Starting phenix.real_space_refine on Fri Feb 14 14:32:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ral_4779/02_2025/6ral_4779.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ral_4779/02_2025/6ral_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6ral_4779/02_2025/6ral_4779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ral_4779/02_2025/6ral_4779.map" model { file = "/net/cci-nas-00/data/ceres_data/6ral_4779/02_2025/6ral_4779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ral_4779/02_2025/6ral_4779.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.06, per 1000 atoms: 0.60 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: 2.36 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.12 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: 3.06 Time building geometry restraints manager: 2.78 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: 0.860 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.390 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.670 ------------------------------------------------------------------------------- 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 10339 Z= 0.420 Angle : 1.186 19.811 14029 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.016 0.002 TRP B 223 HIS 0.007 0.001 HIS A 71 PHE 0.025 0.002 PHE A 229 TYR 0.019 0.002 TYR B 155 ARG 0.003 0.000 ARG A 110 *********************** 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 : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.8566 (mt) cc_final: 0.8181 (mt) REVERT: A 205 MET cc_start: 0.7732 (tmm) cc_final: 0.7530 (tmm) REVERT: A 479 ILE cc_start: 0.9153 (mm) cc_final: 0.8873 (mm) REVERT: B 259 THR cc_start: 0.9131 (m) cc_final: 0.8760 (p) REVERT: B 430 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6821 (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: 0.7963 (pt0) cc_final: 0.7720 (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: 0.3191 time to fit residues: 88.2468 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 : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 0.7980 chunk 96 optimal weight: 0.0670 chunk 53 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 99 optimal weight: 0.0570 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 ASN B 191 GLN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.137395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.114858 restraints weight = 15615.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.118285 restraints weight = 8205.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.120593 restraints weight = 5429.038| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10339 Z= 0.171 Angle : 0.620 11.335 14029 Z= 0.310 Chirality : 0.041 0.141 1600 Planarity : 0.005 0.045 1773 Dihedral : 6.444 97.149 1473 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.77 % Allowed : 14.77 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.52 (0.18), residues: 1269 helix: -3.43 (0.13), residues: 705 sheet: -1.33 (0.41), residues: 142 loop : -2.36 (0.25), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 446 HIS 0.006 0.001 HIS C 80 PHE 0.015 0.001 PHE A 70 TYR 0.015 0.001 TYR A 588 ARG 0.006 0.000 ARG B 188 *********************** 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 188 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 180 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.8152 (mt) cc_final: 0.7618 (tt) REVERT: A 321 MET cc_start: 0.7593 (tmm) cc_final: 0.7108 (tmm) REVERT: A 334 GLU cc_start: 0.7584 (tt0) cc_final: 0.7344 (pt0) REVERT: A 467 GLU cc_start: 0.7466 (tm-30) cc_final: 0.7204 (tm-30) REVERT: B 163 PHE cc_start: 0.8064 (t80) cc_final: 0.7588 (t80) REVERT: B 561 GLN cc_start: 0.7911 (pt0) cc_final: 0.7682 (pp30) REVERT: C 53 LYS cc_start: 0.8889 (ttpp) cc_final: 0.8335 (ttmm) REVERT: C 65 LYS cc_start: 0.8770 (ptmm) cc_final: 0.8474 (ptpp) outliers start: 8 outliers final: 5 residues processed: 186 average time/residue: 0.2747 time to fit residues: 68.3612 Evaluate side-chains 169 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 164 time to evaluate : 1.175 ------------------------------------------------------------------------------- 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 58 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 3 optimal weight: 0.0980 chunk 14 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- 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 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.135618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.112977 restraints weight = 15999.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.116282 restraints weight = 8559.