Starting phenix.real_space_refine on Sun May 3 00:01:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n1p_48820/05_2026/9n1p_48820.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n1p_48820/05_2026/9n1p_48820.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n1p_48820/05_2026/9n1p_48820.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n1p_48820/05_2026/9n1p_48820.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n1p_48820/05_2026/9n1p_48820.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n1p_48820/05_2026/9n1p_48820.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.096 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 54 5.16 5 C 5845 2.51 5 N 1595 2.21 5 O 1698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9192 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1881 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 2 Chain: "B" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2615 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} 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: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 249 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AIB:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3031 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 14, 'TRANS': 359} Chain breaks: 3 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2, 'PHE:plan': 2, 'ARG:plan': 1, 'TRP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 56 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "R" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 1.98, per 1000 atoms: 0.22 Number of scatterers: 9192 At special positions: 0 Unit cell: (96.1053, 100.514, 171.931, 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 54 16.00 O 1698 8.00 N 1595 7.00 C 5845 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.02 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.04 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 367.3 milliseconds 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2176 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 12 sheets defined 39.5% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 11 through 30 removed outlier: 3.736A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS A 28 " --> pdb=" O LYS A 24 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 39 Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.633A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.517A pdb=" N LEU A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.788A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 350 removed outlier: 3.860A pdb=" N LYS A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TYR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 2 through 26 removed outlier: 3.571A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP B 20 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.539A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 22 removed outlier: 3.533A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.656A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.684A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'P' and resid 2 through 27 removed outlier: 4.559A pdb=" N ASP P 15 " --> pdb=" O SER P 11 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE P 23 " --> pdb=" O ALA P 19 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 53 removed outlier: 3.875A pdb=" N THR R 51 " --> pdb=" O GLN R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 169 removed outlier: 3.943A pdb=" N PHE R 143 " --> pdb=" O GLU R 139 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL R 150 " --> pdb=" O ILE R 146 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL R 160 " --> pdb=" O PHE R 156 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER R 163 " --> pdb=" O LEU R 159 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE R 165 " --> pdb=" O ILE R 161 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU R 166 " --> pdb=" O ALA R 162 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU R 167 " --> pdb=" O SER R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 205 removed outlier: 3.620A pdb=" N ARG R 190 " --> pdb=" O SER R 186 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL R 194 " --> pdb=" O ARG R 190 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE R 195 " --> pdb=" O ALA R 191 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE R 196 " --> pdb=" O LEU R 192 " (cutoff:3.500A) Processing helix chain 'R' and resid 214 through 222 removed outlier: 3.913A pdb=" N TYR R 220 " --> pdb=" O GLY R 216 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN R 221 " --> pdb=" O LEU R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 239 removed outlier: 3.979A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU R 232 " --> pdb=" O LEU R 228 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN R 234 " --> pdb=" O PHE R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 242 through 256 removed outlier: 3.605A pdb=" N GLY R 248 " --> pdb=" O LEU R 244 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU R 255 " --> pdb=" O LEU R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 