Starting phenix.real_space_refine on Fri Jan 17 02:49:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9auc_43877/01_2025/9auc_43877.cif Found real_map, /net/cci-nas-00/data/ceres_data/9auc_43877/01_2025/9auc_43877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9auc_43877/01_2025/9auc_43877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9auc_43877/01_2025/9auc_43877.map" model { file = "/net/cci-nas-00/data/ceres_data/9auc_43877/01_2025/9auc_43877.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9auc_43877/01_2025/9auc_43877.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 75 5.16 5 C 6629 2.51 5 N 1771 2.21 5 O 1894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 10369 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1882 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "E" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 946 Classifications: {'peptide': 117} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 110} Chain: "P" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 265 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "R" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 3055 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 16, 'TRANS': 351} Chain: "P" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 184 Unusual residues: {'NAG': 3, 'PLM': 4, 'Y01': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 7.37, per 1000 atoms: 0.71 Number of scatterers: 10369 At special positions: 0 Unit cell: (97.5, 98.8, 163.15, 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 75 16.00 O 1894 8.00 N 1771 7.00 C 6629 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS E 27 " - pdb=" SG CYS E 82 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 104 " distance=2.03 Simple disulfide: pdb=" SG CYS P 2 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG R 502 " - " ASN R 73 " " NAG R 503 " - " ASN R 125 " " NAG R 504 " - " ASN R 130 " Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 1.3 seconds 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2396 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 12 sheets defined 43.5% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 11 through 40 removed outlier: 3.859A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.584A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.524A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.738A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.908A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.595A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 4.510A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.518A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP B 20 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 22 removed outlier: 3.566A pdb=" N GLN G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 43 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.924A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 36 removed outlier: 3.567A pdb=" N ALA E 34 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU E 36 " --> pdb=" O TYR E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 52 removed outlier: 3.531A pdb=" N VAL E 46 " --> pdb=" O THR E 42 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP E 47 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA E 50 " --> pdb=" O VAL E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 58 removed outlier: 4.274A pdb=" N CYS E 57 " --> pdb=" O THR E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 81 removed outlier: 4.091A pdb=" N SER E 65 " --> pdb=" O ARG E 61 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU E 78 " --> pdb=" O TRP E 74 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU E 80 " --> pdb=" O MET E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 100 Processing helix chain 'E' and resid 115 through 120 Processing helix chain 'E' and resid 120 through 143 Proline residue: E 126 - end of helix removed outlier: 3.516A pdb=" N LYS E 142 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG E 143 " --> pdb=" O TRP E 139 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 6 No H-bonds generated for 'chain 'P' and resid 4 through 6' Processing helix chain 'P' and resid 7 through 19 Processing helix chain 