Starting phenix.real_space_refine on Fri Sep 19 06:45:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6bbm_7076/09_2025/6bbm_7076.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bbm_7076/09_2025/6bbm_7076.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6bbm_7076/09_2025/6bbm_7076.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bbm_7076/09_2025/6bbm_7076.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6bbm_7076/09_2025/6bbm_7076.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bbm_7076/09_2025/6bbm_7076.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 78 5.16 5 C 14763 2.51 5 N 4344 2.21 5 O 4761 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 162 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23956 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3164 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 15, 'TRANS': 389} Chain breaks: 1 Chain: "B" Number of atoms: 3482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3482 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 18, 'TRANS': 428} Chain breaks: 1 Chain: "C" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3526 Classifications: {'peptide': 453} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 18, 'TRANS': 434} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3550 Classifications: {'peptide': 455} Link IDs: {'PTRANS': 19, 'TRANS': 435} Chain: "E" Number of atoms: 3539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3539 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 19, 'TRANS': 434} Chain breaks: 2 Chain: "F" Number of atoms: 3490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3490 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 18, 'TRANS': 429} Chain breaks: 1 Chain: "V" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 621 Classifications: {'peptide': 125} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 121} Link IDs: {'TRANS': 124} Unresolved non-hydrogen bonds: 254 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 125} Unresolved non-hydrogen planarities: 125 Chain: "W" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 621 Classifications: {'peptide': 125} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 121} Link IDs: {'TRANS': 124} Chain breaks: 2 Unresolved non-hydrogen bonds: 254 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 125} Unresolved non-hydrogen planarities: 125 Chain: "X" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 601 Classifications: {'peptide': 121} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 117} Link IDs: {'TRANS': 120} Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 371 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 121} Unresolved non-hydrogen planarities: 121 Chain: "Y" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 616 Classifications: {'peptide': 124} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 120} Link IDs: {'TRANS': 123} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 380 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 124} Unresolved non-hydrogen planarities: 124 Chain: "Z" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 611 Classifications: {'peptide': 123} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 119} Link IDs: {'TRANS': 122} Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 377 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 123} Unresolved non-hydrogen planarities: 123 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.06, per 1000 atoms: 0.21 Number of scatterers: 23956 At special positions: 0 Unit cell: (157.29, 131.61, 145.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 78 16.00 P 10 15.00 O 4761 8.00 N 4344 7.00 C 14763 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 928.4 milliseconds Enol-peptide restraints added in 1.2 microseconds 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6178 Finding SS restraints... Secondary structure from input PDB file: 166 helices and 14 sheets defined 55.1% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 31 through 41 removed outlier: 3.965A pdb=" N VAL A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY A 40 " --> pdb=" O SER A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.820A pdb=" N GLU A 53 " --> pdb=" O ASP A 49 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG A 54 " --> pdb=" O ASP A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 68 Processing helix chain 'A' and resid 71 through 79 removed outlier: 3.786A pdb=" N LEU A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN A 76 " --> pdb=" O MET A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 91 Processing helix chain 'A' and resid 101 through 105 removed outlier: 3.919A pdb=" N ALA A 104 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR A 105 " --> pdb=" O GLY A 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 101 through 105' Processing helix chain 'A' and resid 119 through 130 removed outlier: 3.578A pdb=" N ASP A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL A 126 " --> pdb=" O TYR A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 140 removed outlier: 3.785A pdb=" N ILE A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 211 through 219 removed outlier: 3.909A pdb=" N LYS A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 248 Processing helix chain 'A' and resid 264 through 277 removed outlier: 3.562A pdb=" N MET A 269 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 271 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ALA A 