.098 2.00e-02 2.50e+03 pdb=" N PHE S 108 " 0.088 2.00e-02 2.50e+03 ... (remaining 1602 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 64 2.54 - 3.13: 7585 3.13 - 3.72: 14282 3.72 - 4.31: 21462 4.31 - 4.90: 35088 Nonbonded interactions: 78481 Sorted by model distance: nonbonded pdb=" O ASN R 164 " pdb=" OD1 ASN R 164 " model vdw 1.954 3.040 nonbonded pdb=" N HIS R 85 " pdb=" O HIS R 85 " model vdw 2.210 2.496 nonbonded pdb=" O TRP R 83 " pdb=" C ILE R 84 " model vdw 2.245 3.270 nonbonded pdb=" O TRP R 83 " pdb=" N HIS R 85 " model vdw 2.281 3.120 nonbonded pdb=" OE2 GLU R 145 " pdb=" C4 CLR R 402 " model vdw 2.318 3.440 ... (remaining 78476 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.100 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 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 : 0.025 0.189 9362 Z= 1.351 Angle : 1.783 21.764 12698 Z= 1.195 Chirality : 0.107 0.523 1420 Planarity : 0.013 0.161 1605 Dihedral : 9.593 83.787 3456 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.36 % Favored : 97.38 % Rotamer: Outliers : 0.10 % Allowed : 0.91 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.24), residues: 1145 helix: -0.13 (0.22), residues: 398 sheet: 1.14 (0.30), residues: 273 loop : 0.84 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG S 98 TYR 0.048 0.008 TYR R 102 PHE 0.038 0.007 PHE B 199 TRP 0.056 0.010 TRP B 99 HIS 0.007 0.002 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.02541 ( 9358) covalent geometry : angle 1.77976 (12690) SS BOND : bond 0.06127 ( 4) SS BOND : angle 4.89137 ( 8) hydrogen bonds : bond 0.16587 ( 473) hydrogen bonds : angle 7.14550 ( 1305) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 199 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 43 TYR cc_start: 0.7432 (t80) cc_final: 0.6998 (t80) REVERT: R 83 TRP cc_start: 0.7607 (t-100) cc_final: 0.7263 (t-100) REVERT: R 252 LEU cc_start: 0.8197 (mt) cc_final: 0.7996 (pp) REVERT: C 28 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7193 (mt-10) REVERT: C 49 ILE cc_start: 0.8258 (mt) cc_final: 0.7568 (mp) REVERT: C 197 LYS cc_start: 0.8425 (ttmt) cc_final: 0.8208 (ttpp) REVERT: C 322 HIS cc_start: 0.7025 (m-70) cc_final: 0.6483 (m90) outliers start: 1 outliers final: 0 residues processed: 200 average time/residue: 0.6180 time to fit residues: 130.0646 Evaluate side-chains 127 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 10 HIS R 100 ASN R 303 ASN C 22 ASN C 204 GLN C 333 GLN S 186 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.132504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.101615 restraints weight = 14033.902| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.12 r_work: 0.3333 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9362 Z= 0.166 Angle : 0.649 8.510 12698 Z= 0.343 Chirality : 0.045 0.138 1420 Planarity : 0.004 0.033 1605 Dihedral : 5.780 51.522 1394 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.57 % Favored : 98.34 % Rotamer: Outliers : 3.15 % Allowed : 8.74 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.24), residues: 1145 helix: 1.16 (0.25), residues: 415 sheet: 0.90 (0.29), residues: 287 loop : 0.30 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 127 TYR 0.017 0.002 TYR R 251 PHE 0.024 0.002 PHE R 159 TRP 0.021 0.002 TRP R 73 HIS 0.007 0.002 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 9358) covalent geometry : angle 0.64519 (12690) SS BOND : bond 0.00605 ( 4) SS BOND : angle 2.85519 ( 8) hydrogen bonds : bond 0.04762 ( 473) hydrogen bonds : angle 4.96952 ( 1305) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8007 (mp10) REVERT: R 70 LEU cc_start: 0.8670 (tt) cc_final: 0.8422 (tp) REVERT: R 75 ASP cc_start: 0.8033 (t70) cc_final: 0.7428 (t0) REVERT: R 83 TRP cc_start: 0.7765 (t-100) cc_final: 0.7392 (t-100) REVERT: R 263 ARG cc_start: 0.6942 (ptt180) cc_final: 0.6613 (ptp-170) REVERT: R 302 HIS cc_start: 0.4447 (OUTLIER) cc_final: 0.4240 (m-70) REVERT: C 22 ASN cc_start: 0.8907 (m-40) cc_final: 0.8693 (m110) REVERT: C 247 MET cc_start: 0.8692 (mtm) cc_final: 0.8488 (mtm) REVERT: C 248 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8415 (mppt) REVERT: S 39 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8477 (tp40) REVERT: S 65 LYS cc_start: 0.8821 (ttpt) cc_final: 0.8604 (ttmp) REVERT: S 171 ASN cc_start: 0.9131 (m-40) cc_final: 0.8899 (m110) outliers