Starting phenix.real_space_refine on Sat Aug 23 02:52:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m54_63637/08_2025/9m54_63637.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m54_63637/08_2025/9m54_63637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m54_63637/08_2025/9m54_63637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m54_63637/08_2025/9m54_63637.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m54_63637/08_2025/9m54_63637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m54_63637/08_2025/9m54_63637.map" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.009 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 65 5.16 5 C 5736 2.51 5 N 1526 2.21 5 O 1662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8989 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2290 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 3, 'TYR:plan': 4, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "L" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 53 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 5} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2631 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 5, 'TRANS': 337} Chain: "G" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 450 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "A" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1807 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "S" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1757 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 2.22, per 1000 atoms: 0.25 Number of scatterers: 8989 At special positions: 0 Unit cell: (89.79, 116.8, 134.32, 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 65 16.00 O 1662 8.00 N 1526 7.00 C 5736 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 220 " - pdb=" SG CYS R 308 " distance=2.03 Simple disulfide: pdb=" SG CYS R 248 " - pdb=" SG CYS A 351 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 262.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2178 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 14 sheets defined 36.9% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'R' and resid 146 through 173 removed outlier: 3.961A pdb=" N PHE R 150 " --> pdb=" O VAL R 146 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU R 160 " --> pdb=" O LEU R 156 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASN R 165 " --> pdb=" O CYS R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 180 removed outlier: 3.708A pdb=" N THR R 180 " --> pdb=" O HIS R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 199 removed outlier: 3.865A pdb=" N PHE R 185 " --> pdb=" O VAL R 181 " (cutoff:3.500A) Processing helix chain 'R' and resid 199 through 210 removed outlier: 3.891A pdb=" N ILE R 209 " --> pdb=" O LEU R 205 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 251 removed outlier: 3.522A pdb=" N VAL R 249 " --> pdb=" O ARG R 245 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR R 251 " --> pdb=" O GLN R 247 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 276 Processing helix chain 'R' and resid 277 through 283 removed outlier: 3.975A pdb=" N MET R 283 " --> pdb=" O PRO R 279 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 330 removed outlier: 3.506A pdb=" N TYR R 321 " --> pdb=" O MET R 317 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR R 323 " --> pdb=" O LYS R 319 " (cutoff:3.500A) Processing helix chain 'R' and resid 330 through 350 removed outlier: 3.626A pdb=" N PHE R 349 " --> pdb=" O GLY R 345 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG R 350 " --> pdb=" O ILE R 346 " (cutoff:3.500A) Processing helix chain 'R' and resid 371 through 389 removed outlier: 3.793A pdb=" N ILE R 375 " --> pdb=" O LYS R 371 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TRP R 389 " --> pdb=" O PHE R 385 " (cutoff:3.500A) Processing helix chain 'R' and resid 389 through 401 removed outlier: 3.807A pdb=" N TRP R 393 " --> pdb=" O TRP R 389 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR R 394 " --> pdb=" O LEU R 390 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP R 400 " --> pdb=" O MET R 396 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 438 removed outlier: 4.937A pdb=" N TYR R 417 " --> pdb=" O ASN R 413 " (cutoff:3.500A) Proline residue: R 418 - end of helix removed outlier: 4.073A pdb=" N SER R 428 " --> pdb=" O ALA R 424 " (cutoff:3.500A) Proline residue: R 432 - end of helix Processing helix chain 'B' and resid 2 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.734A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.584A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 215 removed outlier: 4.824A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.516A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.570A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.551A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.820A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.501A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.845A 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 'S' and resid 87 through 91 removed outlier: 3.530A pdb=" N ASP S 90 " --> pdb=" O ARG S 87 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'R' and resid 135 through 138 removed outlier: 5.923A pdb=" N THR R 135 " --> pdb=" O ARG R 293 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ARG R 295 " --> pdb=" O THR R 135 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL R 137 " --> pdb=" O ARG R 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 51 removed outlier: 5.594A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 60 through 63 removed outlier: 3.689A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.772A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.534A 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: 6.846A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.374A 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: 6.761A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.296A 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: 3.625A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.775A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 185 through 189 removed outlier: 6.610A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 9.005A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.882A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 4.147A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.561A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 425 hydrogen bonds defined for protein. 