274 " --> pdb=" O MET A 270 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER A 275 " --> pdb=" O ARG A 271 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 305 Processing helix chain 'A' and resid 319 through 331 removed outlier: 3.735A pdb=" N ARG A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 348 removed outlier: 3.517A pdb=" N LEU A 347 " --> pdb=" O TYR A 344 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET A 348 " --> pdb=" O LEU A 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 344 through 348' Processing helix chain 'A' and resid 356 through 363 Processing helix chain 'A' and resid 364 through 373 removed outlier: 4.496A pdb=" N ALA A 370 " --> pdb=" O ARG A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 392 Processing helix chain 'A' and resid 398 through 402 removed outlier: 3.540A pdb=" N ASP A 401 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 402 " --> pdb=" O ASN A 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 398 through 402' Processing helix chain 'A' and resid 420 through 425 removed outlier: 3.855A pdb=" N TYR A 424 " --> pdb=" O ARG A 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 Processing helix chain 'B' and resid 37 through 44 removed outlier: 3.531A pdb=" N MET B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 43 " --> pdb=" O GLY B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.759A pdb=" N ALA B 52 " --> pdb=" O TRP B 48 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU B 53 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG B 54 " --> pdb=" O ASP B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 72 removed outlier: 3.651A pdb=" N HIS B 67 " --> pdb=" O ARG B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 95 Processing helix chain 'B' and resid 103 through 111 Processing helix chain 'B' and resid 118 through 129 removed outlier: 3.981A pdb=" N ASP B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL B 126 " --> pdb=" O TYR B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 142 removed outlier: 4.091A pdb=" N ILE B 136 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER B 137 " --> pdb=" O ARG B 133 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA B 139 " --> pdb=" O MET B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 166 removed outlier: 4.102A pdb=" N ASP B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER B 163 " --> pdb=" O ASP B 159 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 191 removed outlier: 3.844A pdb=" N ASP B 187 " --> pdb=" O ALA B 183 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 217 Processing helix chain 'B' and resid 236 through 249 removed outlier: 3.603A pdb=" N PHE B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA B 241 " --> pdb=" O LYS B 237 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU B 246 " --> pdb=" O MET B 242 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN B 247 " --> pdb=" O ASN B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 275 removed outlier: 4.077A pdb=" N SER B 275 " --> pdb=" O ARG B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 284 removed outlier: 3.976A pdb=" N LYS B 283 " --> pdb=" O ASP B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 300 removed outlier: 3.594A pdb=" N ILE B 297 " --> pdb=" O ASP B 293 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR B 300 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.541A pdb=" N LEU B 305 " --> pdb=" O GLY B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 334 removed outlier: 3.853A pdb=" N ARG B 328 " --> pdb=" O ARG B 324 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG B 329 " --> pdb=" O SER B 325 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU B 333 " --> pdb=" O ARG B 329 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS B 334 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 348 Processing helix chain 'B' and resid 357 through 375 removed outlier: 3.510A pdb=" N ILE B 361 " --> pdb=" O ARG B 357 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLU B 363 " --> pdb=" O LEU B 359 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE B 364 " --> pdb=" O GLU B 360 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER B 367 " --> pdb=" O GLU B 363 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS B 369 " --> pdb=" O SER B 365 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ALA B 370 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS B 373 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LEU B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 392 removed outlier: 3.550A pdb=" N GLN B 391 " --> pdb=" O SER B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 412 removed outlier: 3.799A pdb=" N ALA B 412 " --> pdb=" O GLU B 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 44 removed outlier: 3.567A pdb=" N LEU C 38 " --> pdb=" O GLU C 34 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY C 39 " --> pdb=" O GLN C 35 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY C 40 " --> pdb=" O SER C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 52 removed outlier: 3.650A pdb=" N ALA C 52 " --> pdb=" O TRP C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 78 removed outlier: 3.634A pdb=" N GLN C 76 " --> pdb=" O MET C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 94 removed outlier: 3.628A pdb=" N GLU C 89 " --> pdb=" O ILE C 85 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER C 90 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU