Starting phenix.real_space_refine on Thu Jul 2 16:15:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tyo_26190/07_2026/7tyo_26190.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyo_26190/07_2026/7tyo_26190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tyo_26190/07_2026/7tyo_26190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyo_26190/07_2026/7tyo_26190.map" model { file = "/net/cci-nas-00/data/ceres_data/7tyo_26190/07_2026/7tyo_26190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyo_26190/07_2026/7tyo_26190.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tyo_26190/07_2026/7tyo_26190.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tyo_26190/07_2026/7tyo_26190.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 64 5.16 5 C 5781 2.51 5 N 1561 2.21 5 O 1646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9052 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1889 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 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: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 238 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 2, 'TRANS': 29} 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: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2837 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 14, 'TRANS': 344} Chain breaks: 2 Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 7, 'TYR:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 3, 'PHE:plan': 2, 'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 97 Chain: "R" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'NAG': 1, 'Y01': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.68, per 1000 atoms: 0.19 Number of scatterers: 9052 At special positions: 0 Unit cell: (116.086, 100.547, 140.766, 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 64 16.00 O 1646 8.00 N 1561 7.00 C 5781 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 1 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " distance=2.04 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 Links applied NAG-ASN " NAG R 501 " - " ASN R 130 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 363.4 milliseconds 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 41.0% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 11 through 39 removed outlier: 3.774A pdb=" N GLU A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.911A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.526A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.710A pdb=" N VAL A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.522A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.507A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 3.969A 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 25 removed outlier: 4.068A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.526A pdb=" N ARG G 13 " --> pdb=" O ILE G 9 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.516A pdb=" N TYR G 40 " --> pdb=" O ASP G 36 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.623A 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 removed outlier: 3.607A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 18 removed outlier: 3.543A pdb=" N THR P 11 " --> pdb=" O CYS P 7 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS P 18 " --> pdb=" O GLN P 14 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 60 Processing helix chain 'R' and resid 140 through 173 Processing helix chain 'R' and resid 174 through 177 Processing helix chain 'R' and resid 178 through 205 removed outlier: 3.671A pdb=" N LEU R 183 " --> pdb=" O GLN R 179 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE R 199 " --> pdb=" O SER R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 215 Processing helix chain 'R' and resid 216 through 249 removed outlier: 3.872A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET R 237 " --> pdb=" O ASN R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 267 removed outlier: 4.134A pdb=" N TYR R 262 " --> pdb=" O ARG R 258 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 284 Processing helix chain 'R' and resid 287 through 291 Processing helix chain 'R' and resid 298 through 329 Proline residue: R 304 - end of helix Processing helix chain 'R' and resid 333 through 353 removed outlier: 4.353A pdb=" N LEU R 339 " --> pdb=" O SER R 335 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL R 342 " --> pdb=" O TYR R 338 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS R 343 " --> pdb=" O LEU R 339 " (cutoff:3.500A) Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 367 through 382 Processing helix chain 'R' and resid 382 through 392 Processing helix chain 'R' and resid 395 through 409 removed outlier: 3.526A pdb=" N THR R 401 " --> pdb=" O GLU R 397 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG R 404 " --> pdb=" O THR R 400 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA R 407 " --> pdb=" O LYS R 403 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.527A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.589A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.993A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.699A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.503A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.408A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.166A 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: 3.676A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.780A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.806A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 75 through 77 removed outlier: 3.651A pdb=" N THR R 75 " --> pdb=" O TRP R 82 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TRP R 82 " --> pdb=" O THR R 75 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU R 80 " --> pdb=" O ASP R 77 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 89 through 90 removed outlier: 3.778A pdb=" N VAL R 89 " --> pdb=" O CYS R 112 " (cutoff:3.500A) 441 hydrogen bonds defined for protein. 