Starting phenix.real_space_refine on Tue Jul 29 20:02:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ybq_39121/07_2025/8ybq_39121.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ybq_39121/07_2025/8ybq_39121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ybq_39121/07_2025/8ybq_39121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ybq_39121/07_2025/8ybq_39121.map" model { file = "/net/cci-nas-00/data/ceres_data/8ybq_39121/07_2025/8ybq_39121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ybq_39121/07_2025/8ybq_39121.cif" } resolution = 2.59 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= 0.001 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 7767 2.51 5 N 1845 2.21 5 O 2028 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11700 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3871 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 20, 'TRANS': 481} Chain: "B" Number of atoms: 3871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3871 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 20, 'TRANS': 481} Chain: "C" Number of atoms: 3871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3871 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 20, 'TRANS': 481} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'CHT': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'CHT': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'CHT': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Time building chain proxies: 7.88, per 1000 atoms: 0.67 Number of scatterers: 11700 At special positions: 0 Unit cell: (113.52, 114.38, 78.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 2028 8.00 N 1845 7.00 C 7767 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.98 Conformation dependent library (CDL) restraints added in 1.5 seconds 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2700 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 3 sheets defined 85.3% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 15 through 36 removed outlier: 3.718A pdb=" N PHE A 21 " --> pdb=" O PRO A 17 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE A 25 " --> pdb=" O PHE A 21 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 33 " --> pdb=" O PHE A 29 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 34 " --> pdb=" O GLY A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 55 removed outlier: 3.941A pdb=" N ALA A 42 " --> pdb=" O GLN A 38 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TRP A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN A 53 " --> pdb=" O ASN A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 76 removed outlier: 3.682A pdb=" N TYR A 59 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR A 64 " --> pdb=" O MET A 60 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A 65 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU A 67 " --> pdb=" O MET A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 81 removed outlier: 3.552A pdb=" N LYS A 80 " --> pdb=" O GLY A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 106 removed outlier: 3.553A pdb=" N MET A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 101 " --> pdb=" O TRP A 97 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA A 104 " --> pdb=" O MET A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 111 removed outlier: 3.520A pdb=" N LEU A 110 " --> pdb=" O SER A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.642A pdb=" N LEU A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 147 removed outlier: 3.673A pdb=" N ALA A 136 " --> pdb=" O THR A 132 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN A 141 " --> pdb=" O ARG A 137 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE A 144 " --> pdb=" O MET A 140 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 168 removed outlier: 3.656A pdb=" N TRP A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL A 154 " --> pdb=" O HIS A 150 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE A 155 " --> pdb=" O GLY A 151 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 156 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.594A pdb=" N SER A 177 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA A 178 " --> pdb=" O LEU A 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 174 through 178' Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 185 through 188 removed outlier: 3.652A pdb=" N ASN A 188 " --> pdb=" O LYS A 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 185 through 188' Processing helix chain 'A' and resid 189 through 226 removed outlier: 3.528A pdb=" N ALA A 194 " --> pdb=" O PRO A 190 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 195 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A 199 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA A 202 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY A 221 " --> pdb=" O HIS A 217 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 251 removed outlier: 3.506A pdb=" N VAL A 236 " --> pdb=" O GLN A 232 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY A 237 " --> pdb=" O TRP A 233 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 279 removed outlier: 3.617A pdb=" N ASP A 263 " --> pdb=" O ARG A 259 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS A 270 " --> pdb=" O MET A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 304 Proline residue: A 301 - end of helix removed outlier: 3.672A pdb=" N SER A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 340 Proline residue: A 333 - end of helix removed outlier: 3.556A pdb=" N LEU A 337 " --> pdb=" O PRO A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 347 through 356 Processing helix chain 'A' and resid 357 through 380 removed outlier: 3.808A pdb=" N GLY A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N PHE A 362 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR A 363 " --> pdb=" O PRO A 359 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 374 " --> pdb=" O PHE A 370 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 393 removed outlier: 3.910A pdb=" N GLY A 387 " --> pdb=" O MET A 383 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP A 392 " --> pdb=" O GLN