C 91 " --> pdb=" O LEU C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 101 Processing helix chain 'C' and resid 102 through 107 removed outlier: 3.665A pdb=" N LEU C 106 " --> pdb=" O GLY C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 118 through 132 removed outlier: 3.743A pdb=" N VAL C 126 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA C 130 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL C 132 " --> pdb=" O GLU C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 136 removed outlier: 3.807A pdb=" N ILE C 136 " --> pdb=" O ARG C 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 133 through 136' Processing helix chain 'C' and resid 154 through 164 removed outlier: 3.717A pdb=" N LEU C 160 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER C 163 " --> pdb=" O ASP C 159 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG C 164 " --> pdb=" O LEU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 191 removed outlier: 4.383A pdb=" N ALA C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 194 No H-bonds generated for 'chain 'C' and resid 192 through 194' Processing helix chain 'C' and resid 236 through 246 removed outlier: 3.973A pdb=" N PHE C 240 " --> pdb=" O GLY C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 277 removed outlier: 3.561A pdb=" N MET C 269 " --> pdb=" O SER C 265 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA C 274 " --> pdb=" O MET C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 304 removed outlier: 4.092A pdb=" N ARG C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY C 302 " --> pdb=" O SER C 298 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE C 303 " --> pdb=" O GLY C 299 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU C 304 " --> pdb=" O THR C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 333 removed outlier: 4.117A pdb=" N ARG C 324 " --> pdb=" O PRO C 320 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ARG C 326 " --> pdb=" O GLU C 322 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ARG C 329 " --> pdb=" O SER C 325 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE C 330 " --> pdb=" O ARG C 326 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA C 331 " --> pdb=" O ALA C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 348 Processing helix chain 'C' and resid 356 through 361 removed outlier: 4.291A pdb=" N ILE C 361 " --> pdb=" O ARG C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.968A pdb=" N LYS C 369 " --> pdb=" O SER C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 392 removed outlier: 3.759A pdb=" N LEU C 389 " --> pdb=" O ASN C 386 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN C 391 " --> pdb=" O SER C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 402 Processing helix chain 'C' and resid 422 through 424 No H-bonds generated for 'chain 'C' and resid 422 through 424' Processing helix chain 'D' and resid 31 through 43 removed outlier: 4.018A pdb=" N SER D 36 " --> pdb=" O GLU D 32 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N GLY D 40 " --> pdb=" O SER D 36 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU D 41 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 removed outlier: 3.734A pdb=" N VAL D 51 " --> pdb=" O ARG D 47 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA D 52 " --> pdb=" O TRP D 48 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLU D 53 " --> pdb=" O ASP D 49 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG D 54 " --> pdb=" O ASP D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 71 removed outlier: 3.595A pdb=" N ARG D 66 " --> pdb=" O THR D 62 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE D 68 " --> pdb=" O PRO D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 79 removed outlier: 3.735A pdb=" N GLN D 76 " --> pdb=" O MET D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 93 removed outlier: 3.558A pdb=" N SER D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG D 93 " --> pdb=" O GLU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 112 Processing helix chain 'D' and resid 121 through 128 removed outlier: 3.997A pdb=" N ILE D 125 " --> pdb=" O ALA D 121 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL D 126 " --> pdb=" O TYR D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 139 removed outlier: 3.614A pdb=" N SER D 137 " --> pdb=" O ARG D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 165 removed outlier: 3.542A pdb=" N ALA D 161 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 192 removed outlier: 4.515A pdb=" N ALA D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 217 removed outlier: 3.604A pdb=" N LYS D 216 " --> pdb=" O ASP D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 removed outlier: 3.577A pdb=" N ALA D 241 " --> pdb=" O LYS D 237 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL D 245 " --> pdb=" O ALA D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 277 removed outlier: 3.738A pdb=" N MET D 269 " --> pdb=" O SER D 265 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET D 270 " --> pdb=" O GLU D 266 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG D 271 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ALA D 274 " --> pdb=" O MET D 270 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER D 277 " --> pdb=" O LEU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 286 removed outlier: 3.928A pdb=" N THR D 286 " --> pdb=" O THR D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 307 