1188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.14 Time building geometry restraints manager: 0.93 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: 1455 1.32 - 1.44: 2509 1.44 - 1.57: 5113 1.57 - 1.69: 0 1.69 - 1.82: 98 Bond restraints: 9175 Sorted by residual: bond pdb=" C LEU R 284 " pdb=" O LEU R 284 " ideal model delta sigma weight residual 1.235 1.189 0.047 1.26e-02 6.30e+03 1.37e+01 bond pdb=" N VAL R 282 " pdb=" CA VAL R 282 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.22e+00 bond pdb=" N PRO R 304 " pdb=" CA PRO R 304 " ideal model delta sigma weight residual 1.466 1.499 -0.033 1.17e-02 7.31e+03 7.76e+00 bond pdb=" N VAL R 286 " pdb=" CA VAL R 286 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.22e-02 6.72e+03 7.70e+00 bond pdb=" C SER R 405 " pdb=" O SER R 405 " ideal model delta sigma weight residual 1.233 1.198 0.035 1.26e-02 6.30e+03 7.69e+00 ... (remaining 9170 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 12017 2.02 - 4.03: 363 4.03 - 6.05: 45 6.05 - 8.06: 8 8.06 - 10.08: 3 Bond angle restraints: 12436 Sorted by residual: angle pdb=" CA GLU R 289 " pdb=" C GLU R 289 " pdb=" O GLU R 289 " ideal model delta sigma weight residual 121.07 116.94 4.13 1.10e+00 8.26e-01 1.41e+01 angle pdb=" N LEU L 4 " pdb=" CA LEU L 4 " pdb=" C LEU L 4 " ideal model delta sigma weight residual 109.04 103.37 5.67 1.52e+00 4.33e-01 1.39e+01 angle pdb=" C PHE B 235 " pdb=" N PRO B 236 " pdb=" CA PRO B 236 " ideal model delta sigma weight residual 119.32 115.09 4.23 1.14e+00 7.69e-01 1.38e+01 angle pdb=" N THR R 275 " pdb=" CA THR R 275 " pdb=" C THR R 275 " ideal model delta sigma weight residual 111.14 114.99 -3.85 1.08e+00 8.57e-01 1.27e+01 angle pdb=" N LEU R 257 " pdb=" CA LEU R 257 " pdb=" C LEU R 257 " ideal model delta sigma weight residual 107.88 112.87 -4.99 1.41e+00 5.03e-01 1.25e+01 ... (remaining 12431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 4577 17.11 - 34.21: 602 34.21 - 51.32: 219 51.32 - 68.42: 41 68.42 - 85.53: 14 Dihedral angle restraints: 5453 sinusoidal: 2082 harmonic: 3371 Sorted by residual: dihedral pdb=" CA PHE R 199 " pdb=" C PHE R 199 " pdb=" N CYS R 200 " pdb=" CA CYS R 200 " ideal model delta harmonic sigma weight residual -180.00 -161.28 -18.72 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CD ARG R 309 " pdb=" NE ARG R 309 " pdb=" CZ ARG R 309 " pdb=" NH1 ARG R 309 " ideal model delta sinusoidal sigma weight residual 0.00 -29.23 29.23 1 1.00e+01 1.00e-02 1.22e+01 dihedral pdb=" CA ASP B 254 " pdb=" CB ASP B 254 " pdb=" CG ASP B 254 " pdb=" OD1 ASP B 254 " ideal model delta sinusoidal sigma weight residual -30.00 -89.09 59.09 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 5450 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1164 0.062 - 0.124: 226 0.124 - 0.185: 28 0.185 - 0.247: 3 0.247 - 0.309: 1 Chirality restraints: 1422 Sorted by residual: chirality pdb=" CG LEU G 50 " pdb=" CB LEU G 50 " pdb=" CD1 LEU G 50 " pdb=" CD2 LEU G 50 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CA ILE A 221 " pdb=" N ILE A 221 " pdb=" C ILE A 221 " pdb=" CB ILE A 221 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ILE R 269 " pdb=" N ILE R 269 " pdb=" C ILE R 269 " pdb=" CB ILE R 269 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.95e-01 ... (remaining 1419 not shown) Planarity restraints: 1570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 309 " -0.533 9.50e-02 1.11e+02 2.39e-01 3.49e+01 pdb=" NE ARG R 309 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG R 309 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG R 309 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG R 309 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 253 " -0.016 2.00e-02 2.50e+03 2.38e-02 9.90e+00 pdb=" CG PHE R 253 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE R 253 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE R 253 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE R 253 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE R 253 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE R 253 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 253 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.82e+00 pdb=" C PHE R 253 " -0.038 2.00e-02 2.50e+03 pdb=" O PHE R 253 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS R 254 " 0.013 2.00e-02 2.50e+03 ... (remaining 1567 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 408 2.71 - 3.26: 9073 3.26 - 3.81: 15145 3.81 - 4.35: 18319 4.35 - 4.90: 31109 Nonbonded interactions: 74054 Sorted by model distance: nonbonded pdb=" O ILE R 149 " pdb=" OG SER R 153 " model vdw 2.166 3.040 nonbonded pdb=" O ILE S 100 " pdb=" OG SER S 105 " model vdw 2.258 3.040 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.272 3.040 nonbonded pdb=" NZ LYS B 57 " pdb=" OE1 GLU A 216 " model vdw 2.281 3.120 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.293 3.120 ... (remaining 74049 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: 3.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.710 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 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 0.105 9180 Z= 0.285 Angle : 0.806 10.075 12444 Z= 0.486 Chirality : 0.049 0.309 1422 Planarity : 0.008 0.239 1570 Dihedral : 18.155 85.528 3263 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.14 % Allowed : 32.57 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.25), residues: 1144 helix: 0.73 (0.27), residues: 378 sheet: -0.79 (0.31), residues: 271 loop : -1.31 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 245 TYR 0.015 0.002 TYR S 173 PHE 0.054 0.002 PHE R 253 TRP 0.016 0.002 TRP R 389 HIS 0.005 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 9175) covalent geometry : angle 0.80659 (12436) SS BOND : bond 0.00554 ( 4) SS BOND : angle 0.61891 ( 8) hydrogen bonds : bond 0.19310 ( 418) hydrogen bonds : angle 7.79649 ( 1188) Misc. bond : bond 0.10513 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 464 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 159 PHE cc_start: 0.8013 (t80) cc_final: 0.6867 (t80) REVERT: R 172 VAL cc_start: 0.8601 (t) cc_final: 0.8379 (t) REVERT: R 194 LEU cc_start: 0.8898 (mt) cc_final: 0.8348 (mt) REVERT: R 266 ILE cc_start: 0.8924 (mt) cc_final: 0.8367 (mt) REVERT: R 284 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.6073 (tt) REVERT: B 36 ASN cc_start: 0.8307 (m110) cc_final: 0.8077 (m110) REVERT: B 285 LEU cc_start: 0.9192 (tp) cc_final: 0.8988 (tt) REVERT: B 297 TRP cc_start: 0.8538 (m100) cc_final: 0.8214 (m100) REVERT: G 32 LYS cc_start: 0.8900 (tptm) cc_final: 0.8407 (tptp) REVERT: A 22 ASN cc_start: 0.8478 (m-40) cc_final: 0.7988 (m-40) REVERT: A 228 SER cc_start: 0.8810 (p) cc_final: 0.8507 (p) REVERT: A 269 ASN cc_start: 0.7235 (m-40) cc_final: 0.6769 (m-40) REVERT: S 19 LYS cc_start: 0.8275 (tptm) cc_final: 0.7916 (tptp) outliers start: 11 outliers final: 2 residues processed: 469 average time/residue: 0.0906 time to fit residues: 56.8371 Evaluate side-chains 303 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 300 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 305 VAL Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 177 HIS R 183 ASN B 110 ASN B 259 GLN B 268 ASN G 24 ASN A 188 HIS A 204 GLN A 347 ASN S 183 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.100832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.071835 restraints weight = 23537.868| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 4.15 r_work: 0.2988 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9180 Z= 0.157 Angle : 0.733 10.516 12444 Z= 0.379 Chirality : 0.046 0.231 1422 Planarity : 0.005 0.053 1570 Dihedral : 5.082 58.960 1251 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 5.20 % Allowed : 30.07 % Favored : 64.