Starting phenix.real_space_refine on Sat Jun 7 16:07:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tyl_26184/06_2025/7tyl_26184.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyl_26184/06_2025/7tyl_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7tyl_26184/06_2025/7tyl_26184.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyl_26184/06_2025/7tyl_26184.map" model { file = "/net/cci-nas-00/data/ceres_data/7tyl_26184/06_2025/7tyl_26184.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyl_26184/06_2025/7tyl_26184.cif" } resolution = 3.3 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= -0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 5, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 3, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 177 Time building chain proxies: 5.62, per 1000 atoms: 0.63 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: 2.26 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.93 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: 2.45 Time building geometry restraints manager: 2.67 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: 2.120 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.850 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.570 ------------------------------------------------------------------------------- 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 (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: -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 TRP 0.010 0.001 TRP A 281 HIS 0.003 0.000 HIS R 121 PHE 0.008 0.001 PHE N 108 TYR 0.012 0.001 TYR N 60 ARG 0.004 0.000 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.25346 ( 407) hydrogen bonds : angle 8.19093 ( 1158) SS BOND : bond 0.00646 ( 7) SS BOND : angle 2.43367 ( 14) covalent geometry : bond 0.00303 ( 9175) covalent geometry : angle 0.59058 (12449) 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 : 1.014 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: 0.2252 time to fit residues: 44.7352 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 : 0.897 ------------------------------------------------------------------------------- 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 93 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4598 r_free = 0.4598 target = 0.244319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.205052 restraints weight = 10212.508| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 1.82 r_work: 0.4013 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9183 Z= 0.149 Angle : 0.545 8.135 12463 Z= 0.287 Chirality : 0.042 0.151 1393 Planarity : 0.004 0.038 1600 Dihedral : 3.665 26.577 1256 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.38 % Allowed : 9.25 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.86 (0.24), residues: 1140 helix: 0.51 (0.25), residues: 421 sheet: -0.81 (0.31), residues: 243 loop : -1.35 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 236 HIS 0.005 0.001 HIS A 357 PHE 0.014 0.001 PHE R 359 TYR 0.013 0.001 TYR N 95 ARG 0.005 0.000 ARG N 67 Details of bonding type rmsd hydrogen bonds : bond 0.04259 ( 407) hydrogen bonds : angle 5.00223 ( 1158) SS BOND : bond 0.00257 ( 7) SS BOND : angle 1.75561 ( 14) covalent geometry : bond 0.00313 ( 9175) covalent geometry : angle 0.54167 (12449) Misc. bond : bond 0.00082 ( 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: 13 poor density : 129 time to evaluate : 1.067 Fit side-chains REVERT: B 16 ASN cc_start: 0.7220 (m110) cc_final: 0.6938 (m110) REVERT: R 55 CYS cc_start: 0.1106 (OUTLIER) cc_final: 0.0244 (p) REVERT: R 336 HIS cc_start: 0.7312 (t-90) cc_final: 0.7090 (t-90) outliers start: 13 outliers final: 7 residues processed: 137 average time/residue: 0.2380 time to fit residues: 44.7164 Evaluate side-chains 124 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 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 4 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 79 optimal weight: 40.0000 chunk 37 optimal weight: 0.1980 chunk 94 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 16 ASN P 22 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.242626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.204587 restraints weight = 10381.894| |-----------------------------------------------------------------------------| r_work (start): 0.4225 rms_B_bonded: 2.26 r_work: 0.3973 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9183 Z= 0.120 Angle : 0.496 8.111 12463 Z= 0.262 Chirality : 0.040 0.152 1393 Planarity : 0.004 0.037 1600 Dihedral : 3.575 15.948 1254 