Starting phenix.real_space_refine on Wed Sep 17 18:01:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9auc_43877/09_2025/9auc_43877.cif Found real_map, /net/cci-nas-00/data/ceres_data/9auc_43877/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9auc_43877/09_2025/9auc_43877.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9auc_43877/09_2025/9auc_43877.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9auc_43877/09_2025/9auc_43877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9auc_43877/09_2025/9auc_43877.map" } resolution = 2.4 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= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2} 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: 2.69, per 1000 atoms: 0.26 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: 1.03 Conformation dependent library (CDL) restraints added in 386.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.35 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: 1.89 Time building geometry restraints manager: 1.31 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: 3.240 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: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.340 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:6.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.890 ------------------------------------------------------------------------------- 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 10606 Z= 0.154 Angle : 0.483 8.253 14372 Z= 0.288 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 : 4.47 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 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: -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 ARG 0.001 0.000 ARG G 13 TYR 0.018 0.001 TYR R 150 PHE 0.006 0.001 PHE E 101 TRP 0.005 0.001 TRP E 56 HIS 0.002 0.000 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00267 (10593) covalent geometry : angle 0.47577 (14343) SS BOND : bond 0.00134 ( 10) SS BOND : angle 0.84827 ( 20) hydrogen bonds : bond 0.27121 ( 476) hydrogen bonds : angle 8.46892 ( 1359) link_NAG-ASN : bond 0.00509 ( 3) link_NAG-ASN : angle 3.11410 ( 9) *********************** 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 : 0.422 Fit side-chains revert: symmetry clash REVERT: A 35 GLN cc_start: 0.8012 (mm110) cc_final: 0.7807 (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: 0.5776 (t70) outliers start: 10 outliers final: 3 residues processed: 218 average time/residue: 0.7681 time to fit residues: 177.4815 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 : 0.412 ------------------------------------------------------------------------------- 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 108 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 226 HIS R 383 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.181434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.125053 restraints weight = 12971.556| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.91 r_work: 0.3433 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10606 Z= 0.186 Angle : 0.593 9.572 14372 Z= 0.313 Chirality : 0.044 0.303 1583 Planarity : 0.005 0.041 1809 Dihedral : 6.036 59.561 1676 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.02 % Allowed : 18.37 % 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 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: -0.86 (0.22), residues: 1256 helix: 0.07 (0.21), residues: 524 sheet: -0.49 (0.33), residues: 236 loop : -1.18 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 283 TYR 0.012 0.002 TYR R 191 PHE 0.017 0.002 PHE R 253 TRP 0.019 0.002 TRP B 332 HIS 0.007 0.002 HIS R 277 Details of bonding type rmsd covalent geometry : bond 0.00420 (10593) covalent geometry : angle 0.58725 (14343) SS BOND : bond 0.00387 ( 10) SS BOND : angle 1.13223 ( 20) hydrogen bonds : bond 0.04699 ( 476) hydrogen bonds : angle 4.97504 ( 1359) link_NAG-ASN : bond 0.00355 ( 3) link_NAG-ASN : angle 2.95475 ( 9) *********************** 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 175 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 0.446 Fit side-chains REVERT: A 35 GLN cc_start: 0.7927 (mm110) cc_final: 0.7436 (pt0) REVERT: N 87 LYS cc_start: 0.7614 (mtmt) cc_final: 0.7133 (mttt) REVERT: E 76 MET cc_start: 0.3575 (ppp) cc_final: 0.3299 (ppp) REVERT: E 111 VAL cc_start: 0.7557 (t) cc_final: 0.7309 (p) REVERT: E 139 TRP cc_start: 0.7769 (t60) cc_final: 0.7379 (t60) REVERT: R 49 MET cc_start: 0.6380 (tpp) cc_final: 0.5432 (mtp) REVERT: R 120 LYS cc_start: 0.6538 (mttt) cc_final: 0.6284 (mmtt) REVERT: R 144 ASN cc_start: 0.7406 (m-40) cc_final: 0.7188 (m-40) REVERT: R 174 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7138 (mtm-85) REVERT: R 215 ASP cc_start: 0.5814 (t0) cc_final: 0.5138 (m-30) REVERT: R 227 GLN cc_start: 0.7817 (mt0) cc_final: 0.7334 (mm110) REVERT: R 294 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7512 (mp0) REVERT: R 306 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8406 (mmm) REVERT: R 336 HIS cc_start: 0.6423 (OUTLIER) cc_final: 0.6204 (t-90) REVERT: R 403 LYS cc_start: 0.6502 (ptpp) cc_final: 0.6067 (mmmt) outliers start: 33 outliers final: 12 residues processed: 164 average time/residue: 0.7705 time to fit residues: 134.2881 Evaluate side-chains 134 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 136 SER 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 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 78 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 294 GLU 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 0 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 94 optimal weight: 0.0050 overall best weight: 1.3798 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.180023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.123757 restraints weight = 12888.209| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.90 r_work: 0.3423 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10606 Z= 0.138 Angle : 0.527 9.331 14372 Z= 0.276 Chirality : 0.042 0.301 1583 Planarity : 0.004 0.054 1809 Dihedral : 5.709 59.915 1672 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.11 % Allowed : 18.56 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.00 (0.24), residues: 1256 helix: 1.01 (0.23), residues: 529 sheet: -0.33 (0.34), residues: 236 loop : -0.86 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 214 TYR 0.010 0.001 TYR R 191 PHE 0.016 0.001 PHE B 151 TRP 0.011 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00307 (10593) covalent geometry : angle 0.52061 (14343) SS BOND : bond 0.00352 ( 10) SS BOND : angle 1.23882 ( 20) hydrogen bonds : bond 0.04052 ( 476) hydrogen bonds : angle 4.61927 ( 1359) link_NAG-ASN : bond 0.00287 ( 3) link_NAG-ASN : angle 2.76354 ( 9) *********************** 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: 34 poor density : 130 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7810 (mm110) cc_final: 0.7430 (pt0) REVERT: A 368 ASP cc_start: 0.6769 (p0) cc_final: 0.6295 (p0) REVERT: B 32 GLN cc_start: 0.6869 (mt0) cc_final: 0.6487 (mt0) REVERT: B 61 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8165 (ppp) REVERT: B 134 ARG cc_start: 0.8164 (ptp-110) cc_final: 0.7846 (ptm160) REVERT: B 195 ASP cc_start: 0.7035 (OUTLIER) cc_final: 0.6284 (p0) REVERT: G 54 VAL cc_start: 0.4484 (OUTLIER) cc_final: 0.4248 (t) REVERT: E 139 TRP cc_start: 0.7767 (t60) cc_final: 0.7425 (t60) REVERT: R 49 MET cc_start: 0.6359 (tpp) cc_final: 0.5465 (mtp) REVERT: R 120 LYS cc_start: 0.6577 (mttt) cc_final: 0.6319 (mmtt) REVERT: R 144 ASN cc_start: 0.7376 (m-40) cc_final: 0.7173 (m-40) REVERT: R 174 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.7147 (mtm-85) REVERT: R 215 ASP cc_start: 0.5634 (t0) cc_final: 0.5342 (t0) REVERT: R 227 GLN cc_start: 0.7775 (mt0) cc_final: 0.7283 (mm110) REVERT: R 294 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7482 (mp0) REVERT: R 306 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8384 (mmm) REVERT: R 403 LYS cc_start: 0.6529 (ptpp) cc_final: 0.6283 (mmmt) REVERT: R 404 ARG cc_start: 0.7025 (ttp80) cc_final: 0.6602 (mtm-85) outliers start: 34 outliers final: 10 residues processed: 152 average time/residue: 0.7460 time to fit residues: 120.8542 Evaluate side-chains 136 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 61 MET Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 126 VAL 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 50 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 0.0870 overall best weight: 1.5364 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.178253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.122393 restraints weight = 12935.298| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.89 