Starting phenix.real_space_refine on Tue Mar 3 21:38:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tyl_26184/03_2026/7tyl_26184.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyl_26184/03_2026/7tyl_26184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tyl_26184/03_2026/7tyl_26184.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyl_26184/03_2026/7tyl_26184.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tyl_26184/03_2026/7tyl_26184.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyl_26184/03_2026/7tyl_26184.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5691 2.51 5 N 1579 2.21 5 O 1645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8978 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1886 Classifications: {'peptide': 228} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 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: "P" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2815 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 16, 'TRANS': 352} Unresolved non-hydrogen bonds: 267 Unresolved non-hydrogen angles: 344 Unresolved non-hydrogen dihedrals: 236 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'TYR:plan': 7, 'ARG:plan': 4, 'ASP:plan': 8, 'GLN:plan1': 5, 'GLU:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 3, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 177 Time building chain proxies: 2.00, per 1000 atoms: 0.22 Number of scatterers: 8978 At special positions: 0 Unit cell: (80.464, 100.152, 151.512, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1645 8.00 N 1579 7.00 C 5691 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, 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 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=2.04 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=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 263.9 milliseconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2174 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 15 sheets defined 40.9% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 12 through 38 removed outlier: 3.603A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 58 removed outlier: 4.283A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.572A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.864A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.531A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.558A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.746A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.551A pdb=" N CYS G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 removed outlier: 4.096A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'P' and resid 4 through 7 Processing helix chain 'P' and resid 8 through 19 removed outlier: 3.586A pdb=" N PHE P 15 " --> pdb=" O ARG P 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 61 removed outlier: 3.674A pdb=" N MET R 49 " --> pdb=" O ARG R 45 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP R 50 " --> pdb=" O LYS R 46 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP R 57 " --> pdb=" O TYR R 53 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN R 61 " --> pdb=" O ASP R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 136 Processing helix chain 'R' and resid 137 through 156 Processing helix chain 'R' and resid 157 through 159 No H-bonds generated for 'chain 'R' and resid 157 through 159' Processing helix chain 'R' and resid 160 through 173 removed outlier: 3.872A pdb=" N ILE R 165 " --> pdb=" O PHE R 161 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER R 166 " --> pdb=" O THR R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 204 Processing helix chain 'R' and resid 208 through 214 removed outlier: 4.385A pdb=" N VAL R 212 " --> pdb=" O ASN R 208 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG R 214 " --> pdb=" O GLU R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 249 removed outlier: 3.513A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET R 237 " --> pdb=" O ASN R 233 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU R 238 " --> pdb=" O TYR R 234 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU R 247 " --> pdb=" O TYR R 243 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE R 248 " --> pdb=" O LEU R 244 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 267 Processing helix chain 'R' and resid 270 through 281 removed outlier: 3.590A pdb=" N THR R 274 " --> pdb=" O PRO R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 287 through 291 removed outlier: 3.837A pdb=" N TRP R 290 " --> pdb=" O ASP R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 330 Proline residue: R 