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.25), residues: 1144 helix: 1.25 (0.27), residues: 382 sheet: -0.30 (0.31), residues: 279 loop : -1.17 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 62 TYR 0.025 0.002 TYR A 302 PHE 0.027 0.002 PHE R 246 TRP 0.018 0.002 TRP R 213 HIS 0.003 0.001 HIS R 285 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 9175) covalent geometry : angle 0.73305 (12436) SS BOND : bond 0.00265 ( 4) SS BOND : angle 0.62773 ( 8) hydrogen bonds : bond 0.04518 ( 418) hydrogen bonds : angle 5.56545 ( 1188) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 337 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 145 GLN cc_start: 0.8162 (mm-40) cc_final: 0.7889 (pm20) REVERT: R 236 PHE cc_start: 0.9296 (m-10) cc_final: 0.8665 (m-80) REVERT: R 247 GLN cc_start: 0.8236 (pp30) cc_final: 0.7948 (pp30) REVERT: R 256 LYS cc_start: 0.6402 (pttm) cc_final: 0.5745 (pttm) REVERT: R 267 MET cc_start: 0.9097 (mmp) cc_final: 0.8864 (mmm) REVERT: R 277 MET cc_start: 0.9050 (mmm) cc_final: 0.8515 (mmm) REVERT: R 282 VAL cc_start: 0.8726 (t) cc_final: 0.8428 (m) REVERT: R 284 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6541 (tt) REVERT: R 317 MET cc_start: 0.8380 (mmp) cc_final: 0.8113 (mmp) REVERT: R 329 ILE cc_start: 0.9351 (mp) cc_final: 0.8501 (mp) REVERT: R 340 MET cc_start: 0.9181 (mpp) cc_final: 0.8727 (mpp) REVERT: R 376 LYS cc_start: 0.8903 (mmtt) cc_final: 0.8395 (mttt) REVERT: R 389 TRP cc_start: 0.8912 (OUTLIER) cc_final: 0.8706 (m100) REVERT: R 393 TRP cc_start: 0.8831 (m100) cc_final: 0.8285 (m100) REVERT: R 397 MET cc_start: 0.7955 (ttt) cc_final: 0.7512 (ttt) REVERT: R 401 TYR cc_start: 0.8100 (OUTLIER) cc_final: 0.7229 (m-80) REVERT: R 422 TRP cc_start: 0.9280 (t60) cc_final: 0.9031 (t60) REVERT: B 17 GLN cc_start: 0.9476 (tt0) cc_final: 0.9222 (pt0) REVERT: B 32 GLN cc_start: 0.9443 (mt0) cc_final: 0.9103 (pt0) REVERT: B 124 TYR cc_start: 0.9330 (m-80) cc_final: 0.8820 (m-80) REVERT: B 138 GLU cc_start: 0.9290 (mt-10) cc_final: 0.8545 (pm20) REVERT: B 234 PHE cc_start: 0.9520 (OUTLIER) cc_final: 0.9048 (m-10) REVERT: B 239 ASN cc_start: 0.8483 (m-40) cc_final: 0.8161 (m110) REVERT: B 262 MET cc_start: 0.8392 (mtp) cc_final: 0.7726 (mtp) REVERT: B 297 TRP cc_start: 0.9347 (m100) cc_final: 0.8435 (m100) REVERT: B 339 TRP cc_start: 0.8792 (m100) cc_final: 0.8169 (m-10) REVERT: G 24 ASN cc_start: 0.8249 (OUTLIER) cc_final: 0.8042 (p0) REVERT: G 59 ASN cc_start: 0.8595 (t0) cc_final: 0.8198 (t0) REVERT: A 25 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8884 (mm-30) REVERT: A 33 GLU cc_start: 0.8524 (tt0) cc_final: 0.8200 (mm-30) REVERT: A 38 LEU cc_start: 0.9166 (tt) cc_final: 0.8500 (mt) REVERT: A 194 LEU cc_start: 0.8148 (tp) cc_final: 0.7894 (tp) REVERT: A 224 CYS cc_start: 0.9228 (m) cc_final: 0.8643 (m) REVERT: A 230 TYR cc_start: 0.8123 (p90) cc_final: 0.6379 (p90) REVERT: A 231 ASP cc_start: 0.9094 (t70) cc_final: 0.8768 (m-30) REVERT: A 243 MET cc_start: 0.9330 (tpp) cc_final: 0.8840 (tpp) REVERT: A 247 MET cc_start: 0.8892 (ptt) cc_final: 0.8397 (ptt) REVERT: A 269 ASN cc_start: 0.8214 (m-40) cc_final: 0.7758 (m-40) REVERT: A 276 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8818 (mm-30) REVERT: A 287 TYR cc_start: 0.9296 (m-10) cc_final: 0.9033 (m-10) REVERT: A 310 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9182 (mp) REVERT: A 346 ASN cc_start: 0.9695 (m-40) cc_final: 0.9461 (m110) REVERT: S 19 LYS cc_start: 0.8905 (tptm) cc_final: 0.8668 (tptp) outliers start: 50 outliers final: 28 residues processed: 367 average time/residue: 0.0934 time to fit residues: 45.9832 Evaluate side-chains 323 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 288 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 220 CYS Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 259 ILE Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 285 HIS Chi-restraints excluded: chain R residue 323 THR Chi-restraints excluded: chain R residue 384 LEU Chi-restraints excluded: chain R residue 389 TRP Chi-restraints excluded: chain R residue 401 TYR Chi-restraints excluded: chain L residue 8 PHE Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 135 SER Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 74 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 175 ASN ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 208 ASN R 372 GLN ** R 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 179 GLN S 183 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.095790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.066480 restraints weight = 23792.981| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 4.12 r_work: 0.2874 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9180 Z= 0.235 Angle : 0.722 8.598 12444 Z= 0.375 Chirality : 0.046 0.186 1422 Planarity : 0.005 0.053 1570 Dihedral : 5.021 59.931 1249 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 7.91 % Allowed : 29.55 % Favored : 62.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.25), residues: 1144 helix: 1.07 (0.27), residues: 382 sheet: -0.39 (0.31), residues: 280 loop : -1.10 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 245 TYR 0.023 0.002 TYR A 302 PHE 0.019 0.002 PHE R 246 TRP 0.018 0.001 TRP R 213 HIS 0.006 0.001 HIS R 177 Details of bonding type rmsd covalent geometry : bond 0.00520 ( 9175) covalent geometry : angle 0.72154 (12436) SS BOND : bond 0.00355 ( 4) SS BOND : angle 0.77236 ( 8) hydrogen bonds : bond 0.04265 ( 418) hydrogen bonds : angle 5.40573 ( 1188) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 285 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 145 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7986 (pm20) REVERT: R 173 MET cc_start: 0.8937 (mmm) cc_final: 0.8475 (mmm) REVERT: R 213 TRP cc_start: 0.6805 (t-100) cc_final: 0.6569 (t-100) REVERT: R 236 PHE cc_start: 0.9376 (m-10) cc_final: 0.8761 (m-80) REVERT: R 241 ILE cc_start: 0.9509 (OUTLIER) cc_final: 0.9049 (mm) REVERT: R 245 ARG cc_start: 0.9317 (ttm-80) cc_final: 0.9047 (ttm110) REVERT: R 265 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.8001 (tp) REVERT: R 267 MET cc_start: 0.8945 (mmp) cc_final: 0.8692 (mmm) REVERT: R 284 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.6682 (tt) REVERT: R 317 MET cc_start: 0.8447 (mmp) cc_final: 0.8183 (mmp) REVERT: R 325 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9029 (mt) REVERT: R 329 ILE cc_start: 0.9089 (mp) cc_final: 0.8761 (mp) REVERT: R 343 ARG cc_start: 0.8800 (tpt170) cc_final: 0.8524 (ttt180) REVERT: R 376 LYS cc_start: 0.8962 (mmtt) cc_final: 0.8497 (mttt) REVERT: R 389 TRP cc_start: 0.9072 (OUTLIER) cc_final: 0.8863 (m100) REVERT: R 393 TRP cc_start: 0.8930 (m100) cc_final: 0.8429 (m100) REVERT: R 401 TYR cc_start: 0.8230 (OUTLIER) cc_final: 0.7247 (m-80) REVERT: R 422 TRP cc_start: 0.9263 (t60) cc_final: 0.9056 (t60) REVERT: R 431 ASN cc_start: 0.8951 (m-40) cc_final: 0.8561 (m-40) REVERT: B 23 LYS cc_start: 0.9581 (mttm) cc_final: 0.9201 (mtmm) REVERT: B 138 GLU cc_start: 0.9357 (mt-10) cc_final: 0.8641 (pm20) REVERT: B 234 PHE cc_start: 0.9511 (OUTLIER) cc_final: 0.9162 (m-10) REVERT: B 239 ASN cc_start: 0.8684 (m-40) cc_final: 0.8322 (m110) REVERT: B 262 MET cc_start: 0.8454 (mtp) cc_final: 0.7972 (mtp) REVERT: B 264 TYR cc_start: 0.9489 (m-10) cc_final: 0.9149 (m-10) REVERT: B 297 TRP cc_start: 0.9400 (m100) cc_final: 0.8641 (m100) REVERT: G 22 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8415 (mt-10) REVERT: G 27 ARG cc_start: 0.8953 (mmt90) cc_final: 0.8230 (mmt90) REVERT: G 59 ASN cc_start: 0.8563 (t0) cc_final: 0.8258 (t0) REVERT: A 38 LEU cc_start: 0.9186 (tt) cc_final: 0.8548 (mt) REVERT: A 230 TYR cc_start: 0.8174 (p90) cc_final: 0.6578 (p90) REVERT: A 231 ASP cc_start: 0.9179 (OUTLIER) cc_final: 0.8856 (m-30) REVERT: A 243 MET cc_start: 0.9334 (tpp) cc_final: 0.8858 (tpp) REVERT: A 247 MET cc_start: 0.8972 (ptt) cc_final: 0.8576 (ptt) REVERT: A 265 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8865 (mt) REVERT: A 276 GLU cc_start: 0.9192 (OUTLIER) cc_final: 0.8932 (pt0) REVERT: A 287 TYR cc_start: 0.9374 (m-10) cc_final: 0.8962 (m-10) REVERT: S 13 GLN cc_start: 0.9344 (mm-40) cc_final: 0.9099 (pp30) REVERT: S 19 LYS cc_start: 0.8972 (tptm) cc_final: 0.8630 (tptp) REVERT: S 62 ASP cc_start: 0.9432 (m-30) cc_final: 0.8975 (p0) REVERT: S 234 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8650 (mt-10) outliers start: 76 outliers final: 47 residues processed: 333 average time/residue: 0.0861 time to fit residues: 38.1854 Evaluate side-chains 315 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 258 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 220 CYS Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 241 ILE Chi-restraints excluded: chain R residue 260 LYS Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 280 SER Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 285 HIS Chi-restraints excluded: chain R residue 323 THR Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain R residue 389 TRP Chi-restraints excluded: chain R residue 401 TYR Chi-restraints excluded: chain R residue 409 LEU Chi-restraints excluded: chain R residue 433 ILE Chi-restraints excluded: chain R residue 442 PHE Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 135 SER Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 70 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 49 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 188 ASN ** R 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN S 183 GLN S 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.097593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.067700 restraints weight = 23751.951| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 4.36 r_work: 0.2888 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9180 Z= 0.155 Angle : 0.697 10.231 12444 Z= 0.358 Chirality : 0.044 0.220 1422 Planarity : 0.004 0.049 1570 Dihedral : 5.000 57.930 1249 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 7.08 % Allowed : 30.80 % Favored : 62.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.25), residues: 1144 helix: 0.92 (0.27), residues: 384 sheet: -0.29 (0.31), residues: 280 loop : -1.05 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 21 TYR 0.012 0.001 TYR S 95 PHE 0.017 0.001 PHE S 212 TRP 0.014 0.001 TRP R 213 HIS 0.005 0.001 HIS R 177 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9175) covalent geometry : angle 0.69631 (12436) SS BOND : bond 0.00251 ( 4) SS BOND : angle 1.06545 ( 8) hydrogen bonds : bond 0.04060 ( 418) hydrogen bonds : angle 5.23796 ( 1188) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 282 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 145 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7848 (pm20) REVERT: R 169 CYS cc_start: 0.9713 (m) cc_final: 0.9494 (m) REVERT: R 173 MET cc_start: 0.8904 (mmm) cc_final: 0.8543 (mmm) REVERT: R 188 ASN cc_start: 0.9264 (t160) cc_final: 0.8832 (m-40) REVERT: R 236 PHE cc_start: 0.9350 (m-10) cc_final: 0.9112 (m-10) REVERT: R 284 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.6841 (tt) REVERT: R 317 MET cc_start: 0.8501 (mmp) cc_final: 0.8231 (mmp) REVERT: R 325 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8985 (mt) REVERT: R 329 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8696 (mp) REVERT: R 343 ARG cc_start: 0.8777 (tpt170) cc_final: 0.8503 (ttt180) REVERT: R 376 LYS cc_start: 0.8952 (mmtt) cc_final: 0.8507 (mttt) REVERT: R 393 TRP cc_start: 0.8960 (m100) cc_final: 0.8623 (m100) REVERT: R 401 TYR cc_start: 0.8254 (OUTLIER) cc_final: 0.7249 (m-80) REVERT: R 422 TRP cc_start: 0.9364 (t60) cc_final: 0.8990 (t60) REVERT: R 431 ASN cc_start: 0.8985 (m-40) cc_final: 0.8645 (m-40) REVERT: R 444 ARG cc_start: 0.7341 (ptp-170) cc_final: 0.7075 (ptp-170) REVERT: B 138 GLU cc_start: 0.9398 (mt-10) cc_final: 0.8643 (pm20) REVERT: B 146 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8326 (tt) REVERT: B 215 GLU cc_start: 0.8761 (mp0) cc_final: 0.8150 (mp0) REVERT: B 217 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8275 (ppp) REVERT: B 234 PHE cc_start: 0.9458 (OUTLIER) cc_final: 0.9133 (m-10) REVERT: B 239 ASN cc_start: 0.8596 (m-40) cc_final: 0.8259 (m110) REVERT: B 262 MET cc_start: 0.8324 (mtp) cc_final: 0.7793 (mtp) REVERT: B 264 TYR cc_start: 0.9385 (m-10) cc_final: 0.8815 (m-10) REVERT: B 297 TRP cc_start: 0.9413 (m100) cc_final: 0.8494 (m-10) REVERT: G 27 ARG cc_start: 0.8852 (mmt90) cc_final: 0.8202 (mmt90) REVERT: G 32 LYS cc_start: 0.9292 (tptm) cc_final: 0.8990 (tptp) REVERT: G 59 ASN cc_start: 0.8544 (t0) cc_final: 0.8166 (t0) REVERT: A 38 LEU cc_start: 0.9076 (tt) cc_final: 0.8543 (mt) REVERT: A 230 TYR cc_start: 0.7910 (p90) cc_final: 0.5994 (p90) REVERT: A 231 ASP cc_start: 0.9119 (t70) cc_final: 0.8713 (m-30) REVERT: A 242 ARG cc_start: 0.9180 (mtp85) cc_final: 0.8922 (ttm110) REVERT: A 243 MET cc_start: 0.9282 (tpp) cc_final: 0.9069 (tpp) REVERT: A 247 MET cc_start: 0.8972 (ptt) cc_final: 0.8615 (ptt) REVERT: A 276 GLU cc_start: 0.9157 (OUTLIER) cc_final: 0.8882 (mm-30) REVERT: A 287 TYR cc_start: 0.9359 (m-10) cc_final: 0.9034 (m-10) REVERT: S 19 LYS cc_start: 0.8927 (tptm) cc_final: 0.8554 (tptp) REVERT: S 183 GLN cc_start: 0.9059 (mt0) cc_final: 0.8839 (mt0) outliers start: 68 outliers final: 42 residues processed: 322 average time/residue: 0.0945 time to fit residues: 40.6483 Evaluate side-chains 315 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 265 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 220 CYS Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 253 PHE Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 280 SER Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 285 HIS Chi-restraints excluded: chain R residue 323 THR Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain R residue 401 TYR Chi-restraints excluded: chain R residue 433 ILE Chi-restraints excluded: chain R residue 442 PHE Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 135 SER Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 37 optimal weight: 0.0770 chunk 47 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN S 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.094757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.064829 restraints weight = 24001.921| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 4.29 r_work: 0.2816 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 9180 Z= 0.234 Angle : 0.732 9.886 12444 Z= 0.379 Chirality : 0.045 0.223 1422 Planarity : 0.004 0.054 1570 Dihedral : 5.066 51.270 1249 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 7.60 % Allowed : 30.59 % Favored : 61.