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.118464 restraints weight = 5730.071| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10339 Z= 0.284 Angle : 0.627 8.027 14029 Z= 0.309 Chirality : 0.043 0.134 1600 Planarity : 0.004 0.052 1773 Dihedral : 6.315 103.125 1473 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.11 % Allowed : 16.30 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.21), residues: 1269 helix: -2.62 (0.17), residues: 698 sheet: -1.31 (0.41), residues: 137 loop : -1.89 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 359 HIS 0.006 0.001 HIS C 80 PHE 0.018 0.001 PHE B 341 TYR 0.013 0.001 TYR A 588 ARG 0.006 0.000 ARG C 107 *********************** 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 183 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.8174 (mt) cc_final: 0.7616 (tt) REVERT: A 467 GLU cc_start: 0.7539 (tm-30) cc_final: 0.7285 (tm-30) REVERT: B 163 PHE cc_start: 0.8212 (t80) cc_final: 0.7809 (t80) REVERT: C 19 ARG cc_start: 0.6997 (mmm-85) cc_final: 0.6600 (mmt90) REVERT: C 53 LYS cc_start: 0.8898 (ttpp) cc_final: 0.8361 (ttmm) REVERT: C 65 LYS cc_start: 0.8867 (ptmm) cc_final: 0.8407 (ptpp) outliers start: 22 outliers final: 15 residues processed: 178 average time/residue: 0.2510 time to fit residues: 61.6468 Evaluate side-chains 169 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 70 optimal weight: 0.0670 chunk 77 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 33 optimal weight: 0.0470 chunk 69 optimal weight: 0.7980 chunk 90 optimal weight: 0.1980 overall best weight: 0.3216 ------------------------------------------------------------------------------- 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 531 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.137861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.115403 restraints weight = 15490.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.118856 restraints weight = 8060.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.121134 restraints weight = 5320.588| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 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 : 0.002 0.051 10339 Z= 0.148 Angle : 0.552 7.184 14029 Z= 0.270 Chirality : 0.039 0.173 1600 Planarity : 0.004 0.039 1773 Dihedral : 5.865 101.239 1473 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.11 % Allowed : 17.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.22), residues: 1269 helix: -2.10 (0.18), residues: 699 sheet: -0.99 (0.43), residues: 137 loop : -1.72 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 262 HIS 0.005 0.001 HIS C 80 PHE 0.009 0.001 PHE A 257 TYR 0.012 0.001 TYR A 202 ARG 0.006 0.000 ARG A 493 *********************** 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 186 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7882 (mt) REVERT: A 92 TYR cc_start: 0.7456 (t80) cc_final: 0.6865 (t80) REVERT: A 178 LEU cc_start: 0.8104 (mt) cc_final: 0.7651 (tt) REVERT: A 334 GLU cc_start: 0.7595 (tt0) cc_final: 0.7341 (pt0) REVERT: A 441 GLN cc_start: 0.8159 (tp40) cc_final: 0.7905 (tp40) REVERT: B 163 PHE cc_start: 0.8196 (t80) cc_final: 0.7731 (t80) REVERT: B 301 LEU cc_start: 0.8379 (mt) cc_final: 0.8147 (mt) REVERT: B 303 GLN cc_start: 0.8040 (tp40) cc_final: 0.7821 (tp-100) REVERT: B 489 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8191 (tp) REVERT: C 53 LYS cc_start: 0.8951 (ttpp) cc_final: 0.8444 (ttmm) REVERT: C 65 LYS cc_start: 0.8886 (ptmm) cc_final: 0.8432 (ptpp) outliers start: 22 outliers final: 11 residues processed: 178 average time/residue: 0.2480 time to fit residues: 60.4758 Evaluate side-chains 165 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 357 ASP 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 416 VAL Chi-restraints excluded: chain B residue 489 LEU 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 119 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 chunk 96 optimal weight: 0.1980 chunk 81 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 67 optimal weight: 0.0870 chunk 27 optimal weight: 0.6980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN A 308 GLN ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.137798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.115177 restraints weight = 15486.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.118657 restraints weight = 8098.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.120944 restraints weight = 5340.686| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 10339 Z= 0.161 Angle : 0.534 7.016 14029 Z= 0.260 Chirality : 0.040 0.136 1600 Planarity : 0.003 0.037 1773 Dihedral : 5.758 101.186 1473 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.07 % Allowed : 17.64 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.22), residues: 1269 helix: -1.72 (0.19), residues: 694 sheet: -0.94 (0.44), residues: 138 loop : -1.59 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 262 HIS 0.005 0.001 HIS C 80 PHE 0.008 0.001 PHE B 341 TYR 0.010 0.001 TYR A 202 ARG 0.007 0.000 ARG A 493 *********************** 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 192 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 TYR cc_start: 0.7458 (t80) cc_final: 0.6948 (t80) REVERT: A 178 LEU cc_start: 0.8074 (mt) cc_final: 0.7661 (tt) REVERT: A 305 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7724 (mm-40) REVERT: A 334 GLU cc_start: 0.7644 (tt0) cc_final: 0.7373 (pt0) REVERT: A 441 GLN cc_start: 