304 - end of helix removed outlier: 3.670A 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 Processing helix chain 'R' and resid 383 through 392 Processing helix chain 'R' and resid 395 through 408 removed outlier: 3.619A pdb=" N GLN R 408 " --> pdb=" O ARG R 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 213 removed outlier: 3.650A pdb=" N MET A 221 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN A 292 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.580A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.352A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.509A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR B 124 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN B 125 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 4.289A 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: 3.588A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.658A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.385A 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: 5.903A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 277 Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 8 removed outlier: 3.567A pdb=" N SER N 7 " --> pdb=" O SER N 21 " (cutoff:3.500A) removed outlier: 3.932A 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 Processing sheet with id=AB2, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.870A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN N 35 " --> pdb=" O ALA N 97 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL N 93 " --> pdb=" O GLN N 39 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N TYR N 94 " --> pdb=" O GLY N 121 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLY N 121 " --> pdb=" O TYR N 94 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N CYS N 96 " --> pdb=" O GLY N 119 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 71 through 72 Processing sheet with id=AB4, first strand: chain 'R' and resid 75 through 76 removed outlier: 3.517A pdb=" N THR R 75 " --> pdb=" O TRP R 82 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP R 82 " --> pdb=" O THR R 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'R' and resid 92 through 94 Processing sheet with id=AB6, first strand: chain 'R' and resid 112 through 113 removed outlier: 3.535A pdb=" N VAL R 117 " --> pdb=" O ASP R 113 " (cutoff:3.500A) 407 hydrogen bonds defined for protein. 1158 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: 1.34 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1463 1.32 - 1.44: 2560 1.44 - 1.57: 5064 1.57 - 1.69: 0 1.69 - 1.82: 88 Bond restraints: 9175 Sorted by residual: bond pdb=" N ASP R 215 " pdb=" CA ASP R 215 " ideal model delta sigma weight residual 1.458 1.492 -0.034 7.40e-03 1.83e+04 2.11e+01 bond pdb=" N THR A 285 " pdb=" CA THR A 285 " ideal model delta sigma weight residual 1.455 1.507 -0.052 1.21e-02 6.83e+03 1.82e+01 bond pdb=" C VAL A 287 " pdb=" O VAL A 287 " ideal model delta sigma weight residual 1.236 1.194 0.042 1.04e-02 9.25e+03 1.62e+01 bond pdb=" CA SER A 286 " pdb=" CB SER A 286 " ideal model delta sigma weight residual 1.529 1.463 0.066 1.65e-02 3.67e+03 1.58e+01 bond pdb=" N LYS A 271 " pdb=" CA LYS A 271 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.28e-02 6.10e+03 1.08e+01 ... (remaining 9170 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 12104 1.53 - 3.06: 263 3.06 - 4.59: 65 4.59 - 6.12: 15 6.12 - 7.65: 2 Bond angle restraints: 12449 Sorted by residual: angle pdb=" N LEU R 222 " pdb=" CA LEU R 222 " pdb=" C LEU R 222 " ideal model delta sigma weight residual 112.54 105.16 7.38 1.22e+00 6.72e-01 3.66e+01 angle pdb=" N ARG A 283 " pdb=" CA ARG A 283 " pdb=" C ARG A 283 " ideal model delta sigma weight residual 110.53 102.88 7.65 1.29e+00 6.01e-01 3.52e+01 angle pdb=" CA ARG A 283 " pdb=" C ARG A 283 " pdb=" O ARG A 283 " ideal model delta sigma weight residual 121.94 117.25 4.69 1.15e+00 7.56e-01 1.66e+01 angle pdb=" CA ASP R 215 " pdb=" C ASP R 215 " pdb=" N PRO R 216 " ideal model delta sigma weight residual 118.09 121.28 -3.19 8.20e-01 1.49e+00 1.51e+01 angle pdb=" CA SER A 286 " pdb=" C SER A 286 " pdb=" O SER A 286 " ideal model delta sigma weight residual 121.89 117.44 4.45 1.17e+00 7.31e-01 1.45e+01 ... (remaining 12444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 5021 17.73 - 35.47: 352 35.47 - 53.20: 62 53.20 - 70.94: 14 70.94 - 88.67: 7 Dihedral angle restraints: 5456 sinusoidal: 2093 harmonic: 3363 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 -167.34 81.34 1 1.00e+01 1.00e-02 8.15e+01 dihedral pdb=" CB CYS P 2 " pdb=" SG CYS P 2 " pdb=" SG CYS P 7 " pdb=" CB CYS P 7 " ideal model delta sinusoidal sigma weight