Starting phenix.real_space_refine on Thu Feb 13 05:17:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jlk_36400/02_2025/8jlk_36400.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jlk_36400/02_2025/8jlk_36400.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jlk_36400/02_2025/8jlk_36400.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jlk_36400/02_2025/8jlk_36400.map" model { file = "/net/cci-nas-00/data/ceres_data/8jlk_36400/02_2025/8jlk_36400.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jlk_36400/02_2025/8jlk_36400.cif" } resolution = 3.22 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= 0.084 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 5617 2.51 5 N 1506 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8824 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1915 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2593 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 2084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2084 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 255} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "S" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1775 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "Y" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'UJL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.47, per 1000 atoms: 0.62 Number of scatterers: 8824 At special positions: 0 Unit cell: (110.4, 134.32, 105.8, 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 1638 8.00 N 1506 7.00 C 5617 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 181 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 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: 2.34 Conformation dependent library (CDL) restraints added in 1.0 seconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 15 sheets defined 37.6% alpha, 19.5% 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 32 removed outlier: 3.631A pdb=" N GLU A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.683A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 removed outlier: 4.038A pdb=" N GLN A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 245 removed outlier: 3.555A pdb=" N ASN A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 269 removed outlier: 3.771A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 285 Processing helix chain 'A' and resid 298 through 318 removed outlier: 4.358A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 removed outlier: 3.859A pdb=" N ARG A 352 " --> pdb=" O ASP A 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.841A pdb=" N ARG B 8 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP B 20 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA B 21 " --> pdb=" O GLN B 17 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 4.195A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 20 through 50 removed outlier: 3.573A pdb=" N VAL R 43 " --> pdb=" O GLY R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 85 removed outlier: 4.462A pdb=" N MET R 76 " --> pdb=" O GLY R 72 " (cutoff:3.500A) Proline residue: R 77 - end of helix removed outlier: 3.652A pdb=" N THR R 83 " --> pdb=" O SER R 79 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL R 84 " --> pdb=" O MET R 80 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU R 85 " --> pdb=" O VAL R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 126 removed outlier: 3.663A pdb=" N CYS R 95 " --> pdb=" O GLY R 91 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS R 96 " --> pdb=" O GLU R 92 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL R 97 " --> pdb=" O ILE R 93 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP R 126 " --> pdb=" O CYS R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 134 removed outlier: 3.695A pdb=" N LYS R 133 " --> pdb=" O ARG R 129 " (cutoff:3.500A) Processing helix chain 'R' and resid 135 through 159 removed outlier: 3.825A pdb=" N LEU R 149 " --> pdb=" O VAL R 145 " (cutoff:3.500A) Proline residue: R 150 - end of helix Processing helix chain 'R' and resid 167 through 174 Processing helix chain 'R' and resid 186 through 222 removed outlier: 4.066A pdb=" N VAL R 191 " --> pdb=" O LYS R 187 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ILE R 200 " --> pdb=" O THR R 196 " (cutoff:3.500A) Proline residue: R 201 - end of helix removed outlier: 4.118A pdb=" N TYR R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE