Starting phenix.real_space_refine on Wed Mar 4 02:52:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ral_4779/03_2026/6ral_4779.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ral_4779/03_2026/6ral_4779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ral_4779/03_2026/6ral_4779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ral_4779/03_2026/6ral_4779.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ral_4779/03_2026/6ral_4779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ral_4779/03_2026/6ral_4779.map" } resolution = 3.5 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= 0.003 sd= 0.065 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: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 2 5.21 5 S 25 5.16 5 C 6532 2.51 5 N 1783 2.21 5 O 1780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10127 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4662 Classifications: {'peptide': 583} Link IDs: {'PTRANS': 24, 'TRANS': 558} Chain: "B" Number of atoms: 4508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4508 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 18, 'TRANS': 552} Chain: "C" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 897 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.16, per 1000 atoms: 0.21 Number of scatterers: 10127 At special positions: 0 Unit cell: (102.315, 82.929, 155.088, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 25 16.00 P 5 15.00 Mg 2 11.99 O 1780 8.00 N 1783 7.00 C 6532 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 108 " distance=2.06 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: 0.65 Conformation dependent library (CDL) restraints added in 425.8 milliseconds 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2332 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 7 sheets defined 54.0% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 13 through 23 removed outlier: 3.558A pdb=" N ARG A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR A 21 " --> pdb=" O ARG A 17 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 22 " --> pdb=" O ILE A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 30 removed outlier: 3.661A pdb=" N VAL A 30 " --> pdb=" O ARG A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 44 removed outlier: 3.848A pdb=" N LEU A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.794A pdb=" N LYS A 51 " --> pdb=" O PRO A 47 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 118 removed outlier: 3.746A pdb=" N THR A 91 " --> pdb=" O HIS A 87 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU A 97 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP A 108 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 111 " --> pdb=" O PHE A 107 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASP A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 128 removed outlier: 3.766A pdb=" N ARG A 127 " --> pdb=" O GLY A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 138 through 152 removed outlier: 3.521A pdb=" N ASP A 142 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR A 149 " --> pdb=" O ASN A 145 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 152 " --> pdb=" O ILE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 159 Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.630A pdb=" N GLY A 164 " --> pdb=" O PHE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 173 removed outlier: 3.554A pdb=" N LEU A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 172 " --> pdb=" O PHE A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 181 removed outlier: 3.744A pdb=" N LEU A 178 " --> pdb=" O PRO A 174 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 200 removed outlier: 3.891A pdb=" N THR A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY A 197 " --> pdb=" O TRP A 193 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 216 removed outlier: 3.730A pdb=" N MET A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU A 207 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 222 Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 231 through 242 removed outlier: 3.618A pdb=" N GLU A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 253 through 276 removed outlier: 3.626A pdb=" N ALA A 258 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LEU A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE A 260 " --> pdb=" O TRP A 256 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N PHE A 261 " --> pdb=" O PHE A 257 " (cutoff:3.500A) Proline residue: A 262 - end of helix removed outlier: 3.546A pdb=" N ASP A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 286 removed outlier: 3.785A pdb=" N VAL A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 294 removed outlier: 3.547A pdb=" N LEU A 293 " --> pdb=" O SER A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 304 Processing helix chain 'A' and resid 304 through 313 Processing helix chain 'A' and resid 313 through 322 Processing helix chain 'A' and resid 323 through 331 Processing helix chain 'A' and resid 399 through 403 Processing helix chain 'A' and resid 423 through 427 removed outlier: 3.935A pdb=" N TYR A 427 " --> pdb=" O VAL A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 435 removed outlier: 3.859A pdb=" N ARG A 433 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 473 removed outlier: 3.592A pdb=" N VAL A 466 " --> pdb=" O PRO A 462 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU A 468 " --> pdb=" O GLU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 482 removed outlier: 4.107A pdb=" N ILE A 479 " --> pdb=" O ALA A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 487 removed outlier: 4.021A pdb=" N GLN A 487 " --> pdb=" O LYS A 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 484 through 