A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 403 Processing helix chain 'A' and resid 407 through 438 removed outlier: 3.547A pdb=" N VAL A 411 " --> pdb=" O TRP A 407 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA A 413 " --> pdb=" O LYS A 409 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER A 429 " --> pdb=" O THR A 425 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL A 432 " --> pdb=" O ASP A 428 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A 433 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 472 removed outlier: 4.202A pdb=" N VAL A 454 " --> pdb=" O LYS A 450 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A 455 " --> pdb=" O TRP A 451 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR A 460 " --> pdb=" O TRP A 456 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.832A pdb=" N LEU A 476 " --> pdb=" O SER A 472 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS A 477 " --> pdb=" O ILE A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 509 removed outlier: 4.040A pdb=" N SER A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE A 490 " --> pdb=" O PRO A 486 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N MET A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 36 removed outlier: 3.717A pdb=" N PHE B 21 " --> pdb=" O PRO B 17 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE B 25 " --> pdb=" O PHE B 21 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE B 28 " --> pdb=" O SER B 24 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE B 31 " --> pdb=" O LEU B 27 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE B 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 55 removed outlier: 3.941A pdb=" N ALA B 42 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TRP B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN B 53 " --> pdb=" O ASN B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 76 removed outlier: 3.681A pdb=" N TYR B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR B 64 " --> pdb=" O MET B 60 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU B 65 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU B 67 " --> pdb=" O MET B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 81 removed outlier: 3.552A pdb=" N LYS B 80 " --> pdb=" O GLY B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 106 removed outlier: 3.617A pdb=" N MET B 100 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 101 " --> pdb=" O TRP B 97 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 103 " --> pdb=" O GLY B 99 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA B 104 " --> pdb=" O MET B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 111 removed outlier: 3.519A pdb=" N LEU B 110 " --> pdb=" O SER B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 124 removed outlier: 3.642A pdb=" N LEU B 119 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 147 removed outlier: 3.673A pdb=" N ALA B 136 " --> pdb=" O THR B 132 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN B 141 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE B 144 " --> pdb=" O MET B 140 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP B 147 " --> pdb=" O LEU B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 168 removed outlier: 3.656A pdb=" N TRP B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL B 154 " --> pdb=" O HIS B 150 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE B 155 " --> pdb=" O GLY B 151 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 156 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 166 " --> pdb=" O LEU B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 178 removed outlier: 3.594A pdb=" N SER B 177 " --> pdb=" O ALA B 174 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA B 178 " --> pdb=" O LEU B 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 174 through 178' Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 185 through 188 removed outlier: 3.652A pdb=" N ASN B 188 " --> pdb=" O LYS B 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 185 through 188' Processing helix chain 'B' and resid 189 through 226 removed outlier: 3.527A pdb=" N ALA B 194 " --> pdb=" O PRO B 190 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 195 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B 199 " --> pdb=" O VAL B 195 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE B 201 " --> pdb=" O GLY B 197 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA B 202 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR B 203 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER B 220 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY B 221 " --> pdb=" O HIS B 217 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 251 removed outlier: 3.506A pdb=" N VAL B 236 " --> pdb=" O GLN B 232 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY B 237 " --> pdb=" O TRP B 233 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 246 " --> pdb=" O MET B 242 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B 248 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 279 removed outlier: 3.559A pdb=" N ASP B 263 " --> pdb=" O ARG B 259 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS B 270 " --> pdb=" O MET B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 304 Proline residue: B 301 - end of helix removed outlier: 3.672A pdb=" N SER B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 340 Proline residue: B 333 - end of helix removed outlier: 3.557A pdb=" N LEU B 337 " --> pdb=" O PRO B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 343 No H-bonds generated for 'chain 'B' and resid 341 through 343' Processing helix chain 'B' and resid 347 through 356 Processing helix chain 'B' and resid 357 through 380 removed outlier: 3.809A pdb=" N GLY B 361 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N PHE B 362 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR B 363 " --> pdb=" O PRO B 359 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA B 374 " --> pdb=" O PHE B 370 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 393 removed outlier: 3.909A pdb=" N GLY B 387 " --> pdb=" O MET B 383 