Starting phenix.real_space_refine on Sun Jul 27 03:03:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z9p_39866/07_2025/8z9p_39866.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z9p_39866/07_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_39866/07_2025/8z9p_39866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z9p_39866/07_2025/8z9p_39866.map" model { file = "/net/cci-nas-00/data/ceres_data/8z9p_39866/07_2025/8z9p_39866.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z9p_39866/07_2025/8z9p_39866.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.063 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.85, per 1000 atoms: 0.64 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: 2.98 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.50 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: 2.68 Time building geometry restraints manager: 2.90 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 26.020 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:93.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.700 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (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 TRP 0.056 0.010 TRP B 99 HIS 0.007 0.002 HIS B 62 PHE 0.038 0.007 PHE B 199 TYR 0.048 0.008 TYR R 102 ARG 0.012 0.001 ARG S 98 Details of bonding type rmsd hydrogen bonds : bond 0.16587 ( 473) hydrogen bonds : angle 7.14550 ( 1305) SS BOND : bond 0.06127 ( 4) SS BOND : angle 4.89137 ( 8) covalent geometry : bond 0.02541 ( 9358) covalent geometry : angle 1.77976 (12690) *********************** 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 : 1.065 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: 1.9226 time to fit residues: 407.6630 Evaluate side-chains 125 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.132090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.101390 restraints weight = 13861.115| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.09 r_work: 0.3340 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2833 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= 0.169 Angle : 0.653 8.482 12698 Z= 0.345 Chirality : 0.045 0.145 1420 Planarity : 0.004 0.035 1605 Dihedral : 5.759 51.478 1394 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.50 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.24), residues: 1145 helix: 1.18 (0.25), residues: 415 sheet: 0.88 (0.29), residues: 288 loop : 0.32 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 73 HIS 0.008 0.002 HIS C 322 PHE 0.022 0.002 PHE R 159 TYR 0.016 0.002 TYR R 251 ARG 0.005 0.001 ARG R 127 Details of bonding type rmsd hydrogen bonds : bond 0.04823 ( 473) hydrogen bonds : angle 4.96777 ( 1305) SS BOND : bond 0.00526 ( 4) SS BOND : angle 2.91802 ( 8) covalent geometry : bond 0.00385 ( 9358) covalent geometry : angle 0.64881 (12690) *********************** 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 185 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8011 (mp10) REVERT: R 65 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7353 (mp) REVERT: R 75 ASP cc_start: 0.8056 (t70) cc_final: 0.7467 (t0) REVERT: R 83 TRP cc_start: 0.7770 (t-100) cc_final: 0.7387 (t-100) REVERT: R 302 HIS cc_start: 0.4540 (OUTLIER) cc_final: 0.4338 (m-70) REVERT: C 22 ASN cc_start: 0.8915 (m-40) cc_final: 0.8700 (m110) REVERT: C 248 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8397 (mppt) REVERT: S 65 LYS cc_start: 0.8821 (ttpt) cc_final: 0.8600 (ttmp) REVERT: S 171 ASN cc_start: 0.9131 (m-40) cc_final: 0.8910 (m110) outliers start: 31 outliers final: 6 residues processed: 170 average time/residue: 1.2332 time to fit residues: 223.6604 Evaluate side-chains 148 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 65 LEU 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 46 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 17 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 R 155 HIS C 52 GLN C 213 HIS C 331 ASN S 39 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.127694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.096438 restraints weight = 14179.132| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.13 r_work: 0.3243 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 9362 Z= 0.251 Angle : 0.662 7.914 12698 Z= 0.350 Chirality : 0.048 0.184 1420 Planarity : 0.004 0.040 1605 Dihedral : 5.741 48.039 1394 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.79 % Favored : 97.12 % Rotamer: Outliers : 3.66 % Allowed : 12.30 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.24), residues: 