Starting phenix.real_space_refine on Mon Jul 28 11:22:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ral_4779/07_2025/6ral_4779.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ral_4779/07_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_4779/07_2025/6ral_4779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ral_4779/07_2025/6ral_4779.map" model { file = "/net/cci-nas-00/data/ceres_data/6ral_4779/07_2025/6ral_4779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ral_4779/07_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 6.63, per 1000 atoms: 0.65 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: 2.24 Conformation dependent library (CDL) restraints added in 1.2 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: 1.19 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: 2.98 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1603 1.31 - 1.43: 2783 1.43 - 1.56: 5894 1.56 - 1.69: 14 1.69 - 1.81: 45 Bond restraints: 10339 Sorted by residual: bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.50e+01 bond pdb=" C5 ATP B 601 " pdb=" C6 ATP B 601 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.42e+01 bond pdb=" CA LEU B 122 " pdb=" C LEU B 122 " ideal model delta sigma weight residual 1.524 1.594 -0.070 1.24e-02 6.50e+03 3.22e+01 bond pdb=" C5 ATP B 601 " pdb=" N7 ATP B 601 " ideal model delta sigma weight residual 1.387 1.339 0.048 1.00e-02 1.00e+04 2.31e+01 bond pdb=" C8 ATP B 601 " pdb=" N7 ATP B 601 " ideal model delta sigma weight residual 1.310 1.354 -0.044 1.00e-02 1.00e+04 1.91e+01 ... (remaining 10334 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.96: 13795 3.96 - 7.92: 195 7.92 - 11.89: 33 11.89 - 15.85: 5 15.85 - 19.81: 1 Bond angle restraints: 14029 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 120.06 19.81 1.00e+00 1.00e+00 3.92e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 123.10 13.73 1.00e+00 1.00e+00 1.89e+02 angle pdb=" N ARG A 233 " pdb=" CA ARG A 233 " pdb=" C ARG A 233 " ideal model delta sigma weight residual 111.07 125.42 -14.35 1.07e+00 8.73e-01 1.80e+02 angle pdb=" N LEU B 122 " pdb=" CA LEU B 122 " pdb=" C LEU B 122 " ideal model delta sigma weight residual 111.03 124.73 -13.70 1.11e+00 8.12e-01 1.52e+02 angle pdb=" N ASN B 123 " pdb=" CA ASN B 123 " pdb=" C ASN B 123 " ideal model delta sigma weight residual 111.07 121.84 -10.77 1.07e+00 8.73e-01 1.01e+02 ... (remaining 14024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.94: 5612 19.94 - 39.89: 458 39.89 - 59.83: 65 59.83 - 79.78: 11 79.78 - 99.72: 5 Dihedral angle restraints: 6151 sinusoidal: 2507 harmonic: 3644 Sorted by residual: dihedral pdb=" C LEU A 72 " pdb=" N LEU A 72 " pdb=" CA LEU A 72 " pdb=" CB LEU A 72 " ideal model delta harmonic sigma weight residual -122.60 -138.97 16.37 0 2.50e+00 1.60e-01 4.29e+01 dihedral pdb=" N LEU A 72 " pdb=" C LEU A 72 " pdb=" CA LEU A 72 " pdb=" CB LEU A 72 " ideal model delta harmonic sigma weight residual 122.80 138.19 -15.39 0 2.50e+00 1.60e-01 3.79e+01 dihedral pdb=" O1B ADP A 701 " pdb=" O3A ADP A 701 " pdb=" PB ADP A 701 " pdb=" PA ADP A 701 " ideal model delta sinusoidal sigma weight residual -60.00 -159.72 99.72 1 2.00e+01 2.50e-03 2.81e+01 ... (remaining 6148 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 1510 0.127 - 0.255: 73 0.255 - 0.382: 11 0.382 - 0.510: 5 0.510 - 0.637: 1 Chirality restraints: 1600 Sorted by residual: chirality pdb=" CA LEU A 72 " pdb=" N LEU A 72 " pdb=" C LEU A 72 " pdb=" CB LEU A 72 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" CA LEU B 122 " pdb=" N LEU B 122 " pdb=" C LEU B 122 " pdb=" CB LEU B 122 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.93e+00 chirality pdb=" CA ILE C 51 " pdb=" N ILE C 51 " pdb=" C ILE C 51 " pdb=" CB ILE C 51 " both_signs ideal model delta sigma weight residual False 2.43 2.89 -0.46 2.00e-01 2.50e+01 5.27e+00 ... (remaining 1597 not shown) Planarity restraints: 1773 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 178 " 0.021 2.00e-02 2.50e+03 