Starting phenix.real_space_refine on Mon Jun 9 04:44:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9auc_43877/06_2025/9auc_43877.cif Found real_map, /net/cci-nas-00/data/ceres_data/9auc_43877/06_2025/9auc_43877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9auc_43877/06_2025/9auc_43877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9auc_43877/06_2025/9auc_43877.map" model { file = "/net/cci-nas-00/data/ceres_data/9auc_43877/06_2025/9auc_43877.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9auc_43877/06_2025/9auc_43877.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 75 5.16 5 C 6629 2.51 5 N 1771 2.21 5 O 1894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10369 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1882 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "E" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 946 Classifications: {'peptide': 117} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 110} Chain: "P" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 265 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "R" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 3055 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 16, 'TRANS': 351} Chain: "P" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 184 Unusual residues: {'NAG': 3, 'PLM': 4, 'Y01': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 7.07, per 1000 atoms: 0.68 Number of scatterers: 10369 At special positions: 0 Unit cell: (97.5, 98.8, 163.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 75 16.00 O 1894 8.00 N 1771 7.00 C 6629 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS E 27 " - pdb=" SG CYS E 82 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 104 " distance=2.03 Simple disulfide: pdb=" SG CYS P 2 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG R 502 " - " ASN R 73 " " NAG R 503 " - " ASN R 125 " " NAG R 504 " - " ASN R 130 " Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.4 seconds 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2396 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 12 sheets defined 43.5% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 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: 2.81 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1678 1.32 - 1.45: 2966 1.45 - 1.57: 5843 1.57 - 1.69: 0 1.69 - 1.82: 106 Bond restraints: 10593 Sorted by residual: bond pdb=" N VAL R 147 " pdb=" CA VAL R 147 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.28e+00 bond pdb=" N ASP R 373 " pdb=" CA ASP R 373 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.15e+00 bond pdb=" N LEU R 148 " pdb=" CA LEU R 148 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.84e+00 bond pdb=" CA ALA R 145 " pdb=" CB ALA R 145 " ideal model delta sigma weight residual 1.528 1.491 0.038 1.56e-02 4.11e+03 5.83e+00 bond pdb=" N VAL R 375 " pdb=" CA VAL R 375 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.22e-02 6.72e+03 5.64e+00 ... (remaining 10588 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 14147 1.65 - 3.30: 164 3.30 - 4.95: 24 4.95 - 6.60: 6 6.60 - 8.25: 2 Bond angle restraints: 14343 Sorted by residual: angle pdb=" C TYR R 150 " pdb=" CA TYR R 150 " pdb=" CB TYR R 150 " ideal model delta sigma weight residual 110.85 119.10 -8.25 1.70e+00 3.46e-01 2.36e+01 angle pdb=" C TYR R 374 " pdb=" CA TYR R 374 " pdb=" CB TYR R 374 " ideal model delta sigma weight residual 110.79 118.35 -7.56 1.66e+00 3.63e-01 2.07e+01 angle pdb=" CA ASP R 373 " pdb=" C ASP R 373 " pdb=" O ASP R 373 " ideal model delta sigma weight residual 120.82 116.46 4.36 1.05e+00 9.07e-01 1.72e+01 angle pdb=" C TYR R 146 " pdb=" CA TYR R 146 " pdb=" CB TYR R 146 " ideal model delta sigma weight residual 110.85 117.30 -6.45 1.70e+00 3.46e-01 1.44e+01 angle pdb=" N ASP R 373 " pdb=" CA ASP R 373 " pdb=" C ASP R 373 " ideal model delta sigma weight residual 111.07 114.84 -3.77 1.07e+00 8.73e-01 1.24e+01 ... (remaining 14338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 5966 17.92 - 35.84: 329 35.84 - 53.76: 96 53.76 - 71.67: 26 71.67 - 89.59: 19 Dihedral angle restraints: 6436 sinusoidal: 2723 harmonic: 3713 Sorted by residual: dihedral pdb=" CB CYS R 72 " pdb=" SG CYS R 72 " pdb=" SG CYS R 112 " pdb=" CB CYS R 112 " ideal model delta sinusoidal sigma weight residual -86.00 -173.19 87.19 1 1.00e+01 