'R' and resid 43 through 62 removed outlier: 3.937A pdb=" N LYS R 47 " --> pdb=" O VAL R 43 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA R 51 " --> pdb=" O LYS R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 132 through 136 removed outlier: 3.536A pdb=" N ALA R 136 " --> pdb=" O MET R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 173 removed outlier: 3.544A pdb=" N VAL R 147 " --> pdb=" O LYS R 143 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE R 165 " --> pdb=" O PHE R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 205 Processing helix chain 'R' and resid 208 through 215 removed outlier: 3.910A pdb=" N VAL R 212 " --> pdb=" O ASN R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 249 removed outlier: 3.637A pdb=" N HIS R 223 " --> pdb=" O CYS R 219 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET R 237 " --> pdb=" O ASN R 233 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU R 238 " --> pdb=" O TYR R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 267 Processing helix chain 'R' and resid 270 through 282 Processing helix chain 'R' and resid 287 through 291 Processing helix chain 'R' and resid 295 through 300 removed outlier: 3.920A pdb=" N LEU R 298 " --> pdb=" O THR R 295 " (cutoff:3.500A) Processing helix chain 'R' and resid 301 through 330 removed outlier: 3.502A pdb=" N THR R 330 " --> pdb=" O LYS R 326 " (cutoff:3.500A) Processing helix chain 'R' and resid 333 through 353 Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 365 through 382 removed outlier: 3.589A pdb=" N PHE R 382 " --> pdb=" O SER R 378 " (cutoff:3.500A) Processing helix chain 'R' and resid 382 through 392 Processing helix chain 'R' and resid 395 through 406 removed outlier: 3.578A pdb=" N THR R 401 " --> pdb=" O GLU R 397 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 213 removed outlier: 6.274A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.613A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.556A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.556A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.834A 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 151 removed outlier: 3.544A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.298A 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: 6.854A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.605A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.765A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.661A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.504A pdb=" N VAL N 124 " --> pdb=" O ALA N 92 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'R' and resid 93 through 94 476 hydrogen bonds defined for protein. 1359 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: 3.05 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1678 1.32 - 1.45: 2966 1.45 - 1.57: 5843 1.57 - 1.69: 0 1.69 - 1.82: 106 Bond restraints: 10593 Sorted by residual: bond pdb=" N VAL R 147 " pdb=" CA VAL R 147 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.28e+00 bond pdb=" N ASP R 373 " pdb=" CA ASP R 373 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.15e+00 bond pdb=" N LEU R 148 " pdb=" CA LEU R 148 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.84e+00 bond pdb=" CA ALA R 145 " pdb=" CB ALA R 145 " ideal model delta sigma weight residual 1.528 1.491 0.038 1.56e-02 4.11e+03 5.83e+00 bond pdb=" N VAL R 375 " pdb=" CA VAL R 375 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.22e-02 6.72e+03 5.64e+00 ... (remaining 10588 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 14147 1.65 - 3.30: 164 3.30 - 4.95: 24 4.95 - 6.60: 6 6.60 - 8.25: 2 Bond angle restraints: 14343 Sorted by residual: angle pdb=" C TYR R 150 " pdb=" CA TYR R 150 " pdb=" CB TYR R 150 " ideal model delta sigma weight residual 110.85 119.10 -8.25 1.70e+00 3.46e-01 2.36e+01 angle pdb=" C TYR R 374 " pdb=" CA TYR R 374 " pdb=" CB TYR R 374 " ideal model delta sigma weight residual 110.79 118.35 -7.56 1.66e+00 3.63e-01 2.07e+01 angle pdb=" CA ASP R 373 " pdb=" C ASP R 373 " pdb=" O ASP R 373 " ideal model delta sigma weight residual 120.82 116.46 4.36 1.05e+00 9.07e-01 1.72e+01 angle pdb=" C TYR R 146 " pdb=" CA TYR R 146 " pdb=" CB TYR R 146 " ideal model delta sigma weight