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.23 % Allowed : 11.80 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.40 (0.25), residues: 1140 helix: 1.21 (0.26), residues: 420 sheet: -0.74 (0.32), residues: 233 loop : -1.31 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 236 HIS 0.005 0.001 HIS R 277 PHE 0.011 0.001 PHE N 108 TYR 0.011 0.001 TYR N 95 ARG 0.006 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03669 ( 407) hydrogen bonds : angle 4.62425 ( 1158) SS BOND : bond 0.00320 ( 7) SS BOND : angle 0.57502 ( 14) covalent geometry : bond 0.00268 ( 9175) covalent geometry : angle 0.49633 (12449) Misc. bond : bond 0.00022 ( 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 138 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 1.032 Fit side-chains REVERT: A 216 LYS cc_start: 0.6764 (mptt) cc_final: 0.5938 (pttt) REVERT: G 21 MET cc_start: 0.7716 (tmm) cc_final: 0.7270 (tmm) REVERT: R 143 LYS cc_start: 0.8103 (tptt) cc_final: 0.7571 (tppt) REVERT: R 204 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7452 (mm-30) outliers start: 21 outliers final: 14 residues processed: 133 average time/residue: 0.2223 time to fit residues: 41.1772 Evaluate side-chains 127 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 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 293 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 68 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 47 optimal weight: 0.3980 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 11 optimal weight: 0.2980 chunk 37 optimal weight: 0.0570 chunk 62 optimal weight: 2.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- 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 = 0.4597 r_free = 0.4597 target = 0.243866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.206993 restraints weight = 10354.418| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 2.00 r_work: 0.4004 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9183 Z= 0.096 Angle : 0.471 8.673 12463 Z= 0.247 Chirality : 0.039 0.144 1393 Planarity : 0.003 0.035 1600 Dihedral : 3.482 16.182 1254 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.91 % Allowed : 12.65 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.05 (0.25), residues: 1140 helix: 1.56 (0.26), residues: 420 sheet: -0.57 (0.33), residues: 232 loop : -1.17 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 236 HIS 0.004 0.001 HIS R 277 PHE 0.008 0.001 PHE R 359 TYR 0.014 0.001 TYR N 95 ARG 0.007 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03054 ( 407) hydrogen bonds : angle 4.34669 ( 1158) SS BOND : bond 0.00199 ( 7) SS BOND : angle 0.50596 ( 14) covalent geometry : bond 0.00210 ( 9175) covalent geometry : angle 0.47048 (12449) Misc. bond : bond 0.00010 ( 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 138 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.933 Fit side-chains REVERT: A 216 LYS cc_start: 0.6742 (mptt) cc_final: 0.5936 (pttt) REVERT: A 392 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7398 (mm-30) REVERT: R 143 LYS cc_start: 0.8046 (tptt) cc_final: 0.7525 (tppt) REVERT: R 204 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7432 (mm-30) outliers start: 18 outliers final: 11 residues processed: 132 average time/residue: 0.2162 time to fit residues: 39.6781 Evaluate side-chains 127 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 N residue 12 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 2 optimal weight: 3.9990 chunk 14 optimal weight: 0.0470 chunk 32 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 28 optimal weight: 0.1980 chunk 35 optimal weight: 6.9990 chunk 43 optimal weight: 0.2980 chunk 97 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** R 186 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.241480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.200394 restraints weight = 10382.924| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 2.03 r_work: 0.3979 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9183 Z= 0.114 Angle : 0.492 7.263 12463 Z= 0.259 Chirality : 0.040 0.142 1393 Planarity : 0.003 0.035 1600 Dihedral : 3.564 16.347 1254 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.91 % Allowed : 14.35 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.10 (0.25), residues: 1140 helix: 1.57 (0.26), residues: 423 sheet: -0.83 (0.31), residues: 251 loop : -1.11 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 236 HIS 0.004 0.001 HIS A 357 PHE 0.011 0.001 PHE N 108 TYR 0.013 0.001 TYR N 95 ARG 0.008 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03254 ( 