residual 93.00 136.87 -43.87 1 1.00e+01 1.00e-02 2.68e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 131.46 -38.46 1 1.00e+01 1.00e-02 2.08e+01 ... (remaining 5453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1282 0.073 - 0.145: 100 0.145 - 0.218: 8 0.218 - 0.290: 2 0.290 - 0.363: 1 Chirality restraints: 1393 Sorted by residual: chirality pdb=" CA ARG A 283 " pdb=" N ARG A 283 " pdb=" C ARG A 283 " pdb=" CB ARG A 283 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CA ARG R 214 " pdb=" N ARG R 214 " pdb=" C ARG R 214 " pdb=" CB ARG R 214 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB ILE R 221 " pdb=" CA ILE R 221 " pdb=" CG1 ILE R 221 " pdb=" CG2 ILE R 221 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1390 not shown) Planarity restraints: 1600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG R 213 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.96e+00 pdb=" C ARG R 213 " 0.042 2.00e-02 2.50e+03 pdb=" O ARG R 213 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG R 214 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 279 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.88e+00 pdb=" C ASN A 279 " -0.034 2.00e-02 2.50e+03 pdb=" O ASN A 279 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS A 280 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 282 " 0.006 2.00e-02 2.50e+03 1.32e-02 1.73e+00 pdb=" C LEU A 282 " -0.023 2.00e-02 2.50e+03 pdb=" O LEU A 282 " 0.008 2.00e-02 2.50e+03 pdb=" N ARG A 283 " 0.008 2.00e-02 2.50e+03 ... (remaining 1597 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2204 2.79 - 3.32: 8280 3.32 - 3.84: 14613 3.84 - 4.37: 17216 4.37 - 4.90: 30160 Nonbonded interactions: 72473 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.260 3.040 nonbonded pdb=" O GLN A 236 " pdb=" ND2 ASN A 239 " model vdw 2.262 3.120 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.290 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.309 3.040 nonbonded pdb=" O SER G 8 " pdb=" OG SER G 8 " model vdw 2.316 3.040 ... (remaining 72468 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=0.00 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: 1.800 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.460 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6383 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 0.105 9183 Z= 0.240 Angle : 0.596 7.649 12463 Z= 0.390 Chirality : 0.043 0.363 1393 Planarity : 0.003 0.032 1600 Dihedral : 12.732 88.670 3261 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.75 % Favored : 98.07 % Rotamer: Outliers : 0.43 % Allowed : 2.34 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.22), residues: 1140 helix: -1.93 (0.18), residues: 411 sheet: -1.17 (0.31), residues: 258 loop : -1.49 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 13 TYR 0.012 0.001 TYR N 60 PHE 0.008 0.001 PHE N 108 TRP 0.010 0.001 TRP A 281 HIS 0.003 0.000 HIS R 121 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9175) covalent geometry : angle 0.59058 (12449) SS BOND : bond 0.00646 ( 7) SS BOND : angle 2.43367 ( 14) hydrogen bonds : bond 0.25346 ( 407) hydrogen bonds : angle 8.19093 ( 1158) Misc. bond : bond 0.10453 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 141 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6237 (mt-10) cc_final: 0.6017 (mt-10) outliers start: 4 outliers final: 1 residues processed: 145 average time/residue: 0.1030 time to fit residues: 20.3328 Evaluate side-chains 115 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 221 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 31 GLN A 59 GLN B 75 GLN B 156 GLN G 44 HIS P 22 ASN R 121 HIS R 184 HIS R 296 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.243300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.203046 restraints weight = 10315.549| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 1.93 r_work: 0.3959 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9183 Z= 0.156 Angle : 0.557 7.944 12463 Z= 0.295 Chirality : 0.042 0.155 1393 Planarity : 0.004 0.039 1600 Dihedral : 3.664 27.774 1256 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.49 % Allowed : 9.25 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.24), residues: 1140 helix: 0.44 (0.24), residues: 421 sheet: -0.84 (0.31), residues: 243 loop : -1.37 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 105 TYR 0.013 0.001 TYR N 95 PHE 0.014 0.001 PHE R 359 TRP 0.011 0.001 TRP R 236 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 9175) covalent geometry : angle 0.55403 (12449) SS BOND : bond 0.00506 ( 7) SS BOND : angle 1.66453 ( 14) hydrogen bonds : bond 0.04699 ( 407) hydrogen bonds : angle 5.08864 ( 