residual 110.85 117.30 -6.45 1.70e+00 3.46e-01 1.44e+01 angle pdb=" N ASP R 373 " pdb=" CA ASP R 373 " pdb=" C ASP R 373 " ideal model delta sigma weight residual 111.07 114.84 -3.77 1.07e+00 8.73e-01 1.24e+01 ... (remaining 14338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 5966 17.92 - 35.84: 329 35.84 - 53.76: 96 53.76 - 71.67: 26 71.67 - 89.59: 19 Dihedral angle restraints: 6436 sinusoidal: 2723 harmonic: 3713 Sorted by residual: dihedral pdb=" CB CYS R 72 " pdb=" SG CYS R 72 " pdb=" SG CYS R 112 " pdb=" CB CYS R 112 " ideal model delta sinusoidal sigma weight residual -86.00 -173.19 87.19 1 1.00e+01 1.00e-02 9.13e+01 dihedral pdb=" CB CYS E 27 " pdb=" SG CYS E 27 " pdb=" SG CYS E 82 " pdb=" CB CYS E 82 " ideal model delta sinusoidal sigma weight residual -86.00 -162.54 76.54 1 1.00e+01 1.00e-02 7.36e+01 dihedral pdb=" CB CYS R 95 " pdb=" SG CYS R 95 " pdb=" SG CYS R 134 " pdb=" CB CYS R 134 " ideal model delta sinusoidal sigma weight residual 93.00 135.73 -42.73 1 1.00e+01 1.00e-02 2.55e+01 ... (remaining 6433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1478 0.076 - 0.151: 97 0.151 - 0.227: 5 0.227 - 0.302: 1 0.302 - 0.378: 2 Chirality restraints: 1583 Sorted by residual: chirality pdb=" CA TYR R 150 " pdb=" N TYR R 150 " pdb=" C TYR R 150 " pdb=" CB TYR R 150 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CA TYR R 146 " pdb=" N TYR R 146 " pdb=" C TYR R 146 " pdb=" CB TYR R 146 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CA TYR R 374 " pdb=" N TYR R 374 " pdb=" C TYR R 374 " pdb=" CB TYR R 374 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 1580 not shown) Planarity restraints: 1812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR R 372 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.63e+00 pdb=" C TYR R 372 " 0.037 2.00e-02 2.50e+03 pdb=" O TYR R 372 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP R 373 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS R 141 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.17e+00 pdb=" C LYS R 141 " -0.025 2.00e-02 2.50e+03 pdb=" O LYS R 141 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU R 142 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.021 5.00e-02 4.00e+02 3.22e-02 1.65e+00 pdb=" N PRO B 236 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.018 5.00e-02 4.00e+02 ... (remaining 1809 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1933 2.77 - 3.30: 9731 3.30 - 3.84: 17117 3.84 - 4.37: 20995 4.37 - 4.90: 35499 Nonbonded interactions: 85275 Sorted by model distance: nonbonded pdb=" O GLY E 52 " pdb=" NE1 TRP E 56 " model vdw 2.239 3.120 nonbonded pdb=" O SER A 306 " pdb=" OG SER A 306 " model vdw 2.314 3.040 nonbonded pdb=" O ALA B 56 " pdb=" OG SER B 334 " model vdw 2.317 3.040 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.320 3.040 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.329 3.040 ... (remaining 85270 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: 2.630 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: 0.000 Extract box with map and model: 0.510 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 26.280 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 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 : 0.003 0.038 10593 Z= 0.172 Angle : 0.476 8.253 14343 Z= 0.287 Chirality : 0.042 0.378 1583 Planarity : 0.003 0.032 1809 Dihedral : 13.242 89.593 4010 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 0.91 % Allowed : 13.89 % Favored : 85.19 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.19), residues: 1256 helix: -2.79 (0.14), residues: 513 sheet: -1.02 (0.33), residues: 220 loop : -1.69 (0.23), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 56 HIS 0.002 0.000 HIS B 142 PHE 0.006 0.001 PHE E 101 TYR 0.018 0.001 TYR R 150 ARG 0.001 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 211 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: A 35 GLN cc_start: 0.8012 (mm110) cc_final: 0.7811 (pt0) REVERT: N 43 LYS cc_start: 0.7903 (mttp) cc_final: 0.7548 (mttm) REVERT: E 111 VAL cc_start: 0.7624 (t) cc_final: 0.7349 (p) REVERT: E 139 TRP cc_start: 0.7506 (t60) cc_final: 0.7246 (t60) REVERT: R 49 MET cc_start: 0.6247 (tpp) cc_final: 0.5393 (mtp) REVERT: R 120 LYS cc_start: 0.6372 (mttt) cc_final: 0.6120 (mmtt) REVERT: R 144 ASN cc_start: 0.7611 (m-40) cc_final: 0.7373 (m110) REVERT: R 215 ASP cc_start: 0.5995 (t0) cc_final: 0.5641 (m-30) REVERT: R 227 GLN cc_start: 0.7881 (mt0) cc_final: 0.7541 (mm110) REVERT: R 287 ASP cc_start: 0.6204 (t70) cc_final: 0.5792 (t70) outliers start: 10 outliers final: 3 residues processed: 218 average time/residue: 1.5266 time to fit residues: 353.5934 Evaluate side-chains 135 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 132 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 106 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.0030 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 59 GLN A 254 ASN B 16 ASN B 75 GLN B 176 GLN B 266 HIS B 293 ASN N 1 GLN E 28 GLN E 45 GLN P 26 ASN R 61 GLN R 179 GLN R 223 HIS R 383 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.185108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.130114 restraints weight = 12922.772| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.90 r_work: 0.3505 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10593 Z= 0.184 Angle : 0.515 9.123 14343 Z= 0.271 Chirality : 0.042 0.289 1583 Planarity : 0.004 0.037 1809 Dihedral : 5.465 59.713 1676 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.83 % Allowed : 18.56 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.22), residues: 1256 helix: 0.07 (0.21), residues: 522 sheet: -0.49 (0.33), residues: 236 loop : -1.19 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 297 HIS 0.007 0.001 HIS R 381 PHE 0.013 0.001 PHE N 103 TYR 0.014 0.001 TYR R 191 ARG 0.008 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 1.154 Fit side-chains REVERT: A 35 GLN cc_start: 0.7957 (mm110) cc_final: 0.7480 (pt0) REVERT: N 87 LYS cc_start: 0.7623 (mtmt) cc_final: 0.7113 (mttt) REVERT: E 76 MET cc_start: 0.3577 (ppp) cc_final: 0.3335 (ppp) REVERT: E 111 VAL cc_start: 0.7586 (t) cc_final: 0.7334 (p) REVERT: E 139 TRP cc_start: 0.7747 (t60) cc_final: 0.7424 (t60) REVERT: R 49 MET cc_start: 0.6347 (tpp) cc_final: 0.5451 (mtp) REVERT: R 120 LYS cc_start: 0.6449 (mttt) cc_final: 0.6197 (mmtt) REVERT: R 144 ASN cc_start: 0.7375 (m-40) cc_final: 0.7101 (m110) REVERT: R 174 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7138 (mtm-85) REVERT: R 215 ASP cc_start: 0.5826 (t0) cc_final: 0.5506 (t0) REVERT: R 227 GLN cc_start: 0.7805 (mt0) cc_final: 0.7329 (mm110) REVERT: R 306 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8345 (mmm) REVERT: R 336 HIS cc_start: 0.6332 (OUTLIER) cc_final: 0.6113 (t-90) outliers start: 31 outliers final: 8 residues processed: 168 average time/residue: 1.5135 time to fit residues: 270.7519 Evaluate side-chains 136 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain R residue 336 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 101 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 93 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 1 GLN R 226 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.183141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.127807 restraints weight = 13115.951| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.91 r_work: 0.3474 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10593 Z= 0.159 Angle : 0.491 9.373 14343 Z= 0.255 Chirality : 0.041 0.295 1583 Planarity : 0.004 0.041 1809 Dihedral : 5.166 59.729 1672 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.65 % Allowed : 19.38 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.24), residues: 1256 helix: 1.14 (0.23), residues: 526 sheet: -0.36 (0.34), residues: 238 loop : -0.94 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 236 HIS 0.006 0.001 HIS R 381 PHE 0.014 0.001 PHE E 44 TYR 0.012 0.001 TYR N 80 ARG 0.006 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7831 (mm110) cc_final: 0.7455 (pt0) REVERT: N 87 LYS cc_start: 0.7583 (mtmt) cc_final: 0.7073 (mttt) REVERT: E 49 GLU cc_start: 0.5231 (OUTLIER) cc_final: 0.4394 (tp30) REVERT: E 139 TRP cc_start: 0.7786 (t60) cc_final: 0.7391 (t60) REVERT: R 49 MET cc_start: 0.6347 (tpp) cc_final: 0.5472 (mtp) REVERT: R 120 LYS cc_start: 0.6540 (mttt) cc_final: 0.6269 (mmtt) REVERT: R 174 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7157 (mtm-85) REVERT: R 215 ASP cc_start: 0.5620 (t0) cc_final: 0.5339 (t0) REVERT: R 227 GLN cc_start: 0.7771 (mt0) cc_final: 0.7290 (mm110) REVERT: R 294 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: R 306 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8351 (mmm) REVERT: R 329 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7370 (mt-10) REVERT: R 336 HIS cc_start: 0.6422 (OUTLIER) cc_final: 0.6217 (t-90) REVERT: R 403 LYS cc_start: 0.6493 (ptpp) cc_final: 0.6138 (mmmt) outliers start: 29 outliers final: 11 residues processed: 153 average time/residue: 1.5421 time to fit residues: 251.1127 Evaluate side-chains 140 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain R residue 329 GLU Chi-restraints excluded: chain R residue 336 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 68 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 13 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 67 optimal weight: 0.0670 chunk 48 optimal weight: 0.9980 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN N 1 GLN N 120 GLN R 144 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.181383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.125968 restraints weight = 12924.184| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.91 r_work: 0.3457 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10593 Z= 0.162 Angle : 0.495 9.402 14343 Z= 0.257 Chirality : 0.041 0.300 1583 Planarity : 0.003 0.045 1809 Dihedral : 5.274 59.830 1672 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.29 % Allowed : 20.11 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.24), residues: 1256 helix: 1.50 (0.23), residues: 526 sheet: -0.20 (0.34), residues: 228 loop : -0.77 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 236 HIS 0.005 0.001 HIS R 381 PHE 0.014 0.001 PHE B 151 TYR 0.010 0.001 TYR R 149 ARG 0.006 0.000 ARG R 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 1.303 Fit side-chains revert: symmetry clash REVERT: A 368 ASP cc_start: 0.6658 (p0) cc_final: 0.6152 (p0) REVERT: N 87 LYS cc_start: 0.7563 (mtmt) cc_final: 0.7142 (mttt) REVERT: E 49 GLU cc_start: 0.5080 (OUTLIER) cc_final: 0.3965 (tp30) REVERT: E 139 TRP cc_start: 0.7769 (t60) cc_final: 0.7379 (t60) REVERT: R 49 MET cc_start: 0.6365 (tpp) cc_final: 0.5509 (mtp) REVERT: R 120 LYS cc_start: 0.6561 (mttt) cc_final: 0.6326 (mmtt) REVERT: R 174 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7146 (mtm-85) REVERT: R 227 GLN cc_start: 0.7742 (mt0) cc_final: 0.7275 (mm110) REVERT: R 288 ASN cc_start: 0.6789 (m-40) cc_final: 0.6475 (m-40) REVERT: R 306 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8380 (mmm) REVERT: R 403 LYS cc_start: 0.6502 (ptpp) cc_final: 0.6183 (mmmt) outliers start: 25 outliers final: 9 residues processed: 143 average time/residue: 1.5946 time to fit residues: 242.9855 Evaluate side-chains 139 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain R residue 85 THR Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 306 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 16 optimal weight: 0.0070 chunk 121 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 1 GLN N 120 GLN P 10 HIS R 121 HIS R 144 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.177641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.122019 restraints weight = 12899.886| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.86 r_work: 0.3392 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10593 Z= 0.289 Angle : 0.584 9.378 14343 Z= 0.307 Chirality : 0.044 0.328 1583 Planarity : 0.004 0.051 1809 Dihedral : 6.583 59.944 1672 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.75 % Allowed : 18.92 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.24), residues: 1256 helix: 1.33 (0.23), residues: 527 sheet: -0.26 (0.33), residues: 233 loop : -0.74 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 332 HIS 0.006 0.001 HIS B 62 PHE 0.020 0.002 PHE B 151 TYR 0.012 0.002 TYR A 311 ARG 0.010 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 127 time to evaluate : 1.274 Fit side-chains revert: symmetry clash REVERT: B 43 ILE cc_start: 0.7349 (mp) cc_final: 0.7054 (tt) REVERT: B 61 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8249 (ppp) REVERT: B 134 ARG cc_start: 0.8187 (ptp-110) cc_final: 0.7799 (ptm160) REVERT: B 195 ASP cc_start: 0.6985 (OUTLIER) cc_final: 0.6189 (p0) REVERT: B 197 ARG cc_start: 0.7789 (mmm-85) cc_final: 0.7538 (mmm160) REVERT: E 49 GLU cc_start: 0.5157 (OUTLIER) cc_final: 0.3970 (tp30) REVERT: E 111 VAL cc_start: 0.7693 (t) cc_final: 0.7442 (p) REVERT: E 139 TRP cc_start: 0.7779 (t60) cc_final: 0.7476 (t60) REVERT: R 49 MET cc_start: 0.6386 (tpp) cc_final: 0.5520 (mtp) REVERT: R 120 LYS cc_start: 0.6640 (mttt) cc_final: 0.6413 (mmmt) REVERT: R 144 ASN cc_start: 0.7562 (m-40) cc_final: 0.7360 (m-40) REVERT: R 174 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7142 (mtm-85) REVERT: R 227 GLN cc_start: 0.7820 (mt0) cc_final: 0.7364 (mm110) REVERT: R 294 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7542 (mp0) REVERT: R 306 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8433 (mmm) outliers start: 41 outliers final: 14 residues processed: 151 average time/residue: 1.5249 time to fit residues: 245.1468 Evaluate side-chains 140 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 306 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 22 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 9 optimal weight: 0.0170 chunk 41 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.1020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN N 1 GLN N 120 GLN P 10 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.179667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.124439 restraints weight = 12943.534| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.86 r_work: 0.3426 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10593 Z= 0.180 Angle : 0.513 9.424 14343 Z= 0.267 Chirality : 0.041 0.299 1583 Planarity : 0.003 0.050 1809 Dihedral : 6.257 59.611 1672 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.74 % Allowed : 19.10 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.24), residues: 1256 helix: 1.64 (0.23), residues: 527 sheet: -0.21 (0.33), residues: 228 loop : -0.66 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.004 0.001 HIS R 277 PHE 0.016 0.001 PHE B 151 TYR 0.011 0.001 TYR R 149 ARG 0.005 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 134 ARG cc_start: 0.8175 (ptp-110) cc_final: 0.7802 (ptm160) REVERT: E 49 GLU cc_start: 0.5245 (OUTLIER) cc_final: 0.4041 (tp30) REVERT: E 111 VAL cc_start: 0.7717 (t) cc_final: 0.7467 (p) REVERT: E 139 TRP cc_start: 0.7756 (t60) cc_final: 0.7404 (t60) REVERT: R 49 MET cc_start: 0.6330 (tpp) cc_final: 0.5469 (mtp) REVERT: R 120 LYS cc_start: 0.6606 (mttt) cc_final: 0.6370 (mmmt) REVERT: R 144 ASN cc_start: 0.7543 (m-40) cc_final: 0.7331 (m-40) REVERT: R 174 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.7088 (mtm-85) REVERT: R 227 GLN cc_start: 0.7792 (mt0) cc_final: 0.7342 (mm110) REVERT: R 306 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8362 (mmm) REVERT: R 329 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7530 (mt-10) outliers start: 30 outliers final: 11 residues processed: 148 average time/residue: 1.4861 time to fit residues: 234.3785 Evaluate side-chains 138 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain R residue 329 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 116 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 1 GLN N 120 GLN P 10 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.175380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.119929 restraints weight = 13060.364| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.87 r_work: 0.3391 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10593 Z= 0.261 Angle : 0.571 9.214 14343 Z= 0.298 Chirality : 0.043 0.303 1583 Planarity : 0.004 0.054 1809 Dihedral : 7.059 59.192 1672 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.83 % Allowed : 19.84 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.24), residues: 1256 helix: 1.52 (0.23), residues: 528 sheet: -0.13 (0.33), residues: 227 loop : -0.69 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 236 HIS 0.005 0.001 HIS B 62 PHE 0.019 0.002 PHE B 151 TYR 0.011 0.002 TYR A 311 ARG 0.006 0.001 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 9 GLN cc_start: 0.6481 (OUTLIER) cc_final: 0.5922 (tm-30) REVERT: B 61 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8259 (ppp) REVERT: B 134 ARG