407) hydrogen bonds : angle 4.28199 ( 1158) SS BOND : bond 0.00190 ( 7) SS BOND : angle 1.73685 ( 14) covalent geometry : bond 0.00258 ( 9175) covalent geometry : angle 0.48913 (12449) Misc. bond : bond 0.00007 ( 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 140 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.971 Fit side-chains REVERT: A 216 LYS cc_start: 0.6640 (mptt) cc_final: 0.5864 (pttt) REVERT: A 392 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7421 (mm-30) REVERT: G 37 LEU cc_start: 0.6874 (OUTLIER) cc_final: 0.6377 (mp) REVERT: R 143 LYS cc_start: 0.8196 (tptt) cc_final: 0.7658 (tppt) REVERT: R 204 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7473 (mm-30) REVERT: R 336 HIS cc_start: 0.7367 (t-90) cc_final: 0.7097 (t-90) outliers start: 18 outliers final: 14 residues processed: 134 average time/residue: 0.2387 time to fit residues: 44.4220 Evaluate side-chains 132 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 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 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 293 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.5980 chunk 41 optimal weight: 0.4980 chunk 83 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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 201 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.235026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.193515 restraints weight = 10325.367| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 1.88 r_work: 0.3899 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2675 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= 0.176 Angle : 0.584 13.115 12463 Z= 0.300 Chirality : 0.043 0.212 1393 Planarity : 0.004 0.050 1600 Dihedral : 3.949 20.263 1254 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.55 % Allowed : 14.45 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.23 (0.25), residues: 1140 helix: 1.45 (0.26), residues: 423 sheet: -1.06 (0.31), residues: 250 loop : -1.07 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 236 HIS 0.007 0.001 HIS A 357 PHE 0.021 0.002 PHE B 151 TYR 0.015 0.002 TYR R 391 ARG 0.009 0.001 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03721 ( 407) hydrogen bonds : angle 4.42883 ( 1158) SS BOND : bond 0.00277 ( 7) SS BOND : angle 1.10634 ( 14) covalent geometry : bond 0.00416 ( 9175) covalent geometry : angle 0.58267 (12449) Misc. bond : bond 0.00017 ( 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 142 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.997 Fit side-chains REVERT: B 192 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6334 (pt) REVERT: G 37 LEU cc_start: 0.6862 (OUTLIER) cc_final: 0.6457 (mp) REVERT: R 143 LYS cc_start: 0.8211 (tptt) cc_final: 0.7634 (tppt) REVERT: R 204 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7499 (mm-30) REVERT: R 284 TYR cc_start: 0.6561 (m-80) cc_final: 0.6248 (m-80) REVERT: R 336 HIS cc_start: 0.7432 (t-90) cc_final: 0.7164 (t-90) outliers start: 24 outliers final: 18 residues processed: 132 average time/residue: 0.2219 time to fit residues: 40.4172 Evaluate side-chains 135 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 100 VAL 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 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 79 LEU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 295 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 81 optimal weight: 20.0000 chunk 57 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 14 ASN ** P 22 ASN ** 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 = 0.4579 r_free = 0.4579 target = 0.241212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.199215 restraints weight = 10299.764| |-----------------------------------------------------------------------------| r_work (start): 0.4168 rms_B_bonded: 2.02 r_work: 0.3913 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2785 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= 0.152 Angle : 0.557 15.505 12463 Z= 0.285 Chirality : 0.042 0.173 1393 Planarity : 0.004 0.037 1600 Dihedral : 3.877 20.661 1254 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.13 % Allowed : 15.30 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.15 (0.26), residues: 1140 helix: 1.53 (0.26), residues: 423 sheet: -1.08 (0.32), residues: 250 loop : -1.00 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 236 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.001 PHE B 151 TYR 0.014 0.001 TYR N 95 ARG 0.008 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03404 ( 407) hydrogen bonds : angle 