1145 helix: 1.44 (0.25), residues: 416 sheet: 0.72 (0.30), residues: 278 loop : 0.02 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 99 HIS 0.007 0.002 HIS G 44 PHE 0.019 0.002 PHE B 151 TYR 0.016 0.002 TYR R 102 ARG 0.005 0.001 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04846 ( 473) hydrogen bonds : angle 4.83480 ( 1305) SS BOND : bond 0.00855 ( 4) SS BOND : angle 3.20009 ( 8) covalent geometry : bond 0.00595 ( 9358) covalent geometry : angle 0.65768 (12690) *********************** 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 177 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8321 (mt0) REVERT: B 175 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8002 (mp10) REVERT: R 75 ASP cc_start: 0.8156 (t70) cc_final: 0.7569 (t0) REVERT: R 83 TRP cc_start: 0.8000 (t-100) cc_final: 0.7458 (t-100) REVERT: R 84 ILE cc_start: 0.8900 (pt) cc_final: 0.8635 (pp) REVERT: R 85 HIS cc_start: 0.8369 (OUTLIER) cc_final: 0.7784 (m-70) REVERT: R 91 LYS cc_start: 0.8347 (mttm) cc_final: 0.8051 (tttm) REVERT: C 22 ASN cc_start: 0.8967 (m-40) cc_final: 0.8716 (m110) REVERT: C 33 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7198 (tp30) REVERT: C 246 SER cc_start: 0.8175 (m) cc_final: 0.7922 (m) REVERT: C 248 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8417 (mppt) REVERT: C 275 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8078 (mm-30) REVERT: C 298 GLU cc_start: 0.8124 (mp0) cc_final: 0.7727 (mp0) REVERT: S 65 LYS cc_start: 0.8861 (ttpt) cc_final: 0.8648 (ttmp) REVERT: S 192 MET cc_start: 0.9126 (ttp) cc_final: 0.8873 (ttp) outliers start: 36 outliers final: 13 residues processed: 158 average time/residue: 1.4676 time to fit residues: 246.0618 Evaluate side-chains 153 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 175 GLN Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 85 HIS Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 209 ARG Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 57 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 45 optimal weight: 0.9980 chunk 26 optimal weight: 0.2980 chunk 88 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 83 optimal weight: 0.0570 chunk 40 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 C 331 ASN S 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.129732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.099870 restraints weight = 14084.833| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.07 r_work: 0.3307 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9362 Z= 0.120 Angle : 0.557 8.322 12698 Z= 0.295 Chirality : 0.043 0.133 1420 Planarity : 0.004 0.042 1605 Dihedral : 5.308 43.309 1394 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.57 % Favored : 98.34 % Rotamer: Outliers : 2.54 % Allowed : 13.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.25), residues: 1145 helix: 1.86 (0.26), residues: 416 sheet: 0.67 (0.30), residues: 282 loop : 0.07 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 83 HIS 0.010 0.001 HIS R 85 PHE 0.029 0.002 PHE R 260 TYR 0.011 0.001 TYR R 102 ARG 0.007 0.000 ARG R 160 Details of bonding type rmsd hydrogen bonds : bond 0.03853 ( 473) hydrogen bonds : angle 4.49293 ( 1305) SS BOND : bond 0.00542 ( 4) SS BOND : angle 2.41906 ( 8) covalent geometry : bond 0.00268 ( 9358) covalent geometry : angle 0.55371 (12690) *********************** 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 170 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8277 (mt0) REVERT: B 129 ARG cc_start: 0.8565 (mtp180) cc_final: 0.8361 (mmm160) REVERT: B 175 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8021 (mp10) REVERT: R 43 TYR cc_start: 0.7520 (t80) cc_final: 0.7094 (t80) REVERT: R 75 ASP cc_start: 0.8118 (t70) cc_final: 0.7541 (t0) REVERT: R 83 TRP cc_start: 0.7940 (t-100) cc_final: 0.7591 (t-100) REVERT: R 85 HIS cc_start: 0.8385 (OUTLIER) cc_final: 0.7687 (m170) REVERT: R 91 LYS cc_start: 0.8183 (mttm) cc_final: 0.7936 (tttm) REVERT: R 227 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7730 (mp) REVERT: C 22 ASN cc_start: 0.8977 (m-40) cc_final: 0.8751 (m110) REVERT: C 246 SER cc_start: 0.8220 (m) cc_final: 0.7953 (m) REVERT: C 275 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8196 (tm-30) outliers start: 25 outliers final: 3 residues processed: 158 average time/residue: 1.5580 time to fit residues: 260.8704 Evaluate side-chains 149 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 142 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 275 SER 