removed outlier: 4.238A pdb=" N ARG D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR D 300 " --> pdb=" O ARG D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 328 Processing helix chain 'D' and resid 344 through 348 Processing helix chain 'D' and resid 356 through 369 removed outlier: 4.967A pdb=" N ALA D 362 " --> pdb=" O THR D 358 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE D 364 " --> pdb=" O GLU D 360 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS D 369 " --> pdb=" O SER D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 392 Processing helix chain 'D' and resid 398 through 402 removed outlier: 3.560A pdb=" N LEU D 402 " --> pdb=" O ASN D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 412 removed outlier: 3.801A pdb=" N ALA D 412 " --> pdb=" O ILE D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 425 removed outlier: 3.783A pdb=" N TYR D 424 " --> pdb=" O ARG D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 458 Processing helix chain 'E' and resid 30 through 43 removed outlier: 3.506A pdb=" N GLU E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU E 38 " --> pdb=" O GLU E 34 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLY E 39 " --> pdb=" O GLN E 35 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU E 43 " --> pdb=" O GLY E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 52 removed outlier: 3.568A pdb=" N VAL E 51 " --> pdb=" O ARG E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 77 removed outlier: 3.741A pdb=" N ARG E 66 " --> pdb=" O THR E 62 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU E 71 " --> pdb=" O HIS E 67 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA E 73 " --> pdb=" O PHE E 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU E 77 " --> pdb=" O ALA E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 94 removed outlier: 4.200A pdb=" N GLU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG E 93 " --> pdb=" O GLU E 89 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN E 94 " --> pdb=" O SER E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 110 removed outlier: 4.172A pdb=" N LEU E 109 " --> pdb=" O TYR E 105 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER E 110 " --> pdb=" O LEU E 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 105 through 110' Processing helix chain 'E' and resid 118 through 121 removed outlier: 3.720A pdb=" N ALA E 121 " --> pdb=" O ASN E 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 118 through 121' Processing helix chain 'E' and resid 122 through 144 removed outlier: 3.537A pdb=" N VAL E 126 " --> pdb=" O TYR E 122 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL E 131 " --> pdb=" O ARG E 127 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL E 132 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG E 133 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER E 137 " --> pdb=" O ARG E 133 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL E 138 " --> pdb=" O GLU E 134 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLU E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 154 No H-bonds generated for 'chain 'E' and resid 153 through 154' Processing helix chain 'E' and resid 155 through 155 No H-bonds generated for 'chain 'E' and resid 155 through 155' Processing helix chain 'E' and resid 156 through 170 removed outlier: 3.541A pdb=" N LEU E 160 " --> pdb=" O ASP E 156 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER E 163 " --> pdb=" O ASP E 159 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG E 164 " --> pdb=" O LEU E 160 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL E 165 " --> pdb=" O ALA E 161 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LYS E 167 " --> pdb=" O SER E 163 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE E 168 " --> pdb=" O ARG E 164 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA E 169 " --> pdb=" O VAL E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 191 removed outlier: 4.112A pdb=" N ASP E 187 " --> pdb=" O ALA E 183 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ALA E 188 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA E 191 " --> pdb=" O ASP E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 218 removed outlier: 4.128A pdb=" N LYS E 217 " --> pdb=" O ASP E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 247 removed outlier: 3.623A pdb=" N PHE E 240 " --> pdb=" O GLY E 236 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA E 241 " --> pdb=" O LYS E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 273 Processing helix chain 'E' and resid 281 through 286 removed outlier: 3.688A pdb=" N THR E 286 " --> pdb=" O THR E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 305 removed outlier: 4.431A pdb=" N ALA E 295 " --> pdb=" O ASP E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 334 removed outlier: 3.663A pdb=" N ARG E 329 " --> pdb=" O SER E 325 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA E 331 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU E 333 " --> pdb=" O ARG E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 367 removed outlier: 3.692A pdb=" N ARG E 366 " --> pdb=" O GLU E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 376 removed outlier: 4.127A pdb=" N ALA E 372 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS E 373 " --> pdb=" O LYS E 369 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU E 374 " --> pdb=" O ALA E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 