Starting phenix.real_space_refine on Thu Feb 13 18:24:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tyo_26190/02_2025/7tyo_26190.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyo_26190/02_2025/7tyo_26190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tyo_26190/02_2025/7tyo_26190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyo_26190/02_2025/7tyo_26190.map" model { file = "/net/cci-nas-00/data/ceres_data/7tyo_26190/02_2025/7tyo_26190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyo_26190/02_2025/7tyo_26190.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4} 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: 5.35, per 1000 atoms: 0.59 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: 2.40 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.95 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: 2.54 Time building geometry restraints manager: 2.75 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.640 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.960 ------------------------------------------------------------------------------- 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 0.034 9264 Z= 0.135 Angle : 0.466 6.965 12575 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (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 TRP 0.007 0.001 TRP A 234 HIS 0.002 0.000 HIS B 62 PHE 0.009 0.001 PHE B 151 TYR 0.007 0.001 TYR N 60 ARG 0.002 0.000 ARG A 333 *********************** 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 : 1.004 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: 0.7326 (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: 0.7339 (tpt) cc_final: 0.7104 (tpt) REVERT: R 210 GLU cc_start: 0.6556 (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: 1.5423 time to fit residues: 275.5193 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 : 1.083 ------------------------------------------------------------------------------- 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 92 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 13 GLN P 14 GLN R 135 ASN R 144 ASN R 179 GLN R 201 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.162640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.124135 restraints weight = 10801.546| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.86 r_work: 0.3343 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9264 Z= 0.315 Angle : 0.647 8.130 12575 Z= 0.348 Chirality : 0.047 0.210 1401 Planarity : 0.005 0.060 1593 Dihedral : 6.836 58.598 1412 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.02 % Allowed : 14.48 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.24), residues: 1121 helix: -0.01 (0.24), residues: 438 sheet: -0.44 (0.32), residues: 236 loop : -1.59 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 236 HIS 0.006 0.001 HIS R 184 PHE 0.028 0.002 PHE A 212 TYR 0.013 0.002 TYR P 12 ARG 0.007 0.001 ARG B 19 *********************** 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 163 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 1.029 Fit side-chains REVERT: A 60 MET cc_start: 0.3291 (mtm) cc_final: 0.2516 (mtm) REVERT: A 265 ARG cc_start: 0.6945 (OUTLIER) cc_final: 0.6729 (tpt90) REVERT: A 283 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.7080 (mtt-85) REVERT: B 101 MET cc_start: 0.8655 (mtp) cc_final: 0.8347 (mtp) REVERT: G 47 GLU cc_start: 0.6128 (mt-10) cc_final: 0.5408 (tm-30) REVERT: N 1 GLN cc_start: 0.7317 (OUTLIER) cc_final: 0.6616 (tm-30) REVERT: N 89 GLU cc_start: 0.7445 (mp0) cc_final: 0.7045 (mp0) REVERT: R 79 TRP cc_start: 0.2900 (OUTLIER) cc_final: 0.1517 (m-90) REVERT: R 131 TYR cc_start: 0.3934 (m-80) cc_final: 0.2840 (m-10) REVERT: R 143 LYS cc_start: 0.5560 (tttm) cc_final: 0.4225 (tptm) REVERT: R 161 PHE cc_start: 0.6692 (t80) cc_final: 0.6464 (t80) REVERT: R 187 MET cc_start: 0.7793 (tpt) cc_final: 0.7379 (tpt) REVERT: R 210 GLU cc_start: 0.6571 (mp0) cc_final: 0.6298 (mp0) REVERT: R 