Starting phenix.real_space_refine on Tue Jul 29 06:40:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y64_33633/07_2025/7y64_33633_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y64_33633/07_2025/7y64_33633.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y64_33633/07_2025/7y64_33633.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y64_33633/07_2025/7y64_33633.map" model { file = "/net/cci-nas-00/data/ceres_data/7y64_33633/07_2025/7y64_33633_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y64_33633/07_2025/7y64_33633_neut.cif" } resolution = 2.9 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= 0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2120 atoms to isotropic. 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 66 5.16 5 C 6058 2.51 5 N 1631 2.21 5 O 1765 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 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: 9520 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1795 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "S" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "D" Number of atoms: 2321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2321 Classifications: {'peptide': 293} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 278} Chain: "E" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 578 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Time building chain proxies: 6.46, per 1000 atoms: 0.68 Number of scatterers: 9520 At special positions: 0 Unit cell: (91.8, 119, 140.25, 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 66 16.00 O 1765 8.00 N 1631 7.00 C 6058 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Simple disulfide: pdb=" SG CYS D 109 " - pdb=" SG CYS D 188 " distance=2.03 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 47 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 54 " distance=2.03 Simple disulfide: pdb=" SG CYS E 34 " - pdb=" SG CYS E 55 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 1.2 seconds 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2280 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 13 sheets defined 39.1% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.732A pdb=" N LYS A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.593A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.662A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.635A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.754A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 2 through 25 removed outlier: 3.501A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 8 through 23 removed outlier: 3.693A pdb=" N ALA C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 45 Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 55 through 59 removed outlier: 3.759A pdb=" N ASN C 59 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.645A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.509A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing helix chain 'D' and resid 34 through 66 removed outlier: 4.132A pdb=" N LEU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE D 64 " --> pdb=" O TRP D 60 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU D 65 " --> pdb=" O VAL D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 88 removed outlier: 3.702A pdb=" N PHE D 75 " --> pdb=" O ASN D 71 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN D 77 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU D 78 " --> pdb=" O TRP D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 98 removed outlier: 4.105A pdb=" N LEU D 92 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL D 97 " --> pdb=" O PHE D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 110 Processing helix chain 'D' and resid 111 through 139 removed outlier: 3.856A pdb=" N LEU D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 147 removed outlier: 3.769A pdb=" N CYS D 144 " --> pdb=" O LYS D 140 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN D 146 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 174 removed outlier: 3.616A pdb=" N TRP D 154 " --> pdb=" O ALA D 150 " (cutoff:3.500A) Proline residue: D 170 - end of helix Processing helix chain 'D' and resid 195 through 209 removed outlier: 3.600A pdb=" N GLU D 199 " --> pdb=" O ASP D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 232 removed outlier: 4.110A pdb=" N ARG