1251 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: 1.43 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1454 1.32 - 1.44: 2620 1.44 - 1.57: 5100 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 9264 Sorted by residual: bond pdb=" N LYS A 280 " pdb=" CA LYS A 280 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.27e-02 6.20e+03 6.96e+00 bond pdb=" N THR A 285 " pdb=" CA THR A 285 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.22e-02 6.72e+03 5.00e+00 bond pdb=" N ASP A 284 " pdb=" CA ASP A 284 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.16e-02 7.43e+03 4.80e+00 bond pdb=" N LYS A 271 " pdb=" CA LYS A 271 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.23e-02 6.61e+03 4.23e+00 bond pdb=" C VAL R 206 " pdb=" N PRO R 207 " ideal model delta sigma weight residual 1.335 1.353 -0.018 9.40e-03 1.13e+04 3.79e+00 ... (remaining 9259 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 12318 1.39 - 2.79: 218 2.79 - 4.18: 32 4.18 - 5.57: 5 5.57 - 6.97: 2 Bond angle restraints: 12575 Sorted by residual: angle pdb=" CA PRO P 32 " pdb=" N PRO P 32 " pdb=" CD PRO P 32 " ideal model delta sigma weight residual 112.00 105.03 6.97 1.40e+00 5.10e-01 2.48e+01 angle pdb=" CA ASP A 274 " pdb=" C ASP A 274 " pdb=" O ASP A 274 " ideal model delta sigma weight residual 120.82 117.05 3.77 1.05e+00 9.07e-01 1.29e+01 angle pdb=" N VAL R 357 " pdb=" CA VAL R 357 " pdb=" C VAL R 357 " ideal model delta sigma weight residual 112.96 109.57 3.39 1.00e+00 1.00e+00 1.15e+01 angle pdb=" C ILE R 248 " pdb=" N VAL R 249 " pdb=" CA VAL R 249 " ideal model delta sigma weight residual 122.97 120.20 2.77 9.80e-01 1.04e+00 7.99e+00 angle pdb=" N ALA A 226 " pdb=" CA ALA A 226 " pdb=" C ALA A 226 " ideal model delta sigma weight residual 109.39 113.75 -4.36 1.59e+00 3.96e-01 7.53e+00 ... (remaining 12570 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 5043 17.91 - 35.81: 316 35.81 - 53.72: 73 53.72 - 71.63: 14 71.63 - 89.53: 7 Dihedral angle restraints: 5453 sinusoidal: 2129 harmonic: 3324 Sorted by residual: dihedral pdb=" CB CYS P 1 " pdb=" SG CYS P 1 " pdb=" SG CYS P 7 " pdb=" CB CYS P 7 " ideal model delta sinusoidal sigma weight residual 93.00 50.74 42.26 1 1.00e+01 1.00e-02 2.49e+01 dihedral pdb=" CB CYS R 219 " pdb=" SG CYS R 219 " pdb=" SG CYS R 289 " pdb=" CB CYS R 289 " ideal model delta sinusoidal sigma weight residual 93.00 53.76 39.24 1 1.00e+01 1.00e-02 2.16e+01 dihedral pdb=" CB CYS R 55 " pdb=" SG CYS R 55 " pdb=" SG CYS R 81 " pdb=" CB CYS R 81 " ideal model delta sinusoidal sigma weight residual -86.00 -121.65 35.65 1 1.00e+01 1.00e-02 1.80e+01 ... (remaining 5450 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1100 0.044 - 0.089: 233 0.089 - 0.133: 63 0.133 - 0.177: 4 0.177 - 0.222: 1 Chirality restraints: 1401 Sorted by residual: chirality pdb=" CBE Y01 R 503 " pdb=" CAP Y01 R 503 " pdb=" CBB Y01 R 503 " pdb=" CBI Y01 R 503 " both_signs ideal model delta sigma weight residual False 2.57 2.35 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA LYS A 280 " pdb=" N LYS A 280 " pdb=" C LYS A 280 " pdb=" CB LYS A 280 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CA PRO P 32 " pdb=" N PRO P 32 " pdb=" C PRO P 32 " pdb=" CB PRO P 32 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.07e-01 ... (remaining 1398 not shown) Planarity restraints: 1594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA P 31 " -0.082 5.00e-02 4.00e+02 1.20e-01 2.32e+01 pdb=" N PRO P 32 " 0.208 5.00e-02 4.00e+02 pdb=" CA PRO P 32 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO P 32 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR R 138 " -0.026 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO R 139 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO R 139 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 139 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.023 5.00e-02 4.00e+02 3.55e-02 2.01e+00 pdb=" N PRO B 236 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.020 5.00e-02 4.00e+02 ... (remaining 1591 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 287 2.72 - 3.27: 9093 3.27 - 3.81: 14602 3.81 - 4.36: 19203 4.36 - 4.90: 31737 Nonbonded interactions: 74922 Sorted by model distance: nonbonded pdb=" OH TYR P 12 " pdb=" O ALA R 145 " model vdw 2.176 3.040 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.236 3.040 nonbonded pdb=" OG1 THR B 34 " pdb=" O LEU B 300 " model vdw 2.294 3.040 nonbonded pdb=" OH TYR R 149 " pdb=" O LEU R 202 " model vdw 2.294 3.040 nonbonded pdb=" O PRO R 270 " pdb=" OG1 THR R 274 " model vdw 2.306 3.040 ... (remaining 74917 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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.190 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 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 : 