R 214 " --> pdb=" O TYR R 210 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA R 220 " --> pdb=" O ALA R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 260 removed outlier: 4.437A pdb=" N PHE R 257 " --> pdb=" O MET R 253 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 275 Proline residue: R 272 - end of helix Processing helix chain 'R' and resid 279 through 303 removed outlier: 3.662A pdb=" N ASN R 283 " --> pdb=" O PRO R 279 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA R 285 " --> pdb=" O SER R 281 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY R 290 " --> pdb=" O LEU R 286 " (cutoff:3.500A) Proline residue: R 298 - end of helix removed outlier: 3.525A pdb=" N TYR R 301 " --> pdb=" O ASN R 297 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 310 removed outlier: 3.755A pdb=" N ARG R 310 " --> pdb=" O PRO R 306 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.841A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'Y' and resid 8 through 24 removed outlier: 3.690A pdb=" N LYS Y 14 " --> pdb=" O ALA Y 10 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU Y 15 " --> pdb=" O GLN Y 11 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL Y 16 " --> pdb=" O ALA Y 12 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN Y 24 " --> pdb=" O LYS Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 28 through 45 removed outlier: 3.910A pdb=" N LYS Y 32 " --> pdb=" O ILE Y 28 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA Y 33 " --> pdb=" O LYS Y 29 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU Y 37 " --> pdb=" O ALA Y 33 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 190 removed outlier: 4.787A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 9.900A pdb=" N ALA A 220 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 47 removed outlier: 3.891A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 47 removed outlier: 3.891A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.136A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA B 73 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.053A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.958A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.600A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.515A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.017A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.553A pdb=" N SER S 7 " --> pdb=" O SER S 21 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 Processing sheet with id=AB3, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.573A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR S 94 " --> pdb=" O THR S 115 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 Processing sheet with id=AB6, first strand: chain 'S' and resid 194 through 195 removed outlier: 3.529A pdb=" N ASN S 194 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) 379 hydrogen bonds defined for protein. 1083 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: 2.63 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1434 1.32 - 1.44: 2537 1.44 - 1.57: 4956 1.57 - 1.69: 0 1.69 - 1.82: 93 Bond restraints: 9020 Sorted by residual: bond pdb=" CA PHE R 264 " pdb=" C PHE R 264 " ideal model delta sigma weight residual 1.524 1.455 0.070 1.24e-02 6.50e+03 3.16e+01 bond pdb=" C GLY R 218 " pdb=" O GLY R 218 " ideal model delta sigma weight residual 1.234 1.287 -0.053 1.20e-02 6.94e+03 1.98e+01 bond pdb=" N ARG R 211 " pdb=" CA ARG R 211 " ideal model delta sigma weight residual 1.459 1.510 -0.051 1.21e-02 6.83e+03 1.74e+01 bond pdb=" C PHE R 264 " pdb=" N PHE R 265 " ideal model delta sigma weight residual 1.335 1.283 0.052 1.34e-02 5.57e+03 1.51e+01 bond pdb=" C ILE R 118 " pdb=" O ILE R 118 " ideal model delta sigma weight residual 1.237 1.194 0.043 1.13e-02 7.83e+03 1.45e+01 ... (remaining 9015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 11827 2.09 - 4.17: 326 4.17 - 6.26: 63 6.26 - 8.35: 10 8.35 - 10.43: 2 Bond angle restraints: 12228 Sorted by residual: angle pdb=" N ARG R 82 " pdb=" CA ARG R 82 " pdb=" C ARG R 82 " ideal model delta sigma weight residual 113.19 123.62 -10.43 1.19e+00 7.06e-01 7.69e+01 angle pdb=" O SER R 117 " pdb=" C SER R 117 " pdb=" N ILE R 118 " ideal model delta sigma weight residual 122.07 115.61 6.46 1.03e+00 9.43e-01 3.94e+01 angle pdb=" C ARG R 211 " pdb=" CA ARG R 211 " pdb=" CB ARG R 211 " ideal model