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 389 " --> pdb=" O ALA B 385 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP B 392 " --> pdb=" O GLN B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 403 Processing helix chain 'B' and resid 407 through 438 removed outlier: 3.547A pdb=" N VAL B 411 " --> pdb=" O TRP B 407 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA B 413 " --> pdb=" O LYS B 409 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE B 417 " --> pdb=" O ALA B 413 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER B 429 " --> pdb=" O THR B 425 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL B 432 " --> pdb=" O ASP B 428 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 433 " --> pdb=" O SER B 429 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER B 438 " --> pdb=" O LEU B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 472 removed outlier: 4.202A pdb=" N VAL B 454 " --> pdb=" O LYS B 450 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B 455 " --> pdb=" O TRP B 451 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR B 460 " --> pdb=" O TRP B 456 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE B 469 " --> pdb=" O SER B 465 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER B 470 " --> pdb=" O GLY B 466 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 484 removed outlier: 3.827A pdb=" N LEU B 476 " --> pdb=" O SER B 472 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS B 477 " --> pdb=" O ILE B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 509 removed outlier: 4.041A pdb=" N SER B 488 " --> pdb=" O SER B 484 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE B 490 " --> pdb=" O PRO B 486 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N MET B 504 " --> pdb=" O LYS B 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 36 removed outlier: 3.718A pdb=" N PHE C 21 " --> pdb=" O PRO C 17 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE C 25 " --> pdb=" O PHE C 21 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE C 26 " --> pdb=" O ALA C 22 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE C 28 " --> pdb=" O SER C 24 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE C 31 " --> pdb=" O LEU C 27 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE C 32 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE C 34 " --> pdb=" O GLY C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 55 removed outlier: 3.941A pdb=" N ALA C 42 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TRP C 43 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN C 53 " --> pdb=" O ASN C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 76 removed outlier: 3.681A pdb=" N TYR C 59 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR C 64 " --> pdb=" O MET C 60 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU C 65 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR C 66 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU C 67 " --> pdb=" O MET C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 81 removed outlier: 3.552A pdb=" N LYS C 80 " --> pdb=" O GLY C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 106 removed outlier: 3.592A pdb=" N MET C 100 " --> pdb=" O SER C 96 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU C 101 " --> pdb=" O TRP C 97 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA C 103 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA C 104 " --> pdb=" O MET C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 111 removed outlier: 3.519A pdb=" N LEU C 110 " --> pdb=" O SER C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 124 removed outlier: 3.642A pdb=" N LEU C 119 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 147 removed outlier: 3.672A pdb=" N ALA C 136 " --> pdb=" O THR C 132 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG C 137 " --> pdb=" O ALA C 133 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN C 141 " --> pdb=" O ARG C 137 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE C 144 " --> pdb=" O MET C 140 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP C 147 " --> pdb=" O LEU C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 168 removed outlier: 3.657A pdb=" N TRP C 152 " --> pdb=" O GLY C 148 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL C 154 " --> pdb=" O HIS C 150 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE C 155 " --> pdb=" O GLY C 151 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA C 156 " --> pdb=" O TRP C 152 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE C 157 " --> pdb=" O GLY C 153 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA C 166 " --> pdb=" O LEU C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 178 removed outlier: 3.593A pdb=" N SER C 177 " --> pdb=" O ALA C 174 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA C 178 " --> pdb=" O LEU C 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 174 through 178' Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'C' and resid 185 through 188 removed outlier: 3.652A pdb=" N ASN C 188 " --> pdb=" O LYS C 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 185 through 188' Processing helix chain 'C' and resid 189 through 226 removed outlier: 3.527A pdb=" N ALA C 194 " --> pdb=" O PRO C 190 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL C 195 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY C 199 " --> pdb=" O VAL C 195 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE C 200 " --> pdb=" O ASP C 196 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA C 202 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR C 203 " --> pdb=" O GLY C 199 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER C 220 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY C 221 " --> pdb=" O HIS C 217 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 251 removed outlier: 3.507A pdb=" N VAL C 236 " --> pdb=" O GLN C 232 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY C 237 " --> pdb=" O TRP C 233 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA C 246 " --> pdb=" O MET C 242 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU C 