0.002 0.107 9273 Z= 0.161 Angle : 0.466 6.965 12592 Z= 0.287 Chirality : 0.039 0.222 1401 Planarity : 0.004 0.120 1593 Dihedral : 12.835 89.532 3284 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.37 % Allowed : 10.78 % Favored : 87.84 % 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: -3.13 (0.21), residues: 1121 helix: -2.90 (0.16), residues: 427 sheet: -0.61 (0.31), residues: 239 loop : -1.84 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 333 TYR 0.007 0.001 TYR N 60 PHE 0.009 0.001 PHE B 151 TRP 0.007 0.001 TRP A 234 HIS 0.002 0.000 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.12 ( 9264) covalent geometry : angle 0.46561 / 0.29 (12575) SS BOND : bond 0.00377 / 0.20 ( 7) SS BOND : angle 0.57567 / 0.34 ( 14) hydrogen bonds : bond 0.27119 / 17.84 ( 441) hydrogen bonds : angle 9.01681 / 6.39 ( 1251) Misc. bond : bond 0.10707 / 5.64 ( 1) link_NAG-ASN : bond 0.00184 / 0.10 ( 1) link_NAG-ASN : angle 0.61725 / 0.37 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.295 Fit side-chains REVERT: A 60 MET cc_start: 0.3277 (mtm) cc_final: 0.2369 (mtm) REVERT: A 356 ARG cc_start: 0.6508 (mtm-85) cc_final: 0.6277 (mtm180) REVERT: A 372 ILE cc_start: 0.8158 (pt) cc_final: 0.7950 (pt) REVERT: B 101 MET cc_start: 0.8307 (mtp) cc_final: 0.7958 (mtp) REVERT: B 186 ASP cc_start: 0.7000 (m-30) cc_final: 0.6617 (m-30) REVERT: B 260 GLU cc_start: 0.7260 (pt0) cc_final: 0.7030 (pt0) REVERT: G 13 ARG cc_start: 0.6247 (mtt90) cc_final: 0.5784 (mmt90) REVERT: G 32 LYS cc_start: 0.7543 (tmtt) cc_final: 0.7325 (ttpp) REVERT: G 47 GLU cc_start: 0.6054 (mt-10) cc_final: 0.5582 (tm-30) REVERT: N 89 GLU cc_start: 0.6790 (mp0) cc_final: 0.6478 (mp0) REVERT: N 106 ASP cc_start: 0.8142 (p0) cc_final: 0.7853 (p0) REVERT: R 143 LYS cc_start: 0.6099 (tttm) cc_final: 0.4797 (tptm) REVERT: R 161 PHE cc_start: 0.6339 (t80) cc_final: 0.6107 (t80) REVERT: R 187 MET cc_start: 0.7340 (tpt) cc_final: 0.7104 (tpt) REVERT: R 210 GLU cc_start: 0.6555 (mp0) cc_final: 0.6314 (mp0) REVERT: R 214 ARG cc_start: 0.5122 (ttp-110) cc_final: 0.4675 (ttp-170) REVERT: R 343 LYS cc_start: 0.6465 (mmtt) cc_final: 0.6104 (tttt) outliers start: 13 outliers final: 7 residues processed: 169 average time/residue: 0.6645 time to fit residues: 118.3601 Evaluate side-chains 122 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 253 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 GLN A 31 GLN A 239 ASN A 294 GLN B 17 GLN B 36 ASN B 75 GLN G 24 ASN N 5 GLN N 13 GLN P 14 GLN R 135 ASN R 144 ASN R 179 GLN R 201 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.163374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.124915 restraints weight = 10908.455| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.88 r_work: 0.3355 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9273 Z= 0.181 Angle : 0.607 7.385 12592 Z= 0.329 Chirality : 0.045 0.203 1401 Planarity : 0.005 0.060 1593 Dihedral : 5.697 57.559 1275 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.59 % Allowed : 14.27 % Favored : 82.14 % 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: -1.07 (0.24), residues: 1121 helix: 0.06 (0.24), residues: 437 sheet: -0.35 (0.32), residues: 228 loop : -1.58 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 19 TYR 0.012 0.002 TYR P 12 PHE 0.025 0.002 PHE A 212 TRP 0.015 0.002 TRP R 236 HIS 0.005 0.001 HIS R 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 ( 9264) covalent geometry : angle 0.60516 / 0.33 (12575) SS BOND : bond 0.00279 / 0.15 ( 7) SS BOND : angle 1.64122 / 0.87 ( 14) hydrogen bonds : bond 0.05742 / 3.67 ( 441) hydrogen bonds : angle 5.27329 / 3.76 ( 1251) Misc. bond : bond 0.00089 / 0.05 ( 1) link_NAG-ASN : bond 0.00017 / 0.01 ( 1) link_NAG-ASN : angle 1.06943 / 0.94 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 0.316 Fit side-chains REVERT: A 60 MET cc_start: 0.3347 (mtm) cc_final: 0.2548 (mtm) REVERT: B 101 MET cc_start: 0.8654 (mtp) cc_final: 0.8394 (mtp) REVERT: B 260 GLU cc_start: 0.7902 (pt0) cc_final: 0.7691 (pt0) REVERT: G 32 LYS cc_start: 0.7746 (tmtt) cc_final: 0.7499 (ttpp) REVERT: G 47 GLU cc_start: 0.6164 (mt-10) cc_final: 0.5427 (tm-30) REVERT: N 1 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.6562 (tm-30) REVERT: N 89 GLU cc_start: 0.7413 (mp0) cc_final: 0.6988 (mp0) REVERT: R 131 TYR cc_start: 0.3939 (m-80) cc_final: 0.2813 (m-10) REVERT: R 143 LYS cc_start: 0.5590 (tttm) cc_final: 0.4180 (tptm) REVERT: R 161 PHE cc_start: 0.6632 (t80) cc_final: 0.6405 (t80) REVERT: R 187 MET cc_start: 0.7820 (tpt) cc_final: 0.7397 (tpt) REVERT: R 210 GLU cc_start: 0.6584 (mp0) cc_final: 0.6291 (mp0) REVERT: R 214 ARG cc_start: 0.4917 (ttp-110) cc_final: 0.4579 (ttp-170) REVERT: R 343 LYS cc_start: 0.6535 (mmtt) cc_final: 0.5862 (tttt) REVERT: R 404 ARG cc_start: 0.5968 (ttp-110) cc_final: 0.5758 (ttp-110) outliers start: 34 outliers final: 14 residues processed: 145 average time/residue: 0.6188 time to fit residues: 94.8431 Evaluate side-chains 128 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 128 SER Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 253 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 61 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 99 optimal weight: 9.