4.35968 ( 1158) SS BOND : bond 0.00219 ( 7) SS BOND : angle 0.85425 ( 14) covalent geometry : bond 0.00359 ( 9175) covalent geometry : angle 0.55662 (12449) Misc. bond : bond 0.00015 ( 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 136 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.911 Fit side-chains REVERT: B 335 PHE cc_start: 0.8210 (m-80) cc_final: 0.7855 (m-10) REVERT: G 37 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6451 (mp) REVERT: R 143 LYS cc_start: 0.8260 (tptt) cc_final: 0.7659 (tppt) REVERT: R 204 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7347 (mt-10) REVERT: R 284 TYR cc_start: 0.6582 (m-80) cc_final: 0.6318 (m-80) outliers start: 20 outliers final: 17 residues processed: 127 average time/residue: 0.2220 time to fit residues: 38.8683 Evaluate side-chains 133 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 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 4 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 13 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 37 optimal weight: 0.4980 chunk 88 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.240751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.199563 restraints weight = 10438.012| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 2.11 r_work: 0.3922 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9183 Z= 0.149 Angle : 0.558 15.394 12463 Z= 0.286 Chirality : 0.041 0.147 1393 Planarity : 0.004 0.038 1600 Dihedral : 3.884 19.308 1254 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % 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 (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: -0.13 (0.25), residues: 1140 helix: 1.55 (0.26), residues: 424 sheet: -1.08 (0.31), residues: 250 loop : -0.98 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 236 HIS 0.005 0.001 HIS A 357 PHE 0.016 0.001 PHE N 108 TYR 0.014 0.001 TYR N 95 ARG 0.010 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03388 ( 407) hydrogen bonds : angle 4.32503 ( 1158) SS BOND : bond 0.00204 ( 7) SS BOND : angle 0.79996 ( 14) covalent geometry : bond 0.00352 ( 9175) covalent geometry : angle 0.55800 (12449) Misc. bond : bond 0.00016 ( 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 141 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.922 Fit side-chains REVERT: B 335 PHE cc_start: 0.8213 (m-80) cc_final: 0.7854 (m-10) REVERT: G 37 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6530 (mp) REVERT: R 143 LYS cc_start: 0.8254 (tptt) cc_final: 0.7661 (tppt) REVERT: R 204 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7320 (mt-10) REVERT: R 336 HIS cc_start: 0.7468 (t-90) cc_final: 0.7250 (t-90) REVERT: R 405 GLN cc_start: 0.7398 (tt0) cc_final: 0.7190 (tt0) outliers start: 22 outliers final: 19 residues processed: 131 average time/residue: 0.2299 time to fit residues: 40.7595 Evaluate side-chains 136 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 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 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 R residue 159 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 101 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 91 optimal weight: 0.0030 chunk 66 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 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 = 0.4583 r_free = 0.4583 target = 0.241568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.201399 restraints weight = 10279.837| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 1.84 r_work: 0.3977 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2984 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= 0.137 Angle : 0.553 15.144 12463 Z= 0.282 Chirality : 0.041 0.161 1393 Planarity : 0.004 0.038 1600 Dihedral : 3.848 19.292 1254 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.44 % Allowed : 16.26 % 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 (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 (0.26), residues: 1140 helix: 1.59 (0.26), residues: 424 sheet: -1.07 (0.32), residues: 250 loop : -0.96 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 236 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.001 PHE N 108 TYR 0.013 0.001 TYR N 95 ARG 0.008 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03257 ( 407) hydrogen bonds : angle 4.27491 ( 1158) SS BOND : bond 0.00194 ( 7) SS BOND : angle 0.69598 ( 14) covalent geometry : bond 0.00321 ( 9175) covalent geometry : angle 0.55270 (12449) Misc. bond : bond 0.00012 ( 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 134 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.928 