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.25), residues: 1144 helix: 0.78 (0.27), residues: 383 sheet: -0.30 (0.31), residues: 281 loop : -1.07 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 208 TYR 0.026 0.002 TYR A 302 PHE 0.021 0.002 PHE S 212 TRP 0.023 0.001 TRP R 213 HIS 0.005 0.001 HIS R 177 Details of bonding type rmsd covalent geometry : bond 0.00528 ( 9175) covalent geometry : angle 0.73123 (12436) SS BOND : bond 0.00352 ( 4) SS BOND : angle 1.14893 ( 8) hydrogen bonds : bond 0.04258 ( 418) hydrogen bonds : angle 5.29154 ( 1188) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 271 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 145 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7849 (pm20) REVERT: R 169 CYS cc_start: 0.9737 (m) cc_final: 0.9519 (m) REVERT: R 173 MET cc_start: 0.8901 (mmm) cc_final: 0.8567 (mmm) REVERT: R 188 ASN cc_start: 0.9317 (t160) cc_final: 0.8809 (m-40) REVERT: R 236 PHE cc_start: 0.9461 (m-10) cc_final: 0.9232 (m-10) REVERT: R 266 ILE cc_start: 0.9151 (tt) cc_final: 0.8838 (pt) REVERT: R 277 MET cc_start: 0.9315 (mmm) cc_final: 0.9113 (mmp) REVERT: R 283 MET cc_start: 0.8365 (pmm) cc_final: 0.8145 (pmm) REVERT: R 284 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7056 (tp) REVERT: R 317 MET cc_start: 0.8514 (mmp) cc_final: 0.8264 (mmp) REVERT: R 325 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9112 (mt) REVERT: R 329 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8711 (mp) REVERT: R 343 ARG cc_start: 0.8805 (tpt170) cc_final: 0.8509 (ttt180) REVERT: R 376 LYS cc_start: 0.9006 (mmtt) cc_final: 0.8561 (mttt) REVERT: R 389 TRP cc_start: 0.8987 (m100) cc_final: 0.8759 (m100) REVERT: R 393 TRP cc_start: 0.8955 (m100) cc_final: 0.8586 (m100) REVERT: R 401 TYR cc_start: 0.8304 (OUTLIER) cc_final: 0.7200 (m-80) REVERT: R 431 ASN cc_start: 0.9131 (m-40) cc_final: 0.8775 (m-40) REVERT: R 444 ARG cc_start: 0.7369 (ptp-170) cc_final: 0.7076 (ptp-170) REVERT: B 23 LYS cc_start: 0.9586 (mttm) cc_final: 0.9253 (mttp) REVERT: B 45 MET cc_start: 0.9161 (mmt) cc_final: 0.8774 (mmt) REVERT: B 215 GLU cc_start: 0.8777 (mp0) cc_final: 0.8133 (mp0) REVERT: B 217 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8203 (ppp) REVERT: B 239 ASN cc_start: 0.8738 (m-40) cc_final: 0.8414 (m110) REVERT: B 264 TYR cc_start: 0.9454 (m-10) cc_final: 0.9008 (m-10) REVERT: B 297 TRP cc_start: 0.9409 (m100) cc_final: 0.8533 (m-10) REVERT: G 27 ARG cc_start: 0.8952 (mmt90) cc_final: 0.8222 (mmt90) REVERT: G 32 LYS cc_start: 0.9264 (tptm) cc_final: 0.8978 (tptp) REVERT: G 59 ASN cc_start: 0.8497 (t0) cc_final: 0.8244 (t0) REVERT: A 38 LEU cc_start: 0.9110 (tt) cc_final: 0.8653 (mt) REVERT: A 185 VAL cc_start: 0.8737 (OUTLIER) cc_final: 0.8424 (m) REVERT: A 197 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7748 (mmtt) REVERT: A 231 ASP cc_start: 0.9184 (OUTLIER) cc_final: 0.8737 (m-30) REVERT: A 242 ARG cc_start: 0.9124 (mtp85) cc_final: 0.8914 (ttm110) REVERT: A 243 MET cc_start: 0.9299 (tpp) cc_final: 0.9048 (tpp) REVERT: A 276 GLU cc_start: 0.9166 (OUTLIER) cc_final: 0.8890 (mt-10) REVERT: A 333 GLN cc_start: 0.9237 (tm-30) cc_final: 0.8919 (tm-30) REVERT: S 19 LYS cc_start: 0.8962 (tptm) cc_final: 0.8542 (tptp) REVERT: S 62 ASP cc_start: 0.9408 (m-30) cc_final: 0.8988 (p0) REVERT: S 218 ARG cc_start: 0.8494 (tmm-80) cc_final: 0.8078 (tmm-80) outliers start: 73 outliers final: 44 residues processed: 313 average time/residue: 0.0983 time to fit residues: 40.8888 Evaluate side-chains 309 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 256 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 149 ILE Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 220 CYS Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 253 PHE Chi-restraints excluded: chain R residue 260 LYS Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 280 SER Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 285 HIS Chi-restraints excluded: chain R residue 323 THR Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain R residue 401 TYR Chi-restraints excluded: chain R residue 433 ILE Chi-restraints excluded: chain R residue 442 PHE Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 135 SER Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 64 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN A 304 GLN S 183 GLN S 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.096510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.066646 restraints weight = 23766.029| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 4.34 r_work: 0.2869 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.5367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9180 Z= 0.156 Angle : 0.728 13.883 12444 Z= 0.368 Chirality : 0.045 0.210 1422 Planarity : 0.004 0.047 1570 Dihedral : 4.876 47.186 1249 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 6.66 % Allowed : 31.53 % Favored : 61.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.25), residues: 1144 helix: 0.72 (0.27), residues: 377 sheet: -0.35 (0.31), residues: 285 loop : -0.88 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 208 TYR 0.014 0.001 TYR S 95 PHE 0.021 0.001 PHE S 212 TRP 0.022 0.001 TRP R 213 HIS 0.006 0.001 HIS R 177 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 9175) covalent geometry : angle 0.72797 (12436) SS BOND : bond 0.00230 ( 4) SS BOND : angle 0.83992 ( 8) hydrogen bonds : bond 0.04078 ( 418) hydrogen bonds : angle 5.19356 ( 1188) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 278 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 145 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7798 (pm20) REVERT: R 169 CYS cc_start: 0.9741 (m) cc_final: 0.9527 (m) REVERT: R 173 MET cc_start: 0.8928 (mmm) cc_final: 0.8633 (mmm) REVERT: R 188 ASN cc_start: 0.9294 (t160) cc_final: 0.8779 (m-40) REVERT: R 227 GLN cc_start: 0.8117 (mm110) cc_final: 0.7583 (mm110) REVERT: R 236 PHE cc_start: 0.9428 (m-10) cc_final: 0.9217 (m-10) REVERT: R 266 ILE cc_start: 0.9091 (tt) cc_final: 0.8835 (pt) REVERT: R 284 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.6952 (tt) REVERT: R 317 MET cc_start: 0.8469 (mmp) cc_final: 0.8220 (mmp) REVERT: R 325 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9016 (mt) REVERT: R 329 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8635 (mp) REVERT: R 336 LEU cc_start: 0.9631 (OUTLIER) cc_final: 0.9396 (tp) REVERT: R 340 MET cc_start: 0.9200 (OUTLIER) cc_final: 0.8804 (mpp) REVERT: R 343 ARG cc_start: 0.8734 (tpt170) cc_final: 0.8448 (ttt180) REVERT: R 376 LYS cc_start: 0.8979 (mmtt) cc_final: 0.8523 (mttt) REVERT: R 393 TRP cc_start: 0.8861 (m100) cc_final: 0.8577 (m100) REVERT: R 401 TYR cc_start: 0.8385 (OUTLIER) cc_final: 0.7298 (m-80) REVERT: R 431 ASN cc_start: 0.9202 (m-40) cc_final: 0.8560 (m-40) REVERT: R 444 ARG cc_start: 0.7266 (ptp-170) cc_final: 0.6971 (ptp-170) REVERT: B 23 LYS cc_start: 0.9567 (mttm) cc_final: 0.9240 (mmtp) REVERT: B 45 MET cc_start: 0.9145 (mmt) cc_final: 0.8908 (mmt) REVERT: B 146 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8464 (tt) REVERT: B 215 GLU cc_start: 0.8875 (mp0) cc_final: 0.8181 (mp0) REVERT: B 217 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8150 (ppp) REVERT: B 239 ASN cc_start: 