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 24 GLN R 179 GLN R 405 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.164348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.125436 restraints weight = 10931.826| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.01 r_work: 0.3368 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9273 Z= 0.130 Angle : 0.526 6.231 12592 Z= 0.283 Chirality : 0.042 0.188 1401 Planarity : 0.004 0.045 1593 Dihedral : 5.280 54.614 1273 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.59 % Allowed : 15.86 % Favored : 80.55 % 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: -0.08 (0.25), residues: 1121 helix: 1.25 (0.26), residues: 433 sheet: -0.12 (0.32), residues: 230 loop : -1.27 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 72 TYR 0.012 0.001 TYR P 12 PHE 0.018 0.002 PHE P 19 TRP 0.015 0.002 TRP R 236 HIS 0.004 0.001 HIS R 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 9264) covalent geometry : angle 0.52387 / 0.28 (12575) SS BOND : bond 0.00152 / 0.09 ( 7) SS BOND : angle 1.52042 / 0.75 ( 14) hydrogen bonds : bond 0.04551 / 2.89 ( 441) hydrogen bonds : angle 4.77661 / 3.39 ( 1251) Misc. bond : bond 0.00004 / 0.00 ( 1) link_NAG-ASN : bond 0.00201 / 0.11 ( 1) link_NAG-ASN : angle 0.97837 / 0.87 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 0.230 Fit side-chains REVERT: A 60 MET cc_start: 0.3435 (mtm) cc_final: 0.2744 (mtm) REVERT: B 101 MET cc_start: 0.8631 (mtp) cc_final: 0.8245 (mtp) REVERT: B 154 ASP cc_start: 0.7801 (m-30) cc_final: 0.7571 (m-30) REVERT: B 260 GLU cc_start: 0.7897 (pt0) cc_final: 0.7685 (pt0) REVERT: G 37 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7537 (mp) REVERT: G 47 GLU cc_start: 0.6218 (mt-10) cc_final: 0.5411 (tm-30) REVERT: N 1 GLN cc_start: 0.7299 (tt0) cc_final: 0.6571 (tm-30) REVERT: N 12 VAL cc_start: 0.8094 (p) cc_final: 0.7876 (p) REVERT: N 89 GLU cc_start: 0.7442 (mp0) cc_final: 0.7026 (mp0) REVERT: P 19 PHE cc_start: 0.7095 (m-80) cc_final: 0.6822 (m-80) REVERT: R 79 TRP cc_start: 0.2940 (OUTLIER) cc_final: 0.1365 (m-90) REVERT: R 131 TYR cc_start: 0.3769 (m-80) cc_final: 0.2743 (m-10) REVERT: R 143 LYS cc_start: 0.5735 (tttm) cc_final: 0.4334 (tptm) REVERT: R 158 LEU cc_start: 0.7445 (tp) cc_final: 0.7156 (tt) REVERT: R 161 PHE cc_start: 0.6678 (t80) cc_final: 0.6443 (t80) REVERT: R 172 PHE cc_start: 0.5464 (t80) cc_final: 0.4948 (t80) REVERT: R 187 MET cc_start: 0.7761 (tpt) cc_final: 0.7299 (tpt) REVERT: R 210 GLU cc_start: 0.6582 (mp0) cc_final: 0.6318 (mp0) REVERT: R 260 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.6346 (ptm160) REVERT: R 397 GLU cc_start: 0.6982 (tt0) cc_final: 0.6579 (tm-30) outliers start: 34 outliers final: 16 residues processed: 144 average time/residue: 0.5616 time to fit residues: 85.7601 Evaluate side-chains 131 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 79 TRP Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 253 PHE Chi-restraints excluded: chain R residue 260 ARG Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 402 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 100 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 chunk 79 optimal weight: 20.0000 chunk 107 optimal weight: 8.9990 chunk 76 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 45 optimal weight: 0.1980 chunk 47 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 GLN R 135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.162412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.124881 restraints weight = 11080.225| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.96 r_work: 0.3346 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9273 Z= 0.155 Angle : 0.560 6.808 12592 Z= 0.300 Chirality : 0.043 0.192 1401 Planarity : 0.004 0.068 1593 Dihedral : 5.432 52.198 1272 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.55 % Allowed : 16.70 % Favored : 78.75 % 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 (0.25), residues: 1121 helix: 1.36 (0.26), residues: 438 sheet: -0.11 (0.33), residues: 228 loop : -1.27 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 404 TYR 0.013 0.001 TYR P 12 PHE 0.021 0.002 PHE A 212 TRP 0.015 0.002 TRP R 236 HIS 0.005 0.001 HIS R 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 9264) covalent geometry : angle 0.55829 / 0.30 (12575) SS BOND : bond 0.00196 / 0.11 ( 7) SS BOND : angle 1.30654 / 0.76 ( 14) hydrogen bonds : bond 0.04571 / 2.92 ( 441) hydrogen bonds : angle 4.80436 / 3.41 ( 1251) Misc. bond : bond 0.00015 / 0.01 ( 1) link_NAG-ASN : bond 0.00057 / 0.03 ( 1) link_NAG-ASN : angle 1.21355 / 1.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 117 time to evaluate : 0.353 Fit side-chains REVERT: A 60 MET cc_start: 0.3496 (mtm) cc_final: 0.2750 (mtm) REVERT: A 240 ASP cc_start: 0.7043 (p0) cc_final: 0.6751 (p0) REVERT: A 307 LYS cc_start: 0.5942 (tptt) cc_final: 0.5270 (pmtt) REVERT: A 372 ILE cc_start: 0.7908 (pt) cc_final: 0.7393 (mp) REVERT: A 378 ASP cc_start: 0.7902 (m-30) cc_final: 0.7680 (m-30) REVERT: B 101 MET cc_start: 0.8646 (mtp) cc_final: 0.8283 (mtp) REVERT: B 260 GLU cc_start: 0.7909 (pt0) cc_final: 0.7705 (pt0) REVERT: N 1 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.6547 (tm-30) REVERT: N 12 VAL cc_start: 0.8137 (p) cc_final: 0.7893 (p) REVERT: R 79 TRP cc_start: 0.3025 (OUTLIER) cc_final: 0.1487 (m-90) REVERT: R 131 TYR cc_start: 0.3728 (m-80) cc_final: 0.2746 (m-10) REVERT: R 143 LYS cc_start: 0.5755 (tttm) cc_final: 0.4347 (tptt) REVERT: R 161 PHE cc_start: 0.6758 (t80) cc_final: 0.6515 (t80) REVERT: R 172 PHE cc_start: 0.5392 (t80) cc_final: 0.4874 (t80) REVERT: R 187 MET cc_start: 