r_work: 0.3406 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10606 Z= 0.148 Angle : 0.541 9.423 14372 Z= 0.280 Chirality : 0.043 0.310 1583 Planarity : 0.004 0.057 1809 Dihedral : 6.097 59.881 1672 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.75 % Allowed : 17.73 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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 (0.24), residues: 1256 helix: 1.29 (0.23), residues: 526 sheet: -0.26 (0.33), residues: 231 loop : -0.80 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 214 TYR 0.010 0.001 TYR R 149 PHE 0.018 0.002 PHE B 151 TRP 0.012 0.002 TRP B 99 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00332 (10593) covalent geometry : angle 0.53450 (14343) SS BOND : bond 0.00169 ( 10) SS BOND : angle 1.31869 ( 20) hydrogen bonds : bond 0.03857 ( 476) hydrogen bonds : angle 4.51115 ( 1359) link_NAG-ASN : bond 0.00260 ( 3) link_NAG-ASN : angle 2.71948 ( 9) *********************** 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 160 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 119 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7820 (mm110) cc_final: 0.7419 (pt0) REVERT: A 368 ASP cc_start: 0.6677 (p0) cc_final: 0.6175 (p0) REVERT: B 61 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8195 (ppp) REVERT: B 195 ASP cc_start: 0.7001 (OUTLIER) cc_final: 0.6283 (p0) REVERT: E 111 VAL cc_start: 0.7662 (t) cc_final: 0.7428 (p) REVERT: E 139 TRP cc_start: 0.7785 (t60) cc_final: 0.7455 (t60) REVERT: R 49 MET cc_start: 0.6415 (tpp) cc_final: 0.5527 (mtp) REVERT: R 120 LYS cc_start: 0.6583 (mttt) cc_final: 0.6364 (mmmt) REVERT: R 144 ASN cc_start: 0.7410 (m-40) cc_final: 0.7195 (m-40) REVERT: R 174 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.7107 (mtm-85) REVERT: R 215 ASP cc_start: 0.5660 (t0) cc_final: 0.5333 (t0) REVERT: R 227 GLN cc_start: 0.7809 (mt0) cc_final: 0.7349 (mm110) REVERT: R 294 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7504 (mp0) REVERT: R 329 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7536 (mt-10) outliers start: 41 outliers final: 16 residues processed: 145 average time/residue: 0.6783 time to fit residues: 105.2759 Evaluate side-chains 135 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 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 266 HIS Chi-restraints excluded: chain B residue 325 MET 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 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 85 THR 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 329 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 58 optimal weight: 0.1980 chunk 50 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 75 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 27 optimal weight: 0.0060 chunk 69 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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 = 0.4213 r_free = 0.4213 target = 0.178952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.124368 restraints weight = 12956.253| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.86 r_work: 0.3451 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10606 Z= 0.098 Angle : 0.484 9.420 14372 Z= 0.249 Chirality : 0.040 0.294 1583 Planarity : 0.003 0.055 1809 Dihedral : 5.672 59.678 1672 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.65 % Allowed : 19.65 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.55 (0.24), residues: 1256 helix: 1.60 (0.24), residues: 528 sheet: -0.18 (0.34), residues: 228 loop : -0.65 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 265 TYR 0.011 0.001 TYR R 149 PHE 0.013 0.001 PHE B 151 TRP 0.020 0.001 TRP R 76 HIS 0.004 0.001 HIS R 381 Details of bonding type rmsd covalent geometry : bond 0.00209 (10593) covalent geometry : angle 0.47908 (14343) SS BOND : bond 0.00149 ( 10) SS BOND : angle 0.77943 ( 20) hydrogen bonds : bond 0.03261 ( 476) hydrogen bonds : angle 4.16008 ( 1359) link_NAG-ASN : bond 0.00267 ( 3) link_NAG-ASN : angle 2.71354 ( 9) *********************** 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 157 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7771 (mm110) cc_final: 0.7392 (pt0) REVERT: A 265 ARG cc_start: 0.7934 (mtp85) cc_final: 0.7642 (ttm-80) REVERT: A 368 ASP cc_start: 0.6548 (p0) cc_final: 0.6091 (p0) REVERT: B 61 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8143 (ppp) REVERT: E 49 GLU cc_start: 0.4825 (OUTLIER) cc_final: 0.3706 (tp30) REVERT: E 111 VAL cc_start: 0.7681 (t) cc_final: 0.7448 (p) REVERT: E 139 TRP cc_start: 0.7765 (t60) cc_final: 0.7398 (t60) REVERT: R 49 MET cc_start: 0.6368 (tpp) cc_final: 0.5491 (ptm) REVERT: R 120 LYS cc_start: 0.6574 (mttt) cc_final: 0.6356 (mmmt) REVERT: R 144 ASN cc_start: 0.7353 (m-40) cc_final: 0.7147 (m-40) REVERT: R 227 GLN cc_start: 0.7755 (mt0) cc_final: 0.7304 (mm110) REVERT: R 288 ASN cc_start: 0.7524 (m-40) cc_final: 0.7146 (m-40) REVERT: R 306 MET cc_start: 0.8487 (mmm) cc_final: 0.8172 (mmm) outliers start: 29 outliers final: 9 residues processed: 147 average time/residue: 0.6853 time to fit residues: 107.8528 Evaluate side-chains 132 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain R residue 85 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 27 optimal weight: 0.7980 chunk 94 optimal weight: 30.0000 chunk 75 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4205 r_free = 0.4205 target = 0.180471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.125718 restraints weight = 12990.493| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.86 r_work: 0.3434 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10606 Z= 0.109 Angle : 0.501 9.217 14372 Z= 0.258 Chirality : 0.041 0.294 1583 Planarity : 0.003 0.056 1809 Dihedral : 5.768 59.284 1671 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.47 % Allowed : 19.93 % 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 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: 0.73 (0.24), residues: 1256 helix: 1.79 (0.24), residues: 528 sheet: -0.19 (0.34), residues: 234 loop : -0.55 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 214 TYR 0.016 0.001 TYR N 80 PHE 0.014 0.001 PHE B 151 TRP 0.011 0.001 TRP R 236 HIS 0.004 0.001 HIS R 381 Details of bonding type rmsd covalent geometry : bond 0.00237 (10593) covalent geometry : angle 0.49180 (14343) SS BOND : bond 0.00105 ( 10) SS BOND : angle 1.80146 ( 20) hydrogen bonds : bond 0.03362 ( 476) hydrogen bonds : angle 4.12920 ( 1359) link_NAG-ASN : bond 0.00215 ( 3) link_NAG-ASN : angle 2.72854 ( 9) *********************** 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 151 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7787 (mm110) cc_final: 0.7402 (pt0) REVERT: A 265 ARG cc_start: 0.7964 (mtp85) cc_final: 0.7677 (ttm-80) REVERT: B 61 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8199 (ppp) REVERT: N 87 LYS cc_start: 0.7561 (mtmt) cc_final: 0.7070 (mttt) REVERT: E 49 GLU cc_start: 0.4837 (OUTLIER) cc_final: 0.3695 (tp30) REVERT: E 111 VAL cc_start: 0.7673 (t) cc_final: 0.7433 (p) REVERT: E 139 TRP cc_start: 0.7766 (t60) cc_final: 0.7422 (t60) REVERT: R 49 MET cc_start: 0.6361 (tpp) cc_final: 0.5446 (ptm) REVERT: R 120 LYS cc_start: 0.6625 (mttt) cc_final: 0.6403 (mmmt) REVERT: R 227 GLN cc_start: 0.7789 (mt0) cc_final: 0.7362 (mm110) REVERT: R 294 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: R 306 MET cc_start: 0.8521 (mmm) cc_final: 0.8203 (mmm) outliers start: 27 outliers final: 13 residues processed: 141 average time/residue: 0.7040 time to fit residues: 106.1109 Evaluate side-chains 137 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 349 SER 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 G residue 29 LYS Chi-restraints excluded: chain G residue 54 VAL 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 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain R residue 85 THR Chi-restraints excluded: chain R residue 294 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 28 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 26 optimal weight: 0.0980 chunk 16 optimal weight: 3.9990 chunk 110 optimal weight: 0.0470 chunk 33 optimal weight: 0.6980 overall best weight: 0.5080 ------------------------------------------------------------------------------- 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 = 0.4217 r_free = 0.4217 target = 0.181770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.127175 restraints weight = 12987.923| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.88 r_work: 0.3458 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10606 Z= 0.092 Angle : 0.478 9.340 14372 Z= 0.245 Chirality : 0.040 0.292 1583 Planarity : 0.003 0.055 1809 Dihedral : 5.538 59.436 1671 