1.00e-02 9.13e+01 dihedral pdb=" CB CYS E 27 " pdb=" SG CYS E 27 " pdb=" SG CYS E 82 " pdb=" CB CYS E 82 " ideal model delta sinusoidal sigma weight residual -86.00 -162.54 76.54 1 1.00e+01 1.00e-02 7.36e+01 dihedral pdb=" CB CYS R 95 " pdb=" SG CYS R 95 " pdb=" SG CYS R 134 " pdb=" CB CYS R 134 " ideal model delta sinusoidal sigma weight residual 93.00 135.73 -42.73 1 1.00e+01 1.00e-02 2.55e+01 ... (remaining 6433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1478 0.076 - 0.151: 97 0.151 - 0.227: 5 0.227 - 0.302: 1 0.302 - 0.378: 2 Chirality restraints: 1583 Sorted by residual: chirality pdb=" CA TYR R 150 " pdb=" N TYR R 150 " pdb=" C TYR R 150 " pdb=" CB TYR R 150 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CA TYR R 146 " pdb=" N TYR R 146 " pdb=" C TYR R 146 " pdb=" CB TYR R 146 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CA TYR R 374 " pdb=" N TYR R 374 " pdb=" C TYR R 374 " pdb=" CB TYR R 374 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 1580 not shown) Planarity restraints: 1812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR R 372 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.63e+00 pdb=" C TYR R 372 " 0.037 2.00e-02 2.50e+03 pdb=" O TYR R 372 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP R 373 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS R 141 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.17e+00 pdb=" C LYS R 141 " -0.025 2.00e-02 2.50e+03 pdb=" O LYS R 141 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU R 142 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.021 5.00e-02 4.00e+02 3.22e-02 1.65e+00 pdb=" N PRO B 236 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.018 5.00e-02 4.00e+02 ... (remaining 1809 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1933 2.77 - 3.30: 9731 3.30 - 3.84: 17117 3.84 - 4.37: 20995 4.37 - 4.90: 35499 Nonbonded interactions: 85275 Sorted by model distance: nonbonded pdb=" O GLY E 52 " pdb=" NE1 TRP E 56 " model vdw 2.239 3.120 nonbonded pdb=" O SER A 306 " pdb=" OG SER A 306 " model vdw 2.314 3.040 nonbonded pdb=" O ALA B 56 " pdb=" OG SER B 334 " model vdw 2.317 3.040 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.320 3.040 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.329 3.040 ... (remaining 85270 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 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: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 26.870 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.520 ------------------------------------------------------------------------------- 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 : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 0.91 % Allowed : 13.89 % Favored : 85.19 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.19), residues: 1256 helix: -2.79 (0.14), residues: 513 sheet: -1.02 (0.33), residues: 220 loop : -1.69 (0.23), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 56 HIS 0.002 0.000 HIS B 142 PHE 0.006 0.001 PHE E 101 TYR 0.018 0.001 TYR R 150 ARG 0.001 0.000 ARG G 13 Details of bonding type rmsd link_NAG-ASN : bond 0.00509 ( 3) link_NAG-ASN : angle 3.11410 ( 9) hydrogen bonds : bond 0.27121 ( 476) hydrogen bonds : angle 8.46892 ( 1359) SS BOND : bond 0.00134 ( 10) SS BOND : angle 0.84827 ( 20) covalent geometry : bond 0.00267 (10593) covalent geometry : angle 0.47577 (14343) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 211 time to evaluate : 1.181 Fit side-chains revert: symmetry clash REVERT: A 35 GLN cc_start: 0.8012 (mm110) cc_final: 0.7811 (pt0) REVERT: N 43 LYS cc_start: 0.7903 (mttp) cc_final: 0.7548 (mttm) REVERT: E 111 VAL cc_start: 0.7624 (t) cc_final: 0.7349 (p) REVERT: E 139 TRP cc_start: 0.7506 (t60) cc_final: 0.7246 (t60) REVERT: R 49 MET cc_start: 0.6247 (tpp) cc_final: 0.5393 (mtp) REVERT: R 120 LYS cc_start: 0.6372 (mttt) cc_final: 0.6120 (mmtt) REVERT: R 144 ASN cc_start: 0.7611 (m-40) cc_final: 0.7373 (m110) REVERT: R 215 ASP cc_start: 0.5995 (t0) cc_final: 0.5641 (m-30) REVERT: R 227 GLN cc_start: 0.7881 (mt0) cc_final: 0.7541 (mm110) REVERT: R 287 ASP cc_start: 0.6204 (t70) cc_final: 0.5792 (t70) outliers start: 10 outliers final: 3 residues processed: 218 average time/residue: 1.5013 time to fit residues: 348.1388 Evaluate side-chains 135 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 