0.7768 (tpt) cc_final: 0.7323 (tpt) REVERT: R 210 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.6355 (mp0) REVERT: R 260 ARG cc_start: 0.6844 (OUTLIER) cc_final: 0.6318 (ptm160) REVERT: R 397 GLU cc_start: 0.6924 (tt0) cc_final: 0.6527 (tm-30) outliers start: 43 outliers final: 20 residues processed: 147 average time/residue: 0.5643 time to fit residues: 88.1452 Evaluate side-chains 136 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 128 SER Chi-restraints excluded: chain R residue 79 TRP Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 210 GLU Chi-restraints excluded: chain R residue 253 PHE Chi-restraints excluded: chain R residue 260 ARG Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 402 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 95 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 14 optimal weight: 0.0070 overall best weight: 2.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 135 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 = 0.3957 r_free = 0.3957 target = 0.163555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.124838 restraints weight = 10974.234| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.95 r_work: 0.3360 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9273 Z= 0.171 Angle : 0.580 6.845 12592 Z= 0.309 Chirality : 0.044 0.195 1401 Planarity : 0.004 0.060 1593 Dihedral : 5.526 48.120 1272 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.86 % Allowed : 16.91 % Favored : 78.22 % 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: 0.06 (0.25), residues: 1121 helix: 1.40 (0.26), residues: 438 sheet: -0.09 (0.33), residues: 228 loop : -1.23 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 42 TYR 0.014 0.002 TYR A 358 PHE 0.023 0.002 PHE P 19 TRP 0.016 0.002 TRP R 236 HIS 0.005 0.001 HIS R 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 ( 9264) covalent geometry : angle 0.57836 / 0.31 (12575) SS BOND : bond 0.00213 / 0.12 ( 7) SS BOND : angle 1.35334 / 0.85 ( 14) hydrogen bonds : bond 0.04602 / 2.93 ( 441) hydrogen bonds : angle 4.79677 / 3.42 ( 1251) Misc. bond : bond 0.00013 / 0.01 ( 1) link_NAG-ASN : bond 0.00008 / 0.00 ( 1) link_NAG-ASN : angle 1.31196 / 1.24 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 113 time to evaluate : 0.349 Fit side-chains REVERT: A 60 MET cc_start: 0.3370 (mtm) cc_final: 0.2681 (mtm) REVERT: A 307 LYS cc_start: 0.5930 (tptt) cc_final: 0.5345 (pmtt) REVERT: A 372 ILE cc_start: 0.7852 (pt) cc_final: 0.7401 (mp) REVERT: B 101 MET cc_start: 0.8600 (mtp) cc_final: 0.8364 (mtp) REVERT: B 130 GLU cc_start: 0.4840 (OUTLIER) cc_final: 0.3872 (mm-30) REVERT: B 260 GLU cc_start: 0.7909 (pt0) cc_final: 0.7686 (pt0) REVERT: G 62 ARG cc_start: 0.3581 (pmm-80) cc_final: 0.3300 (pmm-80) REVERT: N 1 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.6620 (tm-30) REVERT: N 12 VAL cc_start: 0.8184 (p) cc_final: 0.7929 (p) REVERT: N 89 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7364 (mp0) REVERT: R 79 TRP cc_start: 0.2923 (OUTLIER) cc_final: 0.1432 (m-90) REVERT: R 131 TYR cc_start: 0.3612 (m-80) cc_final: 0.2605 (m-10) REVERT: R 143 LYS cc_start: 0.5688 (tttm) cc_final: 0.4348 (tptm) REVERT: R 161 PHE cc_start: 0.6781 (t80) cc_final: 0.6572 (t80) REVERT: R 172 PHE cc_start: 0.5393 (t80) cc_final: 0.4848 (t80) REVERT: R 187 MET cc_start: 0.7790 (tpt) cc_final: 0.7358 (tpt) REVERT: R 210 GLU cc_start: 0.6590 (OUTLIER) cc_final: 0.6350 (mp0) REVERT: R 260 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.6327 (ptm160) REVERT: R 300 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8169 (mt) REVERT: R 334 GLU cc_start: 0.5901 (mp0) cc_final: 0.5683 (mp0) REVERT: R 397 GLU cc_start: 0.6939 (tt0) cc_final: 0.6537 (tm-30) outliers start: 46 outliers final: 24 residues processed: 144 average time/residue: 0.5981 time to fit residues: 91.7997 Evaluate side-chains 139 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 128 SER Chi-restraints excluded: chain R residue 79 TRP Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 210 GLU Chi-restraints excluded: chain R residue 253 PHE Chi-restraints excluded: chain R residue 260 ARG Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 402 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 78 optimal weight: 0.1980 chunk 85 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 64 optimal weight: 0.0870 chunk 92 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 278 ASN P 17 ASN R 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.166366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.128710 restraints weight = 10986.195| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.82 r_work: 0.3400 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9273 Z= 0.094 Angle : 0.475 6.577 12592 Z= 0.253 Chirality : 0.041 0.184 1401 Planarity : 0.003 0.052 1593 Dihedral : 5.039 49.453 1272 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.96 % Allowed : 19.03 % Favored : 78.01 % 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: 0.57 (0.26), residues: 1121 helix: 1.98 (0.26), residues: 433 sheet: 0.16 (0.34), residues: 220 loop : -1.06 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 404 TYR 0.011 0.001 TYR N 60 PHE 0.015 0.001 PHE P 19 TRP 0.015 0.001 TRP B 211 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 ( 9264) covalent geometry : angle 0.47420 / 0.25 (12575) SS BOND : bond 0.00097 / 0.06 ( 7) SS BOND : angle 0.85221 / 0.46 ( 