248 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 279 removed outlier: 3.608A pdb=" N ASP C 263 " --> pdb=" O ARG C 259 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N CYS C 270 " --> pdb=" O MET C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 304 Proline residue: C 301 - end of helix removed outlier: 3.672A pdb=" N SER C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 340 Proline residue: C 333 - end of helix removed outlier: 3.557A pdb=" N LEU C 337 " --> pdb=" O PRO C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 343 No H-bonds generated for 'chain 'C' and resid 341 through 343' Processing helix chain 'C' and resid 347 through 356 Processing helix chain 'C' and resid 357 through 380 removed outlier: 3.808A pdb=" N GLY C 361 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N PHE C 362 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR C 363 " --> pdb=" O PRO C 359 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA C 374 " --> pdb=" O PHE C 370 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN C 377 " --> pdb=" O SER C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 393 removed outlier: 3.910A pdb=" N GLY C 387 " --> pdb=" O MET C 383 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER C 389 " --> pdb=" O ALA C 385 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA C 390 " --> pdb=" O LEU C 386 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE C 391 " --> pdb=" O GLY C 387 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP C 392 " --> pdb=" O GLN C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 403 Processing helix chain 'C' and resid 407 through 438 removed outlier: 3.547A pdb=" N VAL C 411 " --> pdb=" O TRP C 407 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA C 413 " --> pdb=" O LYS C 409 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE C 417 " --> pdb=" O ALA C 413 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER C 429 " --> pdb=" O THR C 425 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL C 432 " --> pdb=" O ASP C 428 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL C 433 " --> pdb=" O SER C 429 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER C 438 " --> pdb=" O LEU C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 472 removed outlier: 4.202A pdb=" N VAL C 454 " --> pdb=" O LYS C 450 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE C 455 " --> pdb=" O TRP C 451 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR C 460 " --> pdb=" O TRP C 456 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE C 469 " --> pdb=" O SER C 465 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER C 470 " --> pdb=" O GLY C 466 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY C 471 " --> pdb=" O LEU C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 484 removed outlier: 3.820A pdb=" N LEU C 476 " --> pdb=" O SER C 472 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS C 477 " --> pdb=" O ILE C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 509 removed outlier: 4.040A pdb=" N SER C 488 " --> pdb=" O SER C 484 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU C 489 " --> pdb=" O LEU C 485 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE C 490 " --> pdb=" O PRO C 486 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N MET C 504 " --> pdb=" O LYS C 500 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 Processing sheet with id=AA2, first strand: chain 'B' and resid 13 through 14 Processing sheet with id=AA3, first strand: chain 'C' and resid 13 through 14 702 hydrogen bonds defined for protein. 2079 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.31 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1746 1.30 - 1.43: 3499 1.43 - 1.56: 6629 1.56 - 1.68: 0 1.68 - 1.81: 114 Bond restraints: 11988 Sorted by residual: bond pdb=" C TRP A 325 " pdb=" O TRP A 325 " ideal model delta sigma weight residual 1.237 1.179 0.058 1.17e-02 7.31e+03 2.46e+01 bond pdb=" C TRP C 325 " pdb=" O TRP C 325 " ideal model delta sigma weight residual 1.237 1.179 0.058 1.17e-02 7.31e+03 2.46e+01 bond pdb=" C TRP B 325 " pdb=" O TRP B 325 " ideal model delta sigma weight residual 1.237 1.181 0.055 1.17e-02 7.31e+03 2.24e+01 bond pdb=" C SER B 472 " pdb=" O SER B 472 " ideal model delta sigma weight residual 1.239 1.207 0.031 9.60e-03 1.09e+04 1.07e+01 bond pdb=" C SER A 472 " pdb=" O SER A 472 " ideal model delta sigma weight residual 1.239 1.209 0.029 9.60e-03 1.09e+04 9.43e+00 ... (remaining 11983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 15774 1.80 - 3.60: 487 3.60 - 5.39: 72 5.39 - 7.19: 25 7.19 - 8.99: 4 Bond angle restraints: 16362 Sorted by residual: angle pdb=" C SER A 472 " pdb=" CA SER A 472 " pdb=" CB SER A 472 " ideal model delta sigma weight residual 116.54 109.35 7.19 1.15e+00 7.56e-01 3.91e+01 angle pdb=" C SER B 472 " pdb=" CA SER B 472 " pdb=" CB SER B 472 " ideal model delta sigma weight residual 116.54 109.85 6.69 1.15e+00 7.56e-01 3.38e+01 angle pdb=" N SER C 93 " pdb=" CA SER C 93 " pdb=" C SER C 93 " ideal model delta sigma weight residual 112.93 118.92 -5.99 1.12e+00 7.97e-01 2.86e+01 angle pdb=" N SER A 93 " pdb=" CA SER A 93 " pdb=" C SER A 93 " ideal model delta sigma weight residual 112.72 118.44 -5.72 1.14e+00 7.69e-01 2.51e+01 angle pdb=" CA LEU B 467 " pdb=" C LEU B 467 " pdb=" N LEU B 468 " ideal model delta sigma weight residual 117.72 124.02 -6.30 1.31e+00 5.83e-01 2.32e+01 ... (remaining 16357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 6125 17.24 - 34.48: 480 34.48 - 51.72: 82 51.72 - 68.96: 6 68.96 - 86.20: 3 Dihedral angle restraints: 6696 sinusoidal: 2445 harmonic: 4251 Sorted by residual: dihedral pdb=" CA TRP B 325 " pdb=" CB TRP B 325 " pdb=" CG TRP B 325 " pdb=" CD1 TRP B 325 " ideal model delta sinusoidal sigma weight residual -90.00 -176.20 86.20 2 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA TRP C 325 " pdb=" CB TRP C 325 " pdb=" CG TRP C 325 " pdb=" CD1 TRP C 325 " ideal model delta sinusoidal sigma weight residual -90.00 -176.10 86.10 2 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA TRP A 325 " pdb=" CB TRP A 325 " pdb=" CG TRP A 325 " pdb=" CD1 TRP