487' Processing helix chain 'A' and resid 504 through 513 removed outlier: 3.549A pdb=" N ALA A 510 " --> pdb=" O ALA A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 541 removed outlier: 3.503A pdb=" N LYS A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR A 541 " --> pdb=" O GLN A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 586 removed outlier: 3.703A pdb=" N LEU A 582 " --> pdb=" O SER A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 593 Processing helix chain 'B' and resid 7 through 12 removed outlier: 3.511A pdb=" N ARG B 11 " --> pdb=" O ALA B 7 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG B 12 " --> pdb=" O PRO B 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 7 through 12' Processing helix chain 'B' and resid 13 through 18 Processing helix chain 'B' and resid 20 through 25 Processing helix chain 'B' and resid 28 through 37 removed outlier: 3.518A pdb=" N VAL B 33 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER B 34 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 53 removed outlier: 3.654A pdb=" N ALA B 48 " --> pdb=" O PHE B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 71 removed outlier: 4.044A pdb=" N LEU B 63 " --> pdb=" O GLY B 59 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 86 removed outlier: 3.654A pdb=" N VAL B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 81 through 86' Processing helix chain 'B' and resid 87 through 101 removed outlier: 3.571A pdb=" N GLU B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP B 97 " --> pdb=" O ASP B 93 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 111 removed outlier: 3.893A pdb=" N TYR B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 106 through 111' Processing helix chain 'B' and resid 114 through 124 removed outlier: 3.769A pdb=" N LEU B 118 " --> pdb=" O ARG B 114 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG B 121 " --> pdb=" O ASP B 117 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN B 123 " --> pdb=" O MET B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 133 removed outlier: 3.536A pdb=" N MET B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 133 " --> pdb=" O VAL B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 155 removed outlier: 3.725A pdb=" N GLY B 140 " --> pdb=" O GLY B 136 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 143 " --> pdb=" O MET B 139 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER B 144 " --> pdb=" O GLY B 140 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR B 155 " --> pdb=" O PHE B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 163 Processing helix chain 'B' and resid 168 through 190 removed outlier: 3.980A pdb=" N ALA B 175 " --> pdb=" O GLY B 171 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG B 177 " --> pdb=" O PHE B 173 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N PHE B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU B 179 " --> pdb=" O ALA B 175 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 182 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 206 removed outlier: 3.728A pdb=" N THR B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B 202 " --> pdb=" O SER B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 223 through 226 removed outlier: 3.546A pdb=" N ASP B 226 " --> pdb=" O TRP B 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 223 through 226' Processing helix chain 'B' and resid 227 through 236 removed outlier: 3.523A pdb=" N VAL B 232 " --> pdb=" O ASN B 228 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU B 233 " --> pdb=" O ARG B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 269 removed outlier: 4.180A pdb=" N GLY B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B 258 " --> pdb=" O GLY B 254 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR B 259 " --> pdb=" O PHE B 255 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 260 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N MET B 267 " --> pdb=" O ALA B 263 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 285 removed outlier: 3.500A pdb=" N PHE B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 308 removed outlier: 4.013A pdb=" N ALA B 300 " --> pdb=" O GLY B 296 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.672A pdb=" N LEU B 312 " --> pdb=" O SER B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 381 removed outlier: 3.609A pdb=" N LEU B 380 " --> pdb=" O GLY B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 405 No H-bonds generated for 'chain 'B' and resid 403 through 405' Processing helix chain 'B' and resid 406 through 411 removed outlier: 3.579A pdb=" N ARG B 411 " --> pdb=" O LEU B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 441 through 448 removed outlier: 3.650A pdb=" N GLU B 445 " --> pdb=" O ARG B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 459 removed outlier: 3.972A pdb=" N LEU B 458 " --> pdb=" O HIS B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 489 removed outlier: 3.598A pdb=" N ALA B 486 " --> pdb=" O ARG B 482 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 518 Processing helix chain 'B' and resid 532 through 538 removed outlier: 3.830A pdb=" N LEU B 536 " --> pdb=" O ARG B 532 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N HIS B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 572 removed outlier: 3.709A pdb=" N ALA B 567 " --> pdb=" O GLY B 563 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU B 568 " --> pdb=" O GLY B 564 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N MET B 569 " --> pdb=" O LEU B 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.925A pdb=" N THR C 91 " --> pdb=" O PRO C 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 374 through 379 removed outlier: 5.744A pdb=" N