14) hydrogen bonds : bond 0.03531 / 2.25 ( 441) hydrogen bonds : angle 4.35593 / 3.09 ( 1251) Misc. bond : bond 0.00000 / 0.00 ( 1) link_NAG-ASN : bond 0.00295 / 0.16 ( 1) link_NAG-ASN : angle 0.72050 / 0.62 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.371 Fit side-chains REVERT: A 60 MET cc_start: 0.3304 (mtm) cc_final: 0.2630 (mtm) REVERT: A 240 ASP cc_start: 0.7115 (p0) cc_final: 0.6831 (p0) REVERT: A 300 LYS cc_start: 0.5100 (mtpt) cc_final: 0.4179 (mttp) REVERT: A 307 LYS cc_start: 0.5725 (tptt) cc_final: 0.5249 (pmtt) REVERT: A 372 ILE cc_start: 0.7843 (pt) cc_final: 0.7449 (mp) REVERT: B 101 MET cc_start: 0.8625 (mtp) cc_final: 0.8344 (mtp) REVERT: B 260 GLU cc_start: 0.7860 (pt0) cc_final: 0.7537 (pt0) REVERT: G 62 ARG cc_start: 0.3669 (pmm-80) cc_final: 0.3378 (pmm-80) REVERT: N 1 GLN cc_start: 0.7356 (tt0) cc_final: 0.6636 (tm-30) REVERT: N 3 GLN cc_start: 0.7865 (tt0) cc_final: 0.7487 (tp40) REVERT: P 19 PHE cc_start: 0.6974 (m-80) cc_final: 0.6742 (m-80) REVERT: R 79 TRP cc_start: 0.2818 (OUTLIER) cc_final: 0.1540 (m100) REVERT: R 131 TYR cc_start: 0.3767 (m-80) cc_final: 0.2696 (m-10) REVERT: R 158 LEU cc_start: 0.7121 (tp) cc_final: 0.6871 (tt) REVERT: R 161 PHE cc_start: 0.6741 (t80) cc_final: 0.6502 (t80) REVERT: R 172 PHE cc_start: 0.5323 (t80) cc_final: 0.4784 (t80) REVERT: R 260 ARG cc_start: 0.6878 (OUTLIER) cc_final: 0.6349 (ptm160) outliers start: 28 outliers final: 11 residues processed: 148 average time/residue: 0.5947 time to fit residues: 93.7908 Evaluate side-chains 128 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 128 SER Chi-restraints excluded: chain R residue 79 TRP Chi-restraints excluded: chain R residue 179 GLN Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 253 PHE Chi-restraints excluded: chain R residue 260 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 102 optimal weight: 0.0770 chunk 60 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 ASN R 179 GLN R 405 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.165007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.125816 restraints weight = 11024.250| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.73 r_work: 0.3395 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9273 Z= 0.102 Angle : 0.489 7.657 12592 Z= 0.260 Chirality : 0.041 0.183 1401 Planarity : 0.003 0.048 1593 Dihedral : 4.793 44.522 1268 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.17 % Allowed : 19.77 % Favored : 77.06 % 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: 0.70 (0.26), residues: 1121 helix: 2.04 (0.26), residues: 434 sheet: 0.25 (0.34), residues: 220 loop : -0.95 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 42 TYR 0.010 0.001 TYR N 60 PHE 0.015 0.001 PHE P 19 TRP 0.014 0.001 TRP R 236 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 ( 9264) covalent geometry : angle 0.48799 / 0.26 (12575) SS BOND : bond 0.00117 / 0.07 ( 7) SS BOND : angle 0.80489 / 0.48 ( 14) hydrogen bonds : bond 0.03584 / 2.29 ( 441) hydrogen bonds : angle 4.31014 / 3.07 ( 1251) Misc. bond : bond 0.00003 / 0.00 ( 1) link_NAG-ASN : bond 0.00190 / 0.10 ( 1) link_NAG-ASN : angle 0.71286 / 0.60 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.221 Fit side-chains REVERT: A 60 MET cc_start: 0.3243 (mtm) cc_final: 0.2614 (mtm) REVERT: A 240 ASP cc_start: 0.7074 (p0) cc_final: 0.6777 (p0) REVERT: A 307 LYS cc_start: 0.5714 (tptt) cc_final: 0.5148 (pmtt) REVERT: A 372 ILE cc_start: 0.7849 (pt) cc_final: 0.7458 (mp) REVERT: B 101 MET cc_start: 0.8586 (mtp) cc_final: 0.8338 (mtp) REVERT: B 130 GLU cc_start: 0.4914 (OUTLIER) cc_final: 0.3938 (mm-30) REVERT: B 217 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7753 (pp-130) REVERT: B 260 GLU cc_start: 0.7857 (pt0) cc_final: 0.7639 (pt0) REVERT: G 20 LYS cc_start: 0.7760 (mttt) cc_final: 0.7559 (mmtt) REVERT: G 62 ARG cc_start: 0.3744 (pmm-80) cc_final: 0.3461 (pmm-80) REVERT: N 1 GLN cc_start: 0.7364 (tt0) cc_final: 0.6565 (tm-30) REVERT: N 3 GLN cc_start: 0.7853 (tt0) cc_final: 0.7475 (tp40) REVERT: P 19 PHE cc_start: 0.7038 (m-80) cc_final: 0.6778 (m-80) REVERT: R 79 TRP cc_start: 0.2832 (OUTLIER) cc_final: 0.1561 (m100) REVERT: R 131 TYR cc_start: 0.3778 (m-80) cc_final: 0.2709 (m-10) REVERT: R 161 PHE cc_start: 0.6716 (t80) cc_final: 0.6455 (t80) REVERT: R 172 PHE cc_start: 0.5306 (t80) cc_final: 0.4762 (t80) REVERT: R 229 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7307 (tpp) outliers start: 30 outliers final: 14 residues processed: 140 average time/residue: 0.5597 time to fit residues: 83.3840 Evaluate side-chains 128 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 128 SER Chi-restraints excluded: chain R residue 79 TRP Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 229 MET Chi-restraints excluded: chain R residue 253 PHE Chi-restraints excluded: chain R residue 337 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 37 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.165236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.124667 restraints weight = 10928.631| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.76 r_work: 0.3385 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9273 Z= 0.115 Angle : 0.508 8.156 12592 Z= 0.272 Chirality : 0.042 0.187 1401 Planarity : 0.004 0.052 1593 Dihedral : 4.813 41.074 1268 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.49 % Allowed : 19.56 % Favored : 76.96 % 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: 