276 removed outlier: 3.565A pdb=" N LEU R 268 " --> pdb=" O TRP R 264 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 279 No H-bonds generated for 'chain 'R' and resid 277 through 279' Processing helix chain 'R' and resid 280 through 291 Processing helix chain 'R' and resid 302 through 338 removed outlier: 4.140A pdb=" N ILE R 308 " --> pdb=" O ASN R 304 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix removed outlier: 3.677A pdb=" N ALA R 316 " --> pdb=" O PRO R 312 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE R 321 " --> pdb=" O ILE R 317 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU R 322 " --> pdb=" O GLY R 318 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA R 337 " --> pdb=" O SER R 333 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN R 338 " --> pdb=" O LYS R 334 " (cutoff:3.500A) Processing helix chain 'R' and resid 345 through 355 removed outlier: 4.168A pdb=" N LYS R 351 " --> pdb=" O CYS R 347 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR R 353 " --> pdb=" O LEU R 349 " (cutoff:3.500A) Processing helix chain 'R' and resid 356 through 361 removed outlier: 3.572A pdb=" N LEU R 360 " --> pdb=" O LEU R 356 " (cutoff:3.500A) Processing helix chain 'R' and resid 362 through 366 removed outlier: 3.943A pdb=" N ILE R 366 " --> pdb=" O HIS R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 371 through 375 removed outlier: 3.793A pdb=" N ALA R 375 " --> pdb=" O ASP R 372 " (cutoff:3.500A) Processing helix chain 'R' and resid 376 through 378 No H-bonds generated for 'chain 'R' and resid 376 through 378' Processing helix chain 'R' and resid 379 through 402 removed outlier: 3.786A pdb=" N LEU R 384 " --> pdb=" O ARG R 380 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE R 385 " --> pdb=" O PHE R 381 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER R 392 " --> pdb=" O LEU R 388 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE R 393 " --> pdb=" O SER R 389 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA R 399 " --> pdb=" O GLY R 395 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 413 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.072A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.408A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.655A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.775A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.893A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.921A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.715A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.471A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.910A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.532A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.955A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 65 through 66 removed outlier: 4.198A pdb=" N THR R 65 " --> pdb=" O TRP R 72 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TRP R 72 " --> pdb=" O THR R 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'R' and resid 79 through 84 removed outlier: 4.000A pdb=" N ARG R 102 " --> pdb=" O VAL R 81 " (cutoff:3.500A) 363 hydrogen bonds defined for protein. 1041 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: 1.26 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1745 1.33 - 1.45: 2478 1.45 - 1.57: 5099 1.57 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 9394 Sorted by residual: bond pdb=" N VAL R 259 " pdb=" CA VAL R 259 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.17e-02 7.31e+03 1.23e+01 bond pdb=" N GLY R 98 " pdb=" CA GLY R 98 " ideal model delta sigma weight residual 1.444 1.478 -0.033 9.60e-03 1.09e+04 1.22e+01 bond pdb=" N VAL R 100 " pdb=" CA VAL R 100 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.14e-02 7.69e+03 1.14e+01 bond pdb=" N VAL R 83 " pdb=" CA VAL R 83 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.14e-02 7.69e+03 1.09e+01 bond pdb=" N ILE R 366 " pdb=" CA ILE R 366 " ideal model delta sigma weight residual 1.460 1.499 -0.039 1.19e-02 7.06e+03 1.08e+01 ... (remaining 9389 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 11915 2.15 - 4.30: 742 4.30 - 6.45: 67 6.45 - 8.60: 8 8.60 - 10.75: 3 Bond angle restraints: 12735 Sorted by residual: angle pdb=" N ASN R 63 " pdb=" CA ASN R 63 " pdb=" C ASN R 63 " ideal model delta sigma weight residual 111.04 121.79 -10.75 1.55e+00 4.16e-01 4.81e+01 angle pdb=" N LYS P 12 " pdb=" CA LYS P 12 " pdb=" C LYS P 12 " ideal model delta sigma weight residual 113.55 105.28 8.27 1.26e+00 6.30e-01 4.31e+01 angle pdb=" C CYS R 296 " pdb=" CA CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sigma weight residual 111.89 119.36 -7.47 1.42e+00 4.96e-01 2.77e+01 angle pdb=" N ARG R 380 " pdb=" CA ARG R 380 " pdb=" C ARG R 380 " ideal model delta sigma weight residual 113.28 106.96 6.32 1.22e+00 6.72e-01 2.69e+01 angle pdb=" C PHE R 369 " pdb=" CA PHE R 369 " pdb=" CB PHE R 369 " ideal model delta sigma weight residual 110.09 118.68 -8.59 1.67e+00 3.59e-01 2.65e+01 ... (remaining 12730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 4927 16.10 - 32.19: 463 32.19 - 48.29: 119 48.29 - 64.38: 28 