4.19e-02 1.75e+01 pdb=" C PHE B 178 " -0.072 2.00e-02 2.50e+03 pdb=" O PHE B 178 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU B 179 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 69 " 0.017 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C ARG A 69 " -0.063 2.00e-02 2.50e+03 pdb=" O ARG A 69 " 0.024 2.00e-02 2.50e+03 pdb=" N PHE A 70 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 71 " 0.015 2.00e-02 2.50e+03 3.00e-02 8.98e+00 pdb=" C HIS A 71 " -0.052 2.00e-02 2.50e+03 pdb=" O HIS A 71 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU A 72 " 0.018 2.00e-02 2.50e+03 ... (remaining 1770 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 107 2.64 - 3.21: 8221 3.21 - 3.77: 14579 3.77 - 4.34: 20886 4.34 - 4.90: 34539 Nonbonded interactions: 78332 Sorted by model distance: nonbonded pdb=" O3B ATP B 601 " pdb="MG MG B 602 " model vdw 2.079 2.170 nonbonded pdb=" O2B ADP A 701 " pdb="MG MG A 702 " model vdw 2.085 2.170 nonbonded pdb=" OG1 THR A 400 " pdb="MG MG A 702 " model vdw 2.092 2.170 nonbonded pdb=" OE1 GLN B 419 " pdb="MG MG B 602 " model vdw 2.120 2.170 nonbonded pdb=" OE1 GLN A 441 " pdb="MG MG A 702 " model vdw 2.206 2.170 ... (remaining 78327 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.130 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 10341 Z= 0.400 Angle : 1.187 19.811 14033 Z= 0.772 Chirality : 0.072 0.637 1600 Planarity : 0.007 0.064 1773 Dihedral : 14.571 99.721 3813 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.57 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.30954 ( 364) hydrogen bonds : angle 10.98269 ( 1059) SS BOND : bond 0.02184 ( 2) SS BOND : angle 2.02881 ( 4) covalent geometry : bond 0.00648 (10339) covalent geometry : angle 1.18640 (14029) *********************** 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 : 1.096 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: 0.3150 time to fit residues: 86.8251 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 : 1.077 ------------------------------------------------------------------------------- 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: 2.9990 overall best weight: 0.5236 ------------------------------------------------------------------------------- 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** B 531 HIS C 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.136848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.114289 restraints weight = 15633.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.117729 restraints weight = 8217.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.120009 restraints weight = 5428.546| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10341 Z= 0.122 Angle : 0.624 10.966 14033 Z= 0.312 Chirality : 0.041 0.143 1600 Planarity : 0.005 0.047 1773 Dihedral : 6.494 96.201 1473 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.77 % Allowed : 14.48 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.55 (0.18), residues: 1269 helix: -3.44 (0.13), residues: 703 sheet: -1.37 (0.41), residues: 142 loop : -2.39 (0.25), residues: 424 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 0.019 0.001 TYR A 588 ARG 0.005 0.000 ARG B 188 Details of bonding type rmsd hydrogen bonds : bond 0.04247 ( 364) hydrogen bonds : angle 5.73368 ( 1059) SS BOND : bond 0.00107 ( 2) SS BOND : angle 0.70617 ( 4) covalent geometry : bond 0.00272 (10339) covalent geometry : angle 0.62419 (14029) *********************** 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 185 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 177 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.8930 (mt) cc_final: 0.8640 (mt) REVERT: A 178 LEU cc_start: 0.8163 (mt) cc_final: 0.7611 (tt) REVERT: A 321 MET cc_start: 0.7608 (tmm) cc_final: 0.7125 (tmm) REVERT: A 467 GLU cc_start: 0.7412 (tm-30) cc_final: 0.7168 (tm-30) REVERT: B 163 PHE cc_start: 0.8065 (t80) cc_final: 0.7581 (t80) REVERT: B 561 GLN cc_start: 0.7931 (pt0) cc_final: 0.7688 (pp30) REVERT: C 53 LYS