A 325 " ideal model delta sinusoidal sigma weight residual -90.00 -175.85 85.85 2 2.00e+01 2.50e-03 1.19e+01 ... (remaining 6693 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1506 0.058 - 0.116: 329 0.116 - 0.174: 13 0.174 - 0.231: 1 0.231 - 0.289: 2 Chirality restraints: 1851 Sorted by residual: chirality pdb=" CA SER C 472 " pdb=" N SER C 472 " pdb=" C SER C 472 " pdb=" CB SER C 472 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA SER B 472 " pdb=" N SER B 472 " pdb=" C SER B 472 " pdb=" CB SER B 472 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA SER A 472 " pdb=" N SER A 472 " pdb=" C SER A 472 " pdb=" CB SER A 472 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.43e-01 ... (remaining 1848 not shown) Planarity restraints: 2004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 485 " 0.033 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO C 486 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO C 486 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 486 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 485 " 0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO A 486 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 486 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 486 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 485 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO B 486 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 486 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 486 " -0.027 5.00e-02 4.00e+02 ... (remaining 2001 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 207 2.70 - 3.25: 10966 3.25 - 3.80: 16998 3.80 - 4.35: 23650 4.35 - 4.90: 39596 Nonbonded interactions: 91417 Sorted by model distance: nonbonded pdb=" O PRO A 444 " pdb=" OD1 ASP A 445 " model vdw 2.153 3.040 nonbonded pdb=" O PRO B 444 " pdb=" OD1 ASP B 445 " model vdw 2.154 3.040 nonbonded pdb=" O PRO C 444 " pdb=" OD1 ASP C 445 " model vdw 2.154 3.040 nonbonded pdb=" NZ LYS A 82 " pdb=" O ASP A 88 " model vdw 2.238 3.120 nonbonded pdb=" NZ LYS C 82 " pdb=" O ASP C 88 " model vdw 2.238 3.120 ... (remaining 91412 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.710 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.500 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 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 : 0.005 0.060 11988 Z= 0.294 Angle : 0.778 8.991 16362 Z= 0.475 Chirality : 0.045 0.289 1851 Planarity : 0.005 0.049 2004 Dihedral : 12.287 86.201 3996 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.67 % Allowed : 4.63 % Favored : 94.70 % 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: -2.76 (0.19), residues: 1500 helix: -1.24 (0.15), residues: 1116 sheet: None (None), residues: 0 loop : -3.23 (0.24), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 320 HIS 0.003 0.001 HIS C 87 PHE 0.011 0.002 PHE B 423 TYR 0.007 0.001 TYR B 94 ARG 0.003 0.000 ARG C 168 Details of bonding type rmsd hydrogen bonds : bond 0.20953 ( 702) hydrogen bonds : angle 6.06785 ( 2079) covalent geometry : bond 0.00530 (11988) covalent geometry : angle 0.77839 (16362) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 159 time to evaluate : 1.234 Fit side-chains REVERT: A 186 ARG cc_start: 0.7834 (mtt90) cc_final: 0.7630 (mtm-85) REVERT: A 256 LYS cc_start: 0.6472 (OUTLIER) cc_final: 0.6215 (mmtp) REVERT: A 440 LYS cc_start: 0.8143 (ttpt) cc_final: 0.7896 (ttpm) REVERT: A 508 ARG cc_start: 0.7671 (ttp80) cc_final: 0.6680 (tpt170) REVERT: B 38 GLN cc_start: 0.7610 (mt0) cc_final: 0.7369 (mp10) REVERT: B 186 ARG cc_start: 0.7883 (mtt90) cc_final: 0.7661 (mtm-85) REVERT: B 440 LYS cc_start: 0.8146 (ttpt) cc_final: 0.7892 (ttpm) REVERT: C 38 GLN cc_start: 0.7636 (mt0) cc_final: 0.7356 (mp10) REVERT: C 440 LYS cc_start: 0.8238 (ttpt) cc_final: 0.7967 (ttpm) outliers start: 8 outliers final: 4 residues processed: 166 average time/residue: 1.4562 time to fit residues: 259.5346 Evaluate side-chains 148 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 143 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain B residue 325 TRP Chi-restraints excluded: chain C residue 325 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 60 optimal weight: 0.4980 chunk 117 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS A 121 HIS A 141 GLN A 170 ASN A 372 ASN B 87 HIS B 121 HIS B 141 GLN B 372 ASN C 87 HIS C 141 GLN C 372 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.117567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.092323 restraints weight = 12570.513| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.48 r_work: 0.2892 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11988 Z= 0.119 Angle : 0.502 5.134 16362 Z= 0.269 Chirality : 0.037 0.121 1851 Planarity : 0.004 0.033 2004 Dihedral : 5.736 89.527 1604 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.02 % Allowed : 8.84 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.22), residues: 1500 helix: 0.08 (0.16), residues: 1113 sheet: None (None), residues: 0 loop : -2.34 (0.28), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 366 HIS 0.003 0.001 HIS A 87 PHE 0.013 0.001 PHE B 423 TYR 0.011 0.001 TYR C 94 ARG 0.003 0.000 ARG C 13 Details of bonding type rmsd hydrogen bonds : bond 0.05939 ( 702) hydrogen bonds : angle 4.04334 ( 2079) covalent geometry : bond 0.00243 (11988) covalent geometry : angle 0.50248 (16362) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 1.186 Fit side-chains REVERT: A 80 LYS cc_start: 0.8576 (mmmt) cc_final: 0.8137 (mmtt) REVERT: A 186 ARG cc_start: 0.7809 (mtt90) cc_final: 0.7523 (mtm-85) REVERT: A 357 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8363 (mp) REVERT: B 38 GLN cc_start: 0.7889 (mt0) cc_final: 0.7495 (mt0) REVERT: B 357 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8321 (mp) REVERT: C 13 ARG cc_start: 0.7351 (ptt-90) cc_final: 0.6467 (ptp90) REVERT: C 38 GLN cc_start: 0.8033 (mt0) cc_final: 0.7725 (mt0) REVERT: C 357 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8330 (mp) outliers start: 24 outliers final: 9 residues processed: 157 average time/residue: 1.2040 time to fit residues: 205.0808 Evaluate side-chains 148 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 