64.38 - 80.48: 13 Dihedral angle restraints: 5550 sinusoidal: 2183 harmonic: 3367 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 165.07 -72.07 1 1.00e+01 1.00e-02 6.64e+01 dihedral pdb=" C CYS R 296 " pdb=" N CYS R 296 " pdb=" CA CYS R 296 " pdb=" CB CYS R 296 " ideal model delta harmonic sigma weight residual -122.60 -140.15 17.55 0 2.50e+00 1.60e-01 4.93e+01 dihedral pdb=" N CYS R 296 " pdb=" C CYS R 296 " pdb=" CA CYS R 296 " pdb=" CB CYS R 296 " ideal model delta harmonic sigma weight residual 122.80 138.54 -15.74 0 2.50e+00 1.60e-01 3.96e+01 ... (remaining 5547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 1287 0.127 - 0.254: 106 0.254 - 0.381: 8 0.381 - 0.507: 0 0.507 - 0.634: 1 Chirality restraints: 1402 Sorted by residual: chirality pdb=" CA CYS R 296 " pdb=" N CYS R 296 " pdb=" C CYS R 296 " pdb=" CB CYS R 296 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" CA PHE R 369 " pdb=" N PHE R 369 " pdb=" C PHE R 369 " pdb=" CB PHE R 369 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" CA LEU R 379 " pdb=" N LEU R 379 " pdb=" C LEU R 379 " pdb=" CB LEU R 379 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.78e+00 ... (remaining 1399 not shown) Planarity restraints: 1621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 52 " 0.040 5.00e-02 4.00e+02 6.16e-02 6.07e+00 pdb=" N PRO G 53 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO G 60 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.73e+00 pdb=" C PRO G 60 " 0.041 2.00e-02 2.50e+03 pdb=" O PRO G 60 " -0.016 2.00e-02 2.50e+03 pdb=" N PHE G 61 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " -0.035 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO G 49 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " -0.029 5.00e-02 4.00e+02 ... (remaining 1618 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1670 2.77 - 3.30: 8186 3.30 - 3.84: 13750 3.84 - 4.37: 18076 4.37 - 4.90: 30505 Nonbonded interactions: 72187 Sorted by model distance: nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.238 3.040 nonbonded pdb=" O LEU R 244 " pdb=" ND2 ASN R 320 " model vdw 2.240 3.120 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.262 3.040 nonbonded pdb=" ND2 ASN B 230 " pdb=" OD1 ASP B 246 " model vdw 2.335 3.120 nonbonded pdb=" NE2 HIS B 225 " pdb=" OG1 THR B 243 " model vdw 2.335 3.120 ... (remaining 72182 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=1.00 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: 1.980 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: 0.160 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 8.770 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 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 : 0.008 0.046 9399 Z= 0.505 Angle : 1.081 10.751 12745 Z= 0.746 Chirality : 0.071 0.634 1402 Planarity : 0.005 0.062 1621 Dihedral : 14.198 80.481 3359 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.41 % Allowed : 2.76 % Favored : 96.84 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.22), residues: 1132 helix: -2.48 (0.21), residues: 406 sheet: 0.02 (0.37), residues: 198 loop : -1.72 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 67 TYR 0.032 0.003 TYR B 105 PHE 0.023 0.002 PHE R 280 TRP 0.033 0.003 TRP B 82 HIS 0.009 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00766 ( 9394) covalent geometry : angle 1.07862 (12735) SS BOND : bond 0.00696 ( 5) SS BOND : angle 2.68083 ( 10) hydrogen bonds : bond 0.30753 ( 363) hydrogen bonds : angle 9.22662 ( 1041) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 136 time to evaluate : 0.338 Fit side-chains REVERT: A 17 LYS cc_start: 0.8006 (mtmt) cc_final: 0.7558 (pmtt) REVERT: B 134 ARG cc_start: 0.6970 (ptm-80) cc_final: 0.6465 (ppt170) REVERT: G 21 MET cc_start: 0.6687 (mmm) cc_final: 0.6391 (tmt) REVERT: G 47 GLU cc_start: 0.7720 (mp0) cc_final: 0.7510 (mp0) REVERT: R 202 LYS cc_start: 0.7227 (ttmt) cc_final: 0.6776 (mmtt) outliers start: 4 outliers final: 1 residues processed: 140 average time/residue: 0.5864 time to fit residues: 87.2785 Evaluate side-chains 108 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 137 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.0770 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN B 268 ASN B 295 ASN R 240 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.182456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.138067 restraints weight = 9708.581| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.90 r_work: 0.3252 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9399 Z= 0.127 Angle : 0.587 7.228 12745 Z= 0.318 Chirality : 0.043 0.163 1402 Planarity : 0.005 0.051 1621 Dihedral : 5.051 23.679 1268 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.24 % Allowed : 9.18 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.36 (0.23), residues: 1132 helix: -0.83 (0.24), residues: 417 sheet: 0.54 (0.35), residues: 216 loop : -1.56 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 38 TYR 0.028 0.001 TYR R 148 PHE 0.012 0.001 PHE A 212 TRP 0.015 0.001 TRP A 234 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9394) covalent geometry : angle 0.58658 (12735) SS BOND : bond 0.00372 ( 5) SS BOND : angle 0.91681 ( 10) hydrogen bonds : bond 0.06074 ( 363) hydrogen bonds : angle 4.95664 ( 1041) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.294 Fit side-chains REVERT: A 17 LYS cc_start: 0.7864 (mtmt) cc_final: 0.7151 (pmtt) REVERT: A 392 GLU cc_start: 0.7407 (mm-30) cc_final: 0.6522 (tm-30) REVERT: B 134 ARG cc_start: 0.7175 (ptm-80) cc_final: 0.6604 (ppt170) REVERT: B 197 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.6599 (mpp-170) REVERT: B 221 THR cc_start: 0.8903 (t) cc_final: 0.8370 (m) REVERT: G 21 MET cc_start: 0.7002 (mmm) cc_final: 0.6069 (tmt) REVERT: P 10 TYR cc_start: 0.6870 (OUTLIER) cc_final: 0.6191 (t80) REVERT: R 34 GLU cc_start: 0.6157 (OUTLIER) cc_final: 0.5183 (pt0) REVERT: R 202 LYS cc_start: 0.6084 (ttmt) cc_final: 0.5426 (mptp) REVERT: R 335 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7120 (pp) REVERT: R 420 TRP cc_start: 0.6518 (t60) cc_final: 0.6193 (t-100) outliers start: 22 outliers final: 6 residues processed: 128 average time/residue: 0.5624 time to fit residues: 76.6681 Evaluate side-chains 106 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain R residue 34 GLU Chi-restraints excluded: chain R residue 306 TRP Chi-restraints excluded: chain R residue 335 LEU Chi-restraints excluded: chain R residue 374 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 49 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 67 optimal weight: 0.0030 chunk 97 optimal weight: 5.9990 chunk 79 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 72 optimal weight: 0.0870 chunk 91 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 overall best weight: 0.7770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN B 88 ASN B 237 ASN B 268 ASN R 406 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.180149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.136924 restraints weight = 9897.696| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.79 r_work: 0.3236 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9399 Z= 0.127 Angle : 0.565 8.231 12745 Z= 0.301 Chirality : 0.042 0.162 1402 Planarity : 0.004 0.047 1621 Dihedral : 4.738 20.282 1265 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.06 % Allowed : 12.14 % Favored : 84.80 % 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: -0.80 (0.24), residues: 1132 helix: 0.08 (0.25), residues: 419 sheet: 0.57 (0.36), residues: 205 loop : -1.51 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 347 TYR 0.022 0.001 TYR R 148 PHE 0.017 0.001 PHE R 280 TRP 0.013 0.001 TRP R 306 HIS 0.009 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9394) covalent geometry : angle 0.56372 (12735) SS BOND : bond 0.00326 ( 5) SS BOND : angle 1.33123 ( 10) hydrogen bonds : bond 0.05287 ( 363) hydrogen bonds : angle 4.43941 ( 1041) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.278 Fit side-chains REVERT: A 17 LYS cc_start: 0.7852 (mtmt) cc_final: 0.7105 (pmtt) REVERT: A 392 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6602 (tm-30) REVERT: B 134 ARG cc_start: 0.7184 (ptm-80) cc_final: 0.6592 (ppt170) REVERT: B 197 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.6828 (mpp-170) REVERT: B 221 THR cc_start: 0.8935 (t) cc_final: 0.8431 (m) REVERT: B 325 MET cc_start: 0.8285 (mmm) cc_final: 0.8008 (mmt) REVERT: G 21 MET cc_start: 0.6952 (mmm) cc_final: 0.6100 (tmt) REVERT: P 10 TYR cc_start: 0.6649 (OUTLIER) cc_final: 0.6133 (t80) REVERT: R 267 ARG cc_start: 0.6913 (mtm180) cc_final: 0.6551 (mtt180) REVERT: R 420 TRP cc_start: 0.6457 (t60) cc_final: 0.6140 (t-100) outliers start: 30 outliers final: 14 residues processed: 125 average time/residue: 0.6049 time to fit residues: 80.2129 Evaluate side-chains 112 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 291 TYR Chi-restraints excluded: chain R residue 306 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 1 optimal weight: 0.9990 chunk 52 optimal weight: 0.0170 chunk 104 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 54 ASN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.181097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.138074 restraints weight = 9959.589| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.86 r_work: 0.3222 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9399 Z= 0.114 Angle : 0.541 13.025 12745 Z= 0.284 Chirality : 0.042 0.156 1402 Planarity : 0.004 0.044 1621 Dihedral : 4.554 19.742 1265 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.96 % Allowed : 13.27 % Favored : 83.78 % 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: -0.47 (0.24), residues: 1132 helix: 0.53 (0.26), residues: 429 sheet: 0.68 (0.35), residues: 217 loop : -1.56 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 347 TYR 0.022 0.001 TYR R 148 PHE 0.014 0.001 PHE R 280 TRP 0.012 0.001 TRP R 306 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 9394) covalent geometry : angle 0.53869 (12735) SS BOND : bond 0.00402 ( 5) SS BOND : angle 1.80311 ( 10) hydrogen bonds : bond 0.04599 ( 363) hydrogen bonds : angle 4.14825 ( 1041) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.357 Fit side-chains REVERT: A 17 LYS cc_start: 