391 removed outlier: 4.122A pdb=" N LEU E 389 " --> pdb=" O ASN E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 402 removed outlier: 3.613A pdb=" N LEU E 402 " --> pdb=" O ASN E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 412 removed outlier: 4.512A pdb=" N ASP E 411 " --> pdb=" O SER E 407 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA E 412 " --> pdb=" O ILE E 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 407 through 412' Processing helix chain 'E' and resid 420 through 424 removed outlier: 3.930A pdb=" N VAL E 423 " --> pdb=" O ARG E 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 43 removed outlier: 3.764A pdb=" N SER F 36 " --> pdb=" O GLU F 32 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU F 38 " --> pdb=" O GLU F 34 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU F 41 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET F 42 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU F 43 " --> pdb=" O GLY F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 47 No H-bonds generated for 'chain 'F' and resid 45 through 47' Processing helix chain 'F' and resid 48 through 53 removed outlier: 3.625A pdb=" N GLU F 53 " --> pdb=" O ASP F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 78 removed outlier: 3.648A pdb=" N HIS F 67 " --> pdb=" O ARG F 63 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE F 68 " --> pdb=" O PRO F 64 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE F 69 " --> pdb=" O HIS F 65 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA F 73 " --> pdb=" O PHE F 69 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG F 74 " --> pdb=" O THR F 70 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN F 76 " --> pdb=" O MET F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 95 removed outlier: 3.595A pdb=" N ALA F 88 " --> pdb=" O LEU F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 112 removed outlier: 4.010A pdb=" N GLU F 108 " --> pdb=" O ALA F 104 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU F 109 " --> pdb=" O TYR F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 129 removed outlier: 3.502A pdb=" N ILE F 125 " --> pdb=" O ALA F 121 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL F 126 " --> pdb=" O TYR F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 147 removed outlier: 3.657A pdb=" N ILE F 136 " --> pdb=" O VAL F 132 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER F 137 " --> pdb=" O ARG F 133 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU F 141 " --> pdb=" O SER F 137 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE F 147 " --> pdb=" O ALA F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 170 removed outlier: 4.220A pdb=" N ARG F 164 " --> pdb=" O LEU F 160 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE F 166 " --> pdb=" O GLU F 162 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LYS F 167 " --> pdb=" O SER F 163 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA F 169 " --> pdb=" O VAL F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 194 Processing helix chain 'F' and resid 214 through 219 Processing helix chain 'F' and resid 238 through 250 removed outlier: 3.721A pdb=" N VAL F 245 " --> pdb=" O ALA F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 273 removed outlier: 4.014A pdb=" N MET F 269 " --> pdb=" O SER F 265 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG F 271 " --> pdb=" O GLN F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 286 Processing helix chain 'F' and resid 293 through 305 Processing helix chain 'F' and resid 320 through 325 removed outlier: 3.792A pdb=" N ARG F 324 " --> pdb=" O PRO F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 334 removed outlier: 3.938A pdb=" N ILE F 330 " --> pdb=" O ARG F 326 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA F 331 " --> pdb=" O ALA F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 348 Processing helix chain 'F' and resid 356 through 365 removed outlier: 3.808A pdb=" N ALA F 362 " --> pdb=" O THR F 358 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU F 363 " --> pdb=" O LEU F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 386 through 392 removed outlier: 3.622A pdb=" N GLU F 390 " --> pdb=" O ARG F 387 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN F 391 " --> pdb=" O SER F 388 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG F 392 " --> pdb=" O LEU F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 402 removed outlier: 3.534A pdb=" N LEU F 402 " --> pdb=" O ASN F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 424 Processing helix chain 'V' and resid 117 through 129 removed outlier: 3.664A pdb=" N UNK V 122 " --> pdb=" O UNK V 118 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N UNK V 123 " --> pdb=" O UNK V 119 " (cutoff:3.500A) Processing helix chain 'V' and resid 140 through 148 Processing helix chain 'V' and resid 154 through 163 removed outlier: 3.987A pdb=" N UNK V 161 " --> pdb=" O UNK V 157 " (cutoff:3.500A) Processing helix chain 'V' and resid 176 through 186 Processing helix chain 'V' and resid 221 through 228 removed outlier: 3.512A pdb=" N UNK V 227 " --> pdb=" O UNK V 223 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N UNK V 228 " --> pdb=" O UNK V 224 " (cutoff:3.500A) Processing helix chain 'W' and resid 120 through 128 Processing helix chain 'W' and resid 141 through 146 Processing helix chain 'W' and resid 147 through 150 Processing helix chain 'W' and resid 153 