Starting phenix.real_space_refine on Tue Mar 3 23:26:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tyo_26190/03_2026/7tyo_26190.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyo_26190/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7tyo_26190/03_2026/7tyo_26190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyo_26190/03_2026/7tyo_26190.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tyo_26190/03_2026/7tyo_26190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyo_26190/03_2026/7tyo_26190.map" } 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-5986/lib/python3.9/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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.14, per 1000 atoms: 0.24 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: 0.78 Conformation dependent library (CDL) restraints added in 366.9 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: 0.44 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: 1.53 Time building geometry restraints manager: 1.03 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: 5168 17.91 - 35.81: 322 35.81 - 53.72: 73 53.72 - 71.63: 20 71.63 - 89.53: 7 Dihedral angle restraints: 5590 sinusoidal: 2266 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 5587 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.960 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 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 : 12.868 89.532 3421 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 covalent geometry : bond 0.00204 ( 9264) covalent geometry : angle 0.46561 (12575) SS BOND : bond 0.00377 ( 7) SS BOND : angle 0.57567 ( 14) hydrogen bonds : bond 0.27119 ( 441) hydrogen bonds : angle 9.01681 ( 1251) Misc. bond : bond 0.10707 ( 1) link_NAG-ASN : bond 0.00184 ( 1) link_NAG-ASN : angle 0.61725 ( 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 : 0.339 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: 0.7596 time to fit residues: 135.0695 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 : 0.400 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.163385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.124831 restraints weight = 10911.064| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.88 r_work: 0.3354 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1857 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= 0.180 Angle : 0.613 7.914 12592 Z= 0.330 Chirality : 0.045 0.206 1401 Planarity : 0.005 0.058 1593 Dihedral : 6.766 59.593 1412 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.70 % Allowed : 14.38 % Favored : 81.92 % 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: -1.06 (0.24), residues: 1121 helix: 0.05 (0.24), residues: 437 sheet: -0.27 (0.32), residues: 225 loop : -1.60 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 72 TYR 0.013 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 covalent geometry : bond 0.00411 ( 9264) covalent geometry : angle 0.61034 (12575) SS BOND : bond 0.00280 ( 7) SS BOND : angle 1.68254 ( 14) hydrogen bonds : bond 0.05663 ( 441) hydrogen bonds : angle 5.24462 ( 1251) Misc. bond : bond 0.00015 ( 1) link_NAG-ASN : bond 0.00044 ( 1) link_NAG-ASN : angle 1.45483 ( 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 160 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 125 time to evaluate : 0.260 Fit side-chains REVERT: A 60 MET cc_start: 0.3349 (mtm) cc_final: 0.2556 (mtm) REVERT: B 101 MET cc_start: 0.8657 (mtp) cc_final: 0.8400 (mtp) REVERT: B 260 GLU cc_start: 0.7909 (pt0) cc_final: 0.7704 (pt0) REVERT: G 32 LYS cc_start: 0.7737 (tmtt) cc_final: 0.7498 (ttpp) REVERT: G 47 GLU cc_start: 0.6155 (mt-10) cc_final: 0.5410 (tm-30) REVERT: G 59 ASN cc_start: 0.6324 (p0) cc_final: 0.6022 (p0) REVERT: N 1 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.6568 (tm-30) REVERT: N 89 GLU cc_start: 0.7428 (mp0) cc_final: 0.7008 (mp0) REVERT: R 79 TRP cc_start: 0.2906 (OUTLIER) cc_final: 0.1443 (m-90) REVERT: R 131 TYR cc_start: 0.3918 (m-80) cc_final: 0.2875 (m-10) REVERT: R 143 LYS cc_start: 0.5585 (tttm) cc_final: 0.4190 (tptm) REVERT: R 161 PHE cc_start: 0.6641 (t80) cc_final: 0.6420 (t80) REVERT: R 187 MET cc_start: 0.7813 (tpt) cc_final: 0.7384 (tpt) REVERT: R 210 GLU cc_start: 0.6582 (mp0) cc_final: 0.6290 (mp0) REVERT: R 214 ARG cc_start: 0.4913 (ttp-110) cc_final: 0.4575 (ttp-170) REVERT: R 219 CYS cc_start: 0.5232 (OUTLIER) cc_final: 0.5015 (t) REVERT: R 343 LYS cc_start: 0.6516 (mmtt) cc_final: 0.5845 (tttt) REVERT: R 404 ARG cc_start: 0.5992 (ttp-110) cc_final: 0.5747 (ttp-110) outliers start: 35 outliers final: 14 residues processed: 148 average time/residue: 0.7423 time to fit residues: 115.7982 Evaluate side-chains 133 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 79 TRP Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 219 CYS 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: 10.0000 chunk 50 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN P 24 GLN R 179 GLN R 405 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.163846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.125036 restraints weight = 10934.554| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.00 r_work: 0.3360 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9273 Z= 0.137 Angle : 0.537 6.226 12592 Z= 0.288 Chirality : 0.043 0.183 1401 Planarity : 0.004 0.047 1593 Dihedral : 6.508 58.093 1411 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.02 % Allowed : 15.86 % Favored : 80.13 % 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: -0.11 (0.25), residues: 1121 helix: 1.24 (0.25), residues: 433 sheet: -0.09 (0.33), residues: 224 loop : -1.32 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 72 TYR 0.013 0.001 TYR R 149 PHE 0.019 0.002 PHE A 212 TRP 0.015 0.002 TRP R 236 HIS 0.004 0.001 HIS R 184 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9264) covalent geometry : angle 0.53448 (12575) SS BOND : bond 0.00227 ( 7) SS BOND : angle 1.54115 ( 14) hydrogen bonds : bond 0.04602 ( 441) hydrogen bonds : angle 4.79300 ( 1251) Misc. bond : bond 0.00012 ( 1) link_NAG-ASN : bond 0.00133 ( 1) link_NAG-ASN : angle 1.40827 ( 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 160 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 0.309 Fit side-chains REVERT: A 60 MET cc_start: 0.3401 (mtm) cc_final: 0.2722 (mtm) REVERT: B 101 MET cc_start: 0.8628 (mtp) cc_final: 0.8242 (mtp) REVERT: B 154 ASP cc_start: 0.7809 (m-30) cc_final: 0.7578 (m-30) REVERT: B 260 GLU cc_start: 0.7891 (pt0) cc_final: 0.7679 (pt0) REVERT: G 20 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7488 (mmtt) REVERT: G 37 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7556 (mp) REVERT: G 47 GLU cc_start: 0.6262 (mt-10) cc_final: 0.5457 (tm-30) REVERT: N 1 GLN cc_start: 0.7319 (tt0) cc_final: 0.6609 (tm-30) REVERT: N 12 VAL cc_start: 0.8136 (p) cc_final: 0.7904 (p) REVERT: N 89 GLU cc_start: 0.7443 (mp0) cc_final: 0.7026 (mp0) REVERT: R 79 TRP cc_start: 0.2983 (OUTLIER) cc_final: 0.1399 (m-90) REVERT: R 131 TYR cc_start: 0.3845 (m-80) cc_final: 0.2852 (m-10) REVERT: R 143 LYS cc_start: 0.5692 (tttm) cc_final: 0.4286 (tptt) REVERT: R 158 LEU cc_start: 0.7405 (tp) cc_final: 0.7098 (tt) REVERT: R 161 PHE cc_start: 0.6690 (t80) cc_final: 0.6464 (t80) REVERT: R 172 PHE cc_start: 0.5437 (t80) cc_final: 0.4891 (t80) REVERT: R 187 MET cc_start: 0.7779 (tpt) cc_final: 0.7316 (tpt) REVERT: R 210 GLU cc_start: 0.6600 (mp0) cc_final: 0.6364 (mp0) REVERT: R 260 ARG cc_start: 0.6841 (OUTLIER) cc_final: 0.6322 (ptm160) REVERT: R 397 GLU cc_start: 0.6989 (tt0) cc_final: 0.6544 (tm-30) outliers start: 38 outliers final: 18 residues processed: 146 average time/residue: 0.6835 time to fit residues: 105.4949 Evaluate side-chains 136 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 20 LYS 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 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 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: 3.9990 chunk 19 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 79 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 76 optimal weight: 20.0000 chunk 57 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 135 ASN R 405 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.162934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.124372 restraints weight = 11090.844| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.97 