D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 268 removed outlier: 3.545A pdb=" N LYS D 242 " --> pdb=" O THR D 238 " (cutoff:3.500A) Proline residue: D 257 - end of helix Processing helix chain 'D' and resid 272 through 280 removed outlier: 3.507A pdb=" N LYS D 280 " --> pdb=" O LEU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 303 removed outlier: 4.394A pdb=" N ASN D 292 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N CYS D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS D 294 " --> pdb=" O TYR D 290 " (cutoff:3.500A) Proline residue: D 297 - end of helix removed outlier: 3.946A pdb=" N TYR D 300 " --> pdb=" O ASN D 296 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D 301 " --> pdb=" O PRO D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 314 removed outlier: 3.735A pdb=" N SER D 314 " --> pdb=" O ARG D 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 11 Processing helix chain 'E' and resid 15 through 26 Processing helix chain 'E' and resid 33 through 39 removed outlier: 3.584A pdb=" N ALA E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 63 removed outlier: 3.933A pdb=" N ALA E 50 " --> pdb=" O ARG E 46 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU E 61 " --> pdb=" O VAL E 57 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.722A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.948A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.832A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.730A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.635A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 152 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.693A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.520A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.798A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.711A pdb=" N VAL S 12 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL S 37 " --> pdb=" O TYR S 95 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.009A pdb=" N VAL S 147 " --> pdb=" O GLU S 246 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR S 227 " --> pdb=" O THR S 243 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 155 through 160 Processing sheet with id=AB4, first strand: chain 'D' and resid 175 through 180 450 hydrogen bonds defined for protein. 1275 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: 2.93 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3080 1.35 - 1.46: 2350 1.46 - 1.58: 4195 1.58 - 1.70: 0 1.70 - 1.82: 91 Bond restraints: 9716 Sorted by residual: bond pdb=" N TYR D 258 " pdb=" CA TYR D 258 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.45e+00 bond pdb=" C LEU D 256 " pdb=" N PRO D 257 " ideal model delta sigma weight residual 1.335 1.365 -0.029 1.30e-02 5.92e+03 5.11e+00 bond pdb=" N TYR D 290 " pdb=" CA TYR D 290 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.35e-02 5.49e+03 4.96e+00 bond pdb=" N GLN E 71 " pdb=" CA GLN E 71 " ideal model delta sigma weight residual 1.454 1.480 -0.026 1.21e-02 6.83e+03 4.60e+00 bond pdb=" N ILE D 291 " pdb=" CA ILE D 291 " ideal model delta sigma weight residual 1.458 1.485 -0.028 1.41e-02 5.03e+03 3.88e+00 ... (remaining 9711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 12815 1.48 - 2.96: 267 2.96 - 4.44: 57 4.44 - 5.92: 15 5.92 - 7.40: 6 Bond angle restraints: 13160 Sorted by residual: angle pdb=" N ILE D 291 " pdb=" CA ILE D 291 " pdb=" C ILE D 291 " ideal model delta sigma weight residual 112.04 105.77 6.27 1.40e+00 5.10e-01 2.00e+01 angle pdb=" CA PHE D 182 " pdb=" C PHE D 182 " pdb=" O PHE D 182 " ideal model delta sigma weight residual 119.99 116.42 3.57 8.70e-01 1.32e+00 1.68e+01 angle pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta sigma weight residual 121.54 127.80 -6.26 1.91e+00 2.74e-01 1.07e+01 angle pdb=" CA TYR D 258 " pdb=" CB TYR D 258 " pdb=" CG TYR D 258 " ideal model delta sigma weight residual 113.90 119.41 -5.51 1.80e+00 3.09e-01 9.36e+00 angle pdb=" CA TYR D 258 " pdb=" C TYR D 258 " pdb=" O TYR D 258 " ideal model delta sigma weight residual 120.90 117.72 3.18 1.07e+00 8.73e-01 8.85e+00 ... (remaining 13155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 5326 17.63 - 35.26: 393 35.26 - 52.89: 61 52.89 - 70.52: 7 70.52 - 88.15: 7 Dihedral angle restraints: 5794 sinusoidal: 2265 harmonic: 3529 Sorted by residual: dihedral pdb=" CB CYS E 21 " pdb=" SG CYS E 21 " pdb=" SG CYS E 47 " pdb=" CB CYS E 47 " ideal model delta sinusoidal sigma weight residual -86.00 -117.28 31.28 1 1.00e+01 1.00e-02 1.40e+01 dihedral pdb=" CA LEU D 173 " pdb=" C LEU D 173 " pdb=" N TYR D 174 " pdb=" CA TYR D 174 " ideal model delta harmonic sigma weight residual -180.00 -161.94 -18.06 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CG ARG A 32 " pdb=" CD ARG A 32 " pdb=" NE ARG A 32 " pdb=" CZ ARG A 32 " ideal model delta sinusoidal sigma weight residual 90.00 41.03 48.97 2 1.50e+01 4.44e-03 1.21e+01 ... (remaining 5791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 989 0.035 - 0.070: 368 0.070 - 0.105: 105 0.105 - 0.140: 33 0.140 - 0.175: 4 Chirality restraints: 1499 Sorted by residual: chirality pdb=" CB VAL A 201 " pdb=" CA VAL A 201 " pdb=" CG1 VAL A 201 " pdb=" CG2 VAL A 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" CA MET S 83 " pdb=" N MET S 83 " pdb=" C MET S 83 " pdb=" CB MET S 83 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.62e-01 chirality pdb=" CA PHE D 182 " pdb=" N PHE D 182 " pdb=" C PHE D 182 " pdb=" CB PHE D 182 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.89e-01 ... (remaining 1496 not shown) Planarity restraints: 1664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR D 181 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.59e+00 pdb=" C TYR D 181 " -0.044 2.00e-02 2.50e+03 pdb=" O TYR D 181 " 0.016 2.00e-02 2.50e+03 pdb=" N PHE D 182 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN D 296 " 0.040 5.00e-02 4.00e+02 6.05e-02 5.85e+00 pdb=" N PRO D 297 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO D 297 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 297 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 257 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.12e+00 pdb=" C PRO D 257 " 0.035 2.00e-02 2.50e+03 pdb=" O PRO D 257 " -0.013 2.00e-02 2.50e+03 pdb=" N TYR D 258 " -0.012 2.00e-02 2.50e+03 ... (remaining 1661 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 145 2.69 - 3.24: 8707 3.24 - 3.80: 13735 3.80 - 4.35: 18098 4.35 - 4.90: 31333 Nonbonded interactions: 72018 Sorted by model distance: nonbonded pdb=" O ARG S 67 " pdb=" OG1 THR S 84 " model vdw 2.139 3.040 nonbonded pdb=" NE2 GLN B 220 " pdb=" OD1 ASP B 258 " model vdw 2.239 3.120 nonbonded pdb=" O PHE S 32 " pdb=" NH2 ARG S 72 " model vdw 2.240 3.120 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.256 3.040 nonbonded pdb=" OE2 GLU D 199 " pdb=" NZ LYS E 68 " model vdw 2.267 3.120 ... (remaining 72013 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.360 Find NCS groups from input model: 0.130 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:12.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 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 : 0.002 0.033 9721 Z= 0.134 Angle : 0.584 7.404 13170 Z= 0.336 Chirality : 0.041 0.175 1499 Planarity : 0.004 0.060 1664 Dihedral : 12.471 88.151 3499 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.19 % Allowed : 0.10 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.58 (0.25), residues: 1202 helix: 2.07 (0.26), residues: 427 sheet: 0.72 (0.32), residues: 284 loop : -1.41 (0.25), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.002 0.001 HIS S 35 PHE 0.017 0.002 PHE S 68 TYR 0.024 0.001 TYR D 258 ARG 0.010 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.15242 ( 450) hydrogen bonds : angle 5.22152 ( 1275) SS BOND : bond 0.00487 ( 5) SS BOND : angle 1.24317 ( 10) covalent geometry : bond 0.00244 ( 9716) covalent geometry : angle 0.58329 (13160) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 243 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.6862 (ttp80) cc_final: 0.6516 (ttp80) REVERT: A 197 LYS cc_start: 0.7839 (ttmm) cc_final: 0.7434 (ttmm) REVERT: A 309 ASP cc_start: 0.6446 (m-30) cc_final: 0.6067 (m-30) REVERT: B 42 ARG cc_start: 0.7370 (tmm160) cc_final: 0.7117 (tmm-80) REVERT: B 155 ASN cc_start: 0.7615 (t0) cc_final: 0.6985 (t0) REVERT: D 137 LEU cc_start: 0.7689 (tp) cc_final: 0.7437 (tp) REVERT: D 193 SER cc_start: 0.8699 (m) cc_final: 0.8414 (m) outliers start: 2 outliers final: 1 residues processed: 244 average time/residue: 1.0570 time to fit residues: 278.2919 Evaluate side-chains 225 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 258 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 294 ASN A 347 ASN B 62 HIS B 