start: 31 outliers final: 6 residues processed: 173 average time/residue: 0.5259 time to fit residues: 96.8578 Evaluate side-chains 145 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 302 HIS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 46 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 34 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 340 ASN R 10 HIS R 85 HIS C 52 GLN C 213 HIS C 331 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.128735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.097730 restraints weight = 14079.174| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.12 r_work: 0.3274 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9362 Z= 0.207 Angle : 0.625 7.542 12698 Z= 0.331 Chirality : 0.046 0.173 1420 Planarity : 0.004 0.041 1605 Dihedral : 5.569 47.275 1394 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.45 % Favored : 97.47 % Rotamer: Outliers : 3.35 % Allowed : 11.48 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.24), residues: 1145 helix: 1.53 (0.25), residues: 416 sheet: 0.82 (0.30), residues: 276 loop : 0.09 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 197 TYR 0.015 0.002 TYR R 102 PHE 0.018 0.002 PHE B 151 TRP 0.012 0.002 TRP B 99 HIS 0.007 0.002 HIS R 85 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 9358) covalent geometry : angle 0.61988 (12690) SS BOND : bond 0.00835 ( 4) SS BOND : angle 3.16461 ( 8) hydrogen bonds : bond 0.04601 ( 473) hydrogen bonds : angle 4.72930 ( 1305) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8274 (mt0) REVERT: R 43 TYR cc_start: 0.7541 (t80) cc_final: 0.7112 (t80) REVERT: R 70 LEU cc_start: 0.8708 (tt) cc_final: 0.8468 (tp) REVERT: R 75 ASP cc_start: 0.8091 (t70) cc_final: 0.7522 (t0) REVERT: R 83 TRP cc_start: 0.7919 (t-100) cc_final: 0.7415 (t-100) REVERT: R 84 ILE cc_start: 0.8826 (pt) cc_final: 0.8560 (pp) REVERT: R 85 HIS cc_start: 0.8313 (OUTLIER) cc_final: 0.7773 (m-70) REVERT: C 22 ASN cc_start: 0.8965 (m-40) cc_final: 0.8723 (m110) REVERT: C 246 SER cc_start: 0.8249 (m) cc_final: 0.8002 (m) REVERT: C 275 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8241 (tm-30) REVERT: S 65 LYS cc_start: 0.8850 (ttpt) cc_final: 0.8639 (ttmp) REVERT: S 192 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8848 (ttp) outliers start: 33 outliers final: 10 residues processed: 156 average time/residue: 0.5598 time to fit residues: 92.2497 Evaluate side-chains 146 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 85 HIS Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 192 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 112 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 38 optimal weight: 8.9990 chunk 26 optimal weight: 0.1980 chunk 37 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN B 340 ASN C 269 ASN S 171 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.129670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.099421 restraints weight = 14360.266| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.10 r_work: 0.3297 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9362 Z= 0.134 Angle : 0.566 8.244 12698 Z= 0.299 Chirality : 0.043 0.133 1420 Planarity : 0.004 0.042 1605 Dihedral : 5.301 42.851 1394 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.83 % Favored : 98.08 % Rotamer: Outliers : 2.24 % Allowed : 14.13 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.25), residues: 1145 helix: 1.86 (0.26), residues: 416 sheet: 0.76 (0.30), residues: 280 loop : 0.09 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 160 TYR 0.012 0.001 TYR R 102 PHE 0.029 0.002 PHE R 260 TRP 0.013 0.001 TRP R 83 HIS 0.012 0.001 HIS R 85 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9358) covalent geometry : angle 0.56309 (12690) SS BOND : bond 0.00607 ( 4) SS BOND : angle 2.49484 ( 8) hydrogen bonds : bond 0.03948 ( 473) hydrogen bonds : angle 4.49488 ( 1305) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 43 TYR cc_start: 0.7520 (t80) cc_final: 0.7089 (t80) REVERT: R 75 ASP cc_start: 0.8087 (t70) cc_final: 0.7495 (t0) REVERT: R 83 TRP cc_start: 0.7885 (t-100) cc_final: 0.7485 (t-100) REVERT: R 85 HIS cc_start: 0.8375 (OUTLIER) cc_final: 0.7693 (m170) REVERT: R 227 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7791 (mp) REVERT: C 22 ASN cc_start: 0.8978 (m-40) cc_final: 0.8752 (m110) REVERT: C 246 SER cc_start: 