through 163 removed outlier: 3.580A pdb=" N UNK W 157 " --> pdb=" O UNK W 153 " (cutoff:3.500A) Processing helix chain 'W' and resid 176 through 178 No H-bonds generated for 'chain 'W' and resid 176 through 178' Processing helix chain 'W' and resid 179 through 185 Processing helix chain 'W' and resid 200 through 205 Processing helix chain 'W' and resid 221 through 232 removed outlier: 3.606A pdb=" N UNK W 225 " --> pdb=" O UNK W 221 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N UNK W 226 " --> pdb=" O UNK W 222 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N UNK W 229 " --> pdb=" O UNK W 225 " (cutoff:3.500A) Processing helix chain 'X' and resid 123 through 134 removed outlier: 3.551A pdb=" N UNK X 127 " --> pdb=" O UNK X 123 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N UNK X 129 " --> pdb=" O UNK X 125 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N UNK X 132 " --> pdb=" O UNK X 128 " (cutoff:3.500A) Processing helix chain 'X' and resid 140 through 144 removed outlier: 3.574A pdb=" N UNK X 144 " --> pdb=" O UNK X 141 " (cutoff:3.500A) Processing helix chain 'X' and resid 145 through 154 removed outlier: 3.754A pdb=" N UNK X 151 " --> pdb=" O UNK X 147 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N UNK X 154 " --> pdb=" O UNK X 150 " (cutoff:3.500A) Processing helix chain 'X' and resid 157 through 165 removed outlier: 3.701A pdb=" N UNK X 162 " --> pdb=" O UNK X 158 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N UNK X 164 " --> pdb=" O UNK X 160 " (cutoff:3.500A) Processing helix chain 'X' and resid 177 through 187 removed outlier: 3.745A pdb=" N UNK X 180 " --> pdb=" O UNK X 177 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N UNK X 181 " --> pdb=" O UNK X 178 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N UNK X 182 " --> pdb=" O UNK X 179 " (cutoff:3.500A) Processing helix chain 'X' and resid 226 through 230 Processing helix chain 'Y' and resid 120 through 129 Processing helix chain 'Y' and resid 143 through 148 removed outlier: 3.885A pdb=" N UNK Y 148 " --> pdb=" O UNK Y 144 " (cutoff:3.500A) Processing helix chain 'Y' and resid 153 through 158 Processing helix chain 'Y' and resid 180 through 189 removed outlier: 4.381A pdb=" N UNK Y 186 " --> pdb=" O UNK Y 182 " (cutoff:3.500A) Processing helix chain 'Y' and resid 200 through 205 removed outlier: 4.189A pdb=" N UNK Y 204 " --> pdb=" O UNK Y 200 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N UNK Y 205 " --> pdb=" O UNK Y 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 200 through 205' Processing helix chain 'Y' and resid 221 through 232 Processing helix chain 'Z' and resid 119 through 131 removed outlier: 4.095A pdb=" N UNK Z 123 " --> pdb=" O UNK Z 119 " (cutoff:3.500A) Processing helix chain 'Z' and resid 140 through 145 Processing helix chain 'Z' and resid 146 through 148 No H-bonds generated for 'chain 'Z' and resid 146 through 148' Processing helix chain 'Z' and resid 153 through 157 Processing helix chain 'Z' and resid 166 through 171 removed outlier: 3.805A pdb=" N UNK Z 171 " --> pdb=" O UNK Z 167 " (cutoff:3.500A) Processing helix chain 'Z' and resid 180 through 188 removed outlier: 3.623A pdb=" N UNK Z 185 " --> pdb=" O UNK Z 181 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N UNK Z 186 " --> pdb=" O UNK Z 182 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N UNK Z 188 " --> pdb=" O UNK Z 184 " (cutoff:3.500A) Processing helix chain 'Z' and resid 202 through 207 removed outlier: 3.644A pdb=" N UNK Z 206 " --> pdb=" O UNK Z 202 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N UNK Z 207 " --> pdb=" O UNK Z 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 202 through 207' Processing helix chain 'Z' and resid 221 through 231 removed outlier: 3.621A pdb=" N UNK Z 225 " --> pdb=" O UNK Z 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 310 through 313 removed outlier: 6.369A pdb=" N VAL A 256 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ASP A 313 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE A 258 " --> pdb=" O ASP A 313 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ILE A 340 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU A 382 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ILE A 342 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE A 228 " --> pdb=" O MET A 416 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ILE A 418 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE A 415 " --> pdb=" O GLY A 439 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ARG A 450 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N TYR A 463 " --> pdb=" O ARG A 450 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N THR A 452 " --> pdb=" O ASP A 461 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 258 through 260 removed outlier: 3.521A pdb=" N LEU B 414 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 230 " --> pdb=" O MET B 416 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE B 415 " --> pdb=" O GLY B 439 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 311 through 313 removed outlier: 6.206A pdb=" N ILE C 258 " --> pdb=" O ASP C 313 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE C 228 " --> pdb=" O MET C 416 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ILE C 418 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA C 230 " --> pdb=" O ILE C 418 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N ARG C 420 " --> pdb=" O ALA C 230 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE C 415 " --> pdb=" O GLY C 439 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR C 419 " --> pdb=" O GLU C 435 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE C 438 " --> pdb=" O GLY C 447 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY C 447 " --> pdb=" O ILE C 438 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 311 through 313 removed outlier: 6.206A pdb=" N ILE C 258 " --> pdb=" O ASP C 313 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE C 228 " --> pdb=" O MET C 416 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ILE C 418 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA C 230 " --> pdb=" O ILE C 418 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N ARG C 420 " --> pdb=" O ALA C 230 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE C 415 " --> pdb=" O GLY C 439 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR C 419 " --> pdb=" O GLU C 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 381 through 383 removed outlier: 6.471A pdb=" N ILE D 415 " --> pdb=" O GLY D 439 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY D 447 " --> pdb=" O ILE D 438 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 258 through 260 removed outlier: 7.069A pdb=" N PHE D 259 " --> pdb=" O ASP D 343 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 451 through 454 Processing sheet with id=AA8, first strand: chain 'E' and resid 179 through 180 Processing sheet with id=AA9, first strand: chain 'E' and resid 227 through 231 removed outlier: 3.740A pdb=" N ILE E 438 " --> pdb=" O GLY E 447 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY E 447 " --> pdb=" O ILE E 438 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 257 through 259 Processing sheet with id=AB2, first strand: chain 'E' and resid 452 through 454 removed outlier: 3.737A pdb=" N ARG E 459 " --> pdb=" O ASN E 454 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 228 through 229 removed outlier: 6.566A pdb=" N ILE F 228 " --> pdb=" O MET F 416 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS F 440 " --> pdb=" O ILE F 415 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 341 through 342 Processing sheet with id=AB5, first strand: chain 'F' and resid 433 through 436 689 hydrogen bonds defined for protein. 1893 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: 4.07 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7871 1.33 - 1.45: 3135 1.45 - 1.57: 13075 1.57 - 1.69: 15 1.69 - 1.81: 156 Bond restraints: 24252 Sorted by residual: bond pdb=" C VAL F 379 " pdb=" N VAL F 380 " ideal model delta sigma weight residual 1.335 1.290 0.045 1.16e-02 7.43e+03 1.49e+01 bond pdb=" N GLU E 170 " pdb=" CA GLU E 170 " ideal model delta sigma weight residual 1.463 1.505 -0.042 1.24e-02 6.50e+03 1.14e+01 bond pdb=" C LEU A 318 " pdb=" N THR A 319 " ideal model delta sigma weight residual 1.330 1.285 0.046 1.37e-02 5.33e+03 1.11e+01 bond pdb=" N GLY A 465 " pdb=" CA GLY A 465 " ideal model delta sigma weight residual 1.443 1.485 -0.043 1.37e-02 5.33e+03 9.75e+00 bond pdb=" N GLU D 170 " pdb=" CA GLU D 170 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.25e-02 6.40e+03 7.61e+00 ... (remaining 24247 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 32009 3.02 - 6.04: 808 6.04 - 9.05: 108 9.05 - 12.07: 14 12.07 - 15.09: 1 Bond angle restraints: 32940 Sorted by residual: angle pdb=" N VAL C 138 " pdb=" CA VAL C 138 " pdb=" C VAL C 138 " ideal model delta sigma weight residual 112.12 106.89 5.23 8.40e-01 1.42e+00 3.88e+01 angle pdb=" C UNK X 169 " pdb=" N UNK X 170 " pdb=" CA UNK X 170 " ideal model delta sigma weight residual 121.70 131.91 -10.21 1.80e+00 3.09e-01 3.21e+01 angle pdb=" C ARG C 152 " pdb=" N THR C 153 " pdb=" CA THR C 153 " ideal model delta sigma weight residual 122.41 134.13 -11.72 2.09e+00 2.29e-01 3.14e+01 angle pdb=" N VAL E 165 " pdb=" CA VAL E 165 " pdb=" C VAL E 165 " ideal model delta sigma weight residual 113.22 106.78 6.44 1.23e+00 6.61e-01 2.74e+01 angle pdb=" C ARG C 54 " pdb=" N VAL C 55 " pdb=" CA VAL C 55 " ideal model delta sigma weight residual 121.97 131.34 -9.37 1.80e+00 3.09e-01 2.71e+01 ... (remaining 32935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.04: 14532 35.04 - 70.08: 324 70.08 - 105.12: 32 105.12 - 140.17: 5 140.17 - 175.21: 4 Dihedral angle restraints: 14897 sinusoidal: 5398 harmonic: 9499 Sorted by residual: dihedral pdb=" CA ALA B 169 " pdb=" C ALA B 169 " pdb=" N GLU B 170 " pdb=" CA GLU B 170 " ideal model delta harmonic sigma weight residual 180.00 93.00 87.00 0 5.00e+00 4.00e-02 3.03e+02 dihedral pdb=" CA LYS F 180 " pdb=" C LYS F 180 " pdb=" N ASN F 181 " pdb=" CA ASN F 181 " ideal model delta harmonic sigma weight residual 180.00 116.20 63.80 0 5.00e+00 4.00e-02 1.63e+02 dihedral pdb=" CA PRO D 27 " pdb=" C PRO D 27 " pdb=" N PRO D 28 " pdb=" CA PRO D 28 " ideal model delta harmonic sigma weight residual 180.00 123.12 56.88 0 5.00e+00 4.00e-02 1.29e+02 ... (remaining 14894 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2450 0.054 - 0.107: 1109 0.107 - 0.161: 239 0.161 - 0.214: 42 0.214 - 0.268: 8 Chirality restraints: 3848 Sorted by residual: chirality pdb=" CB ILE D 227 " pdb=" CA ILE D 227 " pdb=" CG1 ILE D 227 " pdb=" CG2 ILE D 227 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB ILE B 193 " pdb=" CA ILE B 193 " pdb=" CG1 ILE B 193 " pdb=" CG2 ILE B 193 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CB ILE B 227 " pdb=" CA ILE B 227 " pdb=" CG1 ILE B 227 " pdb=" CG2 ILE B 227 