132 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 106 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.0030 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 96 optimal weight: 0.1980 chunk 37 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 59 GLN A 254 ASN B 16 ASN B 75 GLN B 176 GLN B 266 HIS B 293 ASN N 1 GLN E 28 GLN E 45 GLN P 26 ASN R 61 GLN R 179 GLN R 223 HIS R 383 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.185749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.131130 restraints weight = 12861.860| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.91 r_work: 0.3527 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10606 Z= 0.122 Angle : 0.514 9.389 14372 Z= 0.267 Chirality : 0.042 0.295 1583 Planarity : 0.004 0.038 1809 Dihedral : 5.389 59.609 1676 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.29 % Allowed : 17.92 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.22), residues: 1256 helix: 0.12 (0.21), residues: 519 sheet: -0.54 (0.33), residues: 238 loop : -1.19 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 297 HIS 0.007 0.001 HIS R 381 PHE 0.011 0.001 PHE N 103 TYR 0.015 0.001 TYR R 191 ARG 0.008 0.001 ARG B 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00390 ( 3) link_NAG-ASN : angle 2.93577 ( 9) hydrogen bonds : bond 0.04268 ( 476) hydrogen bonds : angle 4.74916 ( 1359) SS BOND : bond 0.00199 ( 10) SS BOND : angle 1.02849 ( 20) covalent geometry : bond 0.00255 (10593) covalent geometry : angle 0.50773 (14343) *********************** 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 186 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 1.165 Fit side-chains REVERT: A 35 GLN cc_start: 0.7956 (mm110) cc_final: 0.7499 (pt0) REVERT: N 43 LYS cc_start: 0.7931 (mttp) cc_final: 0.7545 (mttm) REVERT: N 87 LYS cc_start: 0.7605 (mtmt) cc_final: 0.7090 (mttt) REVERT: E 76 MET cc_start: 0.3607 (ppp) cc_final: 0.3332 (ppp) REVERT: E 111 VAL cc_start: 0.7576 (t) cc_final: 0.7321 (p) REVERT: E 139 TRP cc_start: 0.7728 (t60) cc_final: 0.7401 (t60) REVERT: P 25 ASN cc_start: 0.2538 (OUTLIER) cc_final: 0.2261 (m-40) REVERT: R 49 MET cc_start: 0.6344 (tpp) cc_final: 0.5461 (mtp) REVERT: R 120 LYS cc_start: 0.6460 (mttt) cc_final: 0.6188 (mmtt) REVERT: R 144 ASN cc_start: 0.7361 (m-40) cc_final: 0.7095 (m-40) REVERT: R 174 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.7081 (mtm-85) REVERT: R 215 ASP cc_start: 0.5817 (t0) cc_final: 0.5549 (t0) REVERT: R 227 GLN cc_start: 0.7798 (mt0) cc_final: 0.7312 (mm110) REVERT: R 306 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8400 (mmm) REVERT: R 336 HIS cc_start: 0.6301 (OUTLIER) cc_final: 0.6064 (t-90) outliers start: 36 outliers final: 9 residues processed: 175 average time/residue: 1.4063 time to fit residues: 263.3264 Evaluate side-chains 137 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain P residue 25 ASN Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain R residue 336 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 101 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 112 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 93 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 1 GLN N 31 ASN R 226 HIS R 383 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.180752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.124920 restraints weight = 13060.727| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.89 r_work: 0.3430 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10606 Z= 0.149 Angle : 0.547 9.358 14372 Z= 0.285 Chirality : 0.043 0.305 1583 Planarity : 0.004 0.045 1809 Dihedral : 5.674 59.494 1674 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.74 % Allowed : 18.