0.8251 (m) cc_final: 0.7985 (m) REVERT: C 275 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8203 (tm-30) REVERT: C 330 LYS cc_start: 0.8151 (mtmp) cc_final: 0.7882 (mtmm) outliers start: 22 outliers final: 3 residues processed: 152 average time/residue: 0.5228 time to fit residues: 84.2092 Evaluate side-chains 143 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 138 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 85 HIS Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain C residue 53 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 1 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 87 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 340 ASN G 59 ASN R 85 HIS C 52 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.129244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.099193 restraints weight = 14244.185| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.09 r_work: 0.3289 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9362 Z= 0.143 Angle : 0.576 9.360 12698 Z= 0.301 Chirality : 0.044 0.169 1420 Planarity : 0.004 0.046 1605 Dihedral : 5.221 38.630 1394 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.10 % Favored : 97.82 % Rotamer: Outliers : 2.64 % Allowed : 13.82 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.25), residues: 1145 helix: 2.00 (0.26), residues: 415 sheet: 0.73 (0.31), residues: 274 loop : 0.04 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 160 TYR 0.012 0.001 TYR R 102 PHE 0.030 0.002 PHE R 19 TRP 0.009 0.001 TRP B 63 HIS 0.008 0.001 HIS R 85 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9358) covalent geometry : angle 0.57346 (12690) SS BOND : bond 0.00651 ( 4) SS BOND : angle 2.31745 ( 8) hydrogen bonds : bond 0.03850 ( 473) hydrogen bonds : angle 4.44763 ( 1305) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8267 (mt0) REVERT: B 61 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8777 (tmt) REVERT: B 175 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7944 (mp10) REVERT: R 43 TYR cc_start: 0.7537 (t80) cc_final: 0.7086 (t80) REVERT: R 75 ASP cc_start: 0.8107 (t70) cc_final: 0.7494 (t0) REVERT: R 83 TRP cc_start: 0.7962 (t-100) cc_final: 0.7613 (t-100) REVERT: R 84 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8629 (pp) REVERT: R 85 HIS cc_start: 0.8251 (OUTLIER) cc_final: 0.7449 (m90) REVERT: R 91 LYS cc_start: 0.8091 (mmtt) cc_final: 0.7872 (mmtt) REVERT: R 163 TYR cc_start: 0.7441 (m-80) cc_final: 0.7224 (m-80) REVERT: R 227 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7687 (mp) REVERT: C 22 ASN cc_start: 0.8970 (m-40) cc_final: 0.8746 (m110) REVERT: C 248 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8366 (mppt) REVERT: C 275 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8059 (tm-30) outliers start: 26 outliers final: 7 residues processed: 155 average time/residue: 0.5260 time to fit residues: 86.2590 Evaluate side-chains 149 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 85 HIS Chi-restraints excluded: chain R residue 209 ARG Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 189 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 86 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 68 optimal weight: 0.0040 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN C 52 GLN C 269 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.129644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.099619 restraints weight = 14301.306| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.09 r_work: 0.3297 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9362 Z= 0.127 Angle : 0.563 11.455 12698 Z= 0.293 Chirality : 0.043 0.171 1420 Planarity : 0.004 0.041 1605 Dihedral : 5.068 37.674 1394 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.10 % Favored : 97.82 % Rotamer: Outliers : 2.03 % Allowed : 14.53 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.25), residues: 1145 helix: 2.08 (0.26), residues: 415 sheet: 0.71 (0.31), residues: 274 loop : 0.05 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 160 TYR 0.012 0.001 TYR C 296 PHE 0.033 0.002 PHE R 260 TRP 0.016 0.001 TRP R 83 HIS 0.010 0.001 HIS R 85 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9358) covalent geometry : angle 0.56105 (12690) SS BOND : bond 0.00590 ( 4) SS BOND : angle 2.11095 ( 8) hydrogen bonds : bond 0.03670 ( 473) hydrogen bonds : angle 