0.7831 (mtmt) cc_final: 0.7004 (pmtt) REVERT: A 356 ARG cc_start: 0.7463 (mpt90) cc_final: 0.6786 (mtp180) REVERT: A 392 GLU cc_start: 0.7373 (mm-30) cc_final: 0.6718 (tm-30) REVERT: B 42 ARG cc_start: 0.7777 (tpt170) cc_final: 0.7532 (tpt170) REVERT: B 66 ASP cc_start: 0.7434 (p0) cc_final: 0.7053 (p0) REVERT: B 134 ARG cc_start: 0.7223 (ptm-80) cc_final: 0.6623 (ppt170) REVERT: B 197 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.6740 (mpp-170) REVERT: B 221 THR cc_start: 0.8925 (t) cc_final: 0.8422 (m) REVERT: B 325 MET cc_start: 0.8243 (mmm) cc_final: 0.7944 (mmt) REVERT: B 336 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8660 (mp) REVERT: G 21 MET cc_start: 0.6938 (mmm) cc_final: 0.6077 (tmt) REVERT: N 58 ILE cc_start: 0.8540 (mt) cc_final: 0.8337 (mt) REVERT: P 10 TYR cc_start: 0.6703 (OUTLIER) cc_final: 0.6298 (t80) REVERT: R 267 ARG cc_start: 0.6820 (mtm180) cc_final: 0.6426 (mtt180) REVERT: R 420 TRP cc_start: 0.6399 (t60) cc_final: 0.6052 (t-100) outliers start: 29 outliers final: 12 residues processed: 124 average time/residue: 0.6206 time to fit residues: 81.8016 Evaluate side-chains 116 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 291 TYR Chi-restraints excluded: chain R residue 306 TRP Chi-restraints excluded: chain R residue 374 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 18 optimal weight: 0.0770 chunk 67 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 82 optimal weight: 0.0870 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.5716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN B 237 ASN B 268 ASN N 35 ASN R 180 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.181415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.138448 restraints weight = 9981.503| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.82 r_work: 0.3227 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9399 Z= 0.105 Angle : 0.526 9.855 12745 Z= 0.277 Chirality : 0.041 0.152 1402 Planarity : 0.004 0.042 1621 Dihedral : 4.381 19.022 1265 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.65 % Allowed : 15.61 % Favored : 81.73 % 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: -0.23 (0.24), residues: 1132 helix: 0.84 (0.26), residues: 428 sheet: 0.78 (0.36), residues: 210 loop : -1.50 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 347 TYR 0.021 0.001 TYR R 148 PHE 0.013 0.001 PHE R 280 TRP 0.013 0.001 TRP R 306 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 9394) covalent geometry : angle 0.52228 (12735) SS BOND : bond 0.00274 ( 5) SS BOND : angle 2.17369 ( 10) hydrogen bonds : bond 0.04297 ( 363) hydrogen bonds : angle 3.95610 ( 1041) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.357 Fit side-chains REVERT: A 17 LYS cc_start: 0.7782 (mtmt) cc_final: 0.6845 (pptt) REVERT: A 356 ARG cc_start: 0.7453 (mpt90) cc_final: 0.6801 (mtp180) REVERT: A 392 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6699 (tm-30) REVERT: B 42 ARG cc_start: 0.7752 (tpt170) cc_final: 0.7475 (tpt170) REVERT: B 66 ASP cc_start: 0.7448 (p0) cc_final: 0.7075 (p0) REVERT: B 134 ARG cc_start: 0.7213 (ptm-80) cc_final: 0.6608 (ppt170) REVERT: B 197 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.6698 (mpp-170) REVERT: B 215 GLU cc_start: 0.7982 (pt0) cc_final: 0.7672 (pp20) REVERT: B 221 THR cc_start: 0.8884 (t) cc_final: 0.8403 (m) REVERT: B 325 MET cc_start: 0.8187 (mmm) cc_final: 0.7901 (mmt) REVERT: B 336 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8643 (mp) REVERT: G 21 MET cc_start: 0.6862 (mmm) cc_final: 0.6057 (tmt) REVERT: P 10 TYR cc_start: 0.6784 (OUTLIER) cc_final: 0.6389 (t80) REVERT: R 267 ARG cc_start: 0.6789 (mtm180) cc_final: 0.6400 (mtt180) REVERT: R 289 TYR cc_start: 0.7192 (t80) cc_final: 0.6355 (t80) REVERT: R 294 GLU cc_start: 0.5563 (OUTLIER) cc_final: 0.5132 (mp0) REVERT: R 420 TRP cc_start: 0.6338 (t60) cc_final: 0.5988 (t-100) outliers start: 26 outliers final: 14 residues processed: 120 average time/residue: 0.6112 time to fit residues: 77.8283 Evaluate side-chains 118 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 291 TYR Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 374 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 0 optimal weight: 6.9990 chunk 101 optimal weight: 0.2980 chunk 46 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN B 268 ASN N 35 ASN N 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.179181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.135439 restraints weight = 9987.228| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.98 r_work: 0.3185 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9399 Z= 0.134 Angle : 0.559 7.787 12745 Z= 0.296 Chirality : 0.043 0.159 1402 Planarity : 0.004 0.041 1621 Dihedral : 4.505 19.691 1265 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.06 % Allowed : 16.12 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.24), residues: 1132 helix: 0.90 (0.26), residues: 429 sheet: 0.87 (0.37), residues: 205 loop : -1.49 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 67 TYR 0.020 0.002 TYR R 148 PHE 0.017 0.002 PHE R 280 TRP 0.011 0.001 TRP A 234 HIS 0.010 