325 TRP Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 357 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 100 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 108 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 135 optimal weight: 0.3980 chunk 123 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.112166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.086634 restraints weight = 12692.404| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.49 r_work: 0.2806 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11988 Z= 0.181 Angle : 0.612 5.349 16362 Z= 0.323 Chirality : 0.042 0.126 1851 Planarity : 0.004 0.041 2004 Dihedral : 5.680 87.920 1599 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.36 % Allowed : 9.09 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.22), residues: 1500 helix: 0.33 (0.16), residues: 1131 sheet: None (None), residues: 0 loop : -2.33 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 320 HIS 0.005 0.001 HIS B 121 PHE 0.017 0.002 PHE B 423 TYR 0.007 0.001 TYR B 164 ARG 0.004 0.000 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.08638 ( 702) hydrogen bonds : angle 4.20200 ( 2079) covalent geometry : bond 0.00416 (11988) covalent geometry : angle 0.61168 (16362) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 1.326 Fit side-chains REVERT: A 27 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8293 (mp) REVERT: A 80 LYS cc_start: 0.8605 (mmmt) cc_final: 0.8140 (mmtt) REVERT: A 186 ARG cc_start: 0.7823 (mtt90) cc_final: 0.7558 (mtm-85) REVERT: A 259 ARG cc_start: 0.6468 (ttm170) cc_final: 0.6150 (mtm-85) REVERT: B 38 GLN cc_start: 0.7908 (mt0) cc_final: 0.7455 (mp10) REVERT: C 38 GLN cc_start: 0.8043 (mt0) cc_final: 0.7703 (mt0) outliers start: 28 outliers final: 12 residues processed: 145 average time/residue: 1.4376 time to fit residues: 224.0306 Evaluate side-chains 143 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 325 TRP Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 428 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 130 optimal weight: 0.0770 chunk 44 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 59 optimal weight: 0.0050 chunk 24 optimal weight: 0.0050 chunk 92 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.3966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.121639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.096490 restraints weight = 12608.933| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.49 r_work: 0.2952 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11988 Z= 0.098 Angle : 0.447 5.735 16362 Z= 0.235 Chirality : 0.036 0.121 1851 Planarity : 0.003 0.033 2004 Dihedral : 5.275 88.904 1599 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.09 % Allowed : 10.77 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.22), residues: 1500 helix: 1.09 (0.16), residues: 1107 sheet: None (None), residues: 0 loop : -1.92 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 366 HIS 0.001 0.000 HIS A 121 PHE 0.012 0.001 PHE B 423 TYR 0.008 0.001 TYR C 94 ARG 0.006 0.000 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.04282 ( 702) hydrogen bonds : angle 3.76289 ( 2079) covalent geometry : bond 0.00195 (11988) covalent geometry : angle 0.44710 (16362) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 1.252 Fit side-chains REVERT: A 80 LYS cc_start: 0.8628 (mmmt) cc_final: 0.8186 (mmtt) REVERT: A 186 ARG cc_start: 0.7764 (mtt90) cc_final: 0.7549 (mtm-85) REVERT: B 38 GLN cc_start: 0.7779 (mt0) cc_final: 0.7390 (mp10) REVERT: C 13 ARG cc_start: 0.7360 (ptt-90) cc_final: 0.6600 (ptp90) REVERT: C 38 GLN cc_start: 0.7731 (mt0) cc_final: 0.7406 (mt0) REVERT: C 80 LYS cc_start: 0.8620 (mmtt) cc_final: 0.7907 (mmmt) REVERT: C 129 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7319 (mm-30) outliers start: 13 outliers final: 8 residues processed: 149 average time/residue: 1.2366 time to fit residues: 199.8110 Evaluate side-chains 140 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 325 TRP Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 428 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 32 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 68 optimal weight: 0.0870 chunk 67 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 overall best weight: 1.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.112442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.087022 restraints weight = 12556.152| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.48 r_work: 0.2815 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11988 Z= 0.173 Angle : 0.589 5.358 16362 Z= 0.310 Chirality : 0.041 0.128 1851 Planarity : 0.004 0.040 2004 Dihedral : 5.545 87.980 1599 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.53 % Allowed : 10.27 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.22), residues: 1500 helix: 0.91 (0.16), residues: 1134 sheet: None (None), residues: 0 loop : -1.99 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 320 HIS 0.003 0.001 HIS B 121 PHE 0.019 0.002 PHE A 423 TYR 0.007 0.001 TYR A 66 ARG 0.006 0.000 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.08154 ( 702) hydrogen bonds : angle 4.10040 ( 2079) covalent geometry : bond 0.00395 (11988) covalent geometry : angle 0.58902 (16362) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 1.193 Fit side-chains REVERT: A 80 LYS cc_start: 0.8710 (mmmt) cc_final: 0.8242 (mmtt) REVERT: A 129 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7324 (mm-30) REVERT: A 186 ARG cc_start: 0.7846 (mtt90) cc_final: 0.7555 (mtm-85) REVERT: A 425 THR cc_start: 0.7803 (OUTLIER) cc_final: 0.7527 (t) REVERT: B 38 GLN cc_start: 0.7898 (mt0) cc_final: 0.7466 (mp10) REVERT: C 80 LYS cc_start: 0.8702 (mmtt) cc_final: 0.7937 (mmmt) REVERT: C 129 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7305 (mm-30) outliers start: 30 outliers final: 15 residues processed: 146 average time/residue: 1.4085 time to fit residues: 221.4132 Evaluate side-chains 145 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 325 TRP Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 428 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 108 optimal