r_work: 0.3346 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9273 Z= 0.163 Angle : 0.570 6.538 12592 Z= 0.305 Chirality : 0.044 0.194 1401 Planarity : 0.004 0.069 1593 Dihedral : 6.318 56.107 1409 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.76 % Allowed : 16.70 % Favored : 78.54 % 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: -0.03 (0.25), residues: 1121 helix: 1.33 (0.26), residues: 438 sheet: -0.14 (0.33), residues: 228 loop : -1.29 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG N 72 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 covalent geometry : bond 0.00372 ( 9264) covalent geometry : angle 0.56776 (12575) SS BOND : bond 0.00209 ( 7) SS BOND : angle 1.34053 ( 14) hydrogen bonds : bond 0.04635 ( 441) hydrogen bonds : angle 4.84326 ( 1251) Misc. bond : bond 0.00013 ( 1) link_NAG-ASN : bond 0.00011 ( 1) link_NAG-ASN : angle 1.68191 ( 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 162 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 117 time to evaluate : 0.359 Fit side-chains REVERT: A 60 MET cc_start: 0.3516 (mtm) cc_final: 0.2768 (mtm) REVERT: A 240 ASP cc_start: 0.6984 (p0) cc_final: 0.6693 (p0) REVERT: A 307 LYS cc_start: 0.5972 (tptt) cc_final: 0.5288 (pmtt) REVERT: A 372 ILE cc_start: 0.7910 (pt) cc_final: 0.7407 (mp) REVERT: A 378 ASP cc_start: 0.7900 (m-30) cc_final: 0.7692 (m-30) REVERT: B 101 MET cc_start: 0.8634 (mtp) cc_final: 0.8396 (mtp) REVERT: B 130 GLU cc_start: 0.5006 (OUTLIER) cc_final: 0.3988 (mm-30) REVERT: B 260 GLU cc_start: 0.7915 (pt0) cc_final: 0.7684 (pt0) REVERT: G 20 LYS cc_start: 0.7598 (mmtt) cc_final: 0.7324 (mmtt) REVERT: N 1 GLN cc_start: 0.7320 (OUTLIER) cc_final: 0.6595 (tm-30) REVERT: N 12 VAL cc_start: 0.8159 (p) cc_final: 0.7904 (p) REVERT: R 131 TYR cc_start: 0.3780 (m-80) cc_final: 0.2790 (m-10) REVERT: R 143 LYS cc_start: 0.5585 (tttm) cc_final: 0.4220 (tptt) REVERT: R 161 PHE cc_start: 0.6762 (t80) cc_final: 0.6525 (t80) REVERT: R 172 PHE cc_start: 0.5426 (t80) cc_final: 0.4909 (t80) REVERT: R 187 MET cc_start: 0.7770 (tpt) cc_final: 0.7337 (tpt) REVERT: R 210 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.6368 (mp0) REVERT: R 260 ARG cc_start: 0.6853 (OUTLIER) cc_final: 0.6330 (ptm160) REVERT: R 397 GLU cc_start: 0.6921 (tt0) cc_final: 0.6542 (tm-30) outliers start: 45 outliers final: 22 residues processed: 150 average time/residue: 0.6388 time to fit residues: 101.7145 Evaluate side-chains 140 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 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 128 SER 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 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: 9.9990 chunk 5 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.164370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.125705 restraints weight = 10972.445| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.96 r_work: 0.3371 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9273 Z= 0.142 Angle : 0.543 6.957 12592 Z= 0.290 Chirality : 0.043 0.188 1401 Planarity : 0.004 0.059 1593 Dihedral : 6.232 54.428 1409 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 5.07 % Allowed : 16.60 % Favored : 78.33 % 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: 0.14 (0.25), residues: 1121 helix: 1.52 (0.26), residues: 437 sheet: -0.18 (0.33), residues: 235 loop : -1.16 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 42 TYR 0.012 0.001 TYR P 12 PHE 0.022 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 covalent geometry : bond 0.00320 ( 9264) covalent geometry : angle 0.54086 (12575) SS BOND : bond 0.00200 ( 7) SS BOND : angle 1.42096 ( 14) hydrogen bonds : bond 0.04319 ( 441) hydrogen bonds : angle 4.66898 ( 1251) Misc. bond : bond 0.00010 ( 1) link_NAG-ASN : bond 0.00051 ( 1) link_NAG-ASN : angle 1.58991 ( 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 162 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 114 time to evaluate : 0.359 Fit side-chains REVERT: A 60 MET cc_start: 0.3327 (mtm) cc_final: 0.2635 (mtm) REVERT: A 240 ASP cc_start: 0.6997 (p0) cc_final: 0.6739 (p0) REVERT: A 307 LYS cc_start: 0.5873 (tptt) cc_final: 0.5302 (pmtt) REVERT: A 372 ILE cc_start: 0.7849 (pt) cc_final: 0.7414 (mp) REVERT: A 378 ASP cc_start: 0.7903 (m-30) cc_final: 0.7695 (m-30) REVERT: B 101 MET cc_start: 0.8621 (mtp) cc_final: 0.8311 (mtp) REVERT: B 130 GLU cc_start: 0.4994 (OUTLIER) cc_final: 0.3969 (mm-30) REVERT: B 260 GLU cc_start: 0.7916 (pt0) cc_final: 0.7688 (pt0) REVERT: G 20 LYS cc_start: 0.7599 (mmtt) cc_final: 0.7374 (mttt) REVERT: G 37 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7507 (mp) REVERT: G 62 ARG cc_start: 0.3617 (pmm-80) cc_final: 0.3316 (pmm-80) REVERT: N 1 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.6630 (tm-30) REVERT: N 12 VAL cc_start: 0.8137 (p) cc_final: 0.7923 (p) REVERT: N 89 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: R 79 TRP cc_start: 0.2622 (OUTLIER) cc_final: 0.1257 (m100) REVERT: R 131 TYR cc_start: 0.3794 (m-80) cc_final: 0.2751 (m-10) REVERT: R 143 LYS cc_start: 0.5711 (tttm) cc_final: 0.4337 (tptt) REVERT: R 161 PHE cc_start: 0.6755 (t80) cc_final: 0.6520 (t80) REVERT: R 172 PHE cc_start: 0.5391 (t80) cc_final: 0.4867 (t80) REVERT: R 210 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.6416 (mp0) REVERT: R 260 ARG cc_start: 0.6891 (OUTLIER) cc_final: 0.6307 (ptm160) REVERT: R 334 GLU cc_start: 0.5894 (mp0) cc_final: 0.5682 (mp0) REVERT: R 397 GLU cc_start: 0.6954 (tt0) cc_final: 0.6559 (tm-30) outliers start: 48 outliers final: 23 residues processed: 146 average time/residue: 0.6535 time to fit residues: 101.4133 Evaluate side-chains 140 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 367 VAL 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 214 ARG 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 37 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 78 optimal weight: 20.0000 chunk 85 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 64 optimal weight: 0.0030 chunk 92 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 79 optimal weight: 20.0000 overall best weight: 1.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.164468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.125938 restraints weight = 10951.458| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.96 r_work: 0.3376 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9273 Z= 0.134 Angle : 0.533 6.993 12592 Z= 0.284 Chirality : 0.043 0.190 1401 Planarity : 0.004 0.053 1593 Dihedral : 6.070 48.785 1406 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.86 % Allowed : 17.34 % Favored : 77.80 % 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: 0.31 (0.25), residues: 1121 helix: 1.65 (0.26), residues: 437 sheet: -0.10 (0.33), residues: 232 loop : -1.06 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 42 TYR 0.012 0.001 TYR P 12 PHE 0.021 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 covalent geometry : bond 0.00303 ( 9264) covalent geometry : angle 0.53206 (12575) SS BOND : bond 0.00165 ( 7) SS BOND : angle 1.03247 ( 14) hydrogen bonds : bond 0.04167 ( 441) hydrogen bonds : angle 4.60150 ( 1251) Misc. bond : bond 0.00007 ( 1) link_NAG-ASN : bond 0.00072 ( 1) link_NAG-ASN : angle 1.57012 ( 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 160 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 114 time to evaluate : 0.312 Fit side-chains REVERT: A 60 MET cc_start: 0.3273 (mtm) cc_final: 0.2596 (mtm) REVERT: A 240 ASP cc_start: 0.6931 (p0) cc_final: 0.6615 (p0) REVERT: A 307 LYS cc_start: 0.5774 (tptt) cc_final: 0.5278 (pmtt) REVERT: A 372 ILE cc_start: 0.7832 (pt) cc_final: 0.7423 (mp) REVERT: B 15 LYS cc_start: 0.7238 (OUTLIER) cc_final: 0.7018 (mttm) REVERT: B 101 MET cc_start: 0.8611 (mtp) cc_final: 0.8321 (mtp) REVERT: B 130 GLU cc_start: 0.4950 (OUTLIER) cc_final: 0.3926 (mm-30) REVERT: B 260 GLU cc_start: 0.7904 (pt0) cc_final: 0.7675 (pt0) REVERT: G 20 LYS cc_start: 0.7769 (mmtt) cc_final: 0.7476 (mmtt) REVERT: G 37 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7504 (mp) REVERT: N 1 GLN cc_start: 0.7360 (OUTLIER) cc_final: 0.6639 (tm-30) REVERT: N 89 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7263 (mp0) REVERT: R 79 TRP cc_start: 0.2543 (OUTLIER) cc_final: 0.1252 (m100) REVERT: R 131 TYR cc_start: 0.3632 (m-80) cc_final: 0.2691 (m-10) REVERT: R 143 LYS cc_start: 0.5653 (tttm) cc_final: 0.4332 (tptt) REVERT: R 161 PHE cc_start: 0.6758 (t80) cc_final: 0.6494 (t80) REVERT: R 172 PHE cc_start: 0.5361 (t80) cc_final: 0.4841 (t80) REVERT: R 210 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.6380 (mp0) REVERT: R 253 PHE cc_start: 0.5987 (OUTLIER) cc_final: 0.5729 (m-10) REVERT: R 260 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.6337 (ptm160) REVERT: R 300 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8152 (mt) outliers start: 46 outliers final: 22 residues processed: 146 average time/residue: 0.5721 time to fit residues: 89.0225 Evaluate side-chains 145 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 15 LYS 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 214 ARG 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 37 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 89 GLU 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 300 ILE Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 402 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 102 optimal weight: 0.7980 chunk 60 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3966 r_free = 0.3966 target = 0.164373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.126318 restraints weight = 11007.073| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.89 r_work: 0.3369 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2506 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= 0.117 Angle : 0.511 7.678 12592 Z= 0.272 Chirality : 0.042 0.183 1401 Planarity : 0.004 0.048 1593 Dihedral : 5.909 45.408 1406 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.23 % Allowed : 18.18 % Favored : 77.59 % 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: 0.46 (0.25), residues: 1121 helix: 1.85 (0.26), residues: 433 sheet: -0.07 (0.33), residues: 232 loop : -0.99 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 42 TYR 0.011 0.001 TYR R 149 PHE 0.019 0.001 PHE P 19 TRP 0.015 0.002 TRP R 236 HIS 0.003 0.001 HIS R 184 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9264) covalent geometry : angle 0.50965 (12575) SS BOND : bond 0.00157 ( 7) SS BOND : angle 1.04321 ( 14) hydrogen bonds : bond 0.03919 ( 441) hydrogen bonds : angle 4.53414 ( 1251) Misc. bond : bond 0.00011 ( 1) link_NAG-ASN : bond 0.00122 ( 1) link_NAG-ASN : angle 1.38073 ( 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 166 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 126 time to evaluate : 0.348 Fit side-chains REVERT: A 60 MET cc_start: 0.3267 (mtm) cc_final: 0.2584 (mtm) REVERT: A 240 ASP cc_start: 0.7111 (p0) cc_final: 0.6767 (p0) REVERT: A 307 LYS cc_start: 0.5777 (tptt) cc_final: 0.5301 (pmtt) REVERT: A 372 ILE cc_start: 0.7857 (pt) cc_final: 0.7451 (mp) REVERT: B 15 LYS cc_start: 0.7233 (OUTLIER) cc_final: 0.7011 (mttm) REVERT: B 101 MET cc_start: 0.8634 (mtp) cc_final: 0.8363 (mtp) REVERT: B 217 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7846 (pp-130) REVERT: B 260 GLU cc_start: 0.7887 (pt0) cc_final: 0.7681 (pt0) REVERT: G 20 LYS cc_start: 0.7768 (mmtt) cc_final: 0.7465 (mmtt) REVERT: G 37 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7509 (mp) REVERT: N 1 GLN cc_start: 0.7353 (tt0) cc_final: 0.6628 (tm-30) REVERT: P 17 ASN cc_start: 0.7710 (t0) cc_final: 0.7469 (t0) REVERT: P 19 PHE cc_start: 0.6975 (m-80) cc_final: 0.6693 (m-80) REVERT: R 79 TRP cc_start: 0.2605 (OUTLIER) cc_final: 0.1321 (m100) REVERT: R 131 TYR cc_start: 0.3750 (m-80) cc_final: 0.2722 (m-10) REVERT: R 161 PHE cc_start: 0.6756 (t80) cc_final: 0.6502 (t80) REVERT: R 172 PHE cc_start: 0.5351 (t80) cc_final: 0.4845 (t80) REVERT: R 210 GLU cc_start: 0.6629 (OUTLIER) cc_final: 0.6398 (mp0) REVERT: R 253 PHE cc_start: 0.5919 (OUTLIER) cc_final: 0.5685 (m-10) REVERT: R 260 ARG cc_start: 0.6903 (OUTLIER) cc_final: 0.6306 (ptm160) REVERT: R 300 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8135 (mt) outliers start: 40 outliers final: 22 residues processed: 153 average time/residue: 0.6428 time to fit residues: 104.5430 Evaluate side-chains 146 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 40 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 217 MET 