219 CYS cc_start: 0.5199 (OUTLIER) cc_final: 0.4972 (t) REVERT: R 343 LYS cc_start: 0.6476 (mmtt) cc_final: 0.5785 (tttt) REVERT: R 404 ARG cc_start: 0.6135 (ttp-110) cc_final: 0.5826 (ttp-110) outliers start: 38 outliers final: 14 residues processed: 150 average time/residue: 1.4864 time to fit residues: 235.8664 Evaluate side-chains 133 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 283 ARG 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 243 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 27 optimal weight: 10.0000 chunk 39 optimal weight: 0.0980 chunk 11 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 7 optimal weight: 0.1980 chunk 81 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 5 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 = 0.3973 r_free = 0.3973 target = 0.165156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.126100 restraints weight = 11077.697| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.97 r_work: 0.3381 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9264 Z= 0.154 Angle : 0.496 5.567 12575 Z= 0.267 Chirality : 0.041 0.179 1401 Planarity : 0.004 0.045 1593 Dihedral : 6.325 58.936 1409 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.38 % Allowed : 17.12 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.25), residues: 1121 helix: 1.32 (0.26), residues: 433 sheet: -0.12 (0.33), residues: 226 loop : -1.28 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 236 HIS 0.004 0.001 HIS R 302 PHE 0.015 0.001 PHE P 19 TYR 0.013 0.001 TYR R 149 ARG 0.005 0.000 ARG B 19 *********************** 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 158 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 1.112 Fit side-chains REVERT: A 60 MET cc_start: 0.3454 (mtm) cc_final: 0.2700 (mtm) REVERT: A 307 LYS cc_start: 0.5524 (tptt) cc_final: 0.5069 (pmtt) REVERT: B 101 MET cc_start: 0.8650 (mtp) cc_final: 0.8285 (mtp) REVERT: B 154 ASP cc_start: 0.7770 (m-30) cc_final: 0.7542 (m-30) REVERT: G 37 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7495 (mp) REVERT: G 47 GLU cc_start: 0.6203 (mt-10) cc_final: 0.5407 (tm-30) REVERT: N 1 GLN cc_start: 0.7312 (tt0) cc_final: 0.6561 (tm-30) REVERT: N 83 MET cc_start: 0.8367 (mtp) cc_final: 0.8034 (mtp) REVERT: N 89 GLU cc_start: 0.7418 (mp0) cc_final: 0.7016 (mp0) REVERT: P 19 PHE cc_start: 0.7079 (m-80) cc_final: 0.6836 (m-80) REVERT: R 79 TRP cc_start: 0.2984 (OUTLIER) cc_final: 0.1596 (m100) REVERT: R 131 TYR cc_start: 0.3878 (m-80) cc_final: 0.2831 (m-10) REVERT: R 143 LYS cc_start: 0.5652 (tttm) cc_final: 0.4268 (tptm) REVERT: R 158 LEU cc_start: 0.7356 (tp) cc_final: 0.7077 (tt) REVERT: R 161 PHE cc_start: 0.6707 (t80) cc_final: 0.6476 (t80) REVERT: R 172 PHE cc_start: 0.5376 (t80) cc_final: 0.4841 (t80) REVERT: R 210 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.6339 (mp0) REVERT: R 219 CYS cc_start: 0.5404 (OUTLIER) cc_final: 0.5194 (t) REVERT: R 260 ARG cc_start: 0.6908 (OUTLIER) cc_final: 0.6311 (ptm160) REVERT: R 397 GLU cc_start: 0.6957 (tt0) cc_final: 0.6636 (tm-30) outliers start: 32 outliers final: 12 residues processed: 147 average time/residue: 1.4086 time to fit residues: 219.4342 Evaluate side-chains 129 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL 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 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 210 GLU Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 260 ARG 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 86 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 79 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN N 5 GLN R 135 ASN R 179 GLN R 405 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.162115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.124825 restraints weight = 10896.783| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.92 r_work: 0.3341 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9264 Z= 0.243 Angle : 0.569 6.702 12575 