110 ASN B 125 ASN B 230 ASN B 237 ASN B 239 ASN S 194 ASN D 292 ASN E 71 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.135090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.109805 restraints weight = 13061.985| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.08 r_work: 0.3286 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9721 Z= 0.183 Angle : 0.604 8.058 13170 Z= 0.316 Chirality : 0.043 0.158 1499 Planarity : 0.004 0.045 1664 Dihedral : 4.282 21.314 1320 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.12 % Allowed : 10.41 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.60 (0.24), residues: 1202 helix: 2.04 (0.26), residues: 433 sheet: 0.59 (0.31), residues: 294 loop : -1.33 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 211 HIS 0.005 0.001 HIS S 35 PHE 0.020 0.002 PHE B 199 TYR 0.024 0.002 TYR D 258 ARG 0.008 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.06329 ( 450) hydrogen bonds : angle 4.49366 ( 1275) SS BOND : bond 0.00861 ( 5) SS BOND : angle 1.99566 ( 10) covalent geometry : bond 0.00432 ( 9716) covalent geometry : angle 0.60153 (13160) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 1.053 Fit side-chains revert: symmetry clash REVERT: A 197 LYS cc_start: 0.8425 (ttmm) cc_final: 0.8053 (ttmm) REVERT: A 240 MET cc_start: 0.7489 (pp-130) cc_final: 0.7249 (pp-130) REVERT: A 245 GLU cc_start: 0.7207 (mm-30) cc_final: 0.7003 (mm-30) REVERT: A 247 MET cc_start: 0.8177 (mtm) cc_final: 0.7964 (mtm) REVERT: A 309 ASP cc_start: 0.7073 (m-30) cc_final: 0.6868 (m-30) REVERT: B 42 ARG cc_start: 0.8019 (tmm160) cc_final: 0.7794 (ttp80) REVERT: B 90 VAL cc_start: 0.8406 (t) cc_final: 0.7973 (m) REVERT: B 217 MET cc_start: 0.7998 (ptt) cc_final: 0.7784 (pp-130) REVERT: D 271 SER cc_start: 0.8424 (t) cc_final: 0.8080 (p) outliers start: 22 outliers final: 9 residues processed: 216 average time/residue: 1.1202 time to fit residues: 259.6706 Evaluate side-chains 200 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 191 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 274 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 255 ASN B 155 ASN B 237 ASN D 77 ASN D 101 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.135935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.110578 restraints weight = 13270.658| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.10 r_work: 0.3298 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9721 Z= 0.146 Angle : 0.546 8.148 13170 Z= 0.285 Chirality : 0.042 0.163 1499 Planarity : 0.004 0.042 1664 Dihedral : 4.123 21.433 1318 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.60 % Allowed : 13.50 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.67 (0.24), residues: 1202 helix: 2.20 (0.26), residues: 433 sheet: 0.63 (0.31), residues: 293 loop : -1.39 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS S 35 PHE 0.017 0.002 PHE B 199 TYR 0.020 0.001 TYR D 258 ARG 0.008 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.05508 ( 450) hydrogen bonds : angle 4.33277 ( 1275) SS BOND : bond 0.00765 ( 5) SS BOND : angle 1.68899 ( 10) covalent geometry : bond 0.00335 ( 9716) covalent geometry : angle 0.54455 (13160) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 1.176 Fit side-chains revert: symmetry clash REVERT: A 247 MET cc_start: 0.8175 (mtm) cc_final: 0.7953 (mtm) REVERT: A 276 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6138 (mt-10) REVERT: A 280 LYS cc_start: 0.7553 (mppt) cc_final: 0.7189 (mppt) REVERT: A 294 ASN cc_start: 0.8341 (t0) cc_final: 0.8053 (t0) REVERT: B 90 VAL cc_start: 0.8419 (t) cc_final: 0.7951 (m) REVERT: S 219 LEU cc_start: 0.7682 (mp) cc_final: 0.7415 (mp) REVERT: S 220 GLU cc_start: 0.7330 (mp0) cc_final: 0.6517 (mp0) REVERT: D 52 VAL cc_start: 0.8027 (t) cc_final: 0.7769 (t) REVERT: D 271 SER cc_start: 0.8460 (t) cc_final: 0.8114 (p) REVERT: D 274 THR cc_start: 0.8418 (OUTLIER) cc_final: 0.8204 (p) outliers start: 27 outliers final: 16 residues processed: 204 average time/residue: 1.0726 time to fit residues: 236.5446 Evaluate side-chains 203 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 288 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 61 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 112 optimal weight: 0.4980 chunk 77 optimal weight: 0.0770 chunk 23 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 347 ASN B 155 ASN B 237 