LYS A 377 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N LEU A 360 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU A 354 " --> pdb=" O PHE A 418 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS A 416 " --> pdb=" O ARG A 356 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL A 358 " --> pdb=" O ARG A 414 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG A 414 " --> pdb=" O VAL A 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 439 removed outlier: 6.921A pdb=" N GLY A 437 " --> pdb=" O ILE A 520 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ASP A 522 " --> pdb=" O GLY A 437 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL A 439 " --> pdb=" O ASP A 522 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LEU A 519 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE A 552 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 521 " --> pdb=" O ILE A 552 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA A 390 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N PHE A 568 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A 392 " --> pdb=" O PHE A 568 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL A 567 " --> pdb=" O GLU A 575 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLU A 575 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ARG A 569 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LEU A 573 " --> pdb=" O ARG A 569 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 448 through 449 removed outlier: 3.661A pdb=" N GLY A 448 " --> pdb=" O LEU A 490 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 351 through 361 removed outlier: 6.661A pdb=" N LEU B 353 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LYS B 347 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ARG B 355 " --> pdb=" O GLY B 345 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY B 345 " --> pdb=" O ARG B 355 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU B 357 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N PHE B 341 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TYR B 396 " --> pdb=" O PHE B 341 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLY B 343 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ARG B 394 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU B 392 " --> pdb=" O GLY B 345 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N HIS B 400 " --> pdb=" O VAL B 397 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 414 through 417 removed outlier: 6.242A pdb=" N GLY B 368 " --> pdb=" O ILE B 543 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU B 545 " --> pdb=" O GLY B 368 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR B 370 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU B 552 " --> pdb=" O VAL B 544 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA C 101 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.660A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.530A pdb=" N ALA C 92 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ARG C 38 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLY C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) 364 hydrogen bonds defined for protein. 1059 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: 1.34 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1603 1.31 - 1.43: 2783 1.43 - 1.56: 5894 1.56 - 1.69: 14 1.69 - 1.81: 45 Bond restraints: 10339 Sorted by residual: bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.50e+01 bond pdb=" C5 ATP B 601 " pdb=" C6 ATP B 601 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.42e+01 bond pdb=" CA LEU B 122 " pdb=" C LEU B 122 " ideal model delta sigma weight residual 1.524 1.594 -0.070 1.24e-02 6.50e+03 3.22e+01 bond pdb=" C5 ATP B 601 " pdb=" N7 ATP B 601 " ideal model delta sigma weight residual 1.387 1.339 0.048 1.00e-02 1.00e+04 2.31e+01 bond pdb=" C8 ATP B 601 " pdb=" N7 ATP B 601 " ideal model delta sigma weight residual 1.310 1.354 -0.044 1.00e-02 1.00e+04 1.91e+01 ... (remaining 10334 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.96: 13795 3.96 - 7.92: 195 7.92 - 11.89: 33 11.89 - 15.85: 5 15.85 - 19.81: 1 Bond angle restraints: 14029 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 120.06 19.81 1.00e+00 1.00e+00 3.92e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 123.10 13.73 1.00e+00 1.00e+00 1.89e+02 angle pdb=" N ARG A 233 " pdb=" CA ARG A 233 " pdb=" C ARG A 233 " ideal model delta sigma weight residual 111.07 125.42 -14.35 1.07e+00 8.73e-01 1.80e+02 angle pdb=" N LEU B 122 " pdb=" CA LEU B 122 " pdb=" C LEU B 122 " ideal model delta sigma weight residual 111.03 124.73 -13.70 1.11e+00 8.12e-01 1.52e+02 angle pdb=" N ASN B 123 " pdb=" CA ASN B 123 " pdb=" C ASN B 123 " ideal model delta sigma weight residual 111.07 121.84 -10.77 1.07e+00 8.73e-01 1.01e+02 ... (remaining 14024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.94: 5612 19.94 - 39.89: 458 39.89 - 59.83: 65 59.83 - 79.78: 11 79.78 - 99.72: 5 Dihedral angle restraints: 6151 sinusoidal: 2507 harmonic: 3644 Sorted by residual: dihedral pdb=" C LEU A 72 " pdb=" N LEU A 72 " pdb=" CA LEU A 72 " pdb=" CB LEU A 72 " ideal model delta harmonic sigma weight residual -122.60 -138.97 16.37 0 2.50e+00 1.60e-01 4.29e+01 dihedral pdb=" N LEU A 72 " pdb=" C LEU A 72 " pdb=" CA LEU A 72 " pdb=" CB LEU A 72 " ideal model delta harmonic sigma weight residual 122.80 138.19 -15.39 0 2.50e+00 1.60e-01 3.79e+01 dihedral pdb=" O1B ADP A 701 " pdb=" O3A ADP A 701 " pdb=" PB ADP A 701 " pdb=" PA ADP A 701 " ideal model delta sinusoidal sigma weight residual -60.00 -159.72 99.72 1 2.00e+01 2.50e-03 2.81e+01 ... (remaining 6148 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 1510 0.127 - 0.255: 73 0.255 - 0.382: 11 0.382 - 0.510: 5 0.510 - 0.637: 1 