delta sigma weight residual 110.79 101.72 9.07 1.66e+00 3.63e-01 2.99e+01 angle pdb=" CA SER R 117 " pdb=" C SER R 117 " pdb=" N ILE R 118 " ideal model delta sigma weight residual 117.07 123.27 -6.20 1.14e+00 7.69e-01 2.96e+01 angle pdb=" C ILE R 118 " pdb=" N ASP R 119 " pdb=" CA ASP R 119 " ideal model delta sigma weight residual 120.38 113.57 6.81 1.37e+00 5.33e-01 2.47e+01 ... (remaining 12223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 4805 17.88 - 35.76: 419 35.76 - 53.63: 94 53.63 - 71.51: 18 71.51 - 89.39: 7 Dihedral angle restraints: 5343 sinusoidal: 2066 harmonic: 3277 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 93.00 146.24 -53.24 1 1.00e+01 1.00e-02 3.85e+01 dihedral pdb=" CA GLU S 234 " pdb=" C GLU S 234 " pdb=" N TYR S 235 " pdb=" CA TYR S 235 " ideal model delta harmonic sigma weight residual -180.00 -157.60 -22.40 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA LEU R 74 " pdb=" C LEU R 74 " pdb=" N ILE R 75 " pdb=" CA ILE R 75 " ideal model delta harmonic sigma weight residual -180.00 -158.35 -21.65 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 5340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1054 0.051 - 0.101: 264 0.101 - 0.152: 44 0.152 - 0.203: 6 0.203 - 0.254: 3 Chirality restraints: 1371 Sorted by residual: chirality pdb=" CA ARG R 221 " pdb=" N ARG R 221 " pdb=" C ARG R 221 " pdb=" CB ARG R 221 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA LEU R 282 " pdb=" N LEU R 282 " pdb=" C LEU R 282 " pdb=" CB LEU R 282 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA ILE R 278 " pdb=" N ILE R 278 " pdb=" C ILE R 278 " pdb=" CB ILE R 278 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1368 not shown) Planarity restraints: 1553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 UJL R 401 " 0.101 2.00e-02 2.50e+03 8.43e-02 1.24e+02 pdb=" C5 UJL R 401 " -0.063 2.00e-02 2.50e+03 pdb=" C6 UJL R 401 " -0.015 2.00e-02 2.50e+03 pdb=" C7 UJL R 401 " 0.021 2.00e-02 2.50e+03 pdb=" C8 UJL R 401 " 0.111 2.00e-02 2.50e+03 pdb=" C9 UJL R 401 " -0.006 2.00e-02 2.50e+03 pdb=" S1 UJL R 401 " -0.150 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 209 " 0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C TYR R 209 " -0.061 2.00e-02 2.50e+03 pdb=" O TYR R 209 " 0.023 2.00e-02 2.50e+03 pdb=" N TYR R 210 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 286 " 0.018 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C LEU R 286 " -0.060 2.00e-02 2.50e+03 pdb=" O LEU R 286 " 0.022 2.00e-02 2.50e+03 pdb=" N TYR R 287 " 0.020 2.00e-02 2.50e+03 ... (remaining 1550 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1168 2.75 - 3.29: 8465 3.29 - 3.83: 13828 3.83 - 4.36: 16148 4.36 - 4.90: 28455 Nonbonded interactions: 68064 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.213 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP Y 48 " model vdw 2.237 3.040 nonbonded pdb=" OG1 THR R 55 " pdb=" OD1 ASN R 58 " model vdw 2.253 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.262 3.040 nonbonded pdb=" NH1 ARG B 42 " pdb=" OE1 GLN B 44 " model vdw 2.275 3.120 ... (remaining 68059 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: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 23.020 Find NCS groups from input model: 0.110 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 9020 Z= 0.343 Angle : 0.836 10.434 12228 Z= 0.518 Chirality : 0.047 0.254 1371 Planarity : 0.006 0.084 1553 Dihedral : 14.643 89.390 3222 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.95 % Allowed : 0.42 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1111 helix: 0.38 (0.28), residues: 369 sheet: -0.34 (0.31), residues: 294 loop : -1.63 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP S 47 HIS 0.012 0.002 HIS R 98 PHE 0.027 0.002 PHE S 29 TYR 0.016 0.002 TYR R 305 ARG 0.012 0.001 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 258 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ILE cc_start: 0.7880 (mt) cc_final: 0.7342 (mt) REVERT: A 230 TYR cc_start: 0.6275 (m-80) cc_final: 0.5914 (m-80) REVERT: R 197 SER cc_start: 0.6763 (t) cc_final: 0.6528 (p) REVERT: S 27 PHE cc_start: 0.6767 (p90) cc_final: 0.6442 (p90) outliers start: 9 outliers final: 4 residues processed: 264 average time/residue: 0.2565 time to fit residues: 89.0281 Evaluate side-chains 158 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 154 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 