weight: 0.3980 chunk 75 optimal weight: 0.9990 chunk 146 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.116315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.091100 restraints weight = 12633.592| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.49 r_work: 0.2879 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11988 Z= 0.119 Angle : 0.487 5.163 16362 Z= 0.258 Chirality : 0.037 0.121 1851 Planarity : 0.004 0.036 2004 Dihedral : 5.353 88.425 1599 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.94 % Allowed : 11.11 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.22), residues: 1500 helix: 1.31 (0.16), residues: 1125 sheet: None (None), residues: 0 loop : -1.86 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 366 HIS 0.002 0.001 HIS B 121 PHE 0.015 0.001 PHE B 423 TYR 0.007 0.001 TYR A 94 ARG 0.006 0.000 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.05816 ( 702) hydrogen bonds : angle 3.87812 ( 2079) covalent geometry : bond 0.00248 (11988) covalent geometry : angle 0.48701 (16362) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 1.797 Fit side-chains REVERT: A 80 LYS cc_start: 0.8637 (mmmt) cc_final: 0.8187 (mmtt) REVERT: A 186 ARG cc_start: 0.7770 (mtt90) cc_final: 0.7424 (mtm-85) REVERT: A 425 THR cc_start: 0.7683 (OUTLIER) cc_final: 0.7417 (t) REVERT: B 38 GLN cc_start: 0.7757 (mt0) cc_final: 0.7329 (mp10) REVERT: B 383 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7882 (mtm) REVERT: C 13 ARG cc_start: 0.7326 (ptt-90) cc_final: 0.6529 (ptp90) REVERT: C 38 GLN cc_start: 0.8001 (mt0) cc_final: 0.7620 (mt0) REVERT: C 80 LYS cc_start: 0.8662 (mmtt) cc_final: 0.7908 (mmmt) REVERT: C 129 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7279 (mm-30) outliers start: 23 outliers final: 11 residues processed: 145 average time/residue: 1.8606 time to fit residues: 293.1315 Evaluate side-chains 148 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 3.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 325 TRP Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 325 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 144 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 126 optimal weight: 0.8980 chunk 139 optimal weight: 0.1980 chunk 7 optimal weight: 0.0970 chunk 97 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 130 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.119686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.094329 restraints weight = 12750.541| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.50 r_work: 0.2925 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11988 Z= 0.102 Angle : 0.449 5.193 16362 Z= 0.237 Chirality : 0.036 0.121 1851 Planarity : 0.004 0.034 2004 Dihedral : 5.217 88.794 1599 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.60 % Allowed : 11.78 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.24 (0.22), residues: 1500 helix: 1.63 (0.16), residues: 1125 sheet: None (None), residues: 0 loop : -1.69 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 366 HIS 0.002 0.000 HIS C 217 PHE 0.013 0.001 PHE B 423 TYR 0.007 0.001 TYR A 94 ARG 0.007 0.000 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.04718 ( 702) hydrogen bonds : angle 3.73428 ( 2079) covalent geometry : bond 0.00207 (11988) covalent geometry : angle 0.44888 (16362) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 1.288 Fit side-chains REVERT: A 80 LYS cc_start: 0.8648 (mmmt) cc_final: 0.8194 (mmtt) REVERT: A 129 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7215 (mm-30) REVERT: A 186 ARG cc_start: 0.7755 (mtt90) cc_final: 0.7543 (mtm-85) REVERT: A 425 THR cc_start: 0.7625 (OUTLIER) cc_final: 0.7352 (t) REVERT: B 38 GLN cc_start: 0.7701 (mt0) cc_final: 0.7339 (mp10) REVERT: C 13 ARG cc_start: 0.7339 (ptt-90) cc_final: 0.6567 (ptp90) REVERT: C 38 GLN cc_start: 0.7616 (mt0) cc_final: 0.7227 (mt0) REVERT: C 80 LYS cc_start: 0.8636 (mmtt) cc_final: 0.7901 (mmmt) REVERT: C 129 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7313 (mm-30) outliers start: 19 outliers final: 10 residues processed: 148 average time/residue: 1.2924 time to fit residues: 206.6753 Evaluate side-chains 144 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 MET Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 325 TRP Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 428 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 24 optimal weight: 0.1980 chunk 56 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 0.2980 chunk 109 optimal weight: 6.9990 chunk 129 optimal weight: 0.0030 chunk 31 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.119774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.094527 restraints weight = 12645.859| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.50 r_work: 0.2931 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11988 Z= 0.101 Angle : 0.444 5.150 16362 Z= 0.235 Chirality : 0.036 0.120 1851 Planarity : 0.003 0.034 2004 Dihedral : 5.174 88.829 1599 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.60 % Allowed : 12.12 % Favored : 86.28 % 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: 1.47 (0.22), residues: 1500 helix: 1.80 (0.16), residues: 1125 sheet: None (None), residues: 0 loop : -1.61 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 366 HIS 0.001 0.000 HIS C 217 PHE 0.013 0.001 PHE A 423 TYR 0.007 0.001 TYR A 94 ARG 0.007 0.000 ARG B 13 Details of bonding type rmsd hydrogen bonds : bond 0.04676 ( 702) hydrogen bonds : angle 3.70100 ( 2079) covalent geometry : bond 0.00205 (11988) covalent geometry : angle 0.44445 (16362) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 1.253 Fit side-chains REVERT: A 80 LYS cc_start: 0.8651 (mmmt) cc_final: 0.8194 (mmtt) REVERT: A 129 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7244 (mm-30) REVERT: A 186 ARG cc_start: 0.7735 (mtt90) cc_final: 0.7514 (mtm-85) REVERT: B 38 GLN cc_start: 0.7516 (mt0) cc_final: 0.7132 (mp10) REVERT: B 101 LEU cc_start: 0.5927 (mt) cc_final: 0.5508 (mp) REVERT: C 13 ARG cc_start: 0.7361 (ptt-90) cc_final: 0.6579 (ptp90) REVERT: C 38 GLN cc_start: 0.7406 (mt0) cc_final: 0.7024 (mt0) REVERT: C 80 LYS cc_start: 0.8639 (mmtt) cc_final: 0.7894 (mmmt) REVERT: C 129 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7303 (mm-30) REVERT: C 357 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8290 (mp) outliers start: 19 outliers final: 13 residues processed: 144 average time/residue: 1.3615 time to fit residues: 211.4276 Evaluate side-chains 145 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 MET Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 325 TRP Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 428 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 118 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 93 optimal weight: 0.0270 chunk 142 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 overall best weight: 0.6844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.118328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.092943 restraints weight = 12662.925| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.50 r_work: 0.2907 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11988 Z= 0.109 Angle : 0.462 5.204 16362 Z= 0.244 Chirality : 0.037 0.120 1851 Planarity : 0.003 0.036 2004 Dihedral : 5.204 88.625 1599 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.52 % Allowed : 12.21 % Favored : 86.28 % 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: 1.51 (0.22), residues: 1500 helix: 1.82 (0.16), residues: 1128 sheet: None (None), residues: 0 loop : -1.59 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 366 HIS 0.002 0.000 HIS C 217 PHE 0.014 0.001 PHE B 423 TYR 0.007 0.001 TYR C 94 ARG 0.007 0.000 ARG B 13 Details of bonding type rmsd hydrogen bonds : bond 0.05189 ( 702) hydrogen bonds : angle 3.74118 ( 2079) covalent geometry : bond 0.00225 (11988) covalent geometry : angle 0.46229 (16362) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 1.272 Fit side-chains REVERT: A 80 LYS cc_start: 0.8667 (mmmt) cc_final: 0.8220 (mmtt) REVERT: A 129 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7252 (mm-30) REVERT: A 186 ARG cc_start: 0.7734 (mtt90) cc_final: 0.7511 (mtm-85) REVERT: B 38 GLN cc_start: 0.7526 (mt0) cc_final: 0.7089 (mp10) REVERT: B 101 LEU cc_start: 0.6040 (mt) cc_final: 0.5607 (mp) REVERT: B 440 LYS cc_start: 0.7468 (ttpt) cc_final: 0.7234 (ttpm) REVERT: C 13 ARG cc_start: 0.7367 (ptt-90) cc_final: 0.6582 (ptp90) REVERT: C 38 GLN cc_start: 0.7603 (mt0) cc_final: 0.7218 (mt0) REVERT: C 80 LYS cc_start: 0.8650 (mmtt) cc_final: 0.7897 (mmmt) REVERT: C 129 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7279 (mm-30) outliers start: 18 outliers final: 12 residues processed: 142 average time/residue: 1.3337 time to fit residues: 204.5891 Evaluate side-chains 148 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 325 TRP Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 428 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 58 optimal weight: 0.3980 chunk 123 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 61 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.124057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.097971 restraints weight = 13052.006| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.81 r_work: 0.3153 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11988 Z= 0.109 Angle : 0.467 7.165 16362 Z= 0.245 Chirality : 0.037 0.120 1851 Planarity : 0.003 0.036 2004 Dihedral : 5.199 88.741 1599 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.60 % Allowed : 12.37 % Favored : 86.03 % 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: 1.58 (0.22), residues: 1500 helix: 1.87 (0.16), residues: 1128 sheet: None (None), residues: 0 loop : -1.58 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 366 HIS 0.002 0.000 HIS B 121 PHE 0.014 0.001 PHE B 423 TYR 0.007 0.001 TYR A 94 ARG 0.007 0.000 ARG B 13 Details of bonding type rmsd hydrogen bonds : bond 0.05128 ( 702) hydrogen bonds : angle 3.73946 ( 2079) covalent geometry : bond 0.00225 (11988) covalent geometry : angle 0.46725 (16362) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 1.230 Fit side-chains REVERT: A 80 LYS cc_start: 0.8615 (mmmt) cc_final: 0.8151 (mmtt) REVERT: A 129 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7261 (mm-30) REVERT: A 186 ARG cc_start: 0.7644 (mtt90) cc_final: 0.7410 (mtm-85) REVERT: B 38 GLN cc_start: 0.7429 (mt0) cc_final: 0.6991 (mp10) REVERT: B 101 LEU cc_start: 0.5946 (mt) cc_final: 0.5539 (mp) REVERT: B 440 LYS cc_start: 0.7440 (ttpt) cc_final: 0.7195 (ttpm) REVERT: C 38 GLN cc_start: 0.7441 (mt0) cc_final: 0.7046 (mt0) REVERT: C 80 LYS cc_start: 0.8568 (mmtt) cc_final: 0.7793 (mmmt) REVERT: C 129 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7249 (mm-30) outliers start: 19 outliers final: 15 residues processed: 142 average time/residue: 1.3296 time to fit residues: 204.0327 Evaluate side-chains 148 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 325 TRP Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 428 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 121 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 104 optimal weight: 0.4980 chunk 60 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.122645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.096502 restraints weight = 13121.666| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.82 r_work: 0.3142 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11988 Z= 0.116 Angle : 0.479 5.549 16362 Z= 0.253 Chirality : 0.037 0.119 1851 Planarity : 0.004 0.038 2004 Dihedral : 5.247 88.735 1599 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.52 % Allowed : 12.71 % Favored : 85.77 % 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: 1.52 (0.22), residues: 1500 helix: 1.83 (0.16), residues: 1128 sheet: None (None), residues: 0 loop : -1.62 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 366 HIS 0.002 0.001 HIS B 121 PHE 0.015 0.001 PHE A 423 TYR 0.006 0.001 TYR C 94 ARG 0.007 0.000 ARG B 13 Details of bonding type rmsd hydrogen bonds : bond 0.05652 ( 702) hydrogen bonds : angle 3.79217 ( 2079) covalent geometry : bond 0.00242 (11988) covalent geometry : angle 0.47921 (16362) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8634.24 seconds wall clock time: 150 minutes 50.56 seconds (9050.56 seconds total)