Chirality restraints: 1600 Sorted by residual: chirality pdb=" CA LEU A 72 " pdb=" N LEU A 72 " pdb=" C LEU A 72 " pdb=" CB LEU A 72 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" CA LEU B 122 " pdb=" N LEU B 122 " pdb=" C LEU B 122 " pdb=" CB LEU B 122 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.93e+00 chirality pdb=" CA ILE C 51 " pdb=" N ILE C 51 " pdb=" C ILE C 51 " pdb=" CB ILE C 51 " both_signs ideal model delta sigma weight residual False 2.43 2.89 -0.46 2.00e-01 2.50e+01 5.27e+00 ... (remaining 1597 not shown) Planarity restraints: 1773 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 178 " 0.021 2.00e-02 2.50e+03 4.19e-02 1.75e+01 pdb=" C PHE B 178 " -0.072 2.00e-02 2.50e+03 pdb=" O PHE B 178 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU B 179 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 69 " 0.017 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C ARG A 69 " -0.063 2.00e-02 2.50e+03 pdb=" O ARG A 69 " 0.024 2.00e-02 2.50e+03 pdb=" N PHE A 70 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 71 " 0.015 2.00e-02 2.50e+03 3.00e-02 8.98e+00 pdb=" C HIS A 71 " -0.052 2.00e-02 2.50e+03 pdb=" O HIS A 71 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU A 72 " 0.018 2.00e-02 2.50e+03 ... (remaining 1770 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 107 2.64 - 3.21: 8221 3.21 - 3.77: 14579 3.77 - 4.34: 20886 4.34 - 4.90: 34539 Nonbonded interactions: 78332 Sorted by model distance: nonbonded pdb=" O3B ATP B 601 " pdb="MG MG B 602 " model vdw 2.079 2.170 nonbonded pdb=" O2B ADP A 701 " pdb="MG MG A 702 " model vdw 2.085 2.170 nonbonded pdb=" OG1 THR A 400 " pdb="MG MG A 702 " model vdw 2.092 2.170 nonbonded pdb=" OE1 GLN B 419 " pdb="MG MG B 602 " model vdw 2.120 2.170 nonbonded pdb=" OE1 GLN A 441 " pdb="MG MG A 702 " model vdw 2.206 2.170 ... (remaining 78327 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 group one per residue 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: 1.140 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.620 Find NCS groups from input model: 0.050 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 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 : 0.006 0.081 10341 Z= 0.400 Angle : 1.187 19.811 14033 Z= 0.772 Chirality : 0.072 0.637 1600 Planarity : 0.007 0.064 1773 Dihedral : 14.571 99.721 3813 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.57 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Cbeta Deviations : 0.34 % 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: -5.95 (0.16), residues: 1269 helix: -4.66 (0.09), residues: 695 sheet: -1.26 (0.46), residues: 121 loop : -3.12 (0.21), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 110 TYR 0.019 0.002 TYR B 155 PHE 0.025 0.002 PHE A 229 TRP 0.016 0.002 TRP B 223 HIS 0.007 0.001 HIS A 71 Details of bonding type rmsd covalent geometry : bond 0.00648 (10339) covalent geometry : angle 1.18640 (14029) SS BOND : bond 0.02184 ( 2) SS BOND : angle 2.02881 ( 4) hydrogen bonds : bond 0.30954 ( 364) hydrogen bonds : angle 10.98269 ( 1059) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.8566 (mt) cc_final: 0.8184 (mt) REVERT: A 205 MET cc_start: 0.7732 (tmm) cc_final: 0.7531 (tmm) REVERT: A 479 ILE cc_start: 0.9153 (mm) cc_final: 0.8874 (mm) REVERT: B 259 THR cc_start: 0.9131 (m) cc_final: 0.8762 (p) REVERT: B 430 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6822 (tp30) REVERT: B 455 GLU cc_start: 0.8151 (tp30) cc_final: 0.7909 (tp30) REVERT: B 489 LEU cc_start: 0.8794 (pp) cc_final: 0.8078 (tp) REVERT: B 561 GLN cc_start: 0.7964 (pt0) cc_final: 0.7719 (pp30) REVERT: C 65 LYS cc_start: 0.8693 (ptmm) cc_final: 0.8469 (ptpp) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1408 time to fit residues: 38.9802 Evaluate side-chains 163 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.0980 chunk 123 optimal weight: 8.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.0370 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 ASN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.137111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.114426 restraints weight = 15717.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.117886 restraints weight = 8289.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.120162 restraints weight = 5495.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.121525 restraints weight = 4179.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.122535 restraints weight = 3507.875| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10341 Z= 0.123 Angle : 0.621 11.271 14033 Z= 0.310 Chirality : 0.041 0.148 1600 Planarity : 0.005 0.045 1773 Dihedral : 6.454 97.321 1473 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.77 % Allowed : 14.67 % Favored : 84.56 % 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: -4.53 (0.18), residues: 1269 helix: -3.43 (0.13), residues: 703 sheet: -1.35 (0.41), residues: 142 loop : -2.38 (0.25), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 493 TYR 0.018 0.001 TYR A 588 PHE 0.015 0.001 PHE A 257 TRP 0.014 0.001 TRP B 446 HIS 0.006 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00275 (10339) covalent geometry : angle 0.62128 (14029) SS BOND : bond 0.00219 ( 2) SS BOND : angle 0.72805 ( 4) hydrogen bonds : bond 0.04018 ( 364) hydrogen bonds : angle 5.69861 ( 1059) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 179 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 74 LEU cc_start: 0.8855 (mt) cc_final: 0.8625 (mt) REVERT: A 178 LEU cc_start: 0.8165 (mt) cc_final: 0.7632 (tt) REVERT: A 321 MET cc_start: 0.7569 (tmm) cc_final: 0.7117 (tmm) REVERT: A 334 GLU cc_start: 0.7543 (tt0) cc_final: 0.7306 (pt0) REVERT: A 467 GLU cc_start: 0.7471 (tm-30) cc_final: 0.7232 (tm-30) REVERT: B 163 PHE cc_start: 0.8049 (t80) cc_final: 0.7561 (t80) REVERT: B 561 GLN cc_start: 0.7895 (pt0) cc_final: 0.7671 (pp30) REVERT: C 53 LYS cc_start: 0.8884 (ttpp) cc_final: 0.8322 (ttmm) REVERT: C 65 LYS cc_start: 0.8771 (ptmm) cc_final: 0.8476 (ptpp) outliers start: 8 outliers final: 5 residues processed: 185 average time/residue: 0.1214 time to fit residues: 30.1094 Evaluate side-chains 166 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 161 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain C residue 4 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 83 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.136128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.113433 restraints weight = 15943.