1158) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.315 Fit side-chains REVERT: B 16 ASN cc_start: 0.7144 (m110) cc_final: 0.6912 (m110) REVERT: R 55 CYS cc_start: 0.1011 (OUTLIER) cc_final: 0.0173 (p) REVERT: R 336 HIS cc_start: 0.7343 (t-90) cc_final: 0.7005 (t-90) outliers start: 14 outliers final: 8 residues processed: 136 average time/residue: 0.0918 time to fit residues: 17.2155 Evaluate side-chains 123 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 55 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 96 optimal weight: 0.1980 chunk 72 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 80 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN P 22 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.239351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.198469 restraints weight = 10370.815| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 1.89 r_work: 0.3932 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9183 Z= 0.149 Angle : 0.526 7.654 12463 Z= 0.277 Chirality : 0.041 0.155 1393 Planarity : 0.004 0.039 1600 Dihedral : 3.760 17.869 1254 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.44 % Allowed : 11.16 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.24), residues: 1140 helix: 1.10 (0.26), residues: 420 sheet: -0.90 (0.31), residues: 242 loop : -1.34 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 105 TYR 0.013 0.001 TYR A 339 PHE 0.015 0.001 PHE B 151 TRP 0.015 0.001 TRP R 236 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9175) covalent geometry : angle 0.52616 (12449) SS BOND : bond 0.00314 ( 7) SS BOND : angle 0.71460 ( 14) hydrogen bonds : bond 0.03917 ( 407) hydrogen bonds : angle 4.71041 ( 1158) Misc. bond : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.351 Fit side-chains REVERT: A 216 LYS cc_start: 0.6683 (mptt) cc_final: 0.5854 (pttt) REVERT: G 37 LEU cc_start: 0.6724 (OUTLIER) cc_final: 0.6321 (mp) REVERT: R 204 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7525 (mm-30) REVERT: R 337 MET cc_start: 0.7985 (ttm) cc_final: 0.7621 (ttp) outliers start: 23 outliers final: 15 residues processed: 134 average time/residue: 0.0887 time to fit residues: 16.7302 Evaluate side-chains 128 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 293 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 41 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 14 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN P 22 ASN R 186 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.239564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.197907 restraints weight = 10446.676| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 1.99 r_work: 0.3957 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9183 Z= 0.122 Angle : 0.506 9.399 12463 Z= 0.264 Chirality : 0.040 0.150 1393 Planarity : 0.004 0.037 1600 Dihedral : 3.673 18.068 1254 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.23 % Allowed : 12.65 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.25), residues: 1140 helix: 1.51 (0.26), residues: 415 sheet: -0.84 (0.32), residues: 232 loop : -1.15 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 105 TYR 0.013 0.001 TYR N 95 PHE 0.011 0.001 PHE B 151 TRP 0.013 0.001 TRP R 236 HIS 0.004 0.001 HIS R 277 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9175) covalent geometry : angle 0.50422 (12449) SS BOND : bond 0.00269 ( 7) SS BOND : angle 1.21411 ( 14) hydrogen bonds : bond 0.03406 ( 407) hydrogen bonds : angle 4.46710 ( 1158) Misc. bond : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.332 Fit side-chains REVERT: A 216 LYS cc_start: 0.6646 (mptt) cc_final: 0.5878 (pttt) REVERT: G 37 LEU cc_start: 0.6599 (OUTLIER) cc_final: 0.6205 (mp) REVERT: R 55 CYS cc_start: 0.1345 (OUTLIER) cc_final: 0.0800 (p) REVERT: R 143 LYS cc_start: 0.8160 (tptt) cc_final: 0.7583 (tppt) REVERT: R 204 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7488 (mm-30) REVERT: R 284 TYR cc_start: 0.6298 (m-80) cc_final: 0.5992 (m-80) REVERT: R 337 MET cc_start: 0.7916 (ttm) cc_final: 0.7613 (ttp) outliers start: 21 outliers final: 15 residues processed: 134 average time/residue: 0.0950 time to fit residues: 17.5200 Evaluate side-chains 130 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 55 CYS Chi-restraints excluded: chain R residue 159 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 61 optimal weight: 0.0010 chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 0.2980 chunk 31 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 62 optimal weight: 0.0870 chunk 13 optimal weight: 0.0970 chunk 65 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.2362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 