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.10 % Allowed : 20.66 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.92 (0.25), residues: 1256 helix: 1.96 (0.24), residues: 528 sheet: -0.09 (0.34), residues: 235 loop : -0.48 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 214 TYR 0.013 0.001 TYR N 80 PHE 0.012 0.001 PHE B 151 TRP 0.012 0.001 TRP A 234 HIS 0.004 0.001 HIS R 381 Details of bonding type rmsd covalent geometry : bond 0.00195 (10593) covalent geometry : angle 0.47076 (14343) SS BOND : bond 0.00087 ( 10) SS BOND : angle 1.41848 ( 20) hydrogen bonds : bond 0.03063 ( 476) hydrogen bonds : angle 3.99017 ( 1359) link_NAG-ASN : bond 0.00230 ( 3) link_NAG-ASN : angle 2.71200 ( 9) *********************** 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 150 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7754 (mm110) cc_final: 0.7379 (pt0) REVERT: A 265 ARG cc_start: 0.7949 (mtp85) cc_final: 0.7686 (ttm-80) REVERT: A 327 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6757 (mm-30) REVERT: B 61 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8150 (ppp) REVERT: N 87 LYS cc_start: 0.7591 (mtmt) cc_final: 0.7094 (mttt) REVERT: E 49 GLU cc_start: 0.4851 (OUTLIER) cc_final: 0.3708 (tp30) REVERT: E 111 VAL cc_start: 0.7663 (t) cc_final: 0.7433 (p) REVERT: E 139 TRP cc_start: 0.7783 (t60) cc_final: 0.7436 (t60) REVERT: R 49 MET cc_start: 0.6258 (tpp) cc_final: 0.5381 (ptm) REVERT: R 120 LYS cc_start: 0.6600 (mttt) cc_final: 0.6367 (mmmt) REVERT: R 227 GLN cc_start: 0.7791 (mt0) cc_final: 0.7361 (mm110) REVERT: R 294 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: R 306 MET cc_start: 0.8504 (mmm) cc_final: 0.8137 (mmm) outliers start: 23 outliers final: 13 residues processed: 145 average time/residue: 0.6996 time to fit residues: 108.4527 Evaluate side-chains 138 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain R residue 85 THR Chi-restraints excluded: chain R residue 294 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 45 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 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 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 = 0.4205 r_free = 0.4205 target = 0.180147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.125169 restraints weight = 12867.525| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.88 r_work: 0.3437 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10606 Z= 0.107 Angle : 0.496 9.352 14372 Z= 0.255 Chirality : 0.040 0.296 1583 Planarity : 0.003 0.056 1809 Dihedral : 5.722 59.654 1671 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.56 % Allowed : 20.66 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.96 (0.25), residues: 1256 helix: 1.97 (0.24), residues: 528 sheet: 0.02 (0.34), residues: 238 loop : -0.47 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 197 TYR 0.013 0.001 TYR R 146 PHE 0.013 0.001 PHE B 151 TRP 0.011 0.001 TRP R 76 HIS 0.004 0.001 HIS R 381 Details of bonding type rmsd covalent geometry : bond 0.00233 (10593) covalent geometry : angle 0.48974 (14343) SS BOND : bond 0.00103 ( 10) SS BOND : angle 1.20312 ( 20) hydrogen bonds : bond 0.03264 ( 476) hydrogen bonds : angle 4.03377 ( 1359) link_NAG-ASN : bond 0.00221 ( 3) link_NAG-ASN : angle 2.63408 ( 9) *********************** 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 150 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7775 (mm110) cc_final: 0.7394 (pt0) REVERT: A 265 ARG cc_start: 0.7956 (mtp85) cc_final: 0.7692 (ttm-80) REVERT: A 327 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6510 (mm-30) REVERT: B 9 GLN cc_start: 0.6432 (OUTLIER) cc_final: 0.5752 (tm-30) REVERT: B 61 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.8203 (ppp) REVERT: B 195 ASP cc_start: 0.6948 (OUTLIER) cc_final: 0.6293 (p0) REVERT: B 217 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8353 (pmm) REVERT: N 87 LYS cc_start: 0.7598 (mtmt) cc_final: 0.7121 (mttt) REVERT: E 49 GLU cc_start: 0.4857 (OUTLIER) cc_final: 0.3721 (tp30) REVERT: E 111 VAL cc_start: 0.7653 (t) cc_final: 0.7434 (p) REVERT: E 139 TRP cc_start: 0.7762 (t60) cc_final: 0.7412 (t60) REVERT: R 49 MET cc_start: 0.6270 (tpp) cc_final: 0.5378 (ptm) REVERT: R 120 LYS cc_start: 0.6599 (mttt) cc_final: 0.6375 (mmmt) REVERT: R 227 GLN cc_start: 0.7800 (mt0) cc_final: 0.7370 (mm110) REVERT: R 294 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7438 (mp0) REVERT: R 306 MET cc_start: 0.8532 (mmm) cc_final: 0.8205 (mmm) outliers start: 28 outliers final: 15 residues processed: 142 average time/residue: 0.6751 time to fit residues: 102.5552 Evaluate side-chains 144 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 349 SER 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 217 MET Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL 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 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain R residue 85 THR Chi-restraints excluded: chain R residue 294 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 86 optimal weight: 0.0170 chunk 70 optimal weight: 7.9990 chunk 49 optimal weight: 0.0670 chunk 36 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 67 optimal weight: 0.0670 chunk 56 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.8096 ------------------------------------------------------------------------------- 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 = 0.4206 r_free = 0.4206 target = 0.180608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.125876 restraints weight = 12972.849| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.87 r_work: 0.3443 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10606 Z= 0.105 Angle : 0.494 9.375 14372 Z= 0.254 Chirality : 0.040 0.289 1583 Planarity : 0.003 0.056 1809 Dihedral : 5.756 59.839 1671 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.38 % Allowed : 21.30 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.04 (0.24), residues: 1256 helix: 2.08 (0.23), residues: 522 sheet: 0.02 (0.34), residues: 238 loop : -0.43 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 197 TYR 0.013 0.001 TYR N 80 PHE 0.013 0.001 PHE B 151 TRP 0.018 0.001 TRP R 76 HIS 0.004 0.001 HIS R 381 Details of bonding type rmsd covalent geometry : bond 0.00229 (10593) covalent geometry : angle 0.48760 (14343) SS BOND : bond 0.00100 ( 10) SS BOND : angle 1.43951 ( 20) hydrogen bonds : bond 0.03213 ( 476) hydrogen bonds : angle 4.06515 ( 1359) link_NAG-ASN : bond 0.00229 ( 3) link_NAG-ASN : angle 2.54452 ( 9) *********************** 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 151 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7760 (mm110) cc_final: 0.7378 (pt0) REVERT: A 265 ARG cc_start: 0.7942 (mtp85) cc_final: 0.7690 (ttm-80) REVERT: A 327 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6476 (mm-30) REVERT: A 368 ASP cc_start: 0.6573 (p0) cc_final: 0.5935 (p0) REVERT: B 9 GLN cc_start: 0.6369 (OUTLIER) cc_final: 0.5700 (tm-30) REVERT: B 61 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8146 (ppp) REVERT: B 195 ASP cc_start: 0.6949 (OUTLIER) cc_final: 0.6294 (p0) REVERT: G 37 LEU cc_start: 0.5654 (OUTLIER) cc_final: 0.5293 (mm) REVERT: N 87 LYS cc_start: 0.7604 (mtmt) cc_final: 0.7201 (mttt) REVERT: E 49 GLU cc_start: 0.4924 (OUTLIER) cc_final: 0.3806 (tp30) REVERT: E 111 VAL cc_start: 0.7600 (t) cc_final: 0.7383 (p) REVERT: E 139 TRP cc_start: 0.7763 (t60) cc_final: 0.7421 (t60) REVERT: R 49 MET cc_start: 0.6215 (tpp) cc_final: 0.5350 (ptm) REVERT: R 120 LYS cc_start: 0.6595 (mttt) cc_final: 0.6381 (mmmt) REVERT: R 227 GLN cc_start: 0.7785 (mt0) cc_final: 0.7349 (mm110) REVERT: R 294 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7462 (mp0) REVERT: R 306 MET cc_start: 0.8533 (mmm) cc_final: 0.8205 (mmm) outliers start: 26 outliers final: 14 residues processed: 144 average time/residue: 0.7309 time to fit residues: 112.3094 Evaluate side-chains 144 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 349 SER 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 217 MET Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL 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 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain R residue 85 THR Chi-restraints excluded: chain R residue 294 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 102 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 62 optimal weight: 0.0000 chunk 117 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.8386 ------------------------------------------------------------------------------- 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 E 43 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 = 0.4202 r_free = 0.4202 target = 0.179547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.126096 