0.75 (0.25), residues: 1121 helix: 2.07 (0.26), residues: 433 sheet: 0.28 (0.33), residues: 221 loop : -0.91 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 42 TYR 0.010 0.001 TYR P 12 PHE 0.015 0.001 PHE A 212 TRP 0.013 0.001 TRP R 236 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 9264) covalent geometry : angle 0.50730 / 0.27 (12575) SS BOND : bond 0.00143 / 0.08 ( 7) SS BOND : angle 1.00992 / 0.57 ( 14) hydrogen bonds : bond 0.03787 / 2.42 ( 441) hydrogen bonds : angle 4.39038 / 3.12 ( 1251) Misc. bond : bond 0.00001 / 0.00 ( 1) link_NAG-ASN : bond 0.00123 / 0.06 ( 1) link_NAG-ASN : angle 0.82046 / 0.70 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.356 Fit side-chains REVERT: A 60 MET cc_start: 0.3233 (mtm) cc_final: 0.2628 (mtm) REVERT: A 240 ASP cc_start: 0.7100 (p0) cc_final: 0.6802 (p0) REVERT: A 307 LYS cc_start: 0.5734 (tptt) cc_final: 0.5241 (pmtt) REVERT: A 372 ILE cc_start: 0.7856 (pt) cc_final: 0.7453 (mp) REVERT: B 101 MET cc_start: 0.8607 (mtp) cc_final: 0.8386 (mtp) REVERT: B 130 GLU cc_start: 0.4839 (OUTLIER) cc_final: 0.4077 (mt-10) REVERT: B 217 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7847 (pp-130) REVERT: B 260 GLU cc_start: 0.7857 (pt0) cc_final: 0.7640 (pt0) REVERT: G 19 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7457 (mm) REVERT: G 20 LYS cc_start: 0.7685 (mttt) cc_final: 0.7452 (mmtt) REVERT: N 1 GLN cc_start: 0.7363 (tt0) cc_final: 0.6626 (tm-30) REVERT: R 79 TRP cc_start: 0.2893 (OUTLIER) cc_final: 0.1585 (m100) REVERT: R 131 TYR cc_start: 0.3726 (m-80) cc_final: 0.2696 (m-10) REVERT: R 161 PHE cc_start: 0.6744 (t80) cc_final: 0.6490 (t80) REVERT: R 172 PHE cc_start: 0.5336 (t80) cc_final: 0.4810 (t80) REVERT: R 229 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.7309 (tpp) REVERT: R 300 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8027 (mp) REVERT: R 334 GLU cc_start: 0.6089 (mp0) cc_final: 0.5844 (mp0) outliers start: 33 outliers final: 22 residues processed: 137 average time/residue: 0.5256 time to fit residues: 76.7672 Evaluate side-chains 138 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 128 SER Chi-restraints excluded: chain R residue 79 TRP Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 229 MET Chi-restraints excluded: chain R residue 253 PHE Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 337 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 0.3980 chunk 55 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 chunk 62 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 405 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.164771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.127168 restraints weight = 10947.211| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.03 r_work: 0.3371 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9273 Z= 0.122 Angle : 0.522 9.812 12592 Z= 0.279 Chirality : 0.042 0.189 1401 Planarity : 0.004 0.053 1593 Dihedral : 4.791 41.048 1268 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.59 % Allowed : 19.66 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.77 (0.25), residues: 1121 helix: 2.05 (0.25), residues: 434 sheet: 0.31 (0.33), residues: 221 loop : -0.87 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.011 0.001 TYR A 358 PHE 0.028 0.002 PHE A 222 TRP 0.013 0.001 TRP R 236 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 9264) covalent geometry : angle 0.52130 / 0.28 (12575) SS BOND : bond 0.00154 / 0.09 ( 7) SS BOND : angle 0.96701 / 0.58 ( 14) hydrogen bonds : bond 0.03885 / 2.48 ( 441) hydrogen bonds : angle 4.42795 / 3.16 ( 1251) Misc. bond : bond 0.00002 / 0.00 ( 1) link_NAG-ASN : bond 0.00119 / 0.06 ( 1) link_NAG-ASN : angle 0.92212 / 0.81 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 0.292 Fit side-chains REVERT: A 60 MET cc_start: 0.3176 (mtm) cc_final: 0.2599 (mtm) REVERT: A 222 PHE cc_start: 0.7883 (m-80) cc_final: 0.7433 (m-80) REVERT: A 240 ASP cc_start: 0.7165 (p0) cc_final: 0.6926 (p0) REVERT: A 265 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.6544 (ttt-90) REVERT: A 307 LYS cc_start: 0.5806 (tptt) cc_final: 0.5271 (pmtt) REVERT: A 372 ILE cc_start: 0.7810 (pt) cc_final: 0.7407 (mp) REVERT: B 3 GLU cc_start: 0.4616 (OUTLIER) cc_final: 0.4302 (tp30) REVERT: B 101 MET cc_start: 0.8611 (mtp) cc_final: 0.8392 (mtp) REVERT: B 130 GLU cc_start: 0.4776 (OUTLIER) cc_final: 0.4040 (mt-10) REVERT: B 217 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7891 (pp-130) REVERT: B 260 GLU cc_start: 0.7888 (pt0) cc_final: 0.7673 (pt0) REVERT: G 19 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7426 (mm) REVERT: G 37 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7568 (mp) REVERT: N 1 GLN cc_start: 0.7332 (tt0) cc_final: 0.6606 (tm-30) REVERT: R 79 TRP cc_start: 0.2839 (OUTLIER) cc_final: 0.1526 (m100) REVERT: R 131 TYR cc_start: 0.3729 (m-80) cc_final: 0.2685 (m-10) REVERT: R 161 PHE cc_start: 0.6728 (t80) cc_final: 0.6472 (t80) REVERT: R 172 PHE cc_start: 0.5267 (t80) cc_final: 0.4748 (t80) REVERT: R 258 ARG cc_start: 0.4854 (mtm180) cc_final: 0.4584 (ttp-170) REVERT: R 300 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8036 (mp) REVERT: R 334 GLU cc_start: 0.6041 (mp0) cc_final: 0.5804 (mp0) outliers start: 34 outliers final: 21 residues processed: 136 average time/residue: 0.5581 time to fit residues: 80.8103 Evaluate side-chains 138 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 