153 TYR Chi-restraints excluded: chain R residue 211 ARG Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain R residue 289 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 99 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 324 HIS ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** S 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.199875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.156105 restraints weight = 11620.320| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 3.27 r_work: 0.3856 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9020 Z= 0.228 Angle : 0.661 8.371 12228 Z= 0.350 Chirality : 0.046 0.160 1371 Planarity : 0.005 0.063 1553 Dihedral : 5.623 59.770 1254 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.21 % Allowed : 12.01 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.62 (0.25), residues: 1111 helix: 0.64 (0.27), residues: 391 sheet: 0.41 (0.32), residues: 262 loop : -1.86 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP S 47 HIS 0.007 0.001 HIS A 197 PHE 0.013 0.001 PHE B 241 TYR 0.018 0.002 TYR R 287 ARG 0.005 0.001 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 LYS cc_start: 0.8156 (mmtm) cc_final: 0.7909 (mttt) REVERT: A 198 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.8061 (ttp) REVERT: A 260 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7579 (mtmt) REVERT: R 188 VAL cc_start: 0.8349 (m) cc_final: 0.8068 (p) REVERT: S 34 MET cc_start: 0.7428 (mmm) cc_final: 0.6974 (mmm) REVERT: Y 50 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7967 (mp) outliers start: 21 outliers final: 11 residues processed: 177 average time/residue: 0.2371 time to fit residues: 56.0285 Evaluate side-chains 154 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 47 TRP Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain Y residue 50 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 61 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 10 optimal weight: 0.1980 chunk 51 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 chunk 47 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 92 optimal weight: 0.0030 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN R 58 ASN ** S 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.198031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.156442 restraints weight = 11525.170| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.85 r_work: 0.3866 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9020 Z= 0.148 Angle : 0.550 6.432 12228 Z= 0.289 Chirality : 0.042 0.163 1371 Planarity : 0.004 0.048 1553 Dihedral : 4.520 40.565 1248 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.53 % Allowed : 14.65 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.26 (0.25), residues: 1111 helix: 1.06 (0.27), residues: 390 sheet: 0.50 (0.32), residues: 268 loop : -1.74 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP S 47 HIS 0.003 0.001 HIS A 197 PHE 0.013 0.001 PHE A 343 TYR 0.013 0.001 TYR R 287 ARG 0.009 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8217 (ttmm) REVERT: A 53 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.7262 (mpp) REVERT: A 193 LYS cc_start: 0.8130 (mmtm) cc_final: 0.7892 (mttt) REVERT: A 201 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.8141 (t) REVERT: A 269 LEU cc_start: 0.6258 (OUTLIER) cc_final: 0.5875 (mt) REVERT: B 212 ASP cc_start: 0.6547 (t0) cc_final: 0.5775 (t0) REVERT: R 188 VAL cc_start: 0.8228 (m) cc_final: 0.7965 (p) REVERT: S 34 MET cc_start: 0.7455 (mmm) cc_final: 0.7067 (mmm) outliers start: 24 outliers final: 12 residues processed: 174 average time/residue: 0.2141 time to fit residues: 51.6065 Evaluate side-chains 155 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 47 TRP Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 187 LEU Chi-restraints excluded: chain Y residue 17 GLU Chi-restraints excluded: chain Y residue 51 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 16 optimal weight: 20.0000 chunk 90 optimal weight: 0.0010 chunk 97 optimal weight: 0.0980 chunk 105 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 95 optimal weight: 0.0050 chunk 71 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 40 optimal weight: 0.0670 overall best weight: 0.1738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 213 GLN S 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.201132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.157751 