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.23), residues: 1256 helix: 1.01 (0.23), residues: 527 sheet: -0.38 (0.34), residues: 238 loop : -0.90 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 332 HIS 0.006 0.002 HIS R 277 PHE 0.016 0.002 PHE E 44 TYR 0.011 0.002 TYR N 80 ARG 0.005 0.001 ARG B 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 3) link_NAG-ASN : angle 2.73433 ( 9) hydrogen bonds : bond 0.04218 ( 476) hydrogen bonds : angle 4.66709 ( 1359) SS BOND : bond 0.00313 ( 10) SS BOND : angle 1.53133 ( 20) covalent geometry : bond 0.00332 (10593) covalent geometry : angle 0.54001 (14343) *********************** 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 162 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7857 (mm110) cc_final: 0.7433 (pt0) REVERT: B 134 ARG cc_start: 0.8188 (ptp-110) cc_final: 0.7888 (ptm160) REVERT: N 87 LYS cc_start: 0.7577 (mtmt) cc_final: 0.7072 (mttt) REVERT: E 49 GLU cc_start: 0.5353 (OUTLIER) cc_final: 0.4479 (tp30) REVERT: E 139 TRP cc_start: 0.7771 (t60) cc_final: 0.7405 (t60) REVERT: R 49 MET cc_start: 0.6380 (tpp) cc_final: 0.5510 (mtp) REVERT: R 120 LYS cc_start: 0.6595 (mttt) cc_final: 0.6331 (mmtt) REVERT: R 144 ASN cc_start: 0.7368 (m-40) cc_final: 0.7166 (m-40) REVERT: R 174 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.7123 (mtm-85) REVERT: R 215 ASP cc_start: 0.5710 (t0) cc_final: 0.5412 (t0) REVERT: R 227 GLN cc_start: 0.7784 (mt0) cc_final: 0.7299 (mm110) REVERT: R 294 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7434 (mp0) REVERT: R 403 LYS cc_start: 0.6502 (ptpp) cc_final: 0.6123 (mmmt) outliers start: 30 outliers final: 14 residues processed: 151 average time/residue: 1.9974 time to fit residues: 322.1623 Evaluate side-chains 137 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 270 ILE 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 125 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 294 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 68 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN N 1 GLN N 120 GLN R 121 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.175779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.120025 restraints weight = 12923.263| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.87 r_work: 0.3392 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10606 Z= 0.187 Angle : 0.595 9.211 14372 Z= 0.310 Chirality : 0.045 0.318 1583 Planarity : 0.004 0.053 1809 Dihedral : 6.670 59.589 1672 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.38 % Allowed : 18.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.24), residues: 1256 helix: 1.09 (0.23), residues: 527 sheet: -0.33 (0.33), residues: 234 loop : -0.79 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 332 HIS 0.006 0.001 HIS B 62 PHE 0.019 0.002 PHE B 151 TYR 0.011 0.002 TYR A 311 ARG 0.005 0.001 ARG A 265 Details of bonding type rmsd link_NAG-ASN : bond 0.00239 ( 3) link_NAG-ASN : angle 2.85381 ( 9) hydrogen bonds : bond 0.04243 ( 476) hydrogen bonds : angle 4.71329 ( 1359) SS BOND : bond 0.00407 ( 10) SS BOND : angle 2.55500 ( 20) covalent geometry : bond 0.00431 (10593) covalent geometry : angle 0.58398 (14343) *********************** 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 161 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 32 GLN cc_start: 0.6936 (mt0) cc_final: 0.6545 (mt0) REVERT: B 61 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8264 (ppp) REVERT: B 134 ARG cc_start: 0.8183 (ptp-110) cc_final: 0.7880 (ptm160) REVERT: B 195 ASP cc_start: 0.7003 (OUTLIER) cc_final: 0.6247 (p0) REVERT: G 36 ASP cc_start: 0.7069 (m-30) cc_final: 0.6863 (t70) REVERT: E 49 GLU cc_start: 0.5316 (OUTLIER) cc_final: 0.4144 (tp30) REVERT: E 111 VAL cc_start: 0.7684 (t) cc_final: 0.7433 (p) REVERT: E 139 TRP cc_start: 0.7781 (t60) cc_final: 0.7467 (t60) REVERT: R 49 MET cc_start: 0.6440 (tpp) cc_final: 0.5541 (mtp) REVERT: R 120 LYS cc_start: 0.6645 (mttt) cc_final: 0.6395 (mmtt) REVERT: R 144 ASN cc_start: 0.7377 (m-40) cc_final: 0.7155 (m-40) REVERT: R 174 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.7132 (mtm-85) REVERT: R 215 ASP cc_start: 0.5743 (t0) cc_final: 0.5384 (t0) REVERT: R 227 GLN cc_start: 0.7805 (mt0) cc_final: 0.7338 (mm110) REVERT: R 294 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: R 404 ARG cc_start: 0.7022 (ttp80) cc_final: 0.6664 (mtm-85) outliers start: 37 outliers final: 14 residues processed: 148 average time/residue: 1.6207 time to fit residues: 256.2666 Evaluate side-chains 137 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 37 ILE 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 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 57 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 337 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 16 optimal weight: 0.0570 chunk 121 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN N 1 GLN N 120 GLN P 10 