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.136092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.111007 restraints weight = 13125.354| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.07 r_work: 0.3322 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9721 Z= 0.115 Angle : 0.511 7.758 13170 Z= 0.266 Chirality : 0.040 0.129 1499 Planarity : 0.004 0.040 1664 Dihedral : 3.964 22.702 1318 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.38 % Allowed : 14.37 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.83 (0.24), residues: 1202 helix: 2.35 (0.25), residues: 433 sheet: 0.75 (0.31), residues: 294 loop : -1.36 (0.25), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 213 PHE 0.015 0.001 PHE B 199 TYR 0.015 0.001 TYR D 174 ARG 0.007 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.04739 ( 450) hydrogen bonds : angle 4.19014 ( 1275) SS BOND : bond 0.00606 ( 5) SS BOND : angle 1.35976 ( 10) covalent geometry : bond 0.00251 ( 9716) covalent geometry : angle 0.50971 (13160) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 1.189 Fit side-chains REVERT: A 197 LYS cc_start: 0.8357 (ttmm) cc_final: 0.7998 (ttmm) REVERT: A 247 MET cc_start: 0.8172 (mtm) cc_final: 0.7936 (mtm) REVERT: A 276 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6185 (mt-10) REVERT: A 280 LYS cc_start: 0.7469 (mppt) cc_final: 0.7100 (mppt) REVERT: A 294 ASN cc_start: 0.8323 (t0) cc_final: 0.8013 (t0) REVERT: B 42 ARG cc_start: 0.8021 (ttp80) cc_final: 0.7499 (tmm-80) REVERT: B 219 ARG cc_start: 0.7468 (mpt90) cc_final: 0.7206 (mpt90) REVERT: S 83 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.7009 (mmm) REVERT: D 52 VAL cc_start: 0.8011 (t) cc_final: 0.7747 (t) REVERT: D 120 MET cc_start: 0.7959 (mmm) cc_final: 0.7694 (mtt) REVERT: D 271 SER cc_start: 0.8480 (t) cc_final: 0.8121 (p) outliers start: 35 outliers final: 17 residues processed: 196 average time/residue: 1.0105 time to fit residues: 214.4359 Evaluate side-chains 195 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 288 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 15 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 11 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 347 ASN B 155 ASN B 237 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.135438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.110319 restraints weight = 13082.859| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.06 r_work: 0.3310 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9721 Z= 0.129 Angle : 0.530 9.801 13170 Z= 0.275 Chirality : 0.041 0.131 1499 Planarity : 0.004 0.039 1664 Dihedral : 3.947 22.170 1318 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.18 % Allowed : 15.04 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.85 (0.24), residues: 1202 helix: 2.34 (0.25), residues: 434 sheet: 0.76 (0.31), residues: 293 loop : -1.33 (0.25), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.018 0.002 PHE S 68 TYR 0.018 0.001 TYR D 258 ARG 0.010 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.05066 ( 450) hydrogen bonds : angle 4.20547 ( 1275) SS BOND : bond 0.00700 ( 5) SS BOND : angle 1.43578 ( 10) covalent geometry : bond 0.00292 ( 9716) covalent geometry : angle 0.52900 (13160) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 191 time to evaluate : 1.197 Fit side-chains REVERT: A 48 THR cc_start: 0.8185 (p) cc_final: 0.7974 (t) REVERT: A 197 LYS cc_start: 0.8368 (ttmm) cc_final: 0.8044 (ttmm) REVERT: A 247 MET cc_start: 0.8161 (mtm) cc_final: 0.7924 (mtm) REVERT: A 276 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6240 (mt-10) REVERT: A 280 LYS cc_start: 0.7475 (mppt) cc_final: 0.7132 (mppt) REVERT: A 294 ASN cc_start: 0.8350 (t0) cc_final: 0.8036 (t0) REVERT: B 42 ARG cc_start: 0.8024 (ttp80) cc_final: 0.7542 (tmm-80) REVERT: B 212 ASP cc_start: 0.7784 (m-30) cc_final: 0.6032 (m-30) REVERT: B 219 ARG cc_start: 0.7516 (mpt90) cc_final: 0.7224 (mpt90) REVERT: S 83 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.6203 (mpp) REVERT: S 220 GLU cc_start: 0.7321 (mp0) cc_final: 0.6610 (mp0) REVERT: D 52 VAL cc_start: 0.8034 (t) cc_final: 0.7777 (t) REVERT: D 68 ARG cc_start: 0.7723 (mmt90) cc_final: 0.7383 (mmt90) REVERT: D 120 MET cc_start: 0.7969 (mmm) cc_final: 0.7744 (mtt) REVERT: D 271 SER cc_start: 0.8525 (t) cc_final: 0.8166 (p) outliers start: 33 outliers final: 21 residues processed: 