Z= 0.305 Chirality : 0.044 0.192 1401 Planarity : 0.004 0.068 1593 Dihedral : 6.288 54.967 1405 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.97 % Allowed : 16.38 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.25), residues: 1121 helix: 1.37 (0.26), residues: 438 sheet: -0.12 (0.33), residues: 224 loop : -1.30 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 236 HIS 0.005 0.001 HIS R 184 PHE 0.022 0.002 PHE A 212 TYR 0.013 0.002 TYR P 12 ARG 0.004 0.001 ARG B 42 *********************** 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 167 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 120 time to evaluate : 1.012 Fit side-chains REVERT: A 60 MET cc_start: 0.3515 (mtm) cc_final: 0.2760 (mtm) REVERT: A 372 ILE cc_start: 0.7937 (pt) cc_final: 0.7410 (mp) REVERT: A 378 ASP cc_start: 0.7918 (m-30) cc_final: 0.7711 (m-30) REVERT: B 101 MET cc_start: 0.8641 (mtp) cc_final: 0.8282 (mtp) REVERT: B 130 GLU cc_start: 0.5013 (OUTLIER) cc_final: 0.3964 (mm-30) REVERT: N 1 GLN cc_start: 0.7362 (tt0) cc_final: 0.6587 (tm-30) REVERT: R 131 TYR cc_start: 0.3839 (m-80) cc_final: 0.2839 (m-10) REVERT: R 143 LYS cc_start: 0.5773 (tttm) cc_final: 0.4346 (tptt) REVERT: R 161 PHE cc_start: 0.6772 (t80) cc_final: 0.6537 (t80) REVERT: R 172 PHE cc_start: 0.5401 (t80) cc_final: 0.4870 (t80) REVERT: R 187 MET cc_start: 0.7777 (tpt) cc_final: 0.7352 (tpt) REVERT: R 210 GLU cc_start: 0.6602 (OUTLIER) cc_final: 0.6384 (mp0) REVERT: R 260 ARG cc_start: 0.6853 (OUTLIER) cc_final: 0.6340 (ptm160) REVERT: R 343 LYS cc_start: 0.6323 (mmtt) cc_final: 0.5672 (tttt) REVERT: R 397 GLU cc_start: 0.6950 (tt0) cc_final: 0.6569 (tm-30) outliers start: 47 outliers final: 18 residues processed: 152 average time/residue: 1.4599 time to fit residues: 235.2339 Evaluate side-chains 132 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 130 GLU 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 B residue 336 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 52 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 128 SER 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 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 33 optimal weight: 0.6980 chunk 80 optimal weight: 30.0000 chunk 8 optimal weight: 0.6980 chunk 4 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 77 optimal weight: 0.1980 chunk 102 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN N 5 GLN R 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.164966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.126679 restraints weight = 10927.899| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.90 r_work: 0.3372 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9264 Z= 0.156 Angle : 0.494 6.674 12575 Z= 0.265 Chirality : 0.041 0.180 1401 Planarity : 0.004 0.058 1593 Dihedral : 5.857 56.144 1404 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.02 % Allowed : 17.76 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.25), residues: 1121 helix: 1.80 (0.26), residues: 433 sheet: 0.06 (0.33), residues: 226 loop : -1.07 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 236 HIS 0.003 0.001 HIS B 311 PHE 0.019 0.001 PHE P 19 TYR 0.011 0.001 TYR P 12 ARG 0.005 0.000 ARG R 404 *********************** 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 155 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 117 time to evaluate : 1.079 Fit side-chains REVERT: A 60 MET cc_start: 0.3347 (mtm) cc_final: 0.2650 (mtm) REVERT: A 307 LYS cc_start: 0.5928 (tptt) cc_final: 0.5311 (pmtt) REVERT: A 372 ILE cc_start: 0.7831 (pt) cc_final: 0.7374 (mp) REVERT: A 378 ASP cc_start: 0.7874 (m-30) cc_final: 0.7662 (m-30) REVERT: B 101 MET cc_start: 0.8625 (mtp) cc_final: 0.8365 (mtp) REVERT: G 37 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7592 (mp) REVERT: N 1 GLN cc_start: 0.7370 (OUTLIER) cc_final: 0.6612 (tm-30) REVERT: P 19 PHE cc_start: 0.7006 (m-80) cc_final: 0.6748 (m-80) REVERT: R 79 TRP cc_start: 