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.178415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.122991 restraints weight = 12906.743| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.89 r_work: 0.3435 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3643 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= 0.105 Angle : 0.500 9.366 14372 Z= 0.258 Chirality : 0.040 0.292 1583 Planarity : 0.003 0.050 1809 Dihedral : 6.029 59.444 1672 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.38 % Allowed : 19.56 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.24), residues: 1256 helix: 1.53 (0.23), residues: 528 sheet: -0.20 (0.33), residues: 233 loop : -0.72 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 76 HIS 0.004 0.001 HIS R 381 PHE 0.013 0.001 PHE B 151 TYR 0.012 0.001 TYR R 149 ARG 0.004 0.000 ARG A 283 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 3) link_NAG-ASN : angle 2.72587 ( 9) hydrogen bonds : bond 0.03421 ( 476) hydrogen bonds : angle 4.30327 ( 1359) SS BOND : bond 0.00202 ( 10) SS BOND : angle 1.38943 ( 20) covalent geometry : bond 0.00228 (10593) covalent geometry : angle 0.49357 (14343) *********************** 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: 26 poor density : 131 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 ARG cc_start: 0.7878 (mtp85) cc_final: 0.7661 (ttm-80) REVERT: A 368 ASP cc_start: 0.6585 (p0) cc_final: 0.6205 (p0) REVERT: B 43 ILE cc_start: 0.7377 (mp) cc_final: 0.7148 (tt) REVERT: E 49 GLU cc_start: 0.5136 (OUTLIER) cc_final: 0.3948 (tp30) REVERT: E 111 VAL cc_start: 0.7718 (t) cc_final: 0.7468 (p) REVERT: E 139 TRP cc_start: 0.7752 (t60) cc_final: 0.7379 (t60) REVERT: R 49 MET cc_start: 0.6411 (tpp) cc_final: 0.5552 (mtp) REVERT: R 120 LYS cc_start: 0.6633 (mttt) cc_final: 0.6415 (mmmt) REVERT: R 144 ASN cc_start: 0.7332 (m-40) cc_final: 0.7114 (m-40) REVERT: R 174 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7076 (mtm-85) REVERT: R 215 ASP cc_start: 0.5641 (t0) cc_final: 0.5328 (t0) REVERT: R 227 GLN cc_start: 0.7759 (mt0) cc_final: 0.7315 (mm110) REVERT: R 294 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7474 (mp0) REVERT: R 404 ARG cc_start: 0.7055 (ttp80) cc_final: 0.6603 (mtm-85) outliers start: 26 outliers final: 11 residues processed: 144 average time/residue: 1.4441 time to fit residues: 221.8639 Evaluate side-chains 136 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 1.363 ------------------------------------------------------------------------------- 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 29 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 249 THR 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 E residue 49 GLU Chi-restraints excluded: chain R residue 85 THR Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 294 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 22 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 108 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 106 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN N 1 GLN N 120 GLN P 10 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.179313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.124094 restraints weight = 12899.036| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.85 r_work: 0.3414 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10606 Z= 0.133 Angle : 0.527 9.361 14372 Z= 0.273 Chirality : 0.042 0.301 1583 Planarity : 0.003 0.053 1809 Dihedral : 6.457 59.441 1672 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.02 % Allowed : 19.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.24), residues: 1256 helix: 1.62 (0.23), residues: 528 sheet: -0.08 (0.33), residues: 232 loop : -0.70 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 236 HIS 0.004 0.001 HIS R 277 PHE 0.016 0.001 PHE B 151 TYR 0.010 0.001 TYR N 95 ARG 0.003 0.000 ARG A 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00210 ( 3) link_NAG-ASN : angle 2.80746 ( 9) hydrogen bonds : bond 0.03681 ( 476) hydrogen bonds : angle 4.34299 ( 1359) SS BOND : bond 0.00188 ( 10) SS BOND : angle 1.52937 ( 20) covalent geometry : bond 0.00297 (10593) covalent geometry : angle 0.51993 (14343) *********************** 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 155 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 ARG cc_start: 0.7909 (mtp85) cc_final: 0.7685 (ttm-80) REVERT: B 9 GLN cc_start: 