cc_start: 0.8892 (ttpp) cc_final: 0.8330 (ttmm) REVERT: C 65 LYS cc_start: 0.8801 (ptmm) cc_final: 0.8492 (ptpp) outliers start: 8 outliers final: 6 residues processed: 183 average time/residue: 0.3130 time to fit residues: 78.7603 Evaluate side-chains 166 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 160 time to evaluate : 1.177 ------------------------------------------------------------------------------- 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 162 LEU 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: 0.6980 chunk 69 optimal weight: 3.9990 chunk 61 optimal weight: 0.0050 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- 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 = 0.3724 r_free = 0.3724 target = 0.137074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.114386 restraints weight = 15957.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.117735 restraints weight = 8521.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.119972 restraints weight = 5672.449| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10341 Z= 0.147 Angle : 0.597 8.204 14033 Z= 0.294 Chirality : 0.041 0.135 1600 Planarity : 0.004 0.045 1773 Dihedral : 6.212 101.128 1473 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.11 % Allowed : 16.01 % Favored : 81.88 % 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 (0.20), residues: 1269 helix: -2.61 (0.17), residues: 697 sheet: -1.27 (0.41), residues: 137 loop : -1.91 (0.26), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 262 HIS 0.006 0.001 HIS C 80 PHE 0.014 0.001 PHE B 341 TYR 0.012 0.001 TYR A 588 ARG 0.005 0.000 ARG A 493 Details of bonding type rmsd hydrogen bonds : bond 0.03561 ( 364) hydrogen bonds : angle 5.14843 ( 1059) SS BOND : bond 0.00042 ( 2) SS BOND : angle 0.50798 ( 4) covalent geometry : bond 0.00348 (10339) covalent geometry : angle 0.59677 (14029) *********************** 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 : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.8182 (mt) cc_final: 0.7620 (tt) REVERT: A 467 GLU cc_start: 0.7510 (tm-30) cc_final: 0.7243 (tm-30) REVERT: A 531 GLU cc_start: 0.7551 (tp30) cc_final: 0.7308 (tp30) REVERT: B 148 LEU cc_start: 0.8657 (tp) cc_final: 0.8453 (tp) REVERT: B 163 PHE cc_start: 0.8183 (t80) cc_final: 0.7802 (t80) REVERT: C 53 LYS cc_start: 0.8893 (ttpp) cc_final: 0.8360 (ttmm) REVERT: C 65 LYS cc_start: 0.8886 (ptmm) cc_final: 0.8502 (ptpp) outliers start: 22 outliers final: 14 residues processed: 178 average time/residue: 0.2499 time to fit residues: 61.7486 Evaluate side-chains 164 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 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 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: 0.8980 chunk 104 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 33 optimal weight: 0.0000 chunk 69 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.136976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.114330 restraints weight = 15538.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.117831 restraints weight = 8209.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.120136 restraints weight = 5409.654| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10341 Z= 0.119 Angle : 0.558 7.379 14033 Z= 0.273 Chirality : 0.040 0.177 1600 Planarity : 0.004 0.039 1773 Dihedral : 5.905 102.123 1473 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.78 % Allowed : 16.97 % Favored : 80.25 % 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: -2.95 (0.22), residues: 1269 helix: -2.06 (0.18), residues: 696 sheet: -1.01 (0.43), residues: 138 loop : -1.73 (0.27), residues: 435 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 0.011 0.001 PHE B 341 TYR 0.007 0.001 TYR B 43 ARG 0.007 0.000 ARG A 493 Details of bonding type rmsd hydrogen bonds : bond 0.02986 ( 364) hydrogen bonds : angle 4.78430 ( 1059) SS BOND : bond 0.00062 ( 2) SS BOND : angle 0.29502 ( 4) covalent geometry : bond 0.00279 (10339) covalent geometry : angle 