restraints weight = 11294.275| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 2.74 r_work: 0.3904 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9020 Z= 0.127 Angle : 0.524 7.757 12228 Z= 0.271 Chirality : 0.041 0.161 1371 Planarity : 0.004 0.042 1553 Dihedral : 4.266 40.110 1244 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.11 % Allowed : 15.60 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.02 (0.25), residues: 1111 helix: 1.36 (0.27), residues: 385 sheet: 0.63 (0.32), residues: 268 loop : -1.60 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP S 47 HIS 0.004 0.001 HIS A 197 PHE 0.012 0.001 PHE B 199 TYR 0.009 0.001 TYR A 306 ARG 0.006 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.992 Fit side-chains REVERT: A 53 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7273 (mpp) REVERT: A 198 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7766 (ttp) REVERT: A 269 LEU cc_start: 0.6216 (OUTLIER) cc_final: 0.5812 (mt) REVERT: B 59 TYR cc_start: 0.7871 (m-80) cc_final: 0.7383 (m-80) REVERT: B 217 MET cc_start: 0.6993 (ttp) cc_final: 0.6398 (ppp) REVERT: B 219 ARG cc_start: 0.7246 (mmt90) cc_final: 0.7010 (mmt-90) REVERT: B 325 MET cc_start: 0.6325 (mmm) cc_final: 0.6088 (mmm) REVERT: R 82 ARG cc_start: 0.7499 (tmm-80) cc_final: 0.7257 (tmm-80) REVERT: R 188 VAL cc_start: 0.8219 (m) cc_final: 0.7954 (p) REVERT: S 93 MET cc_start: 0.4873 (tpt) cc_final: 0.4661 (tpt) outliers start: 20 outliers final: 10 residues processed: 164 average time/residue: 0.2200 time to fit residues: 49.7148 Evaluate side-chains 147 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain R residue 304 PHE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 47 TRP Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 184 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 10 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 63 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN A 213 GLN A 261 GLN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.192765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.152889 restraints weight = 11528.170| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.61 r_work: 0.3746 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.6226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9020 Z= 0.199 Angle : 0.592 9.148 12228 Z= 0.307 Chirality : 0.043 0.158 1371 Planarity : 0.004 0.041 1553 Dihedral : 4.575 40.845 1244 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.63 % Allowed : 16.65 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.10 (0.25), residues: 1111 helix: 1.51 (0.27), residues: 380 sheet: 0.71 (0.32), residues: 268 loop : -1.62 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP S 47 HIS 0.006 0.001 HIS S 35 PHE 0.014 0.002 PHE A 343 TYR 0.023 0.001 TYR A 30 ARG 0.005 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.935 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.7286 (mpp) REVERT: A 198 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8214 (ttp) REVERT: A 206 ASP cc_start: 0.7920 (m-30) cc_final: 0.7634 (p0) REVERT: A 269 LEU cc_start: 0.6116 (OUTLIER) cc_final: 0.5630 (mt) REVERT: A 281 GLU cc_start: 0.6864 (tp30) cc_final: 0.6200 (tp30) REVERT: B 59 TYR cc_start: 0.8403 (m-80) cc_final: 0.7717 (m-80) REVERT: B 215 GLU cc_start: 0.8031 (pm20) cc_final: 0.7744 (pm20) REVERT: B 226 GLU cc_start: 0.8296 (tp30) cc_final: 0.8057 (mm-30) REVERT: R 58 ASN cc_start: 0.7184 (m110) cc_final: 0.6952 (m110) REVERT: R 82 ARG cc_start: 0.7563 (tmm-80) cc_final: 0.7298 (tmm-80) REVERT: R 86 ARG cc_start: 0.7314 (mtt90) cc_final: 0.6608 (mpt180) REVERT: R 188 VAL cc_start: 0.8054 (m) cc_final: 0.7800 (p) REVERT: S 34 MET cc_start: 0.7105 (mmm) cc_final: 0.6702 (mmm) REVERT: S 82 GLN cc_start: 0.7718 (mm-40) cc_final: 0.7094 (mp10) REVERT: S 177 PHE cc_start: 0.6174 (m-80) cc_final: 0.5831 (m-80) REVERT: S 184 SER cc_start: 0.8850 (OUTLIER) cc_final: 0.8609 (m) outliers start: 25 outliers final: 16 residues processed: 174 average time/residue: 0.2341 time to fit residues: 55.0586 Evaluate side-chains 161 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 252 ILE Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 260 CYS Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain R residue 304 PHE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 47 TRP Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 