0.6392 (OUTLIER) cc_final: 0.5762 (tm-30) REVERT: B 195 ASP cc_start: 0.7001 (OUTLIER) cc_final: 0.6308 (p0) REVERT: E 49 GLU cc_start: 0.5265 (OUTLIER) cc_final: 0.4071 (tp30) REVERT: E 111 VAL cc_start: 0.7702 (t) cc_final: 0.7458 (p) REVERT: E 139 TRP cc_start: 0.7748 (t60) cc_final: 0.7405 (t60) REVERT: R 49 MET cc_start: 0.6365 (tpp) cc_final: 0.5493 (mtp) REVERT: R 120 LYS cc_start: 0.6601 (mttt) cc_final: 0.6367 (mmmt) REVERT: R 144 ASN cc_start: 0.7340 (m-40) cc_final: 0.7123 (m-40) REVERT: R 174 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7093 (mtm-85) REVERT: R 227 GLN cc_start: 0.7805 (mt0) cc_final: 0.7376 (mm110) REVERT: R 288 ASN cc_start: 0.7611 (m-40) cc_final: 0.7233 (m-40) REVERT: R 294 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7588 (mp0) outliers start: 33 outliers final: 11 residues processed: 141 average time/residue: 1.4322 time to fit residues: 216.0149 Evaluate side-chains 135 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain R residue 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 116 optimal weight: 6.9990 chunk 105 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 103 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.179356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.123968 restraints weight = 13095.574| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.88 r_work: 0.3415 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10606 Z= 0.123 Angle : 0.517 9.587 14372 Z= 0.268 Chirality : 0.041 0.314 1583 Planarity : 0.003 0.053 1809 Dihedral : 6.506 59.722 1672 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.74 % Allowed : 20.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.24), residues: 1256 helix: 1.74 (0.23), residues: 528 sheet: -0.16 (0.33), residues: 233 loop : -0.58 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.004 0.001 HIS R 381 PHE 0.016 0.001 PHE B 151 TYR 0.011 0.001 TYR N 80 ARG 0.004 0.000 ARG A 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00218 ( 3) link_NAG-ASN : angle 3.11319 ( 9) hydrogen bonds : bond 0.03477 ( 476) hydrogen bonds : angle 4.25276 ( 1359) SS BOND : bond 0.00155 ( 10) SS BOND : angle 1.19847 ( 20) covalent geometry : bond 0.00275 (10593) covalent geometry : angle 0.50980 (14343) *********************** 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 149 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.7557 (mttm) cc_final: 0.7349 (tttm) REVERT: A 265 ARG cc_start: 0.7892 (mtp85) cc_final: 0.7669 (ttm-80) REVERT: A 327 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6500 (mm-30) REVERT: B 197 ARG cc_start: 0.7743 (mmm-85) cc_final: 0.7446 (mmm-85) REVERT: E 49 GLU cc_start: 0.5290 (OUTLIER) cc_final: 0.4046 (tp30) REVERT: E 111 VAL cc_start: 0.7699 (t) cc_final: 0.7461 (p) REVERT: E 139 TRP cc_start: 0.7753 (t60) cc_final: 0.7408 (t60) REVERT: P 16 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7872 (mp) REVERT: R 49 MET cc_start: 0.6260 (tpp) cc_final: 0.5398 (mtp) REVERT: R 112 CYS cc_start: 0.1686 (OUTLIER) cc_final: 0.1437 (p) REVERT: R 120 LYS cc_start: 0.6632 (mttt) cc_final: 0.6402 (mmmt) REVERT: R 144 ASN cc_start: 0.7329 (m-40) cc_final: 0.7112 (m-40) REVERT: R 174 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7135 (mtm-85) REVERT: R 227 GLN cc_start: 0.7790 (mt0) cc_final: 0.7359 (mm110) REVERT: R 294 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7629 (mp0) outliers start: 30 outliers final: 11 residues processed: 139 average time/residue: 1.4274 time to fit residues: 211.8246 Evaluate side-chains 136 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 199 ILE 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 111 optimal weight: 1.9990 chunk 75 optimal weight: 0.0370 chunk 15 optimal weight: 0.0070 chunk 29 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 100 optimal weight: 0.3980 chunk 86 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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 = 0.180443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.125491 restraints weight = 12929.086| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.87 r_work: 0.3439 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3945 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= 0.103 Angle : 0.495 9.388 14372 Z= 0.256 Chirality : 0.040 0.298 1583 Planarity : 0.003 0.052 1809 