0.55824 (14029) *********************** 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 197 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 1.212 Fit side-chains revert: symmetry clash REVERT: A 33 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7900 (mt) REVERT: A 92 TYR cc_start: 0.7476 (t80) cc_final: 0.6881 (t80) REVERT: A 178 LEU cc_start: 0.8112 (mt) cc_final: 0.7648 (tt) REVERT: A 305 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7796 (tt0) REVERT: A 334 GLU cc_start: 0.7642 (tt0) cc_final: 0.7378 (pt0) REVERT: A 441 GLN cc_start: 0.8171 (tp40) cc_final: 0.7919 (tp40) REVERT: A 467 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7233 (tm-30) REVERT: B 148 LEU cc_start: 0.8631 (tp) cc_final: 0.8431 (tp) REVERT: B 163 PHE cc_start: 0.8201 (t80) cc_final: 0.7756 (t80) REVERT: B 301 LEU cc_start: 0.8424 (mt) cc_final: 0.8195 (mt) REVERT: B 303 GLN cc_start: 0.8050 (tp40) cc_final: 0.7810 (tp-100) REVERT: B 561 GLN cc_start: 0.7718 (pp30) cc_final: 0.7461 (pp30) REVERT: C 19 ARG cc_start: 0.7242 (mmt90) cc_final: 0.6942 (mmt90) REVERT: C 53 LYS cc_start: 0.8933 (ttpp) cc_final: 0.8409 (ttmm) REVERT: C 65 LYS cc_start: 0.8887 (ptmm) cc_final: 0.8433 (ptpp) outliers start: 29 outliers final: 15 residues processed: 188 average time/residue: 0.2876 time to fit residues: 75.1551 Evaluate side-chains 172 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 1.591 ------------------------------------------------------------------------------- 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 141 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 152 LEU 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 B residue 416 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 46 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 119 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** C 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.136078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.113351 restraints weight = 15569.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.116873 restraints weight = 8262.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.119128 restraints weight = 5456.599| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10341 Z= 0.136 Angle : 0.558 7.424 14033 Z= 0.272 Chirality : 0.041 0.133 1600 Planarity : 0.004 0.039 1773 Dihedral : 5.919 103.777 1473 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.97 % Allowed : 17.83 % Favored : 79.19 % 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: -2.60 (0.22), residues: 1269 helix: -1.73 (0.19), residues: 696 sheet: -1.01 (0.44), residues: 140 loop : -1.60 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 359 HIS 0.005 0.001 HIS C 80 PHE 0.013 0.001 PHE B 341 TYR 0.009 0.001 TYR A 588 ARG 0.007 0.000 ARG A 493 Details of bonding type rmsd hydrogen bonds : bond 0.02929 ( 364) hydrogen bonds : angle 4.74070 ( 1059) SS BOND : bond 0.00077 ( 2) SS BOND : angle 0.29564 ( 4) covalent geometry : bond 0.00324 (10339) covalent geometry : angle 0.55853 (14029) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 1.139 Fit side-chains revert: symmetry clash REVERT: A 33 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7956 (mt) REVERT: A 92 TYR cc_start: 0.7446 (t80) cc_final: 0.6897 (t80) REVERT: A 178 LEU cc_start: 0.8130 (mt) cc_final: 0.7658 (tt) REVERT: A 305 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7632 (tt0) REVERT: A 334 GLU cc_start: 0.7613 (tt0) cc_final: 0.7373 (pt0) REVERT: A 441 GLN cc_start: 0.8202 (tp40) cc_final: 0.7943 (tp40) REVERT: A 467 GLU cc_start: 0.7514 (tm-30) cc_final: 0.7256 (tm-30) REVERT: B 163 PHE cc_start: 0.8217 (t80) cc_final: 0.7746 (t80) REVERT: B 277 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.6370 (mm-30) REVERT: B 301 LEU cc_start: 0.8467 (mt) cc_final: 0.8218 (mt) REVERT: B 561 GLN cc_start: 0.7868 (pp30) cc_final: 0.7501 (pp30) REVERT: C 53 LYS cc_start: 0.8937 (ttpp) cc_final: 0.8409 (ttmm) REVERT: C 65 LYS cc_start: 0.8889 (ptmm) cc_final: 0.8494 (ptpp) outliers start: 31 outliers final: 21 residues processed: 174 average time/residue: 0.2427 time to fit residues: 58.1281 Evaluate side-chains 173 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 120 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 105 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 120 ASN C 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.137657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.115251 restraints weight = 15549.