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 17 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 0 optimal weight: 420.0000 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 R 85 HIS C 52 GLN C 269 ASN C 331 ASN S 171 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.125927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.094812 restraints weight = 14178.570| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.12 r_work: 0.3212 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 9362 Z= 0.301 Angle : 0.696 8.730 12698 Z= 0.363 Chirality : 0.049 0.167 1420 Planarity : 0.005 0.042 1605 Dihedral : 5.847 41.021 1394 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.36 % Favored : 97.55 % Rotamer: Outliers : 3.46 % Allowed : 13.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.25), residues: 1145 helix: 1.63 (0.26), residues: 415 sheet: 0.50 (0.30), residues: 279 loop : -0.16 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 63 HIS 0.007 0.002 HIS R 85 PHE 0.032 0.003 PHE R 19 TYR 0.015 0.002 TYR R 102 ARG 0.007 0.001 ARG R 160 Details of bonding type rmsd hydrogen bonds : bond 0.04827 ( 473) hydrogen bonds : angle 4.87369 ( 1305) SS BOND : bond 0.01216 ( 4) SS BOND : angle 2.63231 ( 8) covalent geometry : bond 0.00723 ( 9358) covalent geometry : angle 0.69264 (12690) *********************** 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 177 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8310 (mt0) REVERT: B 61 MET cc_start: 0.9239 (OUTLIER) cc_final: 0.8890 (tmt) REVERT: B 175 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8063 (mp10) REVERT: R 75 ASP cc_start: 0.8145 (t70) cc_final: 0.7538 (t0) REVERT: R 83 TRP cc_start: 0.8133 (t-100) cc_final: 0.7829 (t-100) REVERT: R 85 HIS cc_start: 0.8339 (OUTLIER) cc_final: 0.7746 (m90) REVERT: R 227 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7785 (mp) REVERT: R 246 SER cc_start: 0.8069 (m) cc_final: 0.7729 (p) REVERT: C 22 ASN cc_start: 0.8962 (m-40) cc_final: 0.8720 (m110) REVERT: C 33 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7230 (tp30) REVERT: C 53 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.6967 (mtm) REVERT: C 247 MET cc_start: 0.8707 (mtm) cc_final: 0.8501 (mtm) REVERT: C 275 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8186 (tm-30) outliers start: 34 outliers final: 13 residues processed: 159 average time/residue: 1.3874 time to fit residues: 234.0135 Evaluate side-chains 155 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 76 ASP 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 46 VAL Chi-restraints excluded: chain R residue 85 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 33 GLU 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 12 VAL 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 39 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 78 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 C 52 GLN C 244 HIS C 269 ASN S 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.127997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.097952 restraints weight = 14212.978| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.08 r_work: 0.3272 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9362 Z= 0.141 Angle : 0.588 11.259 12698 Z= 0.306 Chirality : 0.044 0.145 1420 Planarity : 0.004 0.041 1605 Dihedral : 5.360 39.065 1394 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.48 % Favored : 98.43 % Rotamer: Outliers : 2.44 % Allowed : 15.75 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.25), residues: 1145 helix: 1.91 (0.26), residues: 415 sheet: 0.60 (0.31), residues: 281 loop : -0.10 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 83 HIS 0.011 0.001 HIS R 85 PHE 0.032 0.002 PHE R 260 TYR 0.011 0.001 TYR R 102 ARG 0.006 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 473) hydrogen bonds : angle 4.57829 ( 1305) SS BOND : bond 0.00642 ( 4) SS BOND : angle 2.08070 ( 8) covalent geometry : bond 0.00326 ( 9358) covalent geometry : angle 0.58578 (12690) *********************** 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: 24 poor density : 135 time to evaluate : 1.033 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: 0.8547 (OUTLIER) cc_final: 0.8302 (mt0) REVERT: B 61 MET cc_start: 0.9139 (OUTLIER) cc_final: 0.8813 (tmt) REVERT: B 129 ARG cc_start: 0.8590 (mtp180) cc_final: 0.8350 (mmm160) REVERT: B 175 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8097 (mp10) REVERT: R 43 TYR cc_start: 0.7594 (t80) cc_final: 0.7186 (t80) REVERT: R 75 ASP cc_start: 0.8072 (t70) cc_final: 0.7499 (t0) REVERT: R 91 LYS cc_start: 0.8210 (mttm) cc_final: 0.7955 (mttm) REVERT: R 227 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7712 (mp) REVERT: R 246 SER cc_start: 0.8076 (m) cc_final: 0.7751 (p) REVERT: C 22 ASN cc_start: 0.8980 (m-40) cc_final: 0.8734 (m110) REVERT: C 53 MET cc_start: 0.7420 (OUTLIER) cc_final: 0.6930 (mtm) REVERT: C 247 MET cc_start: 0.8632 (mtm) cc_final: 0.8388 (mtm) REVERT: C 275 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8183 (tm-30) REVERT: C 318 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7251 (tt0) outliers start: 24 outliers final: 4 residues processed: 149 average time/residue: 1.3571 time to fit residues: 215.0795 Evaluate side-chains 140 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 275 SER 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 318 GLU Chi-restraints excluded: chain S residue 79 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 43 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 35 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 104 optimal weight: 8.9990 chunk 3 optimal weight: 0.0170 chunk 48 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 84 optimal weight: 9.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 176 GLN B 259 GLN B 340 ASN R 85 HIS C 52 GLN S 39 GLN S 194 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.129109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.099170 restraints weight = 14282.482| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.09 r_work: 0.3292 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9362 Z= 0.122 Angle : 0.575 13.701 12698 Z= 0.297 Chirality : 0.043 0.132 1420 Planarity : 0.004 0.042 1605 Dihedral : 5.039 36.807 1394 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.01 % Favored : 97.90 % Rotamer: Outliers : 2.24 % Allowed : 15.96 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.25), residues: 1145 helix: 2.04 (0.26), residues: 415 sheet: 0.63 (0.31), residues: 281 loop : -0.06 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.007 0.001 HIS R 85 PHE 0.026 0.002 PHE R 19 TYR 0.018 0.001 TYR R 251 ARG 0.006 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03604 ( 473) hydrogen bonds : angle 4.40198 ( 1305) SS BOND : bond 0.00643 ( 4) SS BOND : angle 2.00499 ( 8) covalent geometry : bond 0.00279 ( 9358) covalent geometry : angle 0.57259 (12690) *********************** 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 166 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8306 (mt0) REVERT: B 61 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.8795 (tmt) REVERT: B 129 ARG cc_start: 0.8583 (mtp180) cc_final: 0.8343 (mmm160) REVERT: R 43 TYR cc_start: 0.7518 (t80) cc_final: 0.7116 (t80) REVERT: R 75 ASP cc_start: 0.8094 (t70) cc_final: 0.7494 (t0) REVERT: R 83 TRP cc_start: 0.7910 (t-100) cc_final: 0.7686 (t-100) REVERT: R 91 LYS cc_start: 0.8106 (mttm) cc_final: 0.7827 (tttt) REVERT: R 227 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7659 (mp) REVERT: R 246 SER cc_start: 0.8005 (m) cc_final: 0.7691 (p) REVERT: R 299 LYS cc_start: 0.8363 (tppt) cc_final: 0.8118 (tptm) REVERT: C 22 ASN cc_start: 0.8967 (m-40) cc_final: 0.8738 (m110) REVERT: C 53 MET cc_start: 0.7316 (OUTLIER) cc_final: 0.7113 (mtm) REVERT: C 247 MET cc_start: 0.8616 (mtm) cc_final: 0.8397 (mtm) REVERT: C 275 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8279 (tm-30) REVERT: S 77 ASN cc_start: 0.8689 (m-40) cc_final: 0.8462 (m110) outliers start: 22 outliers final: 6 residues processed: 158 average time/residue: 1.3572 time to fit residues: 227.6289 Evaluate side-chains 146 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 54 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 79 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 33 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 42 optimal weight: 0.0170 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 0.0770 chunk 90 optimal weight: 0.