Fit side-chains REVERT: B 335 PHE cc_start: 0.8196 (m-80) cc_final: 0.7843 (m-10) REVERT: G 37 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6503 (mp) REVERT: R 143 LYS cc_start: 0.8232 (tptt) cc_final: 0.7635 (tppt) REVERT: R 204 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7290 (mt-10) REVERT: R 284 TYR cc_start: 0.6446 (m-80) cc_final: 0.6076 (m-80) REVERT: R 336 HIS cc_start: 0.7277 (t-90) cc_final: 0.7034 (t-90) REVERT: R 405 GLN cc_start: 0.7438 (tt0) cc_final: 0.7232 (tm-30) outliers start: 23 outliers final: 20 residues processed: 125 average time/residue: 0.2315 time to fit residues: 39.7399 Evaluate side-chains 129 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 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 4 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 31 ASN 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 R residue 325 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 6.9990 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 30 optimal weight: 0.3980 chunk 45 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.242217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.202550 restraints weight = 10288.885| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 2.15 r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9183 Z= 0.117 Angle : 0.537 15.060 12463 Z= 0.275 Chirality : 0.041 0.166 1393 Planarity : 0.004 0.062 1600 Dihedral : 3.791 18.981 1254 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.13 % Allowed : 16.47 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.26), residues: 1140 helix: 1.65 (0.26), residues: 424 sheet: -1.04 (0.32), residues: 250 loop : -0.95 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 236 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.001 PHE N 108 TYR 0.014 0.001 TYR N 95 ARG 0.008 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03109 ( 407) hydrogen bonds : angle 4.22072 ( 1158) SS BOND : bond 0.00181 ( 7) SS BOND : angle 0.67991 ( 14) covalent geometry : bond 0.00268 ( 9175) covalent geometry : angle 0.53665 (12449) Misc. bond : bond 0.00007 ( 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 130 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.939 Fit side-chains REVERT: B 335 PHE cc_start: 0.8144 (m-80) cc_final: 0.7820 (m-10) REVERT: G 27 ARG cc_start: 0.7445 (ptp90) cc_final: 0.7013 (mtt-85) REVERT: G 37 LEU cc_start: 0.6941 (OUTLIER) cc_final: 0.6610 (mp) REVERT: R 143 LYS cc_start: 0.8173 (tptt) cc_final: 0.7714 (tppt) REVERT: R 204 GLU cc_start: 0.7337 (mt-10) cc_final: 0.6931 (mt-10) REVERT: R 284 TYR cc_start: 0.5954 (m-80) cc_final: 0.5603 (m-80) outliers start: 20 outliers final: 17 residues processed: 120 average time/residue: 0.2370 time to fit residues: 38.7419 Evaluate side-chains 125 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 100 VAL 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 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 71 SER Chi-restraints excluded: chain N residue 79 LEU 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 75 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 77 optimal weight: 30.0000 chunk 96 optimal weight: 0.0040 chunk 43 optimal weight: 0.5980 chunk 65 optimal weight: 0.0980 chunk 11 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.4192 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.245420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.204779 restraints weight = 10292.937| |-----------------------------------------------------------------------------| r_work (start): 0.4251 rms_B_bonded: 1.86 r_work: 0.4013 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9183 Z= 0.102 Angle : 0.539 14.892 12463 Z= 0.274 Chirality : 0.040 0.166 1393 Planarity : 0.004 0.043 1600 Dihedral : 3.633 17.921 1254 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.81 % Allowed : 17.22 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.17 (0.26), residues: 1140 helix: 1.91 (0.26), residues: 417 sheet: -0.97 (0.32), residues: 249 loop : -0.86 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS R 277 PHE 0.011 0.001 PHE N 108 TYR 0.014 0.001 TYR N 95 ARG 0.009 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.02828 ( 407) hydrogen bonds : angle 4.08701 ( 1158) SS BOND : bond 0.00177 ( 7) SS BOND : angle 0.58952 ( 14) covalent geometry : bond 0.00234 ( 9175) covalent geometry : angle 0.53877 (12449) Misc. bond : bond 0.00003 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4412.60 seconds wall clock time: 76 minutes 47.58 seconds (4607.58 seconds total)