0.8175 (tp40) cc_final: 0.7923 (tp40) REVERT: A 467 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7216 (tm-30) REVERT: B 163 PHE cc_start: 0.8195 (t80) cc_final: 0.7708 (t80) REVERT: B 301 LEU cc_start: 0.8404 (mt) cc_final: 0.8141 (mt) REVERT: B 489 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8190 (tp) REVERT: C 19 ARG cc_start: 0.7144 (mmm-85) cc_final: 0.6916 (mmt90) REVERT: C 53 LYS cc_start: 0.8902 (ttpp) cc_final: 0.8389 (ttmm) REVERT: C 65 LYS cc_start: 0.8884 (ptmm) cc_final: 0.8471 (ptpp) outliers start: 32 outliers final: 19 residues processed: 182 average time/residue: 0.2471 time to fit residues: 61.7642 Evaluate side-chains 174 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 153 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 357 ASP 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 144 SER 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 489 LEU 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 120 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 105 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 96 optimal weight: 0.0670 chunk 84 optimal weight: 0.2980 chunk 102 optimal weight: 0.7980 overall best weight: 0.5920 ------------------------------------------------------------------------------- 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 561 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 = 0.3752 r_free = 0.3752 target = 0.139581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.116598 restraints weight = 15719.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.120083 restraints weight = 8449.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.122338 restraints weight = 5602.394| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10339 Z= 0.173 Angle : 0.540 6.773 14029 Z= 0.263 Chirality : 0.040 0.132 1600 Planarity : 0.003 0.038 1773 Dihedral : 5.629 101.435 1473 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.30 % Allowed : 18.98 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.23), residues: 1269 helix: -1.42 (0.19), residues: 700 sheet: -0.88 (0.45), residues: 140 loop : -1.49 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 262 HIS 0.004 0.001 HIS C 80 PHE 0.010 0.001 PHE B 341 TYR 0.008 0.001 TYR A 202 ARG 0.006 0.000 ARG A 493 *********************** 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 180 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.6697 (mtp180) cc_final: 0.6386 (ttm110) REVERT: A 92 TYR cc_start: 0.7454 (t80) cc_final: 0.6941 (t80) REVERT: A 178 LEU cc_start: 0.8078 (mt) cc_final: 0.7660 (tt) REVERT: A 334 GLU cc_start: 0.7655 (tt0) cc_final: 0.7386 (pt0) REVERT: A 441 GLN cc_start: 0.8219 (tp40) cc_final: 0.7899 (tp40) REVERT: A 536 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8653 (mp) REVERT: B 163 PHE cc_start: 0.8212 (t80) cc_final: 0.7684 (t80) REVERT: B 301 LEU cc_start: 0.8419 (mt) cc_final: 0.8160 (mt) REVERT: C 19 ARG cc_start: 0.7017 (mmm-85) cc_final: 0.6752 (mmt90) REVERT: C 53 LYS cc_start: 0.8939 (ttpp) cc_final: 0.8429 (ttmm) REVERT: C 65 LYS cc_start: 0.8873 (ptmm) cc_final: 0.8437 (ptpp) outliers start: 24 outliers final: 19 residues processed: 174 average time/residue: 0.2575 time to fit residues: 61.5121 Evaluate side-chains 172 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 1.179 ------------------------------------------------------------------------------- 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 153 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 357 ASP 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 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 489 LEU 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 120 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 124 optimal weight: 0.6980 chunk 20 optimal weight: 0.0980 chunk 99 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.139372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.116815 restraints weight = 15623.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.120397 restraints weight = 8153.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.122700 restraints weight = 5356.026| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10339 Z= 0.181 Angle : 0.542 7.484 14029 Z= 0.262 Chirality : 0.040 0.134 1600 Planarity : 0.003 0.037 1773 Dihedral : 5.558 101.882 1473 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.78 % Allowed : 19.08 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.23), residues: 1269 helix: -1.16 (0.20), residues: 701 sheet: -0.86 (0.44), residues: 140 loop : -1.41 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 290 HIS 0.004 0.001 HIS C 80 PHE 0.011 0.001 PHE A 257 TYR 0.008 0.001 TYR A 202 ARG 0.007 0.000 ARG A 493 *********************** 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 185 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.6825 (mtp180) cc_final: 0.6533 (ttm110) REVERT: A 92 TYR cc_start: 0.7462 (t80) cc_final: 0.6954 (t80) REVERT: A 178 LEU cc_start: 0.8087 (mt) cc_final: 0.7678 (tt) REVERT: A 181 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8248 (tt) REVERT: A 334 GLU cc_start: 0.7650 (tt0) cc_final: 0.7391 (pt0) REVERT: A 467 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7231 (tm-30) REVERT: A 536 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8671 (mp) REVERT: B 163 PHE cc_start: 0.8229 (t80) cc_final: 0.7686 (t80) REVERT: B 277 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.6237 (mm-30) REVERT: B 301 LEU cc_start: 0.8478 (mt) cc_final: 0.8213 (mt) REVERT: C 19 ARG cc_start: 0.7143 (mmm-85) cc_final: 0.6881 (mmt90) REVERT: C 53 LYS cc_start: 0.8922 (ttpp) cc_final: 0.8401 (ttmm) REVERT: C 65 LYS cc_start: 0.8876 (ptmm) cc_final: 0.8410 (ptpp) outliers start: 29 outliers final: 19 residues processed: 176 average time/residue: 0.2553 time to fit residues: 62.0052 Evaluate side-chains 172 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 1.173 ------------------------------------------------------------------------------- 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 153 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 357 ASP 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 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 489 LEU 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 120 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 20 optimal weight: 0.0270 chunk 28 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 109 optimal weight: 0.1980 chunk 120 optimal weight: 1.9990 chunk 126 optimal weight: 0.1980 chunk 73 optimal weight: 1.9990 overall best weight: 0.4440 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.140662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.118115 restraints weight = 15471.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.121711 restraints weight = 8073.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.124037 restraints weight = 5300.814| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 10339 Z= 0.157 Angle : 0.537 6.950 14029 Z= 0.260 Chirality : 0.039 0.131 1600 Planarity : 0.003 0.037 1773 Dihedral : 5.412 99.874 1473 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.78 % Allowed : 19.65 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.24), residues: 1269 helix: -0.88 (0.20), residues: 707 sheet: -0.73 (0.44), residues: 140 loop : -1.30 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 193 HIS 0.004 0.001 HIS C 80 PHE 0.011 0.001 PHE A 257 TYR 0.006 0.001 TYR A 541 ARG 0.006 0.000 ARG A 493 *********************** 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 190 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 TYR cc_start: 0.7451 (t80) cc_final: 0.6978 (t80) REVERT: A 178 LEU cc_start: 0.8041 (mt) cc_final: 0.7677 (tt) REVERT: A 181 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8209 (tt) REVERT: A 205 MET cc_start: 0.7445 (tmm) cc_final: 0.7166 (tmm) REVERT: A 308 GLN cc_start: 0.7750 (mp10) cc_final: 0.7520 (mp10) REVERT: A 334 GLU cc_start: 0.7648 (tt0) cc_final: 0.7384 (pt0) REVERT: A 536 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8683 (mp) REVERT: B 163 PHE cc_start: 0.8268 (t80) cc_final: 0.7635 (t80) REVERT: B 277 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.6127 (mm-30) REVERT: B 301 LEU cc_start: 0.8450 (mt) cc_final: 0.8176 (mt) REVERT: C 19 ARG cc_start: 0.7172 (mmm-85) cc_final: 0.6916 (mmt90) REVERT: C 53 LYS cc_start: 0.8904 (ttpp) cc_final: 0.8404 (ttmm) REVERT: C 65 LYS cc_start: 0.8877 (ptmm) cc_final: 0.8419 (ptpp) outliers start: 29 outliers final: 21 residues processed: 179 average time/residue: 0.2491 time to fit residues: 61.1010 Evaluate side-chains 178 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 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 357 ASP 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 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 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 46 GLU 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: 1.9990 chunk 116 optimal weight: 7.9990 chunk 102 optimal weight: 0.9990 chunk 98 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 84 optimal weight: 0.0770 chunk 44 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 50 optimal weight: 0.0970 chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 191 GLN C 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.142463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.120232 restraints weight = 15343.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.123789 restraints weight = 7953.