128 SER Chi-restraints excluded: chain R residue 79 TRP Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 253 PHE Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 337 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 100 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 74 optimal weight: 0.0170 chunk 72 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 45 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 overall best weight: 0.5220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 179 GLN R 405 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.167174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.129152 restraints weight = 10957.835| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.96 r_work: 0.3412 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9273 Z= 0.094 Angle : 0.485 9.292 12592 Z= 0.258 Chirality : 0.041 0.183 1401 Planarity : 0.003 0.054 1593 Dihedral : 4.516 41.406 1268 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.96 % Allowed : 20.51 % Favored : 76.53 % 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: 1.02 (0.26), residues: 1121 helix: 2.32 (0.26), residues: 433 sheet: 0.42 (0.34), residues: 220 loop : -0.79 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 42 TYR 0.011 0.001 TYR N 60 PHE 0.020 0.001 PHE A 222 TRP 0.014 0.001 TRP B 99 HIS 0.002 0.001 HIS R 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 ( 9264) covalent geometry : angle 0.48433 / 0.26 (12575) SS BOND : bond 0.00115 / 0.06 ( 7) SS BOND : angle 0.73856 / 0.40 ( 14) hydrogen bonds : bond 0.03385 / 2.15 ( 441) hydrogen bonds : angle 4.22174 / 3.02 ( 1251) Misc. bond : bond 0.00003 / 0.00 ( 1) link_NAG-ASN : bond 0.00247 / 0.13 ( 1) link_NAG-ASN : angle 0.53414 / 0.40 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 0.252 Fit side-chains REVERT: A 60 MET cc_start: 0.3120 (mtm) cc_final: 0.2576 (mtm) REVERT: A 222 PHE cc_start: 0.7797 (m-80) cc_final: 0.7403 (m-80) REVERT: A 240 ASP cc_start: 0.7198 (p0) cc_final: 0.6964 (p0) REVERT: A 265 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6569 (ttt-90) REVERT: A 307 LYS cc_start: 0.5768 (tptt) cc_final: 0.5166 (pmtt) REVERT: A 372 ILE cc_start: 0.7802 (pt) cc_final: 0.7412 (mp) REVERT: B 3 GLU cc_start: 0.4635 (OUTLIER) cc_final: 0.4378 (tp30) REVERT: B 101 MET cc_start: 0.8637 (mtp) cc_final: 0.8341 (mtp) REVERT: B 110 ASN cc_start: 0.7090 (m110) cc_final: 0.6781 (m-40) REVERT: B 217 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7471 (ppp) REVERT: B 260 GLU cc_start: 0.7799 (pt0) cc_final: 0.7593 (pt0) REVERT: G 19 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7445 (mm) REVERT: N 1 GLN cc_start: 0.7314 (tt0) cc_final: 0.6505 (tm-30) REVERT: N 3 GLN cc_start: 0.7848 (tt0) cc_final: 0.7470 (tp40) REVERT: N 43 LYS cc_start: 0.7834 (mttm) cc_final: 0.7462 (mmmm) REVERT: R 79 TRP cc_start: 0.2737 (OUTLIER) cc_final: 0.1414 (m100) REVERT: R 131 TYR cc_start: 0.3803 (m-80) cc_final: 0.2796 (m-10) REVERT: R 161 PHE cc_start: 0.6640 (t80) cc_final: 0.6417 (t80) REVERT: R 172 PHE cc_start: 0.5188 (t80) cc_final: 0.4669 (t80) REVERT: R 258 ARG cc_start: 0.4898 (mtm180) cc_final: 0.4641 (ttp-170) REVERT: R 300 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.7992 (mp) REVERT: R 334 GLU cc_start: 0.6072 (mp0) cc_final: 0.5820 (mp0) REVERT: R 346 MET cc_start: 0.7556 (tpp) cc_final: 0.7254 (mmp) outliers start: 28 outliers final: 17 residues processed: 146 average time/residue: 0.5609 time to fit residues: 87.4196 Evaluate side-chains 139 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 128 SER Chi-restraints excluded: chain R residue 79 TRP Chi-restraints excluded: chain R residue 179 GLN Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 253 PHE Chi-restraints excluded: chain R residue 300 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 32 optimal weight: 0.0570 chunk 18 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 108 optimal weight: 0.9980 chunk 83 optimal weight: 0.0770 chunk 4 optimal weight: 10.0000 chunk 81 optimal weight: 0.8980 overall best weight: 0.5856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.166703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.129838 restraints weight = 10902.333| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.98 r_work: 0.3409 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9273 Z= 0.096 Angle : 0.489 9.178 12592 Z= 0.260 Chirality : 0.041 0.182 1401 Planarity : 0.003 0.053 1593 Dihedral : 4.500 41.530 1268 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.85 % Allowed : 20.61 % Favored : 76.53 % 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: 1.09 (0.26), residues: 1121 helix: 2.40 (0.26), residues: 434 sheet: 0.44 (0.33), residues: 220 loop : -0.77 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 214 TYR 0.010 0.001 TYR N 60 PHE 0.018 0.001 PHE A 222 TRP 0.014 0.001 TRP B 211 HIS 0.004 0.001 HIS R 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.10 ( 9264) covalent geometry : angle 0.48852 / 0.26 (12575) SS BOND : bond 0.00128 / 0.07 ( 7) SS BOND : angle 0.74435 / 0.42 ( 14) hydrogen bonds : bond 0.03381 / 2.15 ( 441) hydrogen bonds : angle 4.19248 / 3.00 ( 1251) Misc. bond : bond 0.00001 / 0.00 ( 1) link_NAG-ASN : bond 0.00223 / 0.12 ( 1) link_NAG-ASN : angle 0.50823 / 0.37 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3666.42 seconds wall clock time: 62 minutes 58.38 seconds (3778.38 seconds total)