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9394) covalent geometry : angle 0.55397 (12735) SS BOND : bond 0.00346 ( 5) SS BOND : angle 2.72743 ( 10) hydrogen bonds : bond 0.04716 ( 363) hydrogen bonds : angle 4.02494 ( 1041) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 0.344 Fit side-chains REVERT: A 17 LYS cc_start: 0.7866 (mtmt) cc_final: 0.6943 (pptt) REVERT: A 356 ARG cc_start: 0.7535 (mpt90) cc_final: 0.6877 (mtp180) REVERT: A 392 GLU cc_start: 0.7445 (mm-30) cc_final: 0.6783 (tm-30) REVERT: B 32 GLN cc_start: 0.6862 (OUTLIER) cc_final: 0.6640 (tt0) REVERT: B 42 ARG cc_start: 0.7787 (tpt170) cc_final: 0.7478 (tpt170) REVERT: B 66 ASP cc_start: 0.7517 (p0) cc_final: 0.7132 (p0) REVERT: B 134 ARG cc_start: 0.7224 (ptm-80) cc_final: 0.6612 (ppt170) REVERT: B 197 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.6896 (mpp-170) REVERT: B 221 THR cc_start: 0.8946 (t) cc_final: 0.8466 (m) REVERT: B 251 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.7686 (mtt180) REVERT: B 325 MET cc_start: 0.8267 (mmm) cc_final: 0.7945 (mmt) REVERT: B 336 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8687 (mp) REVERT: G 21 MET cc_start: 0.6891 (mmm) cc_final: 0.6124 (tmt) REVERT: N 5 GLN cc_start: 0.6852 (OUTLIER) cc_final: 0.6533 (mm-40) REVERT: P 10 TYR cc_start: 0.6860 (OUTLIER) cc_final: 0.6429 (t80) REVERT: P 12 LYS cc_start: 0.5473 (OUTLIER) cc_final: 0.4764 (mtmp) REVERT: R 228 LEU cc_start: 0.7340 (mm) cc_final: 0.6678 (tm) REVERT: R 289 TYR cc_start: 0.7281 (t80) cc_final: 0.6513 (t80) REVERT: R 292 GLU cc_start: 0.6229 (OUTLIER) cc_final: 0.5548 (tt0) REVERT: R 294 GLU cc_start: 0.5717 (OUTLIER) cc_final: 0.5241 (mp0) REVERT: R 420 TRP cc_start: 0.6362 (t60) cc_final: 0.6012 (t-100) outliers start: 30 outliers final: 15 residues processed: 120 average time/residue: 0.6235 time to fit residues: 79.3315 Evaluate side-chains 124 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 291 TYR Chi-restraints excluded: chain R residue 292 GLU Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 374 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 99 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 94 optimal weight: 0.0670 chunk 68 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.180590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.138295 restraints weight = 10007.992| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.92 r_work: 0.3235 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9399 Z= 0.111 Angle : 0.528 8.215 12745 Z= 0.279 Chirality : 0.041 0.164 1402 Planarity : 0.004 0.040 1621 Dihedral : 4.364 19.168 1265 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.47 % Allowed : 16.12 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.25), residues: 1132 helix: 1.11 (0.26), residues: 428 sheet: 0.70 (0.36), residues: 211 loop : -1.48 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 347 TYR 0.020 0.001 TYR R 148 PHE 0.014 0.001 PHE R 393 TRP 0.012 0.001 TRP A 234 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 9394) covalent geometry : angle 0.52438 (12735) SS BOND : bond 0.00164 ( 5) SS BOND : angle 2.14258 ( 10) hydrogen bonds : bond 0.04333 ( 363) hydrogen bonds : angle 3.91234 ( 1041) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 106 time to evaluate : 0.351 Fit side-chains REVERT: A 17 LYS cc_start: 0.7898 (mtmt) cc_final: 0.6991 (pptt) REVERT: A 356 ARG cc_start: 0.7466 (mpt90) cc_final: 0.6927 (mtp180) REVERT: A 392 GLU cc_start: 0.7328 (mm-30) cc_final: 0.6691 (tm-30) REVERT: B 32 GLN cc_start: 0.6859 (OUTLIER) cc_final: 0.6638 (tt0) REVERT: B 42 ARG cc_start: 0.7752 (tpt170) cc_final: 0.7437 (tpt170) REVERT: B 66 ASP cc_start: 0.7519 (p0) cc_final: 0.7156 (p0) REVERT: B 134 ARG cc_start: 0.7207 (ptm-80) cc_final: 0.6593 (ppt170) REVERT: B 197 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.6864 (mpp-170) REVERT: B 221 THR cc_start: 0.8925 (t) cc_final: 0.8461 (m) REVERT: B 251 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.7770 (mtt180) REVERT: B 325 MET cc_start: 0.8211 (mmm) cc_final: 0.7931 (mmt) REVERT: B 336 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8654 (mp) REVERT: G 21 MET cc_start: 0.6877 (mmm) cc_final: 0.6159 (tmt) REVERT: N 5 GLN cc_start: 0.6783 (OUTLIER) cc_final: 0.6511 (mm-40) REVERT: P 10 TYR cc_start: 0.6801 (OUTLIER) cc_final: 0.6388 (t80) REVERT: R 228 LEU cc_start: 0.7501 (mm) cc_final: 0.6802 (tm) REVERT: R 289 TYR cc_start: 0.7159 (t80) cc_final: 0.6435 (t80) REVERT: R 290 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.6057 (mp) REVERT: R 382 ILE cc_start: 0.6077 (mm) cc_final: 0.5688 (tp) REVERT: R 420 TRP cc_start: 0.6327 (t60) cc_final: 0.5990 (t-100) outliers start: 34 outliers final: 16 residues processed: 126 average time/residue: 0.5860 time to fit residues: 78.5901 Evaluate side-chains 122 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 290 LEU Chi-restraints excluded: chain R residue 291 TYR Chi-restraints excluded: chain R residue 374 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 62 optimal weight: 0.0470 chunk 69 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 85 optimal weight: 0.0170 