restraints weight = 12822.587| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.83 r_work: 0.3439 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10606 Z= 0.108 Angle : 0.506 10.827 14372 Z= 0.259 Chirality : 0.040 0.287 1583 Planarity : 0.003 0.056 1809 Dihedral : 5.823 59.882 1671 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.01 % Allowed : 21.48 % 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 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: 1.09 (0.25), residues: 1256 helix: 2.14 (0.23), residues: 522 sheet: 0.02 (0.34), residues: 238 loop : -0.41 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 214 TYR 0.012 0.001 TYR N 80 PHE 0.013 0.001 PHE B 151 TRP 0.023 0.001 TRP R 76 HIS 0.004 0.001 HIS R 381 Details of bonding type rmsd covalent geometry : bond 0.00240 (10593) covalent geometry : angle 0.50070 (14343) SS BOND : bond 0.00129 ( 10) SS BOND : angle 1.32184 ( 20) hydrogen bonds : bond 0.03261 ( 476) hydrogen bonds : angle 4.05701 ( 1359) link_NAG-ASN : bond 0.00254 ( 3) link_NAG-ASN : angle 2.48548 ( 9) ********************** 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 142 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7764 (mm110) cc_final: 0.7395 (pt0) REVERT: A 265 ARG cc_start: 0.7951 (mtp85) cc_final: 0.7701 (ttm-80) REVERT: A 327 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6419 (mm-30) REVERT: A 368 ASP cc_start: 0.6576 (p0) cc_final: 0.5981 (p0) REVERT: B 9 GLN cc_start: 0.6411 (OUTLIER) cc_final: 0.5743 (tm-30) REVERT: B 61 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.8141 (ppp) REVERT: B 195 ASP cc_start: 0.6954 (OUTLIER) cc_final: 0.6303 (p0) REVERT: N 87 LYS cc_start: 0.7678 (mtmt) cc_final: 0.7208 (mttt) REVERT: E 49 GLU cc_start: 0.5142 (OUTLIER) cc_final: 0.4177 (tp30) REVERT: E 111 VAL cc_start: 0.7606 (t) cc_final: 0.7397 (p) REVERT: E 139 TRP cc_start: 0.7757 (t60) cc_final: 0.7420 (t60) REVERT: R 49 MET cc_start: 0.6213 (tpp) cc_final: 0.5345 (ptm) REVERT: R 208 ASN cc_start: 0.6596 (t0) cc_final: 0.6212 (p0) REVERT: R 227 GLN cc_start: 0.7788 (mt0) cc_final: 0.7351 (mm110) REVERT: R 294 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7505 (mp0) REVERT: R 306 MET cc_start: 0.8525 (mmm) cc_final: 0.8195 (mmm) outliers start: 22 outliers final: 14 residues processed: 137 average time/residue: 0.7299 time to fit residues: 106.6734 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 : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 349 SER 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 217 MET Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain G residue 54 VAL 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 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain R residue 294 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 100 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 115 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 89 optimal weight: 0.0770 chunk 120 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- 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 = 0.4193 r_free = 0.4193 target = 0.176985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.123455 restraints weight = 12951.618| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.83 r_work: 0.3427 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10606 Z= 0.122 Angle : 0.520 9.445 14372 Z= 0.267 Chirality : 0.041 0.286 1583 Planarity : 0.003 0.057 1809 Dihedral : 6.099 59.570 1671 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.01 % Allowed : 21.48 % 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 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: 1.02 (0.24), residues: 1256 helix: 2.07 (0.23), residues: 522 sheet: 0.04 (0.34), residues: 231 loop : -0.47 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 214 TYR 0.013 0.001 TYR R 146 PHE 0.014 0.001 PHE B 151 TRP 0.026 0.002 TRP R 76 HIS 0.004 0.001 HIS R 381 Details of bonding type rmsd covalent geometry : bond 0.00274 (10593) covalent geometry : angle 0.51418 (14343) SS BOND : bond 0.00132 ( 10) SS BOND : angle 1.32305 ( 20) hydrogen bonds : bond 0.03453 ( 476) hydrogen bonds : angle 4.16230 ( 1359) link_NAG-ASN : bond 0.00253 ( 3) link_NAG-ASN : angle 2.47054 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6474.22 seconds wall clock time: 110 minutes 50.93 seconds (6650.93 seconds total)