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.118810 restraints weight = 8145.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.121072 restraints weight = 5351.281| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10341 Z= 0.140 Angle : 0.558 6.886 14033 Z= 0.271 Chirality : 0.041 0.133 1600 Planarity : 0.004 0.040 1773 Dihedral : 5.809 105.373 1473 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.88 % Allowed : 18.70 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.23), residues: 1269 helix: -1.47 (0.19), residues: 695 sheet: -0.94 (0.44), residues: 140 loop : -1.51 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 359 HIS 0.004 0.001 HIS C 80 PHE 0.013 0.001 PHE B 341 TYR 0.007 0.001 TYR B 92 ARG 0.007 0.000 ARG A 493 Details of bonding type rmsd hydrogen bonds : bond 0.02888 ( 364) hydrogen bonds : angle 4.66853 ( 1059) SS BOND : bond 0.00071 ( 2) SS BOND : angle 0.28293 ( 4) covalent geometry : bond 0.00335 (10339) covalent geometry : angle 0.55842 (14029) *********************** 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 186 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 1.169 Fit side-chains revert: symmetry clash REVERT: A 33 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7853 (mt) REVERT: A 69 ARG cc_start: 0.6874 (mtp180) cc_final: 0.6522 (ttm110) REVERT: A 178 LEU cc_start: 0.8089 (mt) cc_final: 0.7657 (tt) REVERT: A 305 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7773 (tt0) REVERT: A 441 GLN cc_start: 0.8164 (tp40) cc_final: 0.7948 (tp40) REVERT: B 163 PHE cc_start: 0.8223 (t80) cc_final: 0.7704 (t80) REVERT: B 277 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.6329 (mm-30) REVERT: B 301 LEU cc_start: 0.8492 (mt) cc_final: 0.8228 (mt) REVERT: B 561 GLN cc_start: 0.7939 (pp30) cc_final: 0.7600 (pp30) REVERT: C 19 ARG cc_start: 0.6585 (tpp80) cc_final: 0.6277 (tpp80) REVERT: C 53 LYS cc_start: 0.8914 (ttpp) cc_final: 0.8403 (ttmm) REVERT: C 65 LYS cc_start: 0.8907 (ptmm) cc_final: 0.8452 (ptpp) outliers start: 30 outliers final: 23 residues processed: 177 average time/residue: 0.2551 time to fit residues: 61.4656 Evaluate side-chains 173 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain C residue 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: 0.7980 chunk 20 optimal weight: 0.0770 chunk 99 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 126 optimal weight: 0.0040 chunk 13 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.5550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 308 GLN ** 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 = 0.3751 r_free = 0.3751 target = 0.139031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.116443 restraints weight = 15633.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.120118 restraints weight = 8234.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.122409 restraints weight = 5387.307| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10341 Z= 0.109 Angle : 0.539 7.105 14033 Z= 0.262 Chirality : 0.040 0.133 1600 Planarity : 0.003 0.038 1773 Dihedral : 5.662 103.757 1473 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.88 % Allowed : 19.46 % Favored : 77.66 % 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: -2.03 (0.23), residues: 1269 helix: -1.24 (0.20), residues: 699 sheet: -0.84 (0.44), residues: 140 loop : -1.38 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 446 HIS 0.004 0.001 HIS C 80 PHE 0.010 0.001 PHE A 168 TYR 0.007 0.001 TYR B 61 ARG 0.007 0.000 ARG A 493 Details of