4.36351 ( 1305) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8778 (tmt) REVERT: B 129 ARG cc_start: 0.8550 (mtp180) cc_final: 0.8330 (mmm160) REVERT: B 175 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.7962 (mp10) REVERT: R 43 TYR cc_start: 0.7508 (t80) cc_final: 0.7054 (t80) REVERT: R 75 ASP cc_start: 0.8106 (t70) cc_final: 0.7489 (t0) REVERT: R 91 LYS cc_start: 0.8002 (mmtt) cc_final: 0.7713 (mmtt) REVERT: R 227 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7692 (mp) REVERT: C 22 ASN cc_start: 0.8970 (m-40) cc_final: 0.8748 (m110) REVERT: C 247 MET cc_start: 0.8729 (mtm) cc_final: 0.8525 (mtm) REVERT: C 248 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8361 (mppt) REVERT: C 275 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8074 (tm-30) outliers start: 20 outliers final: 8 residues processed: 151 average time/residue: 0.5000 time to fit residues: 80.0178 Evaluate side-chains 142 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 209 ARG Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain S residue 189 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 21 optimal weight: 0.3980 chunk 53 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 102 optimal weight: 0.0050 chunk 38 optimal weight: 7.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 85 HIS C 52 GLN C 244 HIS S 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.128893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.099472 restraints weight = 14253.609| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.06 r_work: 0.3292 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9362 Z= 0.137 Angle : 0.576 13.228 12698 Z= 0.299 Chirality : 0.043 0.157 1420 Planarity : 0.004 0.040 1605 Dihedral : 5.029 37.577 1394 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.01 % Favored : 97.90 % Rotamer: Outliers : 2.64 % Allowed : 14.74 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.25), residues: 1145 helix: 2.09 (0.26), residues: 415 sheet: 0.70 (0.31), residues: 274 loop : 0.05 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 160 TYR 0.016 0.001 TYR R 251 PHE 0.028 0.002 PHE R 167 TRP 0.009 0.001 TRP B 211 HIS 0.007 0.001 HIS R 85 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9358) covalent geometry : angle 0.57242 (12690) SS BOND : bond 0.00804 ( 4) SS BOND : angle 2.50044 ( 8) hydrogen bonds : bond 0.03696 ( 473) hydrogen bonds : angle 4.36805 ( 1305) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8776 (tmt) REVERT: B 175 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.7970 (mp10) REVERT: R 43 TYR cc_start: 0.7524 (t80) cc_final: 0.7035 (t80) REVERT: R 75 ASP cc_start: 0.8117 (t70) cc_final: 0.7502 (t0) REVERT: R 227 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7666 (mp) REVERT: R 246 SER cc_start: 0.7984 (m) cc_final: 0.7674 (p) REVERT: C 22 ASN cc_start: 0.8970 (m-40) cc_final: 0.8739 (m110) REVERT: C 247 MET cc_start: 0.8672 (mtm) cc_final: 0.8450 (mtm) REVERT: C 248 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8384 (mppt) REVERT: C 275 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8178 (tm-30) outliers start: 26 outliers final: 10 residues processed: 156 average time/residue: 0.4626 time to fit residues: 76.8948 Evaluate side-chains 149 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 209 ARG Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain R residue 296 ASP Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain S residue 189 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 88 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 259 GLN B 340 ASN R 85 HIS C 269 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.128760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.098658 restraints weight = 14270.623| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.10 r_work: 0.3277 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9362 Z= 0.151 Angle : 0.595 14.080 12698 Z= 0.308 Chirality : 0.044 0.165 1420 Planarity : 0.004 0.041 1605 Dihedral : 5.064 37.193 1394 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.10 % Favored : 97.82 % Rotamer: Outliers : 2.54 % Allowed : 16.16 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.25), residues: 1145 helix: 2.08 (0.26), residues: 416 sheet: 0.70 (0.31), residues: 276 loop : 0.03 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 160 TYR 