Dihedral : 6.280 59.501 1672 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.38 % Allowed : 20.57 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.24), residues: 1256 helix: 1.94 (0.23), residues: 527 sheet: -0.06 (0.33), residues: 238 loop : -0.49 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.003 0.001 HIS R 381 PHE 0.014 0.001 PHE B 151 TYR 0.011 0.001 TYR N 80 ARG 0.003 0.000 ARG A 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00213 ( 3) link_NAG-ASN : angle 2.90659 ( 9) hydrogen bonds : bond 0.03232 ( 476) hydrogen bonds : angle 4.10233 ( 1359) SS BOND : bond 0.00136 ( 10) SS BOND : angle 1.03249 ( 20) covalent geometry : bond 0.00222 (10593) covalent geometry : angle 0.48843 (14343) *********************** 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 144 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.7516 (mttm) cc_final: 0.7284 (tttm) REVERT: A 265 ARG cc_start: 0.7876 (mtp85) cc_final: 0.7660 (ttm-80) REVERT: A 327 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6617 (mm-30) REVERT: A 368 ASP cc_start: 0.6673 (p0) cc_final: 0.6079 (p0) REVERT: B 197 ARG cc_start: 0.7758 (mmm-85) cc_final: 0.7445 (mmm-85) REVERT: B 217 MET cc_start: 0.8588 (pmt) cc_final: 0.8318 (pmm) REVERT: E 49 GLU cc_start: 0.5301 (OUTLIER) cc_final: 0.4062 (tp30) REVERT: E 111 VAL cc_start: 0.7638 (t) cc_final: 0.7405 (p) REVERT: E 139 TRP cc_start: 0.7740 (t60) cc_final: 0.7392 (t60) REVERT: R 49 MET cc_start: 0.6221 (tpp) cc_final: 0.5383 (mtp) REVERT: R 120 LYS cc_start: 0.6619 (mttt) cc_final: 0.6408 (mmmt) REVERT: R 144 ASN cc_start: 0.7297 (m-40) cc_final: 0.7080 (m-40) REVERT: R 227 GLN cc_start: 0.7811 (mt0) cc_final: 0.7382 (mm110) outliers start: 26 outliers final: 9 residues processed: 135 average time/residue: 1.6099 time to fit residues: 234.0905 Evaluate side-chains 128 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain E residue 49 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 97 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 118 optimal weight: 0.0670 chunk 116 optimal weight: 0.0050 chunk 114 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 115 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 overall best weight: 0.5336 ------------------------------------------------------------------------------- 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 = 0.4215 r_free = 0.4215 target = 0.181428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.126656 restraints weight = 13141.871| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.90 r_work: 0.3451 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10606 Z= 0.096 Angle : 0.495 9.867 14372 Z= 0.252 Chirality : 0.040 0.298 1583 Planarity : 0.003 0.052 1809 Dihedral : 6.053 59.971 1671 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.74 % Allowed : 21.30 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.24), residues: 1256 helix: 2.19 (0.23), residues: 521 sheet: 0.03 (0.34), residues: 238 loop : -0.43 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 76 HIS 0.004 0.001 HIS R 381 PHE 0.013 0.001 PHE B 151 TYR 0.011 0.001 TYR N 80 ARG 0.006 0.000 ARG B 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 3) link_NAG-ASN : angle 2.68364 ( 9) hydrogen bonds : bond 0.03067 ( 476) hydrogen bonds : angle 3.97626 ( 1359) SS BOND : bond 0.00092 ( 10) SS BOND : angle 0.81159 ( 20) covalent geometry : bond 0.00208 (10593) covalent geometry : angle 0.48948 (14343) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 ARG cc_start: 0.7875 (mtp85) cc_final: 0.7653 (ttm-80) REVERT: B 197 ARG cc_start: 0.7768 (mmm-85) cc_final: 0.7447 (mmm-85) REVERT: N 87 LYS cc_start: 0.7598 (mtmt) cc_final: 0.7218 (mttt) REVERT: E 49 GLU cc_start: 0.5501 (OUTLIER) cc_final: 0.4435 (tp30) REVERT: E 111 VAL cc_start: 0.7617 (t) cc_final: 0.7392 (p) REVERT: E 139 TRP cc_start: 0.7746 (t60) cc_final: 0.7403 (t60) REVERT: R 49 MET cc_start: 0.6159 (tpp) cc_final: 0.5354 (mtp) REVERT: R 120 LYS cc_start: 0.6607 (mttt) cc_final: 0.6404 (mmmt) REVERT: R 144 ASN cc_start: 0.7281 (m-40) cc_final: 0.7061 (m-40) REVERT: R 215 ASP cc_start: 0.5917 (t70) cc_final: 0.5205 (m-30) REVERT: R 227 GLN cc_start: 0.7796 (mt0) cc_final: 0.7371 (mm110) outliers start: 19 outliers final: 9 residues processed: 136 average time/residue: 1.5531 time to fit residues: 226.0119 Evaluate side-chains 