cc_start: 0.8176 (ptp-110) cc_final: 0.7808 (ptm160) REVERT: B 195 ASP cc_start: 0.6995 (OUTLIER) cc_final: 0.6303 (p0) REVERT: G 36 ASP cc_start: 0.6952 (m-30) cc_final: 0.6581 (t70) REVERT: E 49 GLU cc_start: 0.5225 (OUTLIER) cc_final: 0.3975 (tp30) REVERT: E 111 VAL cc_start: 0.7714 (t) cc_final: 0.7484 (p) REVERT: E 139 TRP cc_start: 0.7769 (t60) cc_final: 0.7434 (t60) REVERT: R 49 MET cc_start: 0.6288 (tpp) cc_final: 0.5446 (mtp) REVERT: R 120 LYS cc_start: 0.6619 (mttt) cc_final: 0.6384 (mmmt) REVERT: R 144 ASN cc_start: 0.7581 (m-40) cc_final: 0.7372 (m-40) REVERT: R 174 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7101 (mtm-85) REVERT: R 227 GLN cc_start: 0.7838 (mt0) cc_final: 0.7398 (mm110) REVERT: R 306 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8417 (mmm) outliers start: 31 outliers final: 14 residues processed: 139 average time/residue: 1.4329 time to fit residues: 213.1353 Evaluate side-chains 139 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain R residue 85 THR Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 306 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 111 optimal weight: 6.9990 chunk 75 optimal weight: 0.0670 chunk 15 optimal weight: 0.1980 chunk 29 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 86 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.5120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 1 GLN N 120 GLN P 10 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.181643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.126850 restraints weight = 12974.496| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.88 r_work: 0.3459 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10593 Z= 0.135 Angle : 0.490 9.530 14343 Z= 0.253 Chirality : 0.040 0.295 1583 Planarity : 0.003 0.051 1809 Dihedral : 6.333 59.607 1672 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.83 % Allowed : 21.21 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.24), residues: 1256 helix: 2.02 (0.24), residues: 522 sheet: -0.03 (0.33), residues: 237 loop : -0.41 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.003 0.001 HIS R 381 PHE 0.013 0.001 PHE B 151 TYR 0.010 0.001 TYR N 60 ARG 0.006 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 ARG cc_start: 0.7865 (mtp85) cc_final: 0.7632 (ttm-80) REVERT: A 327 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6718 (mm-30) REVERT: B 134 ARG cc_start: 0.8152 (ptp-110) cc_final: 0.7789 (ptm160) REVERT: B 217 MET cc_start: 0.8572 (pmt) cc_final: 0.8268 (pmm) REVERT: E 49 GLU cc_start: 0.5256 (OUTLIER) cc_final: 0.3963 (tp30) REVERT: E 111 VAL cc_start: 0.7667 (t) cc_final: 0.7442 (p) REVERT: E 139 TRP cc_start: 0.7755 (t60) cc_final: 0.7404 (t60) REVERT: R 49 MET cc_start: 0.6214 (tpp) cc_final: 0.5383 (mtp) REVERT: R 112 CYS cc_start: 0.1595 (OUTLIER) cc_final: 0.1376 (p) REVERT: R 120 LYS cc_start: 0.6651 (mttt) cc_final: 0.6428 (mmmt) REVERT: R 227 GLN cc_start: 0.7752 (mt0) cc_final: 0.7322 (mm110) REVERT: R 306 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8283 (mmm) outliers start: 20 outliers final: 6 residues processed: 134 average time/residue: 1.5544 time to fit residues: 223.1790 Evaluate side-chains 130 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 306 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 97 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 118 optimal weight: 0.3980 chunk 116 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 1 GLN N 120 GLN P 10 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.176616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.121112 restraints weight = 13042.992| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.89 r_work: 0.3410 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10593 Z= 0.211 Angle : 0.538 9.372 14343 Z= 0.279 Chirality : 0.042 0.305 1583 Planarity : 0.004 0.053 1809 Dihedral : 6.610 59.809 1671 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.92 % Allowed : 21.48 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.24), residues: 1256 helix: 1.88 (0.23), residues: 526 sheet: -0.01 (0.34), residues: 226 loop : -0.61 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 76 HIS 0.004 0.001 HIS R 277 PHE 0.017 0.001 PHE B 151 TYR 0.012 0.001 