203 average time/residue: 1.0636 time to fit residues: 233.3402 Evaluate side-chains 207 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 288 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 59 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 96 optimal weight: 0.0770 chunk 16 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 347 ASN B 155 ASN B 237 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.135881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.110814 restraints weight = 13212.268| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.08 r_work: 0.3302 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9721 Z= 0.138 Angle : 0.534 8.112 13170 Z= 0.278 Chirality : 0.041 0.147 1499 Planarity : 0.004 0.039 1664 Dihedral : 3.982 22.289 1318 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.09 % Allowed : 15.91 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.85 (0.24), residues: 1202 helix: 2.36 (0.25), residues: 433 sheet: 0.75 (0.31), residues: 298 loop : -1.35 (0.25), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.015 0.002 PHE B 199 TYR 0.019 0.001 TYR D 258 ARG 0.010 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.05268 ( 450) hydrogen bonds : angle 4.25541 ( 1275) SS BOND : bond 0.00650 ( 5) SS BOND : angle 1.74785 ( 10) covalent geometry : bond 0.00318 ( 9716) covalent geometry : angle 0.53207 (13160) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 1.105 Fit side-chains REVERT: A 48 THR cc_start: 0.8187 (p) cc_final: 0.7974 (t) REVERT: A 247 MET cc_start: 0.8166 (mtm) cc_final: 0.7921 (mtm) REVERT: A 276 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6310 (mt-10) REVERT: A 280 LYS cc_start: 0.7480 (mppt) cc_final: 0.7141 (mppt) REVERT: A 294 ASN cc_start: 0.8371 (t0) cc_final: 0.8071 (t0) REVERT: B 42 ARG cc_start: 0.8038 (ttp80) cc_final: 0.7577 (tmm-80) REVERT: B 219 ARG cc_start: 0.7532 (mpt90) cc_final: 0.7242 (mpt90) REVERT: S 116 THR cc_start: 0.8416 (t) cc_final: 0.8042 (p) REVERT: S 220 GLU cc_start: 0.7380 (mp0) cc_final: 0.6669 (mp0) REVERT: D 52 VAL cc_start: 0.8055 (t) cc_final: 0.7800 (t) REVERT: D 68 ARG cc_start: 0.7726 (mmt90) cc_final: 0.7401 (mmt90) REVERT: D 271 SER cc_start: 0.8521 (t) cc_final: 0.8178 (p) outliers start: 32 outliers final: 20 residues processed: 208 average time/residue: 1.0311 time to fit residues: 232.0052 Evaluate side-chains 205 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 288 PHE Chi-restraints excluded: chain D residue 294 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 1 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 347 ASN B 155 ASN B 237 ASN ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.135614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.110624 restraints weight = 13189.785| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.07 r_work: 0.3298 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9721 Z= 0.147 Angle : 0.552 8.419 13170 Z= 0.285 Chirality : 0.042 0.191 1499 Planarity : 0.004 0.039 1664 Dihedral : 4.016 22.101 1318 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.70 % Allowed : 16.59 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.86 (0.24), residues: 1202 helix: 2.36 (0.25), residues: 433 sheet: 0.77 (0.31), residues: 298 loop : -1.35 (0.25), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.015 0.002 PHE B 199 TYR 0.020 0.001 TYR D 258 ARG 0.010 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.05446 ( 450) hydrogen bonds : angle 4.28269 ( 1275) SS BOND : bond 0.00767 ( 5) SS BOND : angle 1.82898 ( 10) covalent geometry : bond 0.00342 ( 9716) covalent geometry : angle 0.54987 (13160) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 189 time to evaluate : 1.120 Fit side-chains REVERT: A 48 THR cc_start: 0.8199 (p) cc_final: 0.7982 (t) REVERT: A 240 MET cc_start: 0.7564 (ppp) cc_final: 0.6912 (ppp) REVERT: A 247 MET cc_start: 0.8159 (mtm) cc_final: 0.7940 (mtm) REVERT: A 276 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6336 (mt-10) REVERT: A 280 LYS cc_start: 0.7470 (mppt) cc_final: 0.7134 (mppt) REVERT: A 294 ASN cc_start: 0.8378 (t0) cc_final: 0.8092 (t0) REVERT: B 42 ARG cc_start: 0.7993 (ttp80) cc_final: 0.7549 (tmm-80) REVERT: B 219 ARG cc_start: 0.7553 (mpt90) cc_final: 0.7233 (mpt90) REVERT: D 52 VAL cc_start: 0.8067 (t) cc_final: 0.7809 (t) REVERT: D 68 ARG cc_start: 0.7715 (mmt90) cc_final: 