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.126089 restraints weight = 5226.260| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 10339 Z= 0.142 Angle : 0.545 7.807 14029 Z= 0.263 Chirality : 0.039 0.142 1600 Planarity : 0.003 0.038 1773 Dihedral : 5.242 96.175 1473 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.49 % Allowed : 20.52 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.24), residues: 1269 helix: -0.67 (0.20), residues: 706 sheet: -0.35 (0.45), residues: 133 loop : -1.24 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 446 HIS 0.004 0.000 HIS C 80 PHE 0.012 0.001 PHE A 257 TYR 0.005 0.001 TYR A 541 ARG 0.007 0.000 ARG A 493 *********************** 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 185 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 TYR cc_start: 0.7379 (t80) cc_final: 0.6946 (t80) REVERT: A 178 LEU cc_start: 0.7988 (mt) cc_final: 0.7653 (tt) REVERT: A 181 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8237 (tt) REVERT: A 205 MET cc_start: 0.7467 (tmm) cc_final: 0.7187 (tmm) REVERT: A 308 GLN cc_start: 0.7744 (mp10) cc_final: 0.7490 (mp10) REVERT: A 334 GLU cc_start: 0.7639 (tt0) cc_final: 0.7391 (pt0) REVERT: A 536 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8685 (mp) REVERT: B 163 PHE cc_start: 0.8229 (t80) cc_final: 0.7585 (t80) REVERT: C 53 LYS cc_start: 0.8897 (ttpp) cc_final: 0.8437 (ttmm) REVERT: C 65 LYS cc_start: 0.8868 (ptmm) cc_final: 0.8420 (ptpp) outliers start: 26 outliers final: 17 residues processed: 174 average time/residue: 0.2630 time to fit residues: 63.0400 Evaluate side-chains 172 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 1.341 ------------------------------------------------------------------------------- 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 81 LEU 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 346 ILE Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 536 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 97 optimal weight: 0.7980 chunk 90 optimal weight: 0.0020 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 118 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 89 optimal weight: 0.3980 overall best weight: 0.5388 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.141738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.119243 restraints weight = 15449.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.122855 restraints weight = 8150.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.125164 restraints weight = 5375.267| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10339 Z= 0.171 Angle : 0.565 8.868 14029 Z= 0.269 Chirality : 0.040 0.148 1600 Planarity : 0.004 0.036 1773 Dihedral : 5.256 96.859 1473 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.21 % Allowed : 21.00 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.24), residues: 1269 helix: -0.55 (0.20), residues: 711 sheet: -0.63 (0.44), residues: 142 loop : -1.20 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 262 HIS 0.003 0.001 HIS C 80 PHE 0.015 0.001 PHE B 58 TYR 0.006 0.001 TYR A 541 ARG 0.008 0.000 ARG A 384 ********************** 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 180 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 TYR cc_start: 0.7432 (t80) cc_final: 0.6996 (t80) REVERT: A 181 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8229 (tt) REVERT: A 205 MET cc_start: 0.7489 (tmm) cc_final: 0.7163 (tmm) REVERT: A 308 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7529 (mp10) REVERT: A 334 GLU cc_start: 0.7590 (tt0) cc_final: 0.7329 (pt0) REVERT: A 536 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8692 (mp) REVERT: B 163 PHE cc_start: 0.8248 (t80) cc_final: 0.7598 (t80) REVERT: B 569 MET cc_start: 0.8178 (ttm) cc_final: 0.7845 (ttm) REVERT: C 53 LYS cc_start: 0.8874 (ttpp) cc_final: 0.8418 (ttmm) REVERT: C 65 LYS cc_start: 0.8880 (ptmm) cc_final: 0.8449 (ptpp) outliers start: 23 outliers final: 20 residues processed: 170 average time/residue: 0.2532 time to fit residues: 58.7788 Evaluate side-chains 172 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 1.182 ------------------------------------------------------------------------------- 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 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 308 GLN Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 536 LEU 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 416 VAL 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 46 GLU 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 125 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3779 r_free = 0.3779 target = 0.141261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.118728 restraints weight = 15369.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.122329 restraints weight = 8107.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.124621 restraints weight = 5348.204| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.173 10339 Z= 0.243 Angle : 0.887 59.169 14029 Z= 0.489 Chirality : 0.041 0.296 1600 Planarity : 0.004 0.039 1773 Dihedral : 5.262 96.949 1473 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.21 % Allowed : 21.38 % Favored : 76.41 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.24), residues: 1269 helix: -0.56 (0.20), residues: 711 sheet: -0.64 (0.44), residues: 142 loop : -1.21 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 262 HIS 0.003 0.001 HIS C 80 PHE 0.014 0.001 PHE B 58 TYR 0.006 0.001 TYR A 541 ARG 0.011 0.000 ARG C 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3198.39 seconds wall clock time: 57 minutes 52.84 seconds (3472.84 seconds total)