0.2505 (OUTLIER) cc_final: 0.1226 (m100) REVERT: R 131 TYR cc_start: 0.3872 (m-80) cc_final: 0.2815 (m-10) REVERT: R 143 LYS cc_start: 0.5672 (tttm) cc_final: 0.4284 (tptt) REVERT: R 158 LEU cc_start: 0.7224 (tp) cc_final: 0.6951 (tt) REVERT: R 161 PHE cc_start: 0.6758 (t80) cc_final: 0.6541 (t80) REVERT: R 172 PHE cc_start: 0.5386 (t80) cc_final: 0.4860 (t80) REVERT: R 210 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.6275 (mp0) REVERT: R 260 ARG cc_start: 0.6934 (OUTLIER) cc_final: 0.6333 (ptm160) REVERT: R 397 GLU cc_start: 0.6956 (tt0) cc_final: 0.6575 (tm-30) outliers start: 38 outliers final: 17 residues processed: 143 average time/residue: 1.4133 time to fit residues: 214.9693 Evaluate side-chains 130 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 40 VAL 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 277 SER 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 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 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 52 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 48 optimal weight: 0.2980 chunk 94 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 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 = 0.3970 r_free = 0.3970 target = 0.164706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.127763 restraints weight = 10876.446| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.94 r_work: 0.3380 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9264 Z= 0.150 Angle : 0.492 6.815 12575 Z= 0.262 Chirality : 0.041 0.181 1401 Planarity : 0.004 0.054 1593 Dihedral : 5.687 53.380 1404 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.81 % Allowed : 18.18 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.26), residues: 1121 helix: 2.01 (0.26), residues: 433 sheet: 0.14 (0.33), residues: 226 loop : -0.93 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 236 HIS 0.004 0.001 HIS A 220 PHE 0.015 0.001 PHE P 19 TYR 0.010 0.001 TYR P 12 ARG 0.006 0.000 ARG R 404 *********************** 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 158 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 1.096 Fit side-chains REVERT: A 60 MET cc_start: 0.3277 (mtm) cc_final: 0.2613 (mtm) REVERT: A 307 LYS cc_start: 0.5709 (tptt) cc_final: 0.5089 (pmtt) REVERT: A 372 ILE cc_start: 0.7801 (pt) cc_final: 0.7398 (mp) REVERT: A 378 ASP cc_start: 0.7892 (m-30) cc_final: 0.7671 (m-30) REVERT: B 9 GLN cc_start: 0.6416 (OUTLIER) cc_final: 0.6175 (mm-40) REVERT: B 101 MET cc_start: 0.8617 (mtp) cc_final: 0.8357 (mtp) REVERT: G 37 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7535 (mp) REVERT: G 62 ARG cc_start: 0.3614 (pmm-80) cc_final: 0.3328 (pmm-80) REVERT: N 1 GLN cc_start: 0.7356 (tt0) cc_final: 0.6596 (tm-30) REVERT: N 89 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7291 (mp0) REVERT: P 19 PHE cc_start: 0.7043 (m-80) cc_final: 0.6789 (m-80) REVERT: R 79 TRP cc_start: 0.2522 (OUTLIER) cc_final: 0.1267 (m100) REVERT: R 131 TYR cc_start: 0.3843 (m-80) cc_final: 0.2808 (m-10) REVERT: R 161 PHE cc_start: 0.6709 (t80) cc_final: 0.6449 (t80) REVERT: R 172 PHE cc_start: 0.5359 (t80) cc_final: 0.4842 (t80) REVERT: R 210 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.6310 (mp0) REVERT: R 397 GLU cc_start: 0.6933 (tt0) cc_final: 0.6420 (mp0) outliers start: 36 outliers final: 17 residues processed: 143 average time/residue: 1.4048 time to fit residues: 213.2022 Evaluate side-chains 135 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 9 GLN 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 277 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 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 179 GLN 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 337 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 91 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 405 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.162407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.122799 