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 G residue 37 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 30 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 37 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 59 optimal weight: 0.0070 chunk 44 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 179 GLN R 186 ASN R 405 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.164602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.125709 restraints weight = 10931.122| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.95 r_work: 0.3376 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9273 Z= 0.146 Angle : 0.554 9.012 12592 Z= 0.295 Chirality : 0.043 0.192 1401 Planarity : 0.004 0.054 1593 Dihedral : 5.888 44.780 1405 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 5.07 % Allowed : 17.76 % Favored : 77.17 % 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: 0.32 (0.25), residues: 1121 helix: 1.64 (0.26), residues: 440 sheet: -0.04 (0.33), residues: 229 loop : -1.08 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 42 TYR 0.013 0.001 TYR A 358 PHE 0.020 0.002 PHE P 19 TRP 0.014 0.002 TRP R 236 HIS 0.006 0.001 HIS R 184 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9264) covalent geometry : angle 0.55249 (12575) SS BOND : bond 0.00180 ( 7) SS BOND : angle 1.06124 ( 14) hydrogen bonds : bond 0.04193 ( 441) hydrogen bonds : angle 4.63016 ( 1251) Misc. bond : bond 0.00011 ( 1) link_NAG-ASN : bond 0.00028 ( 1) link_NAG-ASN : angle 1.46163 ( 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 161 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 113 time to evaluate : 0.365 Fit side-chains REVERT: A 60 MET cc_start: 0.3258 (mtm) cc_final: 0.2609 (mtm) REVERT: A 240 ASP cc_start: 0.7129 (p0) cc_final: 0.6863 (p0) REVERT: A 265 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6555 (ttt-90) REVERT: A 307 LYS cc_start: 0.5794 (tptt) cc_final: 0.5306 (pmtt) REVERT: A 372 ILE cc_start: 0.7860 (pt) cc_final: 0.7452 (mp) REVERT: B 15 LYS cc_start: 0.7273 (OUTLIER) cc_final: 0.6967 (mttm) REVERT: B 101 MET cc_start: 0.8604 (mtp) cc_final: 0.8325 (mtp) REVERT: B 217 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7920 (pp-130) REVERT: B 260 GLU cc_start: 0.7864 (pt0) cc_final: 0.7658 (pt0) REVERT: G 19 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7475 (mm) REVERT: G 20 LYS cc_start: 0.7816 (mmtt) cc_final: 0.7509 (mmtt) REVERT: N 1 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.6650 (tm-30) REVERT: N 89 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7260 (mp0) REVERT: P 17 ASN cc_start: 0.7722 (t0) cc_final: 0.7455 (t0) REVERT: R 79 TRP cc_start: 0.2610 (OUTLIER) cc_final: 0.1339 (m100) REVERT: R 131 TYR cc_start: 0.3713 (m-80) cc_final: 0.2752 (m-10) REVERT: R 161 PHE cc_start: 0.6774 (t80) cc_final: 0.6521 (t80) REVERT: R 172 PHE cc_start: 0.5369 (t80) cc_final: 0.4825 (t80) REVERT: R 210 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.6396 (mp0) REVERT: R 253 PHE cc_start: 0.6003 (OUTLIER) cc_final: 0.5741 (m-10) REVERT: R 260 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.6431 (ptm160) REVERT: R 300 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8142 (mt) REVERT: R 334 GLU cc_start: 0.6125 (mp0) cc_final: 0.5894 (mp0) outliers start: 48 outliers final: 24 residues processed: 146 average time/residue: 0.6758 time to fit residues: 104.9152 Evaluate side-chains 147 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 15 LYS Chi-restraints excluded: chain B residue 40 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 122 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 217 MET 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 19 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 61 optimal weight: 0.0000 chunk 99 optimal weight: 10.0000 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.165692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.128270 restraints weight = 10934.504| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.01 r_work: 0.3381 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2612 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= 0.103 Angle : 0.499 9.276 12592 Z= 