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.116763 restraints weight = 8565.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.118979 restraints weight = 5722.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.120387 restraints weight = 4362.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.121336 restraints weight = 3639.441| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10341 Z= 0.173 Angle : 0.616 8.135 14033 Z= 0.303 Chirality : 0.042 0.137 1600 Planarity : 0.004 0.044 1773 Dihedral : 6.290 102.386 1473 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.21 % Allowed : 16.01 % Favored : 81.78 % 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: -3.60 (0.21), residues: 1269 helix: -2.64 (0.17), residues: 697 sheet: -1.29 (0.41), residues: 137 loop : -1.93 (0.26), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 493 TYR 0.012 0.001 TYR A 588 PHE 0.017 0.001 PHE B 341 TRP 0.011 0.001 TRP B 262 HIS 0.006 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00408 (10339) covalent geometry : angle 0.61561 (14029) SS BOND : bond 0.00062 ( 2) SS BOND : angle 0.55088 ( 4) hydrogen bonds : bond 0.03664 ( 364) hydrogen bonds : angle 5.22552 ( 1059) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.8212 (mt) cc_final: 0.7662 (tt) REVERT: A 467 GLU cc_start: 0.7512 (tm-30) cc_final: 0.7279 (tm-30) REVERT: B 148 LEU cc_start: 0.8641 (tp) cc_final: 0.8436 (tp) REVERT: B 163 PHE cc_start: 0.8175 (t80) cc_final: 0.7783 (t80) REVERT: C 53 LYS cc_start: 0.8885 (ttpp) cc_final: 0.8345 (ttmm) REVERT: C 65 LYS cc_start: 0.8857 (ptmm) cc_final: 0.8429 (ptpp) outliers start: 23 outliers final: 16 residues processed: 178 average time/residue: 0.1070 time to fit residues: 26.2066 Evaluate side-chains 167 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 58 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 43 optimal weight: 0.0670 chunk 6 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 40 optimal weight: 0.0870 chunk 88 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.137296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.114664 restraints weight = 15666.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.118221 restraints weight = 8212.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.120479 restraints weight = 5372.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.121946 restraints weight = 4082.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.122774 restraints weight = 3398.860| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10341 Z= 0.110 Angle : 0.559 6.985 14033 Z= 0.274 Chirality : 0.040 0.181 1600 Planarity : 0.004 0.039 1773 Dihedral : 5.934 101.880 1473 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.30 % Allowed : 17.16 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.22), residues: 1269 helix: -2.12 (0.18), residues: 696 sheet: -1.01 (0.43), residues: 138 loop : -1.75 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 493 TYR 0.015 0.001 TYR A 202 PHE 0.010 0.001 PHE B 341 TRP 0.010 0.001 TRP B 262 HIS 0.005 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00257 (10339) covalent geometry : angle 0.55915 (14029) SS BOND : bond 0.00059 ( 2) SS BOND : angle 0.31318 ( 4) hydrogen bonds : bond 0.02969 ( 364) hydrogen bonds : angle 4.83916 ( 1059) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7915 (mt) REVERT: A 92 TYR cc_start: 0.7451 (t80) cc_final: 0.6861 (t80) REVERT: A 178 LEU cc_start: 0.8123 (mt) cc_final: 0.7680 (tt) REVERT: A 305 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7857 (tt0) REVERT: A 334 GLU cc_start: 0.7588 (tt0) cc_final: 0.7333 (pt0) REVERT: A 441 GLN cc_start: 0.8142 (tp40) cc_final: 0.7929 (tp40) REVERT: A 467 GLU cc_start: 0.7480 (tm-30) cc_final: 0.7258 (tm-30) REVERT: B 163 PHE cc_start: 0.8184 (t80) cc_final: 0.7743 (t80) REVERT: B 301 LEU cc_start: 0.8442 (mt) cc_final: 0.8210 (mt) REVERT: B 303 GLN cc_start: 0.8079 (tp40) cc_final: 0.7850 (tp-100) REVERT: C 19 ARG cc_start: 0.7156 (mmt90) cc_final: 0.6941 (mmt90) REVERT: C 53 LYS cc_start: 0.8941 (ttpp) cc_final: 0.8421 (ttmm) REVERT: C 65 LYS cc_start: 0.8881 (ptmm) cc_final: 0.8449 (ptpp) outliers start: 24 outliers final: 11 residues processed: 183 average time/residue: 0.1075 time to fit residues: 27.0190 Evaluate side-chains 164 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 46 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 89 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.138105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.115485 restraints weight = 15497.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.119018 restraints weight = 8224.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.121326 restraints weight = 5428.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.122794 restraints weight = 4129.