restraints weight = 11069.626| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.71 r_work: 0.3358 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9264 Z= 0.228 Angle : 0.555 8.237 12575 Z= 0.295 Chirality : 0.043 0.194 1401 Planarity : 0.004 0.054 1593 Dihedral : 5.821 45.977 1403 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.12 % Allowed : 18.92 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.25), residues: 1121 helix: 1.70 (0.26), residues: 441 sheet: 0.03 (0.33), residues: 229 loop : -1.04 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 236 HIS 0.006 0.001 HIS R 184 PHE 0.021 0.002 PHE A 212 TYR 0.013 0.001 TYR A 358 ARG 0.005 0.001 ARG A 356 *********************** 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 146 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 107 time to evaluate : 1.082 Fit side-chains REVERT: A 60 MET cc_start: 0.3251 (mtm) cc_final: 0.2603 (mtm) REVERT: A 307 LYS cc_start: 0.5879 (tptt) cc_final: 0.5292 (pmtt) REVERT: A 372 ILE cc_start: 0.7819 (pt) cc_final: 0.7400 (mp) REVERT: B 101 MET cc_start: 0.8631 (mtp) cc_final: 0.8339 (mtp) REVERT: B 130 GLU cc_start: 0.4894 (OUTLIER) cc_final: 0.3849 (mm-30) REVERT: N 1 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.6633 (tm-30) REVERT: N 89 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7319 (mp0) REVERT: R 79 TRP cc_start: 0.2563 (OUTLIER) cc_final: 0.1263 (m100) REVERT: R 131 TYR cc_start: 0.3808 (m-80) cc_final: 0.2819 (m-10) REVERT: R 143 LYS cc_start: 0.5717 (tttm) cc_final: 0.4406 (tptm) REVERT: R 161 PHE cc_start: 0.6766 (t80) cc_final: 0.6509 (t80) REVERT: R 172 PHE cc_start: 0.5361 (t80) cc_final: 0.4854 (t80) REVERT: R 210 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.6393 (mp0) REVERT: R 300 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8173 (mt) REVERT: R 334 GLU cc_start: 0.6063 (mp0) cc_final: 0.5824 (mp0) outliers start: 39 outliers final: 22 residues processed: 134 average time/residue: 1.3352 time to fit residues: 191.0676 Evaluate side-chains 133 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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 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 130 GLU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 214 ARG 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 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 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 84 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 186 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.163886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.125196 restraints weight = 11053.257| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.96 r_work: 0.3371 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 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 : 0.004 0.036 9264 Z= 0.244 Angle : 0.569 7.606 12575 Z= 0.304 Chirality : 0.044 0.198 1401 Planarity : 0.004 0.055 1593 Dihedral : 5.863 44.808 1403 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.33 % Allowed : 18.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.25), residues: 1121 helix: 1.62 (0.26), residues: 440 sheet: 0.08 (0.34), residues: 222 loop : -1.14 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 236 HIS 0.006 0.001 HIS A 220 PHE 0.021 0.002 PHE P 19 TYR 0.015 0.001 TYR A 358 ARG 0.005 0.001 ARG B 42 *********************** 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 149 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 108 time to evaluate : 1.091 Fit side-chains REVERT: A 60 MET cc_start: 0.3221 (mtm) cc_final: 0.2574 (mtm) REVERT: A 209 GLU cc_start: 0.6991 (mm-30) cc_final: 0.6694 (mt-10) REVERT: A 307 LYS cc_start: 0.5853 (tptt) cc_final: 0.5311 (pmtt) REVERT: A 372 ILE cc_start: 0.7852 (pt) cc_final: 0.7434 (mp) REVERT: B 101 MET cc_start: 0.8594 (mtp) cc_final: 0.8372 (mtp) REVERT: G 19 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7514 (mm) REVERT: N 1 GLN cc_start: 0.7356 (OUTLIER) cc_final: 0.6657 (tm-30) REVERT: N 89 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7260 (mp0) REVERT: P 17 ASN cc_start: 0.7723 (t0) cc_final: 0.7442 (t0) REVERT: R 79 TRP cc_start: 0.2423 (OUTLIER) cc_final: 0.1171 (m100) REVERT: R 131 TYR cc_start: 0.3784 (m-80) cc_final: 0.2742 (m-10) REVERT: R 143 LYS cc_start: 0.5780 (tttm) cc_final: 0.4455 (tptm) REVERT: R 161 PHE cc_start: 0.6758 (t80) cc_final: 0.6529 (t80) REVERT: R 172 PHE cc_start: 0.5354 (t80) cc_final: 0.4841 (t80) REVERT: R 187 MET cc_start: 0.7759 (tpt) cc_final: 0.7321 (tpt) REVERT: R 210 GLU cc_start: 0.6545 (OUTLIER) cc_final: 0.6308 (mp0) REVERT: R 271 LEU cc_start: 0.6548 (OUTLIER) cc_final: 0.6339 (mt) REVERT: R 300 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8192 (mt) REVERT: R 334 GLU cc_start: 0.6141 (mp0) cc_final: 0.5929 (mp0) outliers start: 41 outliers final: 20 residues processed: 139 average time/residue: 1.3298 time to fit residues: 196.9690 Evaluate side-chains 130 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 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 277 SER Chi-restraints excluded: chain B residue 318 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 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 271 LEU Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 337 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 58 optimal weight: 0.8980 chunk 9 optimal weight: 0.3980 chunk 20 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 41 optimal weight: 0.2980 chunk 65 optimal weight: 0.6980 chunk 91 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 17 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.165296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.126294 restraints weight = 10941.516| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.71 r_work: 0.3402 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9264 Z= 0.134 Angle : 0.489 6.971 12575 Z= 0.262 Chirality : 0.041 0.179 1401 Planarity : 0.003 0.052 1593 Dihedral : 5.444 44.318 1403 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.54 % Allowed : 20.72 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.25), residues: 1121 helix: 2.09 (0.26), residues: 432 sheet: 0.31 (0.34), residues: 220 loop : -0.95 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 99 HIS 0.006 0.001 HIS A 220 PHE 0.024 0.001 PHE A 222 TYR 0.011 0.001 TYR N 60 ARG 0.005 0.000 ARG R 404 *********************** 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 134 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 1.152 Fit side-chains REVERT: A 60 MET cc_start: 0.3163 (mtm) cc_final: 0.2601 (mtm) REVERT: A 265 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.6558 (ttt-90) REVERT: A 307 LYS cc_start: 0.5885 (tptt) cc_final: 0.5300 (pmtt) REVERT: A 372 ILE cc_start: 0.7846 (pt) cc_final: 0.7454 (mp) REVERT: B 101 MET cc_start: 0.8608 (mtp) cc_final: 0.8366 (mtp) REVERT: N 1 GLN cc_start: 0.7334 (tt0) cc_final: 0.6599 (tm-30) REVERT: N 89 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: P 8 MET cc_start: 0.7950 (ttt) cc_final: 0.7622 (ttt) REVERT: P 17 ASN cc_start: 0.7771 (t0) cc_final: 0.7524 (t0) REVERT: R 79 TRP cc_start: 0.2545 (OUTLIER) cc_final: 0.1440 (m100) REVERT: R 131 TYR cc_start: 0.3842 (m-80) cc_final: 0.2770 (m-10) REVERT: R 161 PHE cc_start: 0.6706 (t80) cc_final: 0.6483 (t80) REVERT: R 172 PHE cc_start: 0.5275 (t80) cc_final: 0.4751 (t80) REVERT: R 210 GLU cc_start: 0.6440 (mp0) cc_final: 0.6161 (mp0) REVERT: R 300 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8073 (mp) REVERT: R 397 GLU cc_start: 0.6914 (tt0) cc_final: 0.6549 (tm-30) outliers start: 24 outliers final: 13 residues processed: 129 average time/residue: 1.3762 time to fit residues: 189.0167 Evaluate side-chains 122 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 40 VAL 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 214 ARG Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 30 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 300 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 87 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 52 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 66 optimal weight: 0.5980 chunk 97 optimal weight: 5.