0.8662 (m-40) cc_final: 0.8330 (m110) REVERT: B 297 TRP cc_start: 0.9415 (m100) cc_final: 0.8497 (m100) REVERT: G 27 ARG cc_start: 0.8989 (mmt90) cc_final: 0.8416 (mmt90) REVERT: G 59 ASN cc_start: 0.8511 (t0) cc_final: 0.8252 (t0) REVERT: A 38 LEU cc_start: 0.8937 (tt) cc_final: 0.8491 (mt) REVERT: A 197 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7711 (mmtm) REVERT: A 227 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8836 (mp) REVERT: A 230 TYR cc_start: 0.7841 (p90) cc_final: 0.5684 (p90) REVERT: A 231 ASP cc_start: 0.9174 (t70) cc_final: 0.8790 (m-30) REVERT: A 243 MET cc_start: 0.9284 (tpp) cc_final: 0.9017 (tpp) REVERT: A 276 GLU cc_start: 0.9144 (OUTLIER) cc_final: 0.8834 (mt-10) REVERT: S 19 LYS cc_start: 0.8981 (tptm) cc_final: 0.8568 (tptp) REVERT: S 183 GLN cc_start: 0.9061 (mt0) cc_final: 0.8715 (mt0) REVERT: S 218 ARG cc_start: 0.8520 (tmm-80) cc_final: 0.8080 (tmm-80) REVERT: S 219 LEU cc_start: 0.9162 (tp) cc_final: 0.8850 (pp) outliers start: 64 outliers final: 40 residues processed: 316 average time/residue: 0.0955 time to fit residues: 39.8302 Evaluate side-chains 310 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 259 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 220 CYS Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 253 PHE Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 285 HIS Chi-restraints excluded: chain R residue 310 GLU Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain R residue 336 LEU Chi-restraints excluded: chain R residue 340 MET Chi-restraints excluded: chain R residue 371 LYS Chi-restraints excluded: chain R residue 401 TYR Chi-restraints excluded: chain R residue 433 ILE Chi-restraints excluded: chain R residue 442 PHE Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 135 SER Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 17 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 53 optimal weight: 0.0060 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN S 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.097885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.067829 restraints weight = 24019.753| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 4.38 r_work: 0.2891 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9180 Z= 0.145 Angle : 0.738 11.824 12444 Z= 0.374 Chirality : 0.046 0.196 1422 Planarity : 0.004 0.052 1570 Dihedral : 4.820 42.850 1249 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 5.62 % Allowed : 33.40 % Favored : 60.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.25), residues: 1144 helix: 0.67 (0.27), residues: 383 sheet: -0.26 (0.31), residues: 277 loop : -0.94 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 21 TYR 0.014 0.001 TYR S 95 PHE 0.021 0.001 PHE S 212 TRP 0.020 0.001 TRP R 213 HIS 0.005 0.001 HIS R 177 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 9175) covalent geometry : angle 0.73816 (12436) SS BOND : bond 0.00219 ( 4) SS BOND : angle 0.86309 ( 8) hydrogen bonds : bond 0.04085 ( 418) hydrogen bonds : angle 5.13256 ( 1188) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 278 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 145 GLN cc_start: 0.8197 (mm-40) cc_final: 0.7857 (pm20) REVERT: R 173 MET cc_start: 0.9022 (mmm) cc_final: 0.8820 (mmm) REVERT: R 187 LEU cc_start: 0.9791 (mm) cc_final: 0.9588 (mm) REVERT: R 188 ASN cc_start: 0.9271 (t160) cc_final: 0.8840 (m110) REVERT: R 227 GLN cc_start: 0.8166 (mm110) cc_final: 0.7647 (mm110) REVERT: R 245 ARG cc_start: 0.9327 (ttm110) cc_final: 0.8953 (ttm110) REVERT: R 266 ILE cc_start: 0.9111 (tt) cc_final: 0.8861 (pt) REVERT: R 284 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.6977 (tt) REVERT: R 317 MET cc_start: 0.8489 (mmp) cc_final: 0.8252 (mmp) REVERT: R 325 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9068 (mt) REVERT: R 329 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8641 (mp) REVERT: R 336 LEU cc_start: 0.9646 (OUTLIER) cc_final: 0.9418 (tp) REVERT: R 340 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8785 (mpp) REVERT: R 343 ARG cc_start: 0.8731 (tpt170) cc_final: 0.8451 (ttt180) REVERT: R 376 LYS cc_start: 0.8966 (mmtt) cc_final: 0.8553 (mttt) REVERT: R 378 LEU cc_start: 0.9518 (tp) cc_final: 0.9276 (mm) REVERT: R 397 MET cc_start: 0.7603 (ttt) cc_final: 0.7067 (ttt) REVERT: R 401 TYR cc_start: 0.8371 (OUTLIER) cc_final: 0.7333 (m-80) REVERT: R 422 TRP cc_start: 0.9325 (t60) cc_final: 0.8993 (t60) REVERT: R 431 ASN cc_start: 0.9157 (m-40) cc_final: 0.8795 (m-40) REVERT: B 9 GLN cc_start: 0.9677 (tm-30) cc_final: 0.9369 (pp30) REVERT: B 23 LYS cc_start: 0.9594 (mttm) cc_final: 0.9206 (mttp) REVERT: B 124 TYR cc_start: 0.9336 (m-80) cc_final: 0.9095 (m-80) REVERT: B 146 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8137 (tt) REVERT: B 215 GLU cc_start: 0.8920 (mp0) cc_final: 0.8428 (mp0) REVERT: B 217 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8291 (ppp) REVERT: B 262 MET cc_start: 0.8371 (tpp) cc_final: 0.7533 (mtp) REVERT: B 297 TRP cc_start: 0.9397 (m100) cc_final: 0.8671 (m100) REVERT: G 27 ARG cc_start: 0.9012 (mmt90) cc_final: 0.8494 (mmt90) REVERT: G 59 ASN cc_start: 0.8502 (t0) cc_final: 0.8239 (t0) REVERT: A 38 LEU cc_start: 0.8866 (tt) cc_final: 0.8431 (mt) REVERT: A 197 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7736 (mmtm) REVERT: A 227 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8872 (mp) REVERT: A 230 TYR cc_start: 0.7631 (p90) cc_final: 0.5232 (p90) REVERT: A 231 ASP cc_start: 0.9133 (t70) cc_final: 0.8778 (m-30) REVERT: A 276 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8799 (mt-10) REVERT: A 333 GLN cc_start: 0.9201 (tm-30) cc_final: 0.8801 (tm-30) REVERT: A 337 ASP cc_start: 0.9441 (m-30) cc_final: 0.9101 (m-30) REVERT: S 19 LYS cc_start: 0.8976 (tptm) cc_final: 0.8548 (tptp) REVERT: S 192 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8846 (ptm) REVERT: S 218 ARG cc_start: 0.8612 (tmm-80) cc_final: 0.8155 (tmm-80) outliers start: 54 outliers final: 35 residues processed: 309 average time/residue: 0.0923 time to fit residues: 37.8688 Evaluate side-chains 313 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 266 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 220 CYS Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 253 PHE Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 285 HIS Chi-restraints excluded: chain R residue 310 GLU Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain R residue 336 LEU Chi-restraints excluded: chain R residue 340 MET Chi-restraints excluded: chain R residue 371 LYS Chi-restraints excluded: chain R residue 401 TYR Chi-restraints excluded: chain R residue 433 ILE Chi-restraints excluded: chain R residue 442 PHE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 76 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 18 optimal weight: 0.1980 chunk 65 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.097720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.069096 restraints weight = 24093.575| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 4.20 r_work: 0.2952 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.5749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9180 Z= 0.144 Angle : 0.749 11.471 12444 Z= 0.378 Chirality : 0.046 0.201 1422 Planarity : 0.004 0.051 1570 Dihedral : 4.766 39.689 1249 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 5.52 % Allowed : 34.24 % Favored : 60.