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.5716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.180217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.138727 restraints weight = 10056.392| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.83 r_work: 0.3227 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9399 Z= 0.104 Angle : 0.508 7.310 12745 Z= 0.270 Chirality : 0.041 0.168 1402 Planarity : 0.004 0.049 1621 Dihedral : 4.240 18.417 1265 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.55 % Allowed : 17.45 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.25), residues: 1132 helix: 1.28 (0.26), residues: 428 sheet: 0.84 (0.36), residues: 210 loop : -1.45 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.020 0.001 TYR R 148 PHE 0.013 0.001 PHE R 393 TRP 0.012 0.001 TRP A 234 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 9394) covalent geometry : angle 0.50510 (12735) SS BOND : bond 0.00230 ( 5) SS BOND : angle 1.92658 ( 10) hydrogen bonds : bond 0.04119 ( 363) hydrogen bonds : angle 3.81888 ( 1041) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.258 Fit side-chains REVERT: A 17 LYS cc_start: 0.7938 (mtmt) cc_final: 0.7018 (pptt) REVERT: A 356 ARG cc_start: 0.7562 (mpt90) cc_final: 0.6904 (mtp180) REVERT: A 392 GLU cc_start: 0.7394 (mm-30) cc_final: 0.6741 (tm-30) REVERT: B 32 GLN cc_start: 0.6849 (OUTLIER) cc_final: 0.6648 (tt0) REVERT: B 42 ARG cc_start: 0.7766 (tpt170) cc_final: 0.7446 (tpt170) REVERT: B 66 ASP cc_start: 0.7592 (p0) cc_final: 0.7236 (p0) REVERT: B 134 ARG cc_start: 0.7273 (ptm-80) cc_final: 0.6646 (ppt170) REVERT: B 197 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.6934 (mpp-170) REVERT: B 217 MET cc_start: 0.7680 (mtp) cc_final: 0.7316 (mtm) REVERT: B 221 THR cc_start: 0.8917 (t) cc_final: 0.8467 (m) REVERT: B 251 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.7820 (mtt180) REVERT: B 325 MET cc_start: 0.8228 (mmm) cc_final: 0.7955 (mmt) REVERT: B 336 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8666 (mp) REVERT: G 21 MET cc_start: 0.6923 (mmm) cc_final: 0.6144 (tmt) REVERT: N 5 GLN cc_start: 0.6804 (OUTLIER) cc_final: 0.6559 (mm-40) REVERT: P 10 TYR cc_start: 0.6870 (OUTLIER) cc_final: 0.6520 (t80) REVERT: R 228 LEU cc_start: 0.7566 (mm) cc_final: 0.6893 (tm) REVERT: R 289 TYR cc_start: 0.7220 (t80) cc_final: 0.6546 (t80) REVERT: R 290 LEU cc_start: 0.6666 (OUTLIER) cc_final: 0.6263 (mp) REVERT: R 345 ILE cc_start: 0.5621 (OUTLIER) cc_final: 0.5159 (mp) REVERT: R 382 ILE cc_start: 0.6126 (mm) cc_final: 0.5846 (tp) REVERT: R 420 TRP cc_start: 0.6278 (t60) cc_final: 0.5918 (t-100) outliers start: 25 outliers final: 13 residues processed: 119 average time/residue: 0.6459 time to fit residues: 81.5386 Evaluate side-chains 119 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 290 LEU Chi-restraints excluded: chain R residue 291 TYR Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 374 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 61 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 66 optimal weight: 0.0570 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 58 optimal weight: 0.0770 chunk 11 optimal weight: 1.9990 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.178636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.135370 restraints weight = 9877.212| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.83 r_work: 0.3193 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9399 Z= 0.132 Angle : 0.561 9.657 12745 Z= 0.296 Chirality : 0.043 0.183 1402 Planarity : 0.004 0.047 1621 Dihedral : 4.435 19.894 1265 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.96 % Allowed : 17.35 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.24), residues: 1132 helix: 1.13 (0.26), residues: 430 sheet: 0.66 (0.36), residues: 206 loop : -1.49 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 347 TYR 0.020 0.002 TYR R 148 PHE 0.017 0.002 PHE R 280 TRP 0.011 0.001 TRP R 306 HIS 0.009 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9394) covalent geometry : angle 0.55845 (12735) SS BOND : bond 0.00325 ( 5) SS BOND : angle 1.84020 ( 10) hydrogen bonds : bond 0.04703 ( 363) hydrogen bonds : angle 3.96950 ( 1041) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.365 Fit side-chains REVERT: A 17 LYS cc_start: 0.7852 (mtmt) cc_final: 0.6921 (pptt) REVERT: A 356 ARG cc_start: 0.7505 (mpt90) cc_final: 0.6891 (mtp180) REVERT: A 392 GLU cc_start: 0.7396 (mm-30) cc_final: 0.6708 (tm-30) REVERT: B 32 GLN cc_start: 0.6834 (OUTLIER) cc_final: 0.6614 (tt0) REVERT: B 42 ARG cc_start: 0.7770 (tpt170) cc_final: 0.7441 (tpt170) REVERT: B 134 ARG cc_start: 0.7190 (ptm-80) cc_final: 0.6564 (ppt170) REVERT: B 197 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.6961 (mpp-170) REVERT: B 217 MET cc_start: 0.7727 (mtp) cc_final: 0.7336 (mtm) REVERT: B 221 THR cc_start: 0.8940 (t) cc_final: 0.8451 (m) REVERT: B 251 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.7706 (mtt180) REVERT: B 325 MET cc_start: 0.8231 (mmm) cc_final: 0.7935 (mmt) REVERT: B 336 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8677 (mp) REVERT: G 21 MET cc_start: 0.6969 (mmm) cc_final: 