187 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 99 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 chunk 32 optimal weight: 0.0020 chunk 16 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 45 optimal weight: 0.0870 overall best weight: 0.9970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.194448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.153469 restraints weight = 11646.889| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 2.74 r_work: 0.3765 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.6762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9020 Z= 0.167 Angle : 0.553 8.138 12228 Z= 0.286 Chirality : 0.041 0.160 1371 Planarity : 0.004 0.041 1553 Dihedral : 4.302 39.965 1244 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.42 % Allowed : 18.23 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.26 (0.26), residues: 1111 helix: 1.71 (0.27), residues: 379 sheet: 0.67 (0.32), residues: 266 loop : -1.48 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP S 47 HIS 0.005 0.001 HIS A 197 PHE 0.013 0.001 PHE S 80 TYR 0.015 0.001 TYR A 327 ARG 0.006 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 1.193 Fit side-chains REVERT: A 53 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7082 (mpp) REVERT: A 269 LEU cc_start: 0.6337 (OUTLIER) cc_final: 0.5770 (mt) REVERT: A 281 GLU cc_start: 0.6968 (tp30) cc_final: 0.6298 (tp30) REVERT: B 59 TYR cc_start: 0.8148 (m-80) cc_final: 0.7606 (m-80) REVERT: B 172 GLU cc_start: 0.7610 (tp30) cc_final: 0.7357 (tm-30) REVERT: B 215 GLU cc_start: 0.8289 (pm20) cc_final: 0.8004 (pm20) REVERT: B 217 MET cc_start: 0.7276 (ttp) cc_final: 0.6800 (ppp) REVERT: B 226 GLU cc_start: 0.8135 (tp30) cc_final: 0.7921 (mm-30) REVERT: R 64 MET cc_start: 0.8425 (ttm) cc_final: 0.8199 (ttm) REVERT: R 188 VAL cc_start: 0.8079 (m) cc_final: 0.7826 (p) REVERT: S 34 MET cc_start: 0.7210 (mmm) cc_final: 0.6769 (mmm) REVERT: S 77 ASN cc_start: 0.6191 (m-40) cc_final: 0.5891 (p0) REVERT: S 82 GLN cc_start: 0.7627 (mm-40) cc_final: 0.7122 (mp10) outliers start: 23 outliers final: 14 residues processed: 166 average time/residue: 0.2173 time to fit residues: 50.1636 Evaluate side-chains 149 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 260 CYS Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 47 TRP Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 187 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 30 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 20 optimal weight: 0.0040 chunk 95 optimal weight: 6.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN B 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.189868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.149191 restraints weight = 11712.861| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 2.88 r_work: 0.3726 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.7179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9020 Z= 0.217 Angle : 0.597 10.101 12228 Z= 0.309 Chirality : 0.043 0.160 1371 Planarity : 0.004 0.041 1553 Dihedral : 4.383 40.504 1242 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.11 % Allowed : 19.28 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.14 (0.25), residues: 1111 helix: 1.64 (0.27), residues: 380 sheet: 0.52 (0.32), residues: 271 loop : -1.54 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP S 47 HIS 0.005 0.001 HIS A 324 PHE 0.014 0.001 PHE A 343 TYR 0.022 0.001 TYR A 30 ARG 0.005 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.838 Fit side-chains REVERT: A 53 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7615 (mpp) REVERT: A 269 LEU cc_start: 0.6358 (OUTLIER) cc_final: 0.5711 (mt) REVERT: A 281 GLU cc_start: 0.6998 (tp30) cc_final: 0.6328 (tp30) REVERT: B 59 TYR cc_start: 0.8289 (m-80) cc_final: 0.7725 (m-80) REVERT: B 215 GLU cc_start: 0.8349 (pm20) cc_final: 0.7990 (pm20) REVERT: R 188 VAL cc_start: 0.8040 (m) cc_final: 0.7812 (p) REVERT: R 195 MET cc_start: 0.7859 (tpp) cc_final: 0.7618 (tpp) REVERT: R 208 VAL cc_start: 0.7714 (OUTLIER) cc_final: 0.7452 (t) REVERT: S 34 MET cc_start: 0.7449 (mmm) cc_final: 0.6999 (mmm) REVERT: S 77 ASN cc_start: 0.6293 (m-40) cc_final: 0.5707 (p0) REVERT: Y 17 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7795 (mp0) REVERT: Y 50 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8262 (mp) outliers start: 20 outliers final: 14 residues processed: 