TYR A 311 ARG 0.006 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.7560 (mttp) cc_final: 0.7334 (tttm) REVERT: A 265 ARG cc_start: 0.7914 (mtp85) cc_final: 0.7666 (ttm-80) REVERT: A 327 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6448 (mm-30) REVERT: B 61 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8228 (ppp) REVERT: B 134 ARG cc_start: 0.8187 (ptp-110) cc_final: 0.7832 (ptm160) REVERT: N 87 LYS cc_start: 0.7703 (mtmt) cc_final: 0.7248 (mttt) REVERT: E 49 GLU cc_start: 0.5267 (OUTLIER) cc_final: 0.3972 (tp30) REVERT: E 111 VAL cc_start: 0.7639 (t) cc_final: 0.7418 (p) REVERT: E 139 TRP cc_start: 0.7752 (t60) cc_final: 0.7430 (t60) REVERT: R 49 MET cc_start: 0.6265 (tpp) cc_final: 0.5401 (mtp) REVERT: R 227 GLN cc_start: 0.7814 (mt0) cc_final: 0.7377 (mm110) outliers start: 21 outliers final: 8 residues processed: 133 average time/residue: 1.6444 time to fit residues: 232.3342 Evaluate side-chains 130 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 49 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 0.0980 chunk 86 optimal weight: 0.0470 chunk 37 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 1 GLN N 120 GLN P 10 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.180406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.125301 restraints weight = 13035.362| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.89 r_work: 0.3437 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10593 Z= 0.156 Angle : 0.507 9.411 14343 Z= 0.261 Chirality : 0.040 0.295 1583 Planarity : 0.003 0.051 1809 Dihedral : 6.330 59.866 1671 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.19 % Allowed : 22.21 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.24), residues: 1256 helix: 2.08 (0.23), residues: 522 sheet: -0.01 (0.33), residues: 238 loop : -0.47 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 76 HIS 0.003 0.001 HIS R 381 PHE 0.014 0.001 PHE B 151 TYR 0.013 0.001 TYR R 146 ARG 0.006 0.000 ARG A 265 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.7519 (mttp) cc_final: 0.7266 (tttm) REVERT: A 265 ARG cc_start: 0.7900 (mtp85) cc_final: 0.7659 (ttm-80) REVERT: A 327 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6472 (mm-30) REVERT: B 134 ARG cc_start: 0.8135 (ptp-110) cc_final: 0.7766 (ptm160) REVERT: B 195 ASP cc_start: 0.6964 (OUTLIER) cc_final: 0.6377 (p0) REVERT: B 217 MET cc_start: 0.8628 (pmt) cc_final: 0.8393 (pmm) REVERT: N 87 LYS cc_start: 0.7713 (mtmt) cc_final: 0.7248 (mttt) REVERT: E 49 GLU cc_start: 0.5355 (OUTLIER) cc_final: 0.4052 (tp30) REVERT: E 139 TRP cc_start: 0.7748 (t60) cc_final: 0.7425 (t60) REVERT: R 49 MET cc_start: 0.6131 (tpp) cc_final: 0.5345 (mtp) REVERT: R 227 GLN cc_start: 0.7801 (mt0) cc_final: 0.7370 (mm110) REVERT: R 306 MET cc_start: 0.8480 (mmm) cc_final: 0.8195 (mmm) REVERT: R 397 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7123 (mp0) outliers start: 13 outliers final: 8 residues processed: 125 average time/residue: 1.4888 time to fit residues: 198.2950 Evaluate side-chains 128 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 49 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 59 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 92 optimal weight: 7.9990 chunk 58 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 1 GLN N 120 GLN P 10 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.177836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.122989 restraints weight = 12900.982| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.88 r_work: 0.3436 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10593 Z= 0.163 Angle : 0.514 9.438 14343 Z= 0.266 Chirality : 0.041 0.289 1583 Planarity : 0.003 0.052 1809 Dihedral : 6.200 59.812 1671 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.28 % Allowed : 22.21 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.24), residues: 1256 helix: 2.09 (0.23), residues: 522 sheet: -0.01 (0.33), residues: 238 loop : -0.46 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 76 HIS 0.003 0.001 HIS R 381 PHE 0.014 0.001 PHE B 151 TYR 0.009 0.001 TYR N 95 ARG 0.006 0.000 ARG A 265 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11924.75 seconds wall clock time: 211 minutes 21.55 seconds (12681.55 seconds total)