0.6224 (tmt) REVERT: N 5 GLN cc_start: 0.6778 (OUTLIER) cc_final: 0.6508 (mm-40) REVERT: P 10 TYR cc_start: 0.6906 (OUTLIER) cc_final: 0.6495 (t80) REVERT: R 228 LEU cc_start: 0.7586 (mm) cc_final: 0.6949 (tm) REVERT: R 289 TYR cc_start: 0.7085 (t80) cc_final: 0.6448 (t80) REVERT: R 290 LEU cc_start: 0.6579 (OUTLIER) cc_final: 0.6134 (mp) REVERT: R 345 ILE cc_start: 0.5544 (OUTLIER) cc_final: 0.5080 (mp) REVERT: R 382 ILE cc_start: 0.6052 (mm) cc_final: 0.5810 (tp) REVERT: R 420 TRP cc_start: 0.6306 (t60) cc_final: 0.5899 (t-100) outliers start: 29 outliers final: 18 residues processed: 116 average time/residue: 0.6062 time to fit residues: 74.8679 Evaluate side-chains 122 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 290 LEU Chi-restraints excluded: chain R residue 291 TYR Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 374 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 31 optimal weight: 0.0570 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.179499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.138091 restraints weight = 10071.334| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.84 r_work: 0.3214 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9399 Z= 0.110 Angle : 0.522 7.302 12745 Z= 0.277 Chirality : 0.041 0.178 1402 Planarity : 0.004 0.044 1621 Dihedral : 4.287 18.898 1265 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.55 % Allowed : 17.86 % Favored : 79.59 % 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: 0.11 (0.25), residues: 1132 helix: 1.29 (0.26), residues: 429 sheet: 0.82 (0.36), residues: 212 loop : -1.41 (0.25), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 347 TYR 0.020 0.001 TYR R 148 PHE 0.015 0.001 PHE R 393 TRP 0.012 0.001 TRP R 306 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 9394) covalent geometry : angle 0.52034 (12735) SS BOND : bond 0.00253 ( 5) SS BOND : angle 1.69486 ( 10) hydrogen bonds : bond 0.04246 ( 363) hydrogen bonds : angle 3.86144 ( 1041) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.307 Fit side-chains REVERT: A 17 LYS cc_start: 0.7962 (mtmt) cc_final: 0.7026 (pptt) REVERT: A 356 ARG cc_start: 0.7550 (mpt90) cc_final: 0.6896 (mtp180) REVERT: A 392 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6732 (tm-30) REVERT: B 23 LYS cc_start: 0.6832 (tmtt) cc_final: 0.6626 (tmtt) REVERT: B 32 GLN cc_start: 0.6860 (OUTLIER) cc_final: 0.6647 (tt0) REVERT: B 42 ARG cc_start: 0.7789 (tpt170) cc_final: 0.7447 (tpt170) REVERT: B 66 ASP cc_start: 0.7575 (p0) cc_final: 0.7199 (p0) REVERT: B 134 ARG cc_start: 0.7240 (ptm-80) cc_final: 0.6615 (ppt170) REVERT: B 197 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.6823 (mpp-170) REVERT: B 217 MET cc_start: 0.7700 (mtp) cc_final: 0.7309 (mtm) REVERT: B 221 THR cc_start: 0.8943 (t) cc_final: 0.8494 (m) REVERT: B 325 MET cc_start: 0.8184 (mmm) cc_final: 0.7940 (mmt) REVERT: B 336 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8664 (mp) REVERT: G 21 MET cc_start: 0.6987 (mmm) cc_final: 0.6312 (tmt) REVERT: N 5 GLN cc_start: 0.6782 (OUTLIER) cc_final: 0.6531 (mm-40) REVERT: P 10 TYR cc_start: 0.6909 (OUTLIER) cc_final: 0.6502 (t80) REVERT: R 228 LEU cc_start: 0.7634 (mm) cc_final: 0.7021 (tm) REVERT: R 289 TYR cc_start: 0.7147 (t80) cc_final: 0.6511 (t80) REVERT: R 290 LEU cc_start: 0.6645 (OUTLIER) cc_final: 0.6200 (mp) REVERT: R 310 ARG cc_start: 0.7717 (mtp180) cc_final: 0.7387 (mtm180) REVERT: R 345 ILE cc_start: 0.5654 (OUTLIER) cc_final: 0.5214 (mp) REVERT: R 420 TRP cc_start: 0.6301 (t60) cc_final: 0.5926 (t-100) outliers start: 25 outliers final: 15 residues processed: 114 average time/residue: 0.6055 time to fit residues: 73.5931 Evaluate side-chains 118 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 290 LEU Chi-restraints excluded: chain R residue 291 TYR Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 374 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 26 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.178566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.136949 restraints weight = 9914.764| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.86 r_work: 0.3192 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9399 Z= 0.123 Angle : 0.550 10.069 12745 Z= 0.290 Chirality : 0.042 0.189 1402 Planarity : 0.004 0.042 1621 Dihedral : 4.365 19.230 1265 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.86 % Allowed : 17.65 % 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 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: 0.07 (0.25), residues: 1132 helix: 1.21 (0.26), residues: 429 sheet: 0.83 (0.36), residues: 212 loop : -1.40 (0.25), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 347 TYR 0.019 0.001 TYR R 148 PHE 0.017 0.001 PHE R 393 TRP 0.016 0.001 TRP R 203 HIS 0.009 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9394) covalent geometry : angle 0.54862 (12735) SS BOND : bond 0.00298 ( 5) SS BOND : angle 1.70119 ( 10) hydrogen bonds : bond 0.04526 ( 363) hydrogen bonds : angle 3.90180 ( 1041) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3602.31 seconds wall clock time: 61 minutes 55.46 seconds (3715.46 seconds total)