22 ASN R 201 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.236514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.200394 restraints weight = 10145.593| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 1.76 r_work: 0.3973 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9183 Z= 0.090 Angle : 0.462 7.956 12463 Z= 0.243 Chirality : 0.039 0.135 1393 Planarity : 0.003 0.037 1600 Dihedral : 3.505 16.249 1254 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.02 % Allowed : 14.03 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.25), residues: 1140 helix: 1.79 (0.26), residues: 415 sheet: -0.69 (0.33), residues: 231 loop : -1.05 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 105 TYR 0.014 0.001 TYR N 95 PHE 0.008 0.001 PHE B 241 TRP 0.010 0.001 TRP A 234 HIS 0.004 0.001 HIS R 277 Details of bonding type rmsd covalent geometry : bond 0.00193 ( 9175) covalent geometry : angle 0.46162 (12449) SS BOND : bond 0.00200 ( 7) SS BOND : angle 0.88470 ( 14) hydrogen bonds : bond 0.02902 ( 407) hydrogen bonds : angle 4.25766 ( 1158) Misc. bond : bond 0.00000 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.207 Fit side-chains REVERT: A 216 LYS cc_start: 0.6644 (mptt) cc_final: 0.5879 (pttt) REVERT: R 143 LYS cc_start: 0.8126 (tptt) cc_final: 0.7602 (tppt) REVERT: R 204 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7518 (mm-30) REVERT: R 229 MET cc_start: 0.8242 (tpp) cc_final: 0.7937 (mmm) REVERT: R 294 GLU cc_start: 0.7808 (pm20) cc_final: 0.7514 (pm20) REVERT: R 337 MET cc_start: 0.8053 (ttm) cc_final: 0.7801 (ttp) outliers start: 19 outliers final: 13 residues processed: 127 average time/residue: 0.0922 time to fit residues: 16.3044 Evaluate side-chains 123 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain P residue 22 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 2 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 76 optimal weight: 20.0000 chunk 96 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 184 HIS ** R 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.232642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.190810 restraints weight = 10398.210| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 2.30 r_work: 0.3861 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9183 Z= 0.233 Angle : 0.622 8.546 12463 Z= 0.321 Chirality : 0.045 0.198 1393 Planarity : 0.004 0.038 1600 Dihedral : 4.064 21.023 1254 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.13 % Allowed : 14.98 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.25), residues: 1140 helix: 1.41 (0.26), residues: 423 sheet: -0.97 (0.33), residues: 228 loop : -1.18 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 105 TYR 0.017 0.002 TYR A 339 PHE 0.027 0.002 PHE B 151 TRP 0.016 0.002 TRP R 236 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00558 ( 9175) covalent geometry : angle 0.62174 (12449) SS BOND : bond 0.00253 ( 7) SS BOND : angle 1.08282 ( 14) hydrogen bonds : bond 0.04034 ( 407) hydrogen bonds : angle 4.49802 ( 1158) Misc. bond : bond 0.00027 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.320 Fit side-chains REVERT: G 37 LEU cc_start: 0.6562 (OUTLIER) cc_final: 0.6194 (mp) REVERT: R 143 LYS cc_start: 0.8222 (tptt) cc_final: 0.7610 (tppt) REVERT: R 204 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7502 (mm-30) REVERT: R 284 TYR cc_start: 0.6574 (m-80) cc_final: 0.6247 (m-80) REVERT: R 294 GLU cc_start: 0.8003 (pm20) cc_final: 0.7523 (pm20) REVERT: R 336 HIS cc_start: 0.7563 (t-90) cc_final: 0.7244 (t-90) REVERT: R 337 MET cc_start: 0.7991 (ttm) cc_final: 0.7736 (ttp) outliers start: 20 outliers final: 17 residues processed: 125 average time/residue: 0.1044 time to fit residues: 17.8046 Evaluate side-chains 128 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 159 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 61 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 9 optimal weight: 0.0870 chunk 4 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.243108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.202152 restraints weight = 10380.438| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 1.93 r_work: 0.3976 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9183 Z= 0.114 Angle : 0.511 12.682 12463 Z= 0.264 Chirality : 0.041 0.178 1393 Planarity : 0.003 0.039 1600 Dihedral : 3.776 20.096 1254 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.91 % Allowed : 15.41 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.26), residues: 1140 helix: 1.68 (0.26), residues: 423 sheet: -0.95 (0.33), residues: 234 loop : -1.03 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 105 