bonding type rmsd hydrogen bonds : bond 0.02683 ( 364) hydrogen bonds : angle 4.52821 ( 1059) SS BOND : bond 0.00068 ( 2) SS BOND : angle 0.29717 ( 4) covalent geometry : bond 0.00261 (10339) covalent geometry : angle 0.53885 (14029) *********************** 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 188 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 1.224 Fit side-chains revert: symmetry clash REVERT: A 33 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7831 (mt) REVERT: A 69 ARG cc_start: 0.6861 (mtp180) cc_final: 0.6567 (ttm110) REVERT: A 178 LEU cc_start: 0.8061 (mt) cc_final: 0.7660 (tt) REVERT: A 181 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8297 (tt) REVERT: A 334 GLU cc_start: 0.7607 (tt0) cc_final: 0.7357 (pt0) REVERT: A 441 GLN cc_start: 0.8157 (tp40) cc_final: 0.7945 (tp40) REVERT: A 536 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8690 (mp) REVERT: B 163 PHE cc_start: 0.8247 (t80) cc_final: 0.7658 (t80) REVERT: B 301 LEU cc_start: 0.8469 (mt) cc_final: 0.8166 (mt) REVERT: B 561 GLN cc_start: 0.8005 (pp30) cc_final: 0.7636 (pp30) REVERT: C 19 ARG cc_start: 0.6384 (tpp80) cc_final: 0.6082 (tpp80) REVERT: C 53 LYS cc_start: 0.8921 (ttpp) cc_final: 0.8411 (ttmm) REVERT: C 65 LYS cc_start: 0.8912 (ptmm) cc_final: 0.8455 (ptpp) outliers start: 30 outliers final: 22 residues processed: 179 average time/residue: 0.2536 time to fit residues: 62.4764 Evaluate side-chains 178 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 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 4 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 120 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 20 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 109 optimal weight: 0.0870 chunk 120 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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** C 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.139072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.116743 restraints weight = 15575.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.120334 restraints weight = 8140.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.122634 restraints weight = 5339.357| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10341 Z= 0.119 Angle : 0.547 7.277 14033 Z= 0.265 Chirality : 0.040 0.130 1600 Planarity : 0.004 0.038 1773 Dihedral : 5.594 103.372 1473 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.97 % Allowed : 19.94 % Favored : 77.09 % 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: -1.80 (0.24), residues: 1269 helix: -1.04 (0.20), residues: 704 sheet: -0.80 (0.45), residues: 135 loop : -1.27 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 446 HIS 0.004 0.001 HIS C 80 PHE 0.012 0.001 PHE A 257 TYR 0.007 0.001 TYR A 541 ARG 0.007 0.000 ARG A 493 Details of bonding type rmsd hydrogen bonds : bond 0.02679 ( 364) hydrogen bonds : angle 4.46111 ( 1059) SS BOND : bond 0.00072 ( 2) SS BOND : angle 0.29926 ( 4) covalent geometry : bond 0.00284 (10339) covalent geometry : angle 0.54709 (14029) *********************** 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 188 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: A 33 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7882 (mt) REVERT: A 69 ARG cc_start: 0.6937 (mtp180) cc_final: 0.6658 (ttm110) REVERT: A 92 TYR cc_start: 0.7507 (t80) cc_final: 0.6952 (t80) REVERT: A 178 LEU cc_start: 0.8055 (mt) cc_final: 0.7664 (tt) REVERT: A 181 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8265 (tt) REVERT: A 305 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7524 (tt0) REVERT: A 334 GLU cc_start: 0.7649 (tt0) cc_final: 0.7394 (pt0) REVERT: A 442 GLU cc_start: 0.8065 (pm20) cc_final: 0.7666 (pm20) REVERT: B 163 PHE cc_start: 0.8295 (t80) cc_final: 0.7653 (t80) REVERT: B 277 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.6168 (mm-30) REVERT: B 301 LEU cc_start: 0.8461 (mt) cc_final: 0.8185 (mt) REVERT: B 561 GLN cc_start: 0.7996 (pp30) cc_final: 0.7647 (pp30) REVERT: C 19 ARG cc_start: 0.6377 (tpp80) cc_final: 0.6074 (tpp80) REVERT: C 53 LYS cc_start: 0.8923 (ttpp) cc_final: 0.8430 (ttmm) REVERT: C 65 LYS cc_start: 0.8921 (ptmm) cc_final: 0.8464 (ptpp) outliers start: 31 outliers final: 24 residues processed: 179 average time/residue: 0.2567 time to fit residues: 62.9388 Evaluate side-chains 178 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 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: 0.9990 chunk 116 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 44 optimal weight: 0.0770 chunk 113 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 11 optimal weight: 0.4980 overall best weight: 0.6342 ------------------------------------------------------------------------------- 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** C 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.139132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.116837 restraints weight = 15451.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.120413 restraints weight = 8084.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.122710 restraints weight = 5320.235| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10341 Z= 0.115 Angle : 0.555 7.914 14033 Z= 0.266 Chirality : 0.040 0.151 1600 Planarity : 0.003 0.038 1773 Dihedral : 5.546 102.754 1473 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.26 % Allowed : 20.13 % Favored : 76.61 % 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: -0.91 (0.20), residues: 704 sheet: -0.74 (0.46), residues: 135 loop : -1.21 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 446 HIS 0.003 0.001 HIS C 80 PHE 0.012 0.001 PHE A 257 TYR 0.007 0.001 TYR A 541 ARG 0.007 0.000 ARG A 493 Details of bonding type rmsd hydrogen bonds : bond 0.02653 ( 364) hydrogen bonds : angle 4.41803 ( 1059) SS BOND : bond 0.00082 ( 2) SS BOND : angle 0.29484 ( 4) covalent geometry : bond 0.00275 (10339) covalent geometry : angle 0.55510 (14029) *********************** 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 187 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 1.089 Fit side-chains REVERT: A 33 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7888 (mt) REVERT: A 69 ARG cc_start: 0.6945 (mtp180) cc_final: 0.6691 (ttm110) REVERT: A 74 LEU cc_start: 0.8865 (mt) cc_final: 0.8586 (tp) REVERT: A 92 TYR cc_start: 0.7500 (t80) cc_final: 0.6942 (t80) REVERT: A 181 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8228 (tt) REVERT: A 205 MET cc_start: 0.7437 (tmm) cc_final: 0.7126 (tmm) REVERT: A 305 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7588 (tt0) REVERT: A 334 GLU cc_start: 0.7621 (tt0) cc_final: 0.7355 (pt0) REVERT: A 442 GLU cc_start: 0.8063 (pm20) cc_final: 0.7658 (pm20) REVERT: A 536 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8668 (mp) REVERT: B 163 PHE cc_start: 0.8285 (t80) cc_final: 0.7631 (t80) REVERT: B 188 ARG cc_start: 0.7443 (ttp-110) cc_final: 0.7233 (ttp80) REVERT: B 277 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.6143 (mm-30) REVERT: B 301 LEU cc_start: 0.8469 (mt) cc_final: 0.8189 (mt) REVERT: B 561 GLN cc_start: 0.8029 (pp30) cc_final: 0.7755 (pp30) REVERT: C 19 ARG cc_start: 0.6408 (tpp80) cc_final: 0.6117 (tpp80) REVERT: C 53 LYS cc_start: 0.8910 (ttpp) cc_final: 0.8424 (ttmm) REVERT: C 65 LYS cc_start: 0.8920 (ptmm) cc_final: 0.8474 (ptpp) outliers start: 34 outliers final: 27 residues processed: 176 average time/residue: 0.2496 time to fit residues: 60.3860 Evaluate side-chains 185 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 181 LEU 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 379 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 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 97 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 118 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 0.3980 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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** C 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.136784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.114509 restraints weight = 15661.