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 S 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.127770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.097492 restraints weight = 14449.647| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.11 r_work: 0.3257 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9362 Z= 0.169 Angle : 0.611 14.059 12698 Z= 0.316 Chirality : 0.044 0.131 1420 Planarity : 0.004 0.040 1605 Dihedral : 5.168 37.332 1394 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.75 % Favored : 98.17 % Rotamer: Outliers : 1.73 % Allowed : 17.68 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.25), residues: 1145 helix: 2.02 (0.26), residues: 416 sheet: 0.62 (0.31), residues: 281 loop : -0.09 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 63 HIS 0.008 0.001 HIS R 85 PHE 0.035 0.002 PHE R 260 TYR 0.011 0.001 TYR C 296 ARG 0.007 0.000 ARG R 127 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 473) hydrogen bonds : angle 4.53465 ( 1305) SS BOND : bond 0.00746 ( 4) SS BOND : angle 2.03364 ( 8) covalent geometry : bond 0.00400 ( 9358) covalent geometry : angle 0.60945 (12690) *********************** 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 157 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8336 (mt0) REVERT: B 46 ARG cc_start: 0.8791 (mtp180) cc_final: 0.8577 (mtp85) REVERT: B 61 MET cc_start: 0.9167 (OUTLIER) cc_final: 0.8809 (tmt) REVERT: B 175 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8077 (mp10) REVERT: R 43 TYR cc_start: 0.7567 (t80) cc_final: 0.7184 (t80) REVERT: R 75 ASP cc_start: 0.8162 (t70) cc_final: 0.7565 (t0) REVERT: R 83 TRP cc_start: 0.7951 (t-100) cc_final: 0.7639 (t-100) REVERT: R 91 LYS cc_start: 0.8148 (mttm) cc_final: 0.7856 (tttt) REVERT: R 227 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7690 (mp) REVERT: R 246 SER cc_start: 0.7991 (m) cc_final: 0.7703 (p) REVERT: C 22 ASN cc_start: 0.8970 (m-40) cc_final: 0.8758 (m110) REVERT: C 53 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.6968 (mtm) REVERT: C 275 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8226 (tm-30) outliers start: 17 outliers final: 7 residues processed: 150 average time/residue: 1.6098 time to fit residues: 256.7693 Evaluate side-chains 149 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 54 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 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 42 optimal weight: 0.8980 chunk 33 optimal weight: 30.0000 chunk 12 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 0 optimal weight: 100.0000 chunk 74 optimal weight: 0.8980 chunk 1 optimal weight: 9.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 S 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.127905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.097760 restraints weight = 14143.852| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.09 r_work: 0.3267 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4300 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= 0.163 Angle : 0.617 14.530 12698 Z= 0.317 Chirality : 0.044 0.129 1420 Planarity : 0.004 0.039 1605 Dihedral : 5.131 36.106 1394 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.01 % Favored : 97.90 % Rotamer: Outliers : 1.83 % Allowed : 17.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.25), residues: 1145 helix: 2.02 (0.26), residues: 416 sheet: 0.62 (0.31), residues: 283 loop : -0.08 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.007 0.001 HIS R 85 PHE 0.025 0.002 PHE R 167 TYR 0.013 0.001 TYR C 296 ARG 0.007 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03849 ( 473) hydrogen bonds : angle 4.54685 ( 1305) SS BOND : bond 0.00733 ( 4) SS BOND : angle 2.02860 ( 8) covalent geometry : bond 0.00385 ( 9358) covalent geometry : angle 0.61463 (12690) *********************** 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 157 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8324 (mt0) REVERT: B 61 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8809 (tmt) REVERT: B 175 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8097 (mp10) REVERT: B 217 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7602 (ptt) REVERT: R 43 TYR cc_start: 0.7573 (t80) cc_final: 0.7183 (t80) REVERT: R 75 ASP cc_start: 0.8179 (t70) cc_final: 0.7579 (t0) REVERT: R 83 TRP cc_start: 0.7984 (t-100) cc_final: 0.7705 (t-100) REVERT: R 91 LYS cc_start: 0.8114 (mttm) cc_final: 0.7822 (tttt) REVERT: R 227 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7674 (mp) REVERT: R 246 SER cc_start: 0.7987 (m) cc_final: 0.7642 (p) REVERT: R 299 LYS cc_start: 0.8444 (tppt) cc_final: 0.8166 (tptp) REVERT: C 22 ASN cc_start: 0.8979 (m-40) cc_final: 0.8767 (m110) REVERT: C 53 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.7051 (mtm) REVERT: C 248 LYS cc_start: 0.8556 (ptpt) cc_final: 0.8320 (ptmm) REVERT: C 275 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8226 (tm-30) outliers start: 18 outliers final: 7 residues processed: 149 average time/residue: 1.4027 time to fit residues: 222.6172 Evaluate side-chains 150 