0.012 0.001 TYR C 296 PHE 0.037 0.002 PHE R 260 TRP 0.010 0.001 TRP B 63 HIS 0.007 0.001 HIS R 85 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 9358) covalent geometry : angle 0.59119 (12690) SS BOND : bond 0.00869 ( 4) SS BOND : angle 2.68653 ( 8) hydrogen bonds : bond 0.03787 ( 473) hydrogen bonds : angle 4.39197 ( 1305) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8786 (tmt) REVERT: B 175 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.7969 (mp10) REVERT: B 217 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7617 (ptt) REVERT: R 10 HIS cc_start: 0.7639 (OUTLIER) cc_final: 0.7396 (m-70) REVERT: R 43 TYR cc_start: 0.7547 (t80) cc_final: 0.7035 (t80) REVERT: R 75 ASP cc_start: 0.8126 (t70) cc_final: 0.7550 (t0) REVERT: R 181 MET cc_start: 0.8285 (tpp) cc_final: 0.8043 (tpt) REVERT: R 227 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7676 (mp) REVERT: R 246 SER cc_start: 0.7922 (m) cc_final: 0.7651 (p) REVERT: R 299 LYS cc_start: 0.8388 (tppt) cc_final: 0.8129 (tptm) REVERT: C 22 ASN cc_start: 0.8968 (m-40) cc_final: 0.8732 (m110) REVERT: C 53 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.7041 (mtm) REVERT: C 247 MET cc_start: 0.8687 (mtm) cc_final: 0.8457 (mtm) REVERT: C 248 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8363 (mppt) REVERT: C 275 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8199 (tm-30) outliers start: 25 outliers final: 8 residues processed: 153 average time/residue: 0.5097 time to fit residues: 83.0040 Evaluate side-chains 152 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 10 HIS Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 209 ARG Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain R residue 296 ASP Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 189 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 22 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 0.5980 chunk 62 optimal weight: 6.9990 chunk 17 optimal weight: 0.0970 chunk 82 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 340 ASN R 85 HIS C 269 ASN S 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.129135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.099026 restraints weight = 14312.537| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.11 r_work: 0.3290 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9362 Z= 0.142 Angle : 0.594 14.498 12698 Z= 0.308 Chirality : 0.044 0.164 1420 Planarity : 0.004 0.041 1605 Dihedral : 5.009 36.728 1394 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.01 % Favored : 97.90 % Rotamer: Outliers : 2.13 % Allowed : 17.17 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.25), residues: 1145 helix: 2.12 (0.26), residues: 417 sheet: 0.67 (0.31), residues: 278 loop : 0.01 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 96 TYR 0.013 0.001 TYR C 296 PHE 0.032 0.002 PHE R 167 TRP 0.010 0.001 TRP R 83 HIS 0.005 0.001 HIS R 85 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9358) covalent geometry : angle 0.59152 (12690) SS BOND : bond 0.00797 ( 4) SS BOND : angle 2.43239 ( 8) hydrogen bonds : bond 0.03691 ( 473) hydrogen bonds : angle 4.37120 ( 1305) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8777 (tmt) REVERT: B 175 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.7949 (mp10) REVERT: B 217 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7622 (ptt) REVERT: R 10 HIS cc_start: 0.7571 (OUTLIER) cc_final: 0.7346 (m-70) REVERT: R 43 TYR cc_start: 0.7529 (t80) cc_final: 0.7040 (t80) REVERT: R 75 ASP cc_start: 0.8096 (t70) cc_final: 0.7544 (t0) REVERT: R 227 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7671 (mp) REVERT: R 246 SER cc_start: 0.7896 (m) cc_final: 0.7594 (p) REVERT: R 263 ARG cc_start: 0.5730 (ptt180) cc_final: 0.4672 (pmt170) REVERT: C 22 ASN cc_start: 0.8973 (m-40) cc_final: 0.8739 (m110) REVERT: C 247 MET cc_start: 0.8680 (mtm) cc_final: 0.8440 (mtm) REVERT: C 248 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8376 (mppt) REVERT: C 275 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8188 (tm-30) outliers start: 21 outliers final: 10 residues processed: 149 average time/residue: 0.5012 time to fit residues: 79.3140 Evaluate side-chains 155 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 10 HIS Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 209 ARG Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain R residue 296 ASP Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 189 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 94 optimal weight: 0.5980 chunk 84 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 85 HIS C 52 GLN C 269 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.129617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.099583 restraints weight = 14209.088| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.10 r_work: 0.3295 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9362 Z= 0.133 Angle : 0.597 14.835 12698 Z= 0.308 Chirality : 0.043 0.143 1420 Planarity : 0.004 0.040 1605 Dihedral : 4.924 35.650 1394 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.45 % Favored : 97.47 % Rotamer: Outliers : 2.03 % Allowed : 17.68 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.25), residues: 1145 helix: 2.18 (0.26), residues: 417 sheet: 0.68 (0.31), residues: 278 loop : 0.02 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 96 TYR 0.013 0.001 TYR C 296 PHE 0.037 0.002 PHE R 260 TRP 0.012 0.001 TRP R 83 HIS 0.005 0.001 HIS R 17 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9358) covalent geometry : angle 0.59416 (12690) SS BOND : bond 0.00808 ( 4) SS BOND : angle 2.39493 ( 8) hydrogen bonds : bond 0.03618 ( 473) hydrogen bonds : angle 4.33854 ( 1305) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 GLN cc_start: 0.8554 (mt0) cc_final: 0.8315 (mt0) REVERT: B 61 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.8771 (tmt) REVERT: B 175 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7946 (mp10) REVERT: B 217 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7612 (ptt) REVERT: R 10 HIS cc_start: 0.7580 (OUTLIER) cc_final: 0.7333 (m-70) REVERT: R 43 TYR cc_start: 0.7525 (t80) cc_final: 0.7026 (t80) REVERT: R 75 ASP cc_start: 0.8123 (t70) cc_final: 0.7578 (t70) REVERT: R 91 LYS cc_start: 0.7867 (mmtt) cc_final: 0.7575 (tmtt) REVERT: R 181 MET cc_start: 0.8282 (tpp) cc_final: 0.8009 (tpt) REVERT: R 227 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7661 (mp) REVERT: R 246 SER cc_start: 0.7904 (m) cc_final: 0.7637 (p) REVERT: R 299 LYS cc_start: 0.8472 (tppt) cc_final: 0.8212 (tptm) REVERT: C 22 ASN cc_start: 0.8960 (m-40) cc_final: 0.8727 (m110) REVERT: C 247 MET cc_start: 0.8677 (mtm) cc_final: 0.8437 (mtm) REVERT: C 275 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8170 (tm-30) REVERT: S 76 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8728 (pttp) outliers start: 20 outliers final: 9 residues processed: 158 average time/residue: 0.4926 time to fit residues: 82.8670 Evaluate side-chains 155 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 10 HIS Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain R residue 296 ASP Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 189 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 110 optimal weight: 0.0050 chunk 11 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 77 optimal weight: 0.0010 chunk 38 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 overall best weight: 0.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 85 HIS C 195 HIS C 269 ASN S 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.130834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.101071 restraints weight = 14180.128| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.09 r_work: 0.3328 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9362 Z= 0.114 Angle : 0.583 15.109 12698 Z= 0.300 Chirality : 0.043 0.147 1420 Planarity : 0.004 0.041 1605 Dihedral : 4.748 33.770 1394 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.01 % Favored : 97.90 % Rotamer: Outliers : 1.63 % Allowed : 18.50 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.25), residues: 1145 helix: 2.30 (0.26), residues: 412 sheet: 0.69 (0.31), residues: 278 loop : 0.09 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 96 TYR 0.018 0.001 TYR R 251 PHE 0.024 0.002 PHE R 167 TRP 0.011 0.001 TRP B 297 HIS 0.005 0.001 HIS R 17 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9358) covalent geometry : angle 0.58061 (12690) SS BOND : bond 0.00752 ( 4) SS BOND : angle 2.25912 ( 8) hydrogen bonds : bond 0.03445 ( 473) hydrogen bonds : angle 4.25303 ( 1305) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3878.48 seconds wall clock time: 66 minutes 36.55 seconds (3996.55 seconds total)