130 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain E residue 49 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.4179 r_free = 0.4179 target = 0.177937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.122754 restraints weight = 12960.891| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.86 r_work: 0.3392 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10606 Z= 0.173 Angle : 0.585 9.486 14372 Z= 0.301 Chirality : 0.043 0.298 1583 Planarity : 0.004 0.055 1809 Dihedral : 6.804 59.680 1671 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.55 % Allowed : 21.76 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.24), residues: 1256 helix: 1.89 (0.23), residues: 521 sheet: -0.02 (0.32), residues: 241 loop : -0.56 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 76 HIS 0.006 0.001 HIS R 331 PHE 0.018 0.002 PHE B 151 TYR 0.014 0.002 TYR A 311 ARG 0.007 0.001 ARG B 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 3) link_NAG-ASN : angle 2.82638 ( 9) hydrogen bonds : bond 0.03930 ( 476) hydrogen bonds : angle 4.39004 ( 1359) SS BOND : bond 0.00192 ( 10) SS BOND : angle 1.21152 ( 20) covalent geometry : bond 0.00400 (10593) covalent geometry : angle 0.57935 (14343) ********************** 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 139 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 1.279 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.7607 (mttp) cc_final: 0.7312 (tttm) REVERT: A 265 ARG cc_start: 0.7885 (mtp85) cc_final: 0.7652 (ttm-80) REVERT: A 368 ASP cc_start: 0.6723 (p0) cc_final: 0.6144 (p0) REVERT: B 61 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8246 (ppp) REVERT: B 195 ASP cc_start: 0.6972 (OUTLIER) cc_final: 0.6221 (p0) REVERT: B 197 ARG cc_start: 0.7768 (mmm-85) cc_final: 0.7492 (mmm-85) REVERT: N 76 LYS cc_start: 0.7542 (mptt) cc_final: 0.7310 (mptm) REVERT: E 48 MET cc_start: 0.0467 (ttp) cc_final: -0.0821 (mtt) REVERT: E 49 GLU cc_start: 0.5309 (OUTLIER) cc_final: 0.4264 (tp30) REVERT: E 111 VAL cc_start: 0.7645 (t) cc_final: 0.7438 (p) REVERT: E 139 TRP cc_start: 0.7725 (t60) cc_final: 0.7421 (t60) REVERT: R 49 MET cc_start: 0.6187 (tpp) cc_final: 0.5332 (mtp) REVERT: R 120 LYS cc_start: 0.6607 (mttt) cc_final: 0.6407 (mmmt) REVERT: R 144 ASN cc_start: 0.7385 (m-40) cc_final: 0.7164 (m-40) REVERT: R 227 GLN cc_start: 0.7838 (mt0) cc_final: 0.7383 (mm110) REVERT: R 288 ASN cc_start: 0.7617 (m-40) cc_final: 0.7220 (m-40) outliers start: 17 outliers final: 7 residues processed: 133 average time/residue: 1.4883 time to fit residues: 211.0060 Evaluate side-chains 130 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain E residue 49 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 59 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 24 optimal weight: 0.0980 chunk 97 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 92 optimal weight: 0.0470 chunk 58 optimal weight: 0.0980 chunk 89 optimal weight: 20.0000 chunk 69 optimal weight: 0.8980 overall best weight: 0.3878 ------------------------------------------------------------------------------- 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 = 0.181282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.127054 restraints weight = 12921.675| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.87 r_work: 0.3458 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10606 Z= 0.098 Angle : 0.513 9.425 14372 Z= 0.263 Chirality : 0.040 0.283 1583 Planarity : 0.004 0.071 1809 Dihedral : 6.161 59.811 1671 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.01 % Allowed : 22.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.24), residues: 1256 helix: 2.20 (0.23), residues: 522 sheet: 0.07 (0.34), residues: 237 loop : -0.40 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 76 HIS 0.003 0.001 HIS R 381 PHE 0.012 0.001 PHE B 151 TYR 0.012 0.001 TYR N 80 ARG 0.016 0.000 ARG B 134 Details of bonding type rmsd link_NAG-ASN : bond 0.00264 ( 3) link_NAG-ASN : angle 2.51049 ( 9) hydrogen bonds : bond 0.03072 ( 476) hydrogen bonds : angle 4.03940 ( 1359) SS BOND : bond 0.00112 ( 10) SS BOND : angle 1.22699 ( 20) covalent geometry : bond 0.00209 (10593) covalent geometry : angle 0.50798 (14343) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13435.22 seconds wall clock time: 234 minutes 37.51 seconds (14077.51 seconds total)