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.123594 restraints weight = 3446.555| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10341 Z= 0.133 Angle : 0.559 7.395 14033 Z= 0.273 Chirality : 0.040 0.134 1600 Planarity : 0.004 0.039 1773 Dihedral : 5.927 103.475 1473 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.78 % Allowed : 18.22 % Favored : 79.00 % 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: -2.65 (0.22), residues: 1269 helix: -1.79 (0.19), residues: 695 sheet: -1.02 (0.44), residues: 140 loop : -1.61 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 493 TYR 0.011 0.001 TYR A 202 PHE 0.012 0.001 PHE B 341 TRP 0.009 0.001 TRP A 359 HIS 0.005 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00317 (10339) covalent geometry : angle 0.55943 (14029) SS BOND : bond 0.00073 ( 2) SS BOND : angle 0.28741 ( 4) hydrogen bonds : bond 0.02911 ( 364) hydrogen bonds : angle 4.74091 ( 1059) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 33 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7963 (mt) REVERT: A 69 ARG cc_start: 0.6870 (mmm-85) cc_final: 0.6641 (mmm-85) REVERT: A 92 TYR cc_start: 0.7428 (t80) cc_final: 0.6878 (t80) REVERT: A 178 LEU cc_start: 0.8109 (mt) cc_final: 0.7684 (tt) REVERT: A 334 GLU cc_start: 0.7610 (tt0) cc_final: 0.7354 (pt0) REVERT: A 441 GLN cc_start: 0.8144 (tp40) cc_final: 0.7909 (tp40) REVERT: A 467 GLU cc_start: 0.7497 (tm-30) cc_final: 0.7270 (tm-30) REVERT: B 163 PHE cc_start: 0.8191 (t80) cc_final: 0.7722 (t80) REVERT: B 301 LEU cc_start: 0.8480 (mt) cc_final: 0.8227 (mt) REVERT: C 53 LYS cc_start: 0.8931 (ttpp) cc_final: 0.8421 (ttmm) REVERT: C 65 LYS cc_start: 0.8875 (ptmm) cc_final: 0.8492 (ptpp) outliers start: 29 outliers final: 21 residues processed: 177 average time/residue: 0.1094 time to fit residues: 26.5320 Evaluate side-chains 175 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 464 TYR Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 120 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 70 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 115 optimal weight: 0.3980 chunk 35 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN C 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.138216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.115798 restraints weight = 15621.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.119364 restraints weight = 8154.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.121640 restraints weight = 5349.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.123058 restraints weight = 4060.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.124034 restraints weight = 3393.431| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10341 Z= 0.127 Angle : 0.553 7.595 14033 Z= 0.268 Chirality : 0.040 0.132 1600 Planarity : 0.004 0.039 1773 Dihedral : 5.744 104.070 1473 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.97 % Allowed : 18.41 % Favored : 78.62 % 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: -2.31 (0.23), residues: 1269 helix: -1.49 (0.19), residues: 695 sheet: -0.92 (0.44), residues: 140 loop : -1.48 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 493 TYR 0.009 0.001 TYR A 202 PHE 0.012 0.001 PHE B 341 TRP 0.008 0.001 TRP A 359 HIS 0.004 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00304 (10339) covalent geometry : angle 0.55334 (14029) SS BOND : bond 0.00077 ( 2) SS BOND : angle 0.26897 ( 4) hydrogen bonds : bond 0.02795 ( 364) hydrogen bonds : angle 4.61517 ( 1059) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 33 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7865 (mt) REVERT: A 92 TYR cc_start: 0.7478 (t80) cc_final: 0.6904 (t80) REVERT: A 178 LEU cc_start: 0.8095 (mt) cc_final: 0.7684 (tt) REVERT: A 334 GLU cc_start: 0.7614 (tt0) cc_final: 0.7337 (pt0) REVERT: A 441 GLN cc_start: 0.8135 (tp40) cc_final: 0.7889 (tp40) REVERT: A 531 GLU cc_start: 0.7575 (tp30) cc_final: 0.7331 (tp30) REVERT: B 163 PHE cc_start: 0.8197 (t80) cc_final: 0.7669 (t80) REVERT: B 277 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.6281 (mm-30) REVERT: B 301 LEU cc_start: 0.8470 (mt) cc_final: 0.8204 (mt) REVERT: B 569 MET cc_start: 0.8266 (ttm) cc_final: 0.7911 (ttm) REVERT: C 19 ARG cc_start: 0.6585 (tpp80) cc_final: 0.6330 (tpp80) REVERT: C 53 LYS cc_start: 0.8908 (ttpp) cc_final: 0.8405 (ttmm) REVERT: C 65 LYS cc_start: 0.8891 (ptmm) cc_final: 0.8444 (ptpp) outliers start: 31 outliers final: 22 residues processed: 182 average time/residue: 0.1092 time to fit residues: 26.8768 Evaluate side-chains 175 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 120 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 78 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 0.1980 chunk 91 optimal weight: 2.9990 chunk 49 optimal weight: 0.0770 chunk 93 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.140122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.117654 restraints weight = 15428.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.121236 restraints weight = 8117.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.123532 restraints weight = 5359.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.125003 restraints weight = 4075.