0.265 Chirality : 0.041 0.177 1401 Planarity : 0.003 0.054 1593 Dihedral : 5.555 43.989 1405 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.49 % Allowed : 19.45 % 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: 0.66 (0.25), residues: 1121 helix: 2.03 (0.26), residues: 433 sheet: 0.23 (0.34), residues: 220 loop : -1.00 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 42 TYR 0.011 0.001 TYR R 149 PHE 0.015 0.001 PHE P 19 TRP 0.015 0.001 TRP R 236 HIS 0.003 0.001 HIS R 302 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 9264) covalent geometry : angle 0.49790 (12575) SS BOND : bond 0.00131 ( 7) SS BOND : angle 0.85538 ( 14) hydrogen bonds : bond 0.03654 ( 441) hydrogen bonds : angle 4.40858 ( 1251) Misc. bond : bond 0.00005 ( 1) link_NAG-ASN : bond 0.00180 ( 1) link_NAG-ASN : angle 1.16970 ( 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 152 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.318 Fit side-chains REVERT: A 60 MET cc_start: 0.3160 (mtm) cc_final: 0.2585 (mtm) REVERT: A 209 GLU cc_start: 0.7022 (mm-30) cc_final: 0.6779 (mt-10) REVERT: A 240 ASP cc_start: 0.7214 (p0) cc_final: 0.6995 (p0) REVERT: A 265 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.6563 (ttt-90) REVERT: A 307 LYS cc_start: 0.5854 (tptt) cc_final: 0.5316 (pmtt) REVERT: A 372 ILE cc_start: 0.7831 (pt) cc_final: 0.7433 (mp) REVERT: B 9 GLN cc_start: 0.6454 (OUTLIER) cc_final: 0.6152 (mm-40) REVERT: B 101 MET cc_start: 0.8633 (mtp) cc_final: 0.8387 (mtp) REVERT: B 130 GLU cc_start: 0.4835 (OUTLIER) cc_final: 0.3900 (mm-30) REVERT: B 154 ASP cc_start: 0.7890 (m-30) cc_final: 0.7598 (m-30) REVERT: B 217 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7832 (pp-130) REVERT: B 260 GLU cc_start: 0.7887 (pt0) cc_final: 0.7672 (pt0) REVERT: G 19 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7454 (mm) REVERT: G 20 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7501 (mmtt) REVERT: N 1 GLN cc_start: 0.7339 (tt0) cc_final: 0.6557 (tm-30) REVERT: N 3 GLN cc_start: 0.7856 (tt0) cc_final: 0.7484 (tp40) REVERT: N 89 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7257 (mp0) REVERT: P 8 MET cc_start: 0.7977 (ttt) cc_final: 0.7653 (ttt) REVERT: P 17 ASN cc_start: 0.7709 (t0) cc_final: 0.7499 (t0) REVERT: R 79 TRP cc_start: 0.2622 (OUTLIER) cc_final: 0.1298 (m100) REVERT: R 131 TYR cc_start: 0.3794 (m-80) cc_final: 0.2815 (m-10) REVERT: R 161 PHE cc_start: 0.6750 (t80) cc_final: 0.6502 (t80) REVERT: R 172 PHE cc_start: 0.5268 (t80) cc_final: 0.4745 (t80) REVERT: R 187 MET cc_start: 0.7719 (tpt) cc_final: 0.7238 (tpt) REVERT: R 253 PHE cc_start: 0.5928 (OUTLIER) cc_final: 0.5685 (m-10) REVERT: R 300 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8126 (mt) REVERT: R 334 GLU cc_start: 0.6142 (mp0) cc_final: 0.5902 (mp0) REVERT: R 397 GLU cc_start: 0.6915 (tt0) cc_final: 0.6557 (tm-30) outliers start: 33 outliers final: 14 residues processed: 141 average time/residue: 0.6996 time to fit residues: 104.4371 Evaluate side-chains 137 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 9 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 130 GLU 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 336 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 52 THR 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 253 PHE Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 402 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 100 optimal weight: 6.9990 chunk 47 optimal weight: 0.4980 chunk 102 optimal weight: 0.8980 chunk 74 optimal weight: 0.0270 chunk 72 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 13 optimal weight: 0.1980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 17 ASN R 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.167113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.130299 restraints weight = 10949.890| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.97 r_work: 0.3412 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9273 Z= 0.093 Angle : 0.482 9.237 12592 Z= 0.256 Chirality : 0.041 0.176 1401 Planarity : 0.004 0.052 1593 Dihedral : 5.283 43.435 1405 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.43 % Allowed : 20.93 % Favored : 76.64 % 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: 0.95 (0.26), residues: 1121 helix: 2.28 (0.26), residues: 434 sheet: 0.34 (0.34), residues: 220 loop : -0.82 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 62 TYR 0.012 0.001 TYR R 149 PHE 0.018 0.001 PHE P 19 TRP 0.015 0.001 TRP R 236 HIS 0.002 0.001 HIS R 302 Details of bonding type rmsd covalent geometry : bond 0.00198 ( 9264) covalent geometry : angle 0.48120 (12575) SS BOND : bond 0.00122 ( 7) SS BOND : angle 0.77129 ( 14) hydrogen bonds : bond 0.03299 ( 441) hydrogen bonds : angle 4.20575 ( 1251) Misc. bond : bond 0.00004 ( 1) link_NAG-ASN : bond 0.00262 ( 1) link_NAG-ASN : angle 0.87585 ( 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 143 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.279 Fit side-chains REVERT: A 60 MET cc_start: 0.3092 (mtm) cc_final: 0.2544 (mtm) REVERT: A 209 GLU cc_start: 0.7050 (mm-30) cc_final: 0.6793 (mt-10) REVERT: A 240 ASP cc_start: 0.7125 (p0) cc_final: 0.6903 (p0) REVERT: A 265 ARG cc_start: 0.7224 (OUTLIER) cc_final: 0.6564 (ttt-90) REVERT: A 307 LYS cc_start: 0.5859 (tptt) cc_final: 0.5293 (pmtt) REVERT: A 372 ILE cc_start: 0.7793 (pt) cc_final: 0.7426 (mp) REVERT: B 9 GLN cc_start: 0.6307 (OUTLIER) cc_final: 0.6059 (mm-40) REVERT: B 101 MET cc_start: 0.8629 (mtp) cc_final: 0.8313 (mtp) REVERT: B 154 ASP cc_start: 0.7869 (m-30) cc_final: 0.7572 (m-30) REVERT: B 260 GLU cc_start: 0.7826 (pt0) cc_final: 0.7616 (pt0) REVERT: G 20 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7505 (mmtt) REVERT: N 1 GLN cc_start: 0.7320 (tt0) cc_final: 0.6507 (tm-30) REVERT: N 3 GLN cc_start: 0.7847 (tt0) cc_final: 0.7469 (tp40) REVERT: N 43 LYS cc_start: 0.7868 (mttm) cc_final: 0.7482 (mmmm) REVERT: P 17 ASN cc_start: 0.7639 (t0) cc_final: 0.7432 (t0) REVERT: P 19 PHE cc_start: 0.6937 (m-80) cc_final: 0.6640 (m-80) REVERT: R 131 TYR cc_start: 0.3713 (m-80) cc_final: 0.2731 (m-10) REVERT: R 161 PHE cc_start: 0.6760 (t80) cc_final: 0.6492 (t80) REVERT: R 172 PHE cc_start: 0.5164 (t80) cc_final: 0.4656 (t80) REVERT: R 346 MET cc_start: 0.7547 (tpp) cc_final: 0.7252 (mmp) REVERT: R 397 GLU cc_start: 0.6922 (tt0) cc_final: 0.6551 (tm-30) outliers start: 23 outliers final: 13 residues processed: 138 average time/residue: 0.6181 time to fit residues: 90.4745 Evaluate side-chains 127 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 9 GLN Chi-restraints excluded: chain B residue 61 MET 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 G residue 20 LYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 128 SER Chi-restraints excluded: chain R residue 179 GLN Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 253 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 32 optimal weight: 0.0060 chunk 18 optimal weight: 7.9990 chunk 91 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 83 optimal weight: 30.0000 chunk 4 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.163380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.125112 restraints weight = 10920.536| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.95 r_work: 0.3356 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9273 Z= 0.174 Angle : 0.589 9.439 12592 Z= 0.313 Chirality : 0.045 0.190 1401 Planarity : 0.004 0.057 1593 Dihedral : 5.730 44.641 1405 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.64 % Allowed : 21.14 % Favored : 76.22 % 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: 0.55 (0.25), residues: 1121 helix: 1.84 (0.25), residues: 440 sheet: 0.16 (0.33), residues: 230 loop : -1.00 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 180 TYR 0.013 0.002 TYR R 391 PHE 0.023 0.002 PHE A 212 TRP 0.013 0.002 TRP R 236 HIS 0.008 0.001 HIS R 184 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 9264) covalent geometry : angle 0.58827 (12575) SS BOND : bond 0.00244 ( 7) SS BOND : angle 1.06077 ( 14) hydrogen bonds : bond 0.04304 ( 441) hydrogen bonds : angle 4.58431 ( 1251) Misc. bond : bond 0.00008 ( 1) link_NAG-ASN : bond 0.00213 ( 1) link_NAG-ASN : angle 1.24139 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4141.28 seconds wall clock time: 70 minutes 59.81 seconds (4259.81 seconds total)