162 average time/residue: 0.2307 time to fit residues: 50.6831 Evaluate side-chains 153 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain R residue 80 MET Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 252 ILE Chi-restraints excluded: chain R residue 260 CYS Chi-restraints excluded: chain S residue 47 TRP Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 187 LEU Chi-restraints excluded: chain Y residue 17 GLU Chi-restraints excluded: chain Y residue 50 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 40 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN A 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.180578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.139571 restraints weight = 11625.142| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.70 r_work: 0.3541 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.7844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9020 Z= 0.307 Angle : 0.665 10.624 12228 Z= 0.345 Chirality : 0.045 0.167 1371 Planarity : 0.004 0.041 1553 Dihedral : 4.767 36.096 1242 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.06 % Allowed : 18.76 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.16 (0.25), residues: 1111 helix: 1.33 (0.27), residues: 384 sheet: 0.37 (0.32), residues: 270 loop : -1.69 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP S 36 HIS 0.007 0.002 HIS A 324 PHE 0.017 0.002 PHE A 343 TYR 0.028 0.002 TYR A 30 ARG 0.005 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 1.007 Fit side-chains REVERT: A 53 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7577 (mpp) REVERT: A 269 LEU cc_start: 0.6234 (OUTLIER) cc_final: 0.5712 (mt) REVERT: A 281 GLU cc_start: 0.6832 (tp30) cc_final: 0.6242 (tp30) REVERT: A 297 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7690 (mm-30) REVERT: A 300 ARG cc_start: 0.8243 (mtm180) cc_final: 0.7808 (mmm160) REVERT: B 59 TYR cc_start: 0.8320 (m-80) cc_final: 0.7825 (m-80) REVERT: B 210 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7928 (tt) REVERT: B 215 GLU cc_start: 0.8397 (pm20) cc_final: 0.8197 (pm20) REVERT: B 219 ARG cc_start: 0.8192 (mmt90) cc_final: 0.7786 (mmt90) REVERT: B 226 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8112 (mm-30) REVERT: B 234 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.6571 (m-80) REVERT: R 188 VAL cc_start: 0.8006 (m) cc_final: 0.7774 (p) REVERT: Y 17 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7815 (mp0) REVERT: Y 50 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8491 (mp) outliers start: 29 outliers final: 16 residues processed: 181 average time/residue: 0.2360 time to fit residues: 57.6372 Evaluate side-chains 163 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 80 MET Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 260 CYS Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 47 TRP Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 187 LEU Chi-restraints excluded: chain Y residue 17 GLU Chi-restraints excluded: chain Y residue 50 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 76 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 32 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN A 261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.189577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.149304 restraints weight = 11760.247| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.85 r_work: 0.3732 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.7996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9020 Z= 0.174 Angle : 0.594 11.761 12228 Z= 0.306 Chirality : 0.042 0.159 1371 Planarity : 0.004 0.056 1553 Dihedral : 4.221 18.848 1242 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.21 % Allowed : 20.55 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.13 (0.25), residues: 1111 helix: 1.73 (0.28), residues: 373 sheet: 0.32 (0.31), residues: 272 loop : -1.47 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP S 47 HIS 0.004 0.001 HIS A 197 PHE 0.013 0.001 PHE S 29 TYR 0.012 0.001 TYR A 30 ARG 0.012 0.000 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7413 (mpp) REVERT: A 269 LEU cc_start: 0.6332 (OUTLIER) cc_final: 0.5717 (mt) REVERT: A 281 GLU cc_start: 0.6783 (tp30) cc_final: 0.6194 (tp30) REVERT: A 297 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7653 (mm-30) REVERT: A 314 ARG cc_start: 0.7546 (ttm110) cc_final: 0.7199 (ttp80) REVERT: B 59 TYR cc_start: 