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.117977 restraints weight = 8275.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.120240 restraints weight = 5477.527| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10341 Z= 0.180 Angle : 0.608 7.231 14033 Z= 0.292 Chirality : 0.042 0.153 1600 Planarity : 0.004 0.040 1773 Dihedral : 5.758 107.547 1473 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.97 % Allowed : 20.33 % Favored : 76.70 % 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: -1.72 (0.24), residues: 1269 helix: -0.97 (0.20), residues: 706 sheet: -0.80 (0.45), residues: 135 loop : -1.21 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 359 HIS 0.003 0.001 HIS C 80 PHE 0.016 0.001 PHE B 341 TYR 0.009 0.001 TYR B 92 ARG 0.008 0.000 ARG A 384 Details of bonding type rmsd hydrogen bonds : bond 0.02975 ( 364) hydrogen bonds : angle 4.57091 ( 1059) SS BOND : bond 0.00079 ( 2) SS BOND : angle 0.38793 ( 4) covalent geometry : bond 0.00430 (10339) covalent geometry : angle 0.60820 (14029) ********************** 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 184 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 1.236 Fit side-chains REVERT: A 33 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7871 (mt) REVERT: A 181 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8334 (tt) REVERT: A 305 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7611 (tt0) REVERT: A 442 GLU cc_start: 0.8089 (pm20) cc_final: 0.7765 (pm20) REVERT: B 163 PHE cc_start: 0.8302 (t80) cc_final: 0.7674 (t80) REVERT: B 277 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.6247 (mm-30) REVERT: B 301 LEU cc_start: 0.8556 (mt) cc_final: 0.8289 (mt) REVERT: B 303 GLN cc_start: 0.8130 (tp40) cc_final: 0.7826 (tp-100) REVERT: B 443 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7266 (ttp-170) REVERT: B 561 GLN cc_start: 0.8057 (pp30) cc_final: 0.7828 (pp30) REVERT: B 569 MET cc_start: 0.8199 (ttm) cc_final: 0.7855 (ttm) REVERT: C 19 ARG cc_start: 0.6379 (tpp80) cc_final: 0.6066 (tpp80) REVERT: C 53 LYS cc_start: 0.8891 (ttpp) cc_final: 0.8415 (ttmm) REVERT: C 65 LYS cc_start: 0.8923 (ptmm) cc_final: 0.8489 (ptpp) outliers start: 31 outliers final: 25 residues processed: 175 average time/residue: 0.2604 time to fit residues: 62.1101 Evaluate side-chains 179 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 4 LEU 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 125 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 68 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 123 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** C 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.137700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.115548 restraints weight = 15518.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.119050 restraints weight = 8135.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.121308 restraints weight = 5348.614| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10341 Z= 0.128 Angle : 0.585 7.375 14033 Z= 0.281 Chirality : 0.041 0.176 1600 Planarity : 0.004 0.077 1773 Dihedral : 5.714 106.056 1473 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.16 % Allowed : 19.94 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.59 (0.24), residues: 1269 helix: -0.87 (0.20), residues: 706 sheet: -0.79 (0.45), residues: 135 loop : -1.15 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 359 HIS 0.003 0.001 HIS C 80 PHE 0.013 0.001 PHE A 168 TYR 0.007 0.001 TYR B 61 ARG 0.016 0.000 ARG A 69 Details of bonding type rmsd hydrogen bonds : bond 0.02804 ( 364) hydrogen bonds : angle 4.55064 ( 1059) SS BOND : bond 0.00064 ( 2) SS BOND : angle 0.40081 ( 4) covalent geometry : bond 0.00307 (10339) covalent geometry : angle 0.58493 (14029) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3978.36 seconds wall clock time: 70 minutes 56.24 seconds (4256.24 seconds total)