0.7392 (mmt90) REVERT: D 271 SER cc_start: 0.8547 (t) cc_final: 0.8206 (p) outliers start: 28 outliers final: 23 residues processed: 203 average time/residue: 1.0704 time to fit residues: 234.4419 Evaluate side-chains 208 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 288 PHE Chi-restraints excluded: chain D residue 294 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 21 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 105 optimal weight: 0.0870 chunk 67 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS A 347 ASN B 155 ASN B 237 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.136282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.111234 restraints weight = 13300.301| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.09 r_work: 0.3305 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9721 Z= 0.131 Angle : 0.531 8.713 13170 Z= 0.276 Chirality : 0.041 0.150 1499 Planarity : 0.004 0.039 1664 Dihedral : 3.967 22.398 1318 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.89 % Allowed : 16.39 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.89 (0.24), residues: 1202 helix: 2.39 (0.25), residues: 433 sheet: 0.77 (0.31), residues: 298 loop : -1.34 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.015 0.002 PHE B 199 TYR 0.017 0.001 TYR D 258 ARG 0.010 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.05075 ( 450) hydrogen bonds : angle 4.24703 ( 1275) SS BOND : bond 0.00708 ( 5) SS BOND : angle 1.62071 ( 10) covalent geometry : bond 0.00298 ( 9716) covalent geometry : angle 0.52929 (13160) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 0.997 Fit side-chains REVERT: A 48 THR cc_start: 0.8210 (p) cc_final: 0.7995 (t) REVERT: A 197 LYS cc_start: 0.8378 (ttmp) cc_final: 0.8110 (ttmm) REVERT: A 240 MET cc_start: 0.7627 (ppp) cc_final: 0.6961 (ppp) REVERT: A 276 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6334 (mt-10) REVERT: A 280 LYS cc_start: 0.7481 (mppt) cc_final: 0.7149 (mppt) REVERT: A 294 ASN cc_start: 0.8356 (t0) cc_final: 0.8088 (t0) REVERT: A 316 THR cc_start: 0.7950 (m) cc_final: 0.7723 (p) REVERT: B 42 ARG cc_start: 0.7994 (ttp80) cc_final: 0.7558 (tmm-80) REVERT: B 212 ASP cc_start: 0.7820 (m-30) cc_final: 0.5973 (m-30) REVERT: B 219 ARG cc_start: 0.7554 (mpt90) cc_final: 0.7152 (mpt90) REVERT: D 52 VAL cc_start: 0.8045 (t) cc_final: 0.7789 (t) REVERT: D 68 ARG cc_start: 0.7732 (mmt90) cc_final: 0.7412 (mmt90) REVERT: D 271 SER cc_start: 0.8545 (t) cc_final: 0.8196 (p) outliers start: 30 outliers final: 23 residues processed: 199 average time/residue: 1.2778 time to fit residues: 275.4396 Evaluate side-chains 207 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 288 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 116 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 114 optimal weight: 0.0470 chunk 31 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS A 347 ASN B 155 ASN B 237 ASN ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.135445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.110498 restraints weight = 13122.341| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.07 r_work: 0.3290 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9721 Z= 0.149 Angle : 0.555 8.785 13170 Z= 0.287 Chirality : 0.042 0.144 1499 Planarity : 0.004 0.039 1664 Dihedral : 4.025 21.555 1318 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.80 % Allowed : 17.45 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.85 (0.24), residues: 1202 helix: 2.34 (0.25), residues: 434 sheet: 0.70 (0.31), residues: 300 loop : -1.31 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.017 0.002 PHE S 68 TYR 0.020 0.001 TYR D 258 ARG 0.010 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.05487 ( 450) hydrogen bonds : angle 4.29161 ( 1275) SS BOND : bond 0.00773 ( 5) SS BOND : angle 1.76671 ( 10) covalent geometry : bond 0.00346 ( 9716) covalent geometry : angle 0.55328 (13160) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 183 time to evaluate : 1.072 Fit side-chains REVERT: A 197 LYS cc_start: 0.8393 (ttmp) cc_final: 0.8127 (ttmm) REVERT: A 276 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6336 (mt-10) REVERT: A 280 LYS cc_start: 0.7475 (mppt) cc_final: 0.7149 (mppt) REVERT: A 294 ASN cc_start: 0.8395 (t0) cc_final: 0.8114 (t0) REVERT: A 316 THR cc_start: 0.7987 (m) cc_final: 0.7745 (p) REVERT: B 42 ARG