0.8365 (m-80) cc_final: 0.7952 (m-80) REVERT: R 188 VAL cc_start: 0.8010 (m) cc_final: 0.7780 (p) REVERT: R 189 SER cc_start: 0.8493 (m) cc_final: 0.8157 (p) REVERT: R 208 VAL cc_start: 0.7820 (OUTLIER) cc_final: 0.7534 (t) REVERT: Y 17 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7709 (mp0) REVERT: Y 50 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8323 (mp) outliers start: 21 outliers final: 12 residues processed: 161 average time/residue: 0.2267 time to fit residues: 49.7310 Evaluate side-chains 158 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 260 CYS Chi-restraints excluded: chain S residue 47 TRP Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 187 LEU Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain Y residue 17 GLU Chi-restraints excluded: chain Y residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 66 optimal weight: 0.9990 chunk 93 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 101 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 100 optimal weight: 0.2980 chunk 107 optimal weight: 9.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN A 261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.191126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.150666 restraints weight = 11889.796| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.63 r_work: 0.3752 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.8136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9020 Z= 0.181 Angle : 0.612 11.317 12228 Z= 0.313 Chirality : 0.042 0.158 1371 Planarity : 0.004 0.051 1553 Dihedral : 4.096 18.052 1242 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.90 % Allowed : 20.76 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.28 (0.26), residues: 1111 helix: 1.87 (0.27), residues: 379 sheet: 0.34 (0.32), residues: 270 loop : -1.38 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP S 47 HIS 0.004 0.001 HIS A 197 PHE 0.013 0.001 PHE A 343 TYR 0.015 0.001 TYR A 30 ARG 0.013 0.000 ARG A 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7283 (mpp) REVERT: A 269 LEU cc_start: 0.6202 (OUTLIER) cc_final: 0.5693 (mt) REVERT: A 281 GLU cc_start: 0.6676 (tp30) cc_final: 0.6080 (tp30) REVERT: A 297 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7589 (mm-30) REVERT: A 300 ARG cc_start: 0.8329 (mtm180) cc_final: 0.7798 (tpp80) REVERT: B 59 TYR cc_start: 0.8304 (m-80) cc_final: 0.7886 (m-80) REVERT: B 217 MET cc_start: 0.7690 (ttp) cc_final: 0.7262 (ppp) REVERT: R 188 VAL cc_start: 0.8000 (m) cc_final: 0.7756 (p) REVERT: R 189 SER cc_start: 0.8458 (m) cc_final: 0.8119 (p) REVERT: R 208 VAL cc_start: 0.7791 (OUTLIER) cc_final: 0.7502 (t) REVERT: S 71 SER cc_start: 0.7805 (p) cc_final: 0.7551 (m) REVERT: Y 50 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8366 (mp) outliers start: 18 outliers final: 12 residues processed: 162 average time/residue: 0.2259 time to fit residues: 49.9736 Evaluate side-chains 156 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 260 CYS Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain S residue 47 TRP Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 187 LEU Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain Y residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 38 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 23 optimal weight: 0.0980 chunk 3 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS A 213 GLN A 261 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.189896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.150487 restraints weight = 11853.077| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 2.80 r_work: 0.3707 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.8242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9020 Z= 0.204 Angle : 0.626 11.688 12228 Z= 0.319 Chirality : 0.042 0.157 1371 Planarity : 0.004 0.049 1553 Dihedral : 4.164 18.443 1242 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.21 % Allowed : 20.76 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.24 (0.26), residues: 1111 helix: 1.80 (0.27), residues: 380 sheet: 0.27 (0.31), residues: 271 loop : -1.35 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP S 47 HIS 0.005 0.001 HIS A 324 PHE 0.015 0.001 PHE S 29 TYR 0.020 0.001 TYR A 30 ARG 0.012 0.000 ARG A 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4754.17 seconds wall clock time: 84 minutes 58.01 seconds (5098.01 seconds total)