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.25), residues: 1144 helix: 0.84 (0.27), residues: 370 sheet: -0.22 (0.31), residues: 277 loop : -0.98 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 21 TYR 0.014 0.001 TYR S 95 PHE 0.020 0.001 PHE S 212 TRP 0.041 0.002 TRP R 393 HIS 0.002 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9175) covalent geometry : angle 0.74873 (12436) SS BOND : bond 0.00205 ( 4) SS BOND : angle 0.94599 ( 8) hydrogen bonds : bond 0.04049 ( 418) hydrogen bonds : angle 5.08523 ( 1188) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 275 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 145 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7872 (pm20) REVERT: R 171 ILE cc_start: 0.9514 (mm) cc_final: 0.9273 (tt) REVERT: R 173 MET cc_start: 0.9096 (mmm) cc_final: 0.8825 (mmm) REVERT: R 188 ASN cc_start: 0.9283 (t160) cc_final: 0.8819 (m110) REVERT: R 227 GLN cc_start: 0.8098 (mm110) cc_final: 0.7349 (mm110) REVERT: R 236 PHE cc_start: 0.9296 (m-10) cc_final: 0.8658 (m-80) REVERT: R 266 ILE cc_start: 0.9092 (tt) cc_final: 0.8860 (pt) REVERT: R 284 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7022 (tt) REVERT: R 317 MET cc_start: 0.8452 (mmp) cc_final: 0.8193 (mmp) REVERT: R 336 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9402 (tp) REVERT: R 340 MET cc_start: 0.9148 (OUTLIER) cc_final: 0.8739 (mpp) REVERT: R 343 ARG cc_start: 0.8739 (tpt170) cc_final: 0.8492 (ttt180) REVERT: R 370 LYS cc_start: 0.8022 (pttm) cc_final: 0.7554 (pttm) REVERT: R 376 LYS cc_start: 0.8974 (mmtt) cc_final: 0.8547 (mttt) REVERT: R 378 LEU cc_start: 0.9520 (tp) cc_final: 0.9290 (mm) REVERT: R 389 TRP cc_start: 0.8903 (m100) cc_final: 0.8647 (m100) REVERT: R 397 MET cc_start: 0.7642 (ttt) cc_final: 0.7108 (ttt) REVERT: R 401 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.7352 (m-80) REVERT: R 422 TRP cc_start: 0.9308 (t60) cc_final: 0.8971 (t60) REVERT: R 431 ASN cc_start: 0.9229 (m-40) cc_final: 0.8871 (m-40) REVERT: B 23 LYS cc_start: 0.9609 (mttm) cc_final: 0.9391 (mttm) REVERT: B 32 GLN cc_start: 0.9466 (mt0) cc_final: 0.9070 (pt0) REVERT: B 45 MET cc_start: 0.9154 (mmt) cc_final: 0.8902 (mmt) REVERT: B 138 GLU cc_start: 0.9351 (mt-10) cc_final: 0.8563 (pm20) REVERT: B 215 GLU cc_start: 0.8962 (mp0) cc_final: 0.8462 (mp0) REVERT: B 217 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8377 (ppp) REVERT: B 262 MET cc_start: 0.8293 (tpp) cc_final: 0.7521 (mtp) REVERT: B 297 TRP cc_start: 0.9383 (m100) cc_final: 0.8705 (m100) REVERT: G 27 ARG cc_start: 0.9054 (mmt90) cc_final: 0.8699 (mmt90) REVERT: G 59 ASN cc_start: 0.8580 (t0) cc_final: 0.8356 (t0) REVERT: A 197 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7890 (mmtm) REVERT: A 230 TYR cc_start: 0.7547 (p90) cc_final: 0.5183 (p90) REVERT: A 231 ASP cc_start: 0.9106 (t70) cc_final: 0.8742 (m-30) REVERT: A 276 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8765 (mt-10) REVERT: A 337 ASP cc_start: 0.9445 (m-30) cc_final: 0.9108 (m-30) REVERT: A 345 LYS cc_start: 0.9494 (tptp) cc_final: 0.9292 (mmmm) REVERT: S 19 LYS cc_start: 0.9068 (tptm) cc_final: 0.8609 (tptp) REVERT: S 183 GLN cc_start: 0.9035 (mt0) cc_final: 0.8740 (mt0) REVERT: S 192 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8754 (ptm) REVERT: S 218 ARG cc_start: 0.8612 (tmm-80) cc_final: 0.8196 (tmm-80) outliers start: 53 outliers final: 34 residues processed: 302 average time/residue: 0.1077 time to fit residues: 42.8818 Evaluate side-chains 310 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 268 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 220 CYS Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 253 PHE Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 285 HIS Chi-restraints excluded: chain R residue 336 LEU Chi-restraints excluded: chain R residue 340 MET Chi-restraints excluded: chain R residue 371 LYS Chi-restraints excluded: chain R residue 395 LEU Chi-restraints excluded: chain R residue 401 TYR Chi-restraints excluded: chain R residue 433 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 41 optimal weight: 3.9990 chunk 86 optimal weight: 0.2980 chunk 11 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.096123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.067110 restraints weight = 24240.657| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 4.17 r_work: 0.2899 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.5858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9180 Z= 0.200 Angle : 0.784 11.807 12444 Z= 0.398 Chirality : 0.047 0.205 1422 Planarity : 0.004 0.054 1570 Dihedral : 4.898 38.037 1249 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.89 % Allowed : 34.76 % Favored : 60.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.25), residues: 1144 helix: 0.81 (0.27), residues: 373 sheet: -0.39 (0.31), residues: 272 loop : -0.89 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 13 TYR 0.031 0.002 TYR A 290 PHE 0.022 0.002 PHE S 212 TRP 0.051 0.002 TRP R 393 HIS 0.007 0.001 HIS R 177 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 9175) covalent geometry : angle 0.78351 (12436) SS BOND : bond 0.00308 ( 4) SS BOND : angle 0.99792 ( 8) hydrogen bonds : bond 0.04116 ( 418) hydrogen bonds : angle 5.22165 ( 1188) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 269 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 145 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7869 (pm20) REVERT: R 173 MET cc_start: 0.9065 (mmm) cc_final: 0.8759 (mmm) REVERT: R 174 ARG cc_start: 0.5184 (ptt180) cc_final: 0.4833 (ptm160) REVERT: R 188 ASN cc_start: 0.9365 (t160) cc_final: 0.8861 (m-40) REVERT: R 227 GLN cc_start: 0.7907 (mm110) cc_final: 0.7381 (mm110) REVERT: R 236 PHE cc_start: 0.9281 (m-10) cc_final: 0.8630 (m-80) REVERT: R 245 ARG cc_start: 0.9374 (ttm110) cc_final: 0.9068 (ttm110) REVERT: R 256 LYS cc_start: 0.7219 (mmtt) cc_final: 0.6938 (pttm) REVERT: R 284 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7043 (tt) REVERT: R 317 MET cc_start: 0.8462 (mmp) cc_final: 0.8248 (mmp) REVERT: R 336 LEU cc_start: 0.9628 (tp) cc_final: 0.9389 (tp) REVERT: R 340 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8776 (mpp) REVERT: R 343 ARG cc_start: 0.8771 (tpt170) cc_final: 0.8484 (ttt180) REVERT: R 370 LYS cc_start: 0.8110 (pttm) cc_final: 0.7635 (pttm) REVERT: R 376 LYS cc_start: 0.8990 (mmtt) cc_final: 0.8557 (mttt) REVERT: R 397 MET cc_start: 0.7667 (ttt) cc_final: 0.7096 (ttt) REVERT: R 401 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.7331 (m-80) REVERT: R 431 ASN cc_start: 0.9202 (m-40) cc_final: 0.8847 (m-40) REVERT: B 9 GLN cc_start: 0.9684 (tm-30) cc_final: 0.9423 (pp30) REVERT: B 23 LYS cc_start: 0.9595 (mttm) cc_final: 0.9365 (mttm) REVERT: B 32 GLN cc_start: 0.9453 (mt0) cc_final: 0.9071 (pt0) REVERT: B 45 MET cc_start: 0.9150 (mmt) cc_final: 0.8842 (mmt) REVERT: B 215 GLU cc_start: 0.8925 (mp0) cc_final: 0.8538 (mp0) REVERT: B 297 TRP cc_start: 0.9379 (m100) cc_final: 0.8750 (m100) REVERT: G 27 ARG cc_start: 0.9185 (mmt90) cc_final: 0.8674 (mmt90) REVERT: A 185 VAL cc_start: 0.8790 (OUTLIER) cc_final: 0.8471 (m) REVERT: A 197 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7831 (mmtm) REVERT: A 230 TYR cc_start: 0.7647 (p90) cc_final: 0.5333 (p90) REVERT: A 231 ASP cc_start: 0.9119 (t70) cc_final: 0.8763 (m-30) REVERT: A 276 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8771 (mt-10) REVERT: A 333 GLN cc_start: 0.9217 (tm-30) cc_final: 0.8892 (tm-30) REVERT: A 337 ASP cc_start: 0.9485 (m-30) cc_final: 0.9156 (m-30) REVERT: A 349 LYS cc_start: 0.9641 (OUTLIER) cc_final: 0.9397 (ptpp) REVERT: S 19 LYS cc_start: 0.9080 (tptm) cc_final: 0.8611 (tptp) REVERT: S 192 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8781 (ptm) REVERT: S 218 ARG cc_start: 0.8689 (tmm-80) cc_final: 0.8263 (tmm-80) REVERT: S 230 MET cc_start: 0.8957 (ttp) cc_final: 0.8725 (ttp) outliers start: 47 outliers final: 35 residues processed: 293 average time/residue: 0.1067 time to fit residues: 41.1791 Evaluate side-chains 304 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 261 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 220 CYS Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 253 PHE Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 285 HIS Chi-restraints excluded: chain R residue 340 MET Chi-restraints excluded: chain R residue 371 LYS Chi-restraints excluded: chain R residue 395 LEU Chi-restraints excluded: chain R residue 401 TYR Chi-restraints excluded: chain R residue 433 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 135 SER Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 40 optimal weight: 0.9990 chunk 66 optimal weight: 0.0040 chunk 91 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 chunk 49 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN S 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.098000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.069065 restraints weight = 24148.144| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 4.21 r_work: 0.2952 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.6050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9180 Z= 0.153 Angle : 0.819 16.914 12444 Z= 0.412 Chirality : 0.047 0.212 1422 Planarity : 0.004 0.050 1570 Dihedral : 4.841 38.914 1249 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.95 % Allowed : 36.52 % Favored : 59.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.25), residues: 1144 helix: 0.66 (0.27), residues: 376 sheet: -0.36 (0.31), residues: 272 loop : -1.03 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 21 TYR 0.016 0.001 TYR S 95 PHE 0.021 0.001 PHE S 212 TRP 0.036 0.002 TRP R 393 HIS 0.006 0.001 HIS R 177 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9175) covalent geometry : angle 0.81899 (12436) SS BOND : bond 0.00235 ( 4) SS BOND : angle 0.95567 ( 8) hydrogen bonds : bond 0.04196 ( 418) hydrogen bonds : angle 5.23642 ( 1188) Misc. bond : bond 0.00006 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 271 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 145 GLN cc_start: 0.8108 (mm-40) cc_final: 0.7790 (pm20) REVERT: R 173 MET cc_start: 0.9077 (mmm) cc_final: 0.8752 (mmm) REVERT: R 174 ARG cc_start: 0.5328 (ptt180) cc_final: 0.4858 (ptm-80) REVERT: R 227 GLN cc_start: 0.7892 (mm110) cc_final: 0.7404 (mm110) REVERT: R 236 PHE cc_start: 0.9242 (m-10) cc_final: 0.8569 (m-80) REVERT: R 245 ARG cc_start: 0.9348 (ttm110) cc_final: 0.9064 (ttm110) REVERT: R 284 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.6924 (tp) REVERT: R 336 LEU cc_start: 0.9631 (tp) cc_final: 0.9405 (tp) REVERT: R 340 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8747 (mpp) REVERT: R 343 ARG cc_start: 0.8763 (tpt170) cc_final: 0.8491 (ttt180) REVERT: R 370 LYS cc_start: 0.7994 (pttm) cc_final: 0.7524 (pttm) REVERT: R 376 LYS cc_start: 0.8966 (mmtt) cc_final: 0.8513 (mttt) REVERT: R 397 MET cc_start: 0.7565 (ttt) cc_final: 0.7043 (ttt) REVERT: R 401 TYR cc_start: 0.8394 (OUTLIER) cc_final: 0.7377 (m-80) REVERT: R 422 TRP cc_start: 0.9262 (t60) cc_final: 0.9028 (t60) REVERT: R 431 ASN cc_start: 0.9306 (m-40) cc_final: 0.8950 (m-40) REVERT: B 9 GLN cc_start: 0.9683 (tm-30) cc_final: 0.9444 (pp30) REVERT: B 23 LYS cc_start: 0.9607 (mttm) cc_final: 0.9366 (mttm) REVERT: B 32 GLN cc_start: 0.9449 (mt0) cc_final: 0.9062 (pt0) REVERT: B 138 GLU cc_start: 0.9369 (mt-10) cc_final: 0.8608 (pm20) REVERT: B 262 MET cc_start: 0.8059 (tpp) cc_final: 0.7392 (mtt) REVERT: B 297 TRP cc_start: 0.9360 (m100) cc_final: 0.8721 (m100) REVERT: A 185 VAL cc_start: 0.8805 (t) cc_final: 0.8496 (m) REVERT: A 197 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7916 (mmtm) REVERT: A 230 TYR cc_start: 0.7614 (p90) cc_final: 0.5244 (p90) REVERT: A 231 ASP cc_start: 0.9082 (t70) cc_final: 0.8741 (m-30) REVERT: A 276 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8743 (mt-10) REVERT: A 333 GLN cc_start: 0.9195 (tm-30) cc_final: 0.8855 (tm-30) REVERT: A 337 ASP cc_start: 0.9459 (m-30) cc_final: 0.9112 (m-30) REVERT: S 19 LYS cc_start: 0.9072 (tptm) cc_final: 0.8596 (tptp) REVERT: S 183 GLN cc_start: 0.9028 (mt0) cc_final: 0.8742 (mt0) REVERT: S 192 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8642 (ptm) REVERT: S 218 ARG cc_start: 0.8713 (tmm-80) cc_final: 0.8305 (tmm-80) outliers start: 38 outliers final: 28 residues processed: 292 average time/residue: 0.1025 time to fit residues: 39.3581 Evaluate side-chains 296 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 262 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 220 CYS Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 253 PHE Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 285 HIS Chi-restraints excluded: chain R residue 340 MET Chi-restraints excluded: chain R residue 371 LYS Chi-restraints excluded: chain R residue 395 LEU Chi-restraints excluded: chain R residue 401 TYR Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 71 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 16 optimal weight: 30.0000 chunk 90 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.097459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.068576 restraints weight = 23670.952| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 4.14 r_work: 0.2933 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.6165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9180 Z= 0.175 Angle : 0.841 11.225 12444 Z= 0.424 Chirality : 0.048 0.320 1422 Planarity : 0.004 0.054 1570 Dihedral : 4.834 41.388 1249 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.85 % Allowed : 37.04 % Favored : 59.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.25), residues: 1144 helix: 0.63 (0.27), residues: 377 sheet: -0.36 (0.31), residues: 272 loop : -0.96 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 13 TYR 0.033 0.002 TYR A 290 PHE 0.023 0.001 PHE R 155 TRP 0.047 0.002 TRP R 393 HIS 0.004 0.001 HIS R 177 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 9175) covalent geometry : angle 0.84035 (12436) SS BOND : bond 0.00290 ( 4) SS BOND : angle 1.18868 ( 8) hydrogen bonds : bond 0.04189 ( 418) hydrogen bonds : angle 5.29103 ( 1188) Misc. bond : bond 0.00015 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2323.97 seconds wall clock time: 40 minutes 39.32 seconds (2439.32 seconds total)