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.125847 restraints weight = 3401.191| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 10341 Z= 0.103 Angle : 0.533 7.039 14033 Z= 0.258 Chirality : 0.039 0.131 1600 Planarity : 0.003 0.037 1773 Dihedral : 5.555 101.753 1473 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.68 % Allowed : 19.56 % Favored : 77.76 % 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: -1.93 (0.23), residues: 1269 helix: -1.15 (0.20), residues: 697 sheet: -0.79 (0.45), residues: 140 loop : -1.36 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 188 TYR 0.008 0.001 TYR A 202 PHE 0.012 0.001 PHE A 257 TRP 0.009 0.001 TRP B 446 HIS 0.004 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00245 (10339) covalent geometry : angle 0.53333 (14029) SS BOND : bond 0.00061 ( 2) SS BOND : angle 0.27950 ( 4) hydrogen bonds : bond 0.02563 ( 364) hydrogen bonds : angle 4.45223 ( 1059) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 33 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7886 (mt) REVERT: A 92 TYR cc_start: 0.7444 (t80) cc_final: 0.6890 (t80) REVERT: A 178 LEU cc_start: 0.8084 (mt) cc_final: 0.7698 (tt) REVERT: A 181 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8242 (tt) REVERT: A 205 MET cc_start: 0.7431 (tmm) cc_final: 0.7135 (tmm) REVERT: A 334 GLU cc_start: 0.7592 (tt0) cc_final: 0.7331 (pt0) REVERT: A 441 GLN cc_start: 0.8174 (tp40) cc_final: 0.7942 (tp40) REVERT: A 442 GLU cc_start: 0.8050 (pm20) cc_final: 0.7756 (pm20) REVERT: A 536 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8692 (mp) REVERT: B 163 PHE cc_start: 0.8222 (t80) cc_final: 0.7640 (t80) REVERT: B 277 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.6165 (mm-30) REVERT: B 301 LEU cc_start: 0.8480 (mt) cc_final: 0.8211 (mt) REVERT: B 569 MET cc_start: 0.8204 (ttm) cc_final: 0.7834 (ttm) REVERT: C 19 ARG cc_start: 0.6405 (tpp80) cc_final: 0.6110 (tpp80) REVERT: C 53 LYS cc_start: 0.8926 (ttpp) cc_final: 0.8407 (ttmm) REVERT: C 65 LYS cc_start: 0.8890 (ptmm) cc_final: 0.8445 (ptpp) outliers start: 28 outliers final: 19 residues processed: 181 average time/residue: 0.1080 time to fit residues: 26.9202 Evaluate side-chains 179 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 120 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 95 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 45 optimal weight: 0.0060 chunk 84 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.137914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.115587 restraints weight = 15493.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.119088 restraints weight = 8123.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.121376 restraints weight = 5368.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.122825 restraints weight = 4075.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.123659 restraints weight = 3396.824| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10341 Z= 0.143 Angle : 0.573 7.256 14033 Z= 0.275 Chirality : 0.041 0.131 1600 Planarity : 0.004 0.039 1773 Dihedral : 5.632 104.551 1473 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.78 % Allowed : 20.33 % Favored : 76.89 % 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: -1.80 (0.24), residues: 1269 helix: -1.04 (0.20), residues: 711 sheet: -0.75 (0.44), residues: 140 loop : -1.30 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 493 TYR 0.008 0.001 TYR A 541 PHE 0.013 0.001 PHE B 341 TRP 0.009 0.001 TRP A 359 HIS 0.003 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00342 (10339) covalent geometry : angle 0.57262 (14029) SS BOND : bond 0.00074 ( 2) SS BOND : angle 0.34271 ( 4) hydrogen bonds : bond 0.02780 ( 364) hydrogen bonds : angle 4.53461 ( 1059) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 33 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7937 (mt) REVERT: A 178 LEU cc_start: 0.8088 (mt) cc_final: 0.7700 (tt) REVERT: A 181 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8304 (tt) REVERT: A 334 GLU cc_start: 0.7601 (tt0) cc_final: 0.7336 (pt0) REVERT: A 442 GLU cc_start: 0.8073 (pm20) cc_final: 0.7758 (pm20) REVERT: A 536 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8700 (mp) REVERT: B 163 PHE cc_start: 0.8279 (t80) cc_final: 0.7629 (t80) REVERT: B 277 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.6226 (mm-30) REVERT: B 301 LEU cc_start: 0.8513 (mt) cc_final: 0.8235 (mt) REVERT: B 317 ASP cc_start: 0.7226 (t0) cc_final: 0.7024 (t0) REVERT: B 569 MET cc_start: 0.8182 (ttm) cc_final: 0.7847 (ttm) REVERT: C 19 ARG cc_start: 0.6313 (tpp80) cc_final: 0.6014 (tpp80) REVERT: C 53 LYS cc_start: 0.8895 (ttpp) cc_final: 0.8396 (ttmm) REVERT: C 65 LYS cc_start: 0.8896 (ptmm) cc_final: 0.8457 (ptpp) outliers start: 29 outliers final: 24 residues processed: 178 average time/residue: 0.1010 time to fit residues: 24.8799 Evaluate side-chains 182 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 120 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 77 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 96 optimal weight: 0.0980 chunk 56 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.139315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.116842 restraints weight = 15601.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.120397 restraints weight = 8189.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.122681 restraints weight = 5414.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.124159 restraints weight = 4129.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.124982 restraints weight = 3448.413| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10341 Z= 0.120 Angle : 0.565 7.175 14033 Z= 0.272 Chirality : 0.040 0.133 1600 Planarity : 0.004 0.038 1773 Dihedral : 5.545 103.217 1473 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.16 % Allowed : 20.33 % Favored : 76.51 % 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: -1.62 (0.24), residues: 1269 helix: -0.90 (0.20), residues: 710 sheet: -0.67 (0.45), residues: 140 loop : -1.20 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 493 TYR 0.006 0.001 TYR B 61 PHE 0.009 0.001 PHE B 58 TRP 0.008 0.001 TRP B 446 HIS 0.003 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00289 (10339) covalent geometry : angle 0.56498 (14029) SS BOND : bond 0.00178 ( 2) SS BOND : angle 0.30451 ( 4) hydrogen bonds : bond 0.02739 ( 364) hydrogen bonds : angle 4.38363 ( 1059) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 33 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7904 (mt) REVERT: A 181 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8244 (tt) REVERT: A 334 GLU cc_start: 0.7611 (tt0) cc_final: 0.7359 (pt0) REVERT: A 442 GLU cc_start: 0.8066 (pm20) cc_final: 0.7727 (pm20) REVERT: A 536 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8696 (mp) REVERT: B 163 PHE cc_start: 0.8304 (t80) cc_final: 0.7628 (t80) REVERT: B 277 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.6148 (mm-30) REVERT: B 301 LEU cc_start: 0.8475 (mt) cc_final: 0.8199 (mt) REVERT: B 303 GLN cc_start: 0.8190 (tp40) cc_final: 0.7876 (tp-100) REVERT: B 317 ASP cc_start: 0.7232 (t0) cc_final: 0.6996 (t0) REVERT: B 443 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7140 (ttp-170) REVERT: B 569 MET cc_start: 0.8158 (ttm) cc_final: 0.7831 (ttm) REVERT: C 19 ARG cc_start: 0.6430 (tpp80) cc_final: 0.6142 (tpp80) REVERT: C 53 LYS cc_start: 0.8897 (ttpp) cc_final: 0.8408 (ttmm) REVERT: C 65 LYS cc_start: 0.8897 (ptmm) cc_final: 0.8459 (ptpp) outliers start: 33 outliers final: 24 residues processed: 183 average time/residue: 0.1150 time to fit residues: 28.7103 Evaluate side-chains 187 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 124 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 0.0030 chunk 79 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 81 optimal weight: 0.0670 chunk 16 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.4528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.140549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.118421 restraints weight = 15383.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.121980 restraints weight = 8079.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.124255 restraints weight = 5316.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.125716 restraints weight = 4034.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.126521 restraints weight = 3361.450| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10341 Z= 0.105 Angle : 0.575 8.900 14033 Z= 0.276 Chirality : 0.040 0.144 1600 Planarity : 0.004 0.039 1773 Dihedral : 5.403 100.028 1473 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.78 % Allowed : 21.00 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.24), residues: 1269 helix: -0.73 (0.21), residues: 704 sheet: -0.62 (0.44), residues: 142 loop : -1.08 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 493 TYR 0.006 0.001 TYR A 541 PHE 0.011 0.001 PHE B 58 TRP 0.009 0.001 TRP B 446 HIS 0.003 0.000 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00251 (10339) covalent geometry : angle 0.57490 (14029) SS BOND : bond 0.00226 ( 2) SS BOND : angle 0.43868 ( 4) hydrogen bonds : bond 0.02678 ( 364) hydrogen bonds : angle 4.28272 ( 1059) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 92 TYR cc_start: 0.7478 (t80) cc_final: 0.6965 (t80) REVERT: A 181 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8255 (tt) REVERT: A 205 MET cc_start: 0.7515 (tmm) cc_final: 0.7194 (tmm) REVERT: A 334 GLU cc_start: 0.7590 (tt0) cc_final: 0.7335 (pt0) REVERT: A 442 GLU cc_start: 0.8030 (pm20) cc_final: 0.7728 (pm20) REVERT: A 536 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8716 (mp) REVERT: B 163 PHE cc_start: 0.8189 (t80) cc_final: 0.7550 (t80) REVERT: B 277 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.6109 (mm-30) REVERT: B 301 LEU cc_start: 0.8447 (mt) cc_final: 0.8141 (mt) REVERT: B 303 GLN cc_start: 0.8116 (tp40) cc_final: 0.7819 (tp-100) REVERT: B 317 ASP cc_start: 0.7201 (t0) cc_final: 0.6963 (t0) REVERT: B 365 MET cc_start: 0.8468 (tpp) cc_final: 0.8206 (tpp) REVERT: B 443 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7201 (ttp-170) REVERT: B 537 ARG cc_start: 0.8138 (tpp80) cc_final: 0.7935 (mmm160) REVERT: B 569 MET cc_start: 0.8130 (ttm) cc_final: 0.7809 (ttm) REVERT: C 19 ARG cc_start: 0.6393 (tpp80) cc_final: 0.6121 (tpp80) REVERT: C 53 LYS cc_start: 0.8875 (ttpp) cc_final: 0.8390 (ttmm) REVERT: C 65 LYS cc_start: 0.8900 (ptmm) cc_final: 0.8482 (ptpp) outliers start: 29 outliers final: 22 residues processed: 177 average time/residue: 0.1120 time to fit residues: 27.2581 Evaluate side-chains 177 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 99 optimal weight: 0.7980 chunk 57 optimal weight: 0.1980 chunk 112 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 50 optimal weight: 0.4980 chunk 105 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.140308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.117948 restraints weight = 15506.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.121540 restraints weight = 8183.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.123832 restraints weight = 5411.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.125338 restraints weight = 4114.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.126345 restraints weight = 3418.230| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.197 10341 Z= 0.185 Angle : 0.895 59.196 14033 Z= 0.493 Chirality : 0.041 0.241 1600 Planarity : 0.004 0.039 1773 Dihedral : 5.403 100.033 1473 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.78 % Allowed : 21.00 % Favored : 76.22 % Cbeta Deviations : 0.09 % 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: -1.39 (0.24), residues: 1269 helix: -0.72 (0.21), residues: 704 sheet: -0.61 (0.44), residues: 142 loop : -1.08 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 493 TYR 0.006 0.001 TYR A 541 PHE 0.011 0.001 PHE B 58 TRP 0.008 0.001 TRP B 446 HIS 0.003 0.000 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00403 (10339) covalent geometry : angle 0.89496 (14029) SS BOND : bond 0.00127 ( 2) SS BOND : angle 1.31359 ( 4) hydrogen bonds : bond 0.02691 ( 364) hydrogen bonds : angle 4.28255 ( 1059) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1690.48 seconds wall clock time: 29 minutes 42.54 seconds (1782.54 seconds total)