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 54 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 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 102 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 71 optimal weight: 0.0010 chunk 105 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 101 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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 ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 ASN S 39 GLN S 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.129771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.099843 restraints weight = 14406.510| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.11 r_work: 0.3300 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4443 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= 0.119 Angle : 0.592 15.118 12698 Z= 0.303 Chirality : 0.043 0.132 1420 Planarity : 0.004 0.039 1605 Dihedral : 4.841 33.896 1394 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.48 % Favored : 98.43 % Rotamer: Outliers : 1.63 % Allowed : 17.89 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.25), residues: 1145 helix: 2.20 (0.26), residues: 410 sheet: 0.66 (0.31), residues: 283 loop : -0.04 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 297 HIS 0.006 0.001 HIS R 85 PHE 0.036 0.002 PHE R 260 TYR 0.017 0.001 TYR C 296 ARG 0.007 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03471 ( 473) hydrogen bonds : angle 4.40026 ( 1305) SS BOND : bond 0.00648 ( 4) SS BOND : angle 1.70460 ( 8) covalent geometry : bond 0.00270 ( 9358) covalent geometry : angle 0.59051 (12690) ********************** 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 154 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8305 (mt0) REVERT: B 46 ARG cc_start: 0.8780 (mtp180) cc_final: 0.8566 (mtp85) REVERT: B 61 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8760 (tmt) REVERT: B 96 ARG cc_start: 0.8658 (ttp-110) cc_final: 0.8443 (mtm-85) REVERT: B 129 ARG cc_start: 0.8561 (mtp180) cc_final: 0.8307 (mmm160) REVERT: B 175 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8057 (mp10) REVERT: B 217 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7673 (ptt) REVERT: R 43 TYR cc_start: 0.7509 (t80) cc_final: 0.7077 (t80) REVERT: R 75 ASP cc_start: 0.8117 (t70) cc_final: 0.7561 (t0) REVERT: R 91 LYS cc_start: 0.8109 (mttm) cc_final: 0.7898 (mttm) REVERT: R 227 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7673 (mp) REVERT: R 246 SER cc_start: 0.7859 (m) cc_final: 0.7610 (p) REVERT: R 299 LYS cc_start: 0.8442 (tppt) cc_final: 0.8197 (tptt) REVERT: C 22 ASN cc_start: 0.8973 (m-40) cc_final: 0.8746 (m110) REVERT: C 248 LYS cc_start: 0.8552 (ptpt) cc_final: 0.8328 (ptmm) REVERT: C 275 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8185 (tm-30) outliers start: 16 outliers final: 6 residues processed: 147 average time/residue: 1.2326 time to fit residues: 193.2798 Evaluate side-chains 144 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain R residue 296 ASP Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 0.0170 chunk 12 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 overall best weight: 1.5424 ------------------------------------------------------------------------------- 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 R 269 HIS ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.127379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.097307 restraints weight = 14201.561| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.08 r_work: 0.3245 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9362 Z= 0.198 Angle : 0.647 14.831 12698 Z= 0.332 Chirality : 0.045 0.168 1420 Planarity : 0.004 0.039 1605 Dihedral : 5.197 34.252 1394 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.83 % Favored : 98.08 % Rotamer: Outliers : 1.73 % Allowed : 17.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.25), residues: 1145 helix: 2.08 (0.26), residues: 411 sheet: 0.65 (0.31), residues: 279 loop : -0.11 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 83 HIS 0.005 0.001 HIS R 17 PHE 0.028 0.002 PHE R 167 TYR 0.021 0.002 TYR R 251 ARG 0.007 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04066 ( 473) hydrogen bonds : angle 4.65080 ( 1305) SS BOND : bond 0.01023 ( 4) SS BOND : angle 2.75455 ( 8) covalent geometry : bond 0.00472 ( 9358) covalent geometry : angle 0.64344 (12690) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11100.16 seconds wall clock time: 195 minutes 34.88 seconds (11734.88 seconds total)