TYR 0.014 0.001 TYR N 95 PHE 0.009 0.001 PHE N 108 TRP 0.013 0.001 TRP R 236 HIS 0.004 0.001 HIS R 277 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 9175) covalent geometry : angle 0.51102 (12449) SS BOND : bond 0.00154 ( 7) SS BOND : angle 0.78051 ( 14) hydrogen bonds : bond 0.03156 ( 407) hydrogen bonds : angle 4.28846 ( 1158) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.220 Fit side-chains REVERT: G 37 LEU cc_start: 0.6581 (OUTLIER) cc_final: 0.6231 (mp) REVERT: N 65 LYS cc_start: 0.7797 (tppt) cc_final: 0.7512 (mmtm) REVERT: P 18 ARG cc_start: 0.8124 (ttm170) cc_final: 0.7871 (ttp-170) REVERT: R 143 LYS cc_start: 0.8203 (tptt) cc_final: 0.7620 (tppt) REVERT: R 204 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7512 (mm-30) REVERT: R 284 TYR cc_start: 0.6587 (m-80) cc_final: 0.6329 (m-80) REVERT: R 294 GLU cc_start: 0.7882 (pm20) cc_final: 0.7602 (pm20) REVERT: R 336 HIS cc_start: 0.7568 (t-90) cc_final: 0.7272 (t-90) outliers start: 18 outliers final: 13 residues processed: 125 average time/residue: 0.0971 time to fit residues: 16.8619 Evaluate side-chains 126 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain R residue 325 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 85 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 61 optimal weight: 0.0070 chunk 100 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 28 optimal weight: 0.1980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 22 ASN R 257 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.244814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.208046 restraints weight = 10378.726| |-----------------------------------------------------------------------------| r_work (start): 0.4222 rms_B_bonded: 2.00 r_work: 0.3961 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9183 Z= 0.104 Angle : 0.504 9.934 12463 Z= 0.258 Chirality : 0.040 0.161 1393 Planarity : 0.003 0.038 1600 Dihedral : 3.637 19.017 1254 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.34 % Allowed : 15.83 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.26), residues: 1140 helix: 1.94 (0.26), residues: 416 sheet: -0.86 (0.33), residues: 234 loop : -0.92 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 105 TYR 0.014 0.001 TYR N 95 PHE 0.010 0.001 PHE N 108 TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS R 277 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9175) covalent geometry : angle 0.50398 (12449) SS BOND : bond 0.00152 ( 7) SS BOND : angle 0.70164 ( 14) hydrogen bonds : bond 0.02954 ( 407) hydrogen bonds : angle 4.16131 ( 1158) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.6683 (mptt) cc_final: 0.5939 (pttt) REVERT: G 37 LEU cc_start: 0.6543 (OUTLIER) cc_final: 0.6232 (mp) REVERT: R 143 LYS cc_start: 0.8186 (tptt) cc_final: 0.7607 (tppt) REVERT: R 204 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7586 (mm-30) REVERT: R 284 TYR cc_start: 0.6515 (m-80) cc_final: 0.6293 (m-80) REVERT: R 294 GLU cc_start: 0.7882 (pm20) cc_final: 0.7593 (pm20) REVERT: R 336 HIS cc_start: 0.7506 (t-90) cc_final: 0.7206 (t-90) outliers start: 22 outliers final: 16 residues processed: 130 average time/residue: 0.0928 time to fit residues: 16.8844 Evaluate side-chains 132 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain R residue 159 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 6 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 9 optimal weight: 0.1980 chunk 61 optimal weight: 0.0770 chunk 40 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.245079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.207902 restraints weight = 10384.377| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 2.08 r_work: 0.3991 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9183 Z= 0.106 Angle : 0.507 8.661 12463 Z= 0.260 Chirality : 0.040 0.159 1393 Planarity : 0.003 0.038 1600 Dihedral : 3.596 16.925 1254 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.34 % Allowed : 16.58 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.26), residues: 1140 helix: 1.99 (0.26), residues: 416 sheet: -0.82 (0.33), residues: 233 loop : -0.88 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 105 TYR 0.014 0.001 TYR N 95 PHE 0.013 0.001 PHE N 108 TRP 0.011 0.001 TRP R 236 HIS 0.004 0.001 HIS R 277 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 9175) covalent geometry : angle 0.50646 (12449) SS BOND : bond 0.00161 ( 7) SS BOND : angle 0.68349 ( 14) hydrogen bonds : bond 0.02915 ( 407) hydrogen bonds : angle 4.10015 ( 1158) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.350 Fit side-chains REVERT: A 216 LYS cc_start: 0.6674 (mptt) cc_final: 0.5916 (pttt) REVERT: B 45 