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 17 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.162588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.124780 restraints weight = 11005.461| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.86 r_work: 0.3354 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9264 Z= 0.342 Angle : 0.648 8.849 12575 Z= 0.345 Chirality : 0.048 0.217 1401 Planarity : 0.005 0.053 1593 Dihedral : 6.058 44.138 1403 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.28 % Allowed : 20.30 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.25), residues: 1121 helix: 1.37 (0.25), residues: 439 sheet: 0.08 (0.34), residues: 222 loop : -1.20 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 236 HIS 0.012 0.002 HIS A 220 PHE 0.033 0.003 PHE A 222 TYR 0.021 0.002 TYR A 358 ARG 0.006 0.001 ARG B 42 ********************** 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 135 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 1.052 Fit side-chains REVERT: A 60 MET cc_start: 0.3321 (mtm) cc_final: 0.2709 (mtm) REVERT: A 265 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.6558 (ttt-90) REVERT: A 307 LYS cc_start: 0.5878 (tptt) cc_final: 0.5373 (pmtt) REVERT: A 372 ILE cc_start: 0.7861 (pt) cc_final: 0.7425 (mp) REVERT: B 101 MET cc_start: 0.8576 (mtp) cc_final: 0.8320 (mtp) REVERT: B 130 GLU cc_start: 0.4856 (OUTLIER) cc_final: 0.4140 (mt-10) REVERT: G 19 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7515 (mm) REVERT: N 1 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.6647 (tm-30) REVERT: N 89 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7370 (mp0) REVERT: R 79 TRP cc_start: 0.2488 (OUTLIER) cc_final: 0.1370 (m100) REVERT: R 161 PHE cc_start: 0.6736 (t80) cc_final: 0.6487 (t80) REVERT: R 172 PHE cc_start: 0.5379 (t80) cc_final: 0.4832 (t80) REVERT: R 300 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8199 (mt) REVERT: R 334 GLU cc_start: 0.6326 (mp0) cc_final: 0.5487 (mp0) REVERT: R 397 GLU cc_start: 0.6867 (tt0) cc_final: 0.6525 (tm-30) outliers start: 31 outliers final: 18 residues processed: 124 average time/residue: 1.4855 time to fit residues: 195.5678 Evaluate side-chains 127 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 1.084 ------------------------------------------------------------------------------- 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 265 ARG Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 61 MET 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 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 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 300 ILE Chi-restraints excluded: chain R residue 337 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.165050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.127416 restraints weight = 10917.748| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.86 r_work: 0.3389 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9264 Z= 0.190 Angle : 0.542 9.562 12575 Z= 0.288 Chirality : 0.043 0.188 1401 Planarity : 0.004 0.053 1593 Dihedral : 5.729 43.797 1403 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.43 % Allowed : 21.56 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.25), residues: 1121 helix: 1.75 (0.25), residues: 435 sheet: 0.34 (0.35), residues: 214 loop : -1.10 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 99 HIS 0.008 0.001 HIS A 220 PHE 0.025 0.002 PHE A 222 TYR 0.012 0.001 TYR A 358 ARG 0.005 0.000 ARG B 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8007.73 seconds wall clock time: 141 minutes 56.09 seconds (8516.09 seconds total)