cc_start: 0.7992 (ttp80) cc_final: 0.7556 (tmm-80) REVERT: B 212 ASP cc_start: 0.7794 (m-30) cc_final: 0.5918 (m-30) REVERT: B 219 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.7099 (mpt90) REVERT: D 52 VAL cc_start: 0.8032 (t) cc_final: 0.7774 (t) REVERT: D 68 ARG cc_start: 0.7728 (mmt90) cc_final: 0.7417 (mmt90) REVERT: D 271 SER cc_start: 0.8564 (t) cc_final: 0.8221 (p) outliers start: 29 outliers final: 25 residues processed: 196 average time/residue: 1.3260 time to fit residues: 278.5616 Evaluate side-chains 209 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 288 PHE Chi-restraints excluded: chain D residue 294 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 116 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS A 347 ASN B 155 ASN B 237 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.136299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.111266 restraints weight = 13357.888| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.08 r_work: 0.3309 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9721 Z= 0.131 Angle : 0.546 8.950 13170 Z= 0.282 Chirality : 0.041 0.156 1499 Planarity : 0.004 0.039 1664 Dihedral : 4.013 21.973 1318 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.70 % Allowed : 17.26 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.89 (0.24), residues: 1202 helix: 2.39 (0.25), residues: 434 sheet: 0.74 (0.31), residues: 298 loop : -1.30 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 213 PHE 0.015 0.002 PHE B 199 TYR 0.017 0.001 TYR D 258 ARG 0.010 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.05113 ( 450) hydrogen bonds : angle 4.30297 ( 1275) SS BOND : bond 0.00682 ( 5) SS BOND : angle 1.92289 ( 10) covalent geometry : bond 0.00298 ( 9716) covalent geometry : angle 0.54314 (13160) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 1.084 Fit side-chains REVERT: A 48 THR cc_start: 0.8190 (p) cc_final: 0.7979 (t) REVERT: A 197 LYS cc_start: 0.8380 (ttmp) cc_final: 0.8114 (ttmm) REVERT: A 240 MET cc_start: 0.7673 (ppp) cc_final: 0.6934 (ppp) REVERT: A 276 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6362 (mt-10) REVERT: A 280 LYS cc_start: 0.7483 (mppt) cc_final: 0.7158 (mppt) REVERT: A 294 ASN cc_start: 0.8385 (t0) cc_final: 0.8127 (t0) REVERT: A 316 THR cc_start: 0.7972 (m) cc_final: 0.7745 (p) REVERT: B 42 ARG cc_start: 0.8009 (ttp80) cc_final: 0.7577 (tmm-80) REVERT: B 212 ASP cc_start: 0.7795 (m-30) cc_final: 0.5950 (m-30) REVERT: B 219 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7104 (mpt90) REVERT: S 230 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7892 (ttp) REVERT: D 52 VAL cc_start: 0.8055 (t) cc_final: 0.7800 (t) REVERT: D 68 ARG cc_start: 0.7721 (mmt90) cc_final: 0.7421 (mmt90) REVERT: D 271 SER cc_start: 0.8545 (t) cc_final: 0.8201 (p) outliers start: 28 outliers final: 22 residues processed: 190 average time/residue: 1.2096 time to fit residues: 248.1012 Evaluate side-chains 202 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 288 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 100 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 48 optimal weight: 0.0670 chunk 87 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS A 347 ASN B 155 ASN B 237 ASN D 292 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.135200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.110238 restraints weight = 13278.765| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.08 r_work: 0.3287 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9721 Z= 0.158 Angle : 0.567 8.894 13170 Z= 0.293 Chirality : 0.042 0.143 1499 Planarity : 0.004 0.039 1664 Dihedral : 4.095 21.341 1318 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.70 % Allowed : 17.74 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.80 (0.24), residues: 1202 helix: 2.32 (0.25), residues: 434 sheet: 0.65 (0.31), residues: 298 loop : -1.33 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.018 0.002 PHE S 68 TYR 0.021 0.002 TYR D 258 ARG 0.010 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.05659 ( 450) hydrogen bonds : angle 4.37433 ( 1275) SS BOND : bond 0.00788 ( 5) SS BOND : angle 1.91574 ( 10) covalent geometry : bond 0.00371 ( 9716) covalent geometry : angle 0.56525 (13160) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7853.05 seconds wall clock time: 138 minutes 34.43 seconds (8314.43 seconds total)