MET cc_start: 0.1993 (tpt) cc_final: 0.1739 (mmt) REVERT: G 37 LEU cc_start: 0.6516 (OUTLIER) cc_final: 0.6196 (mp) REVERT: N 65 LYS cc_start: 0.7756 (tppt) cc_final: 0.7425 (mmtm) REVERT: R 143 LYS cc_start: 0.8178 (tptt) cc_final: 0.7583 (tppt) REVERT: R 204 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7602 (mm-30) REVERT: R 284 TYR cc_start: 0.6522 (m-80) cc_final: 0.6318 (m-80) REVERT: R 294 GLU cc_start: 0.7878 (pm20) cc_final: 0.7673 (pm20) REVERT: R 336 HIS cc_start: 0.7513 (t-90) cc_final: 0.7198 (t-90) outliers start: 22 outliers final: 16 residues processed: 129 average time/residue: 0.0929 time to fit residues: 16.6959 Evaluate side-chains 133 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain R residue 325 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 95 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 109 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 257 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.240147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.198388 restraints weight = 10345.591| |-----------------------------------------------------------------------------| r_work (start): 0.4188 rms_B_bonded: 1.96 r_work: 0.3913 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9183 Z= 0.170 Angle : 0.566 8.524 12463 Z= 0.293 Chirality : 0.042 0.157 1393 Planarity : 0.004 0.037 1600 Dihedral : 3.858 18.487 1254 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.23 % Allowed : 16.47 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.26), residues: 1140 helix: 1.69 (0.26), residues: 424 sheet: -0.98 (0.33), residues: 237 loop : -0.97 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 105 TYR 0.014 0.002 TYR N 95 PHE 0.020 0.002 PHE N 108 TRP 0.014 0.001 TRP R 236 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 9175) covalent geometry : angle 0.56601 (12449) SS BOND : bond 0.00180 ( 7) SS BOND : angle 0.80079 ( 14) hydrogen bonds : bond 0.03487 ( 407) hydrogen bonds : angle 4.25260 ( 1158) Misc. bond : bond 0.00018 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.292 Fit side-chains REVERT: B 4 LEU cc_start: 0.6413 (OUTLIER) cc_final: 0.6208 (tp) REVERT: B 45 MET cc_start: 0.2736 (tpt) cc_final: 0.2441 (mmt) REVERT: B 192 LEU cc_start: 0.6735 (OUTLIER) cc_final: 0.6267 (pt) REVERT: G 27 ARG cc_start: 0.7496 (ptp90) cc_final: 0.7066 (mtt-85) REVERT: G 37 LEU cc_start: 0.6518 (OUTLIER) cc_final: 0.6207 (mp) REVERT: N 31 ASN cc_start: 0.7350 (m-40) cc_final: 0.7122 (m-40) REVERT: N 65 LYS cc_start: 0.7854 (tppt) cc_final: 0.7631 (tppt) REVERT: P 18 ARG cc_start: 0.8161 (ttm170) cc_final: 0.7918 (ttp-170) REVERT: R 143 LYS cc_start: 0.8258 (tptt) cc_final: 0.7651 (tppt) REVERT: R 204 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7456 (mt-10) REVERT: R 284 TYR cc_start: 0.6587 (m-80) cc_final: 0.6386 (m-80) REVERT: R 294 GLU cc_start: 0.8034 (pm20) cc_final: 0.7658 (pm20) REVERT: R 336 HIS cc_start: 0.7536 (t-90) cc_final: 0.7184 (t-90) REVERT: R 405 GLN cc_start: 0.7449 (tt0) cc_final: 0.7237 (tm-30) outliers start: 21 outliers final: 17 residues processed: 126 average time/residue: 0.1016 time to fit residues: 17.2464 Evaluate side-chains 129 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain R residue 325 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 61 optimal weight: 0.9990 chunk 82 optimal weight: 40.0000 chunk 16 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 0.0060 chunk 1 optimal weight: 0.7980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.242828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.202764 restraints weight = 10225.889| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 2.18 r_work: 0.3953 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9183 Z= 0.118 Angle : 0.518 8.955 12463 Z= 0.267 Chirality : 0.041 0.162 1393 Planarity : 0.004 0.073 1600 Dihedral : 3.731 19.093 1254 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.91 % Allowed : 16.90 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.26), residues: 1140 helix: 1.78 (0.26), residues: 424 sheet: -0.89 (0.33), residues: 235 loop : -0.92 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 105 TYR 0.014 0.001 TYR N 95 PHE 0.016 0.001 PHE N 108 TRP 0.012 0.001 TRP R 236 HIS 0.004 0.001 HIS R 277 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9175) covalent geometry : angle 0.51800 (12449) SS BOND : bond 0.00161 ( 7) SS BOND : angle 0.68750 ( 14) hydrogen bonds : bond 0.03079 ( 407) hydrogen bonds : angle 4.17147 ( 1158) Misc. bond : bond 0.00009 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2074.21 seconds wall clock time: 36 minutes 17.61 seconds (2177.61 seconds total)