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 3845 not shown) Planarity restraints: 4404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 169 " 0.034 2.00e-02 2.50e+03 6.81e-02 4.63e+01 pdb=" C ALA D 169 " -0.118 2.00e-02 2.50e+03 pdb=" O ALA D 169 " 0.046 2.00e-02 2.50e+03 pdb=" N GLU D 170 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 169 " 0.033 2.00e-02 2.50e+03 6.52e-02 4.26e+01 pdb=" C ALA C 169 " -0.113 2.00e-02 2.50e+03 pdb=" O ALA C 169 " 0.044 2.00e-02 2.50e+03 pdb=" N GLU C 170 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 464 " 0.031 2.00e-02 2.50e+03 6.14e-02 3.77e+01 pdb=" C ALA E 464 " -0.106 2.00e-02 2.50e+03 pdb=" O ALA E 464 " 0.041 2.00e-02 2.50e+03 pdb=" N GLY E 465 " 0.035 2.00e-02 2.50e+03 ... (remaining 4401 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 5083 2.76 - 3.30: 22686 3.30 - 3.83: 38848 3.83 - 4.37: 45192 4.37 - 4.90: 73213 Nonbonded interactions: 185022 Sorted by model distance: nonbonded pdb=" O ARG C 74 " pdb=" OG SER C 78 " model vdw 2.231 3.040 nonbonded pdb=" O LEU B 109 " pdb=" OG1 THR B 113 " model vdw 2.236 3.040 nonbonded pdb=" OD1 ASN D 140 " pdb=" OG SER F 115 " model vdw 2.238 3.040 nonbonded pdb=" OG SER D 224 " pdb=" O ALA D 372 " model vdw 2.250 3.040 nonbonded pdb=" OH TYR A 344 " pdb=" OD1 ASP F 411 " model vdw 2.252 3.040 ... (remaining 185017 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 27 through 464) selection = (chain 'B' and (resid 27 through 166 or resid 204 through 464)) selection = (chain 'C' and (resid 27 through 166 or resid 204 through 464)) selection = (chain 'D' and (resid 27 through 166 or resid 204 through 464)) selection = (chain 'E' and (resid 27 through 166 or resid 204 through 464)) selection = (chain 'F' and (resid 27 through 166 or resid 204 through 464)) } ncs_group { reference = (chain 'V' and ((resid 113 through 121 and (name N or name CA or name C or name \ O )) or resid 122 through 232)) selection = (chain 'W' and ((resid 114 through 122 and (name N or name CA or name C or name \ O )) or resid 123 through 233)) selection = (chain 'X' and ((resid 113 through 121 and (name N or name CA or name C or name \ O )) or resid 122 through 232)) selection = (chain 'Y' and ((resid 113 through 121 and (name N or name CA or name C or name \ O )) or resid 122 through 232)) selection = (chain 'Z' and ((resid 113 through 121 and (name N or name CA or name C or name \ O )) or resid 122 through 232)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.770 Find NCS groups from input model: 0.610 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 24256 Z= 0.383 Angle : 1.201 15.089 32940 Z= 0.654 Chirality : 0.061 0.268 3848 Planarity : 0.008 0.123 4404 Dihedral : 16.696 175.208 8719 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.19 % Allowed : 13.75 % Favored : 86.06 % Rotamer: Outliers : 0.58 % Allowed : 11.95 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.83 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.97 (0.12), residues: 2640 helix: -4.57 (0.07), residues: 1104 sheet: -3.68 (0.26), residues: 257 loop : -3.39 (0.15), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 152 TYR 0.029 0.002 TYR D 344 PHE 0.031 0.003 PHE D 259 TRP 0.027 0.003 TRP D 457 HIS 0.009 0.002 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00808 (24252) covalent geometry : angle 1.20115 (32940) hydrogen bonds : bond 0.30986 ( 678) hydrogen bonds : angle 10.92248 ( 1893) Misc. bond : bond 0.00265 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 367 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8398 (mm110) cc_final: 0.7898 (mm-40) REVERT: A 270 MET cc_start: 0.6864 (mtp) cc_final: 0.6283 (ttm) REVERT: B 222 GLN cc_start: 0.8395 (mm-40) cc_final: 0.8175 (mp10) REVERT: B 291 ASP cc_start: 0.6987 (t70) cc_final: 0.5870 (t0) REVERT: B 294 TRP cc_start: 0.5092 (m100) cc_final: 0.3699 (t-100) REVERT: B 366 ARG cc_start: 0.7876 (mtm-85) cc_final: 0.7438 (mtm110) REVERT: C 180 LYS cc_start: 0.8305 (mttt) cc_final: 0.7977 (mmtt) REVERT: C 197 PHE cc_start: 0.6280 (m-80) cc_final: 0.5780 (p90) REVERT: C 229 VAL cc_start: 0.8707 (t) cc_final: 0.8461 (p) REVERT: C 243 ASN cc_start: 0.7070 (t0) cc_final: 0.6446 (t0) REVERT: C 357 ARG cc_start: 0.8453 (mmm160) cc_final: 0.8244 (tpp80) REVERT: C 449 VAL cc_start: 0.8244 (OUTLIER) cc_final: 0.7994 (t) REVERT: D 112 ASN cc_start: 0.8399 (m-40) cc_final: 0.7548 (t0) REVERT: D 177 GLU cc_start: 0.5548 (OUTLIER) cc_final: 0.5339 (mm-30) REVERT: E 237 LYS cc_start: 0.7225 (ttpt) cc_final: 0.6903 (ttpp) REVERT: E 244 LEU cc_start: 0.9272 (tt) cc_final: 0.9067 (tt) REVERT: E 310 ILE cc_start: 0.8818 (mt) cc_final: 0.8539 (tt) REVERT: E 341 MET cc_start: 0.7760 (ttp) cc_final: 0.7477 (ttp) REVERT: E 349 ARG cc_start: 0.8467 (mtm110) cc_final: 0.8019 (ptp-110) REVERT: E 401 ASP cc_start: 0.7929 (m-30) cc_final: 0.7516 (t0) REVERT: E 411 ASP cc_start: 0.8048 (m-30) cc_final: 0.7201 (m-30) REVERT: E 443 ASN cc_start: 0.7402 (p0) cc_final: 0.7140 (p0) REVERT: F 366 ARG cc_start: 0.8140 (mtm-85) cc_final: 0.7940 (mtm-85) outliers start: 13 outliers final: 5 residues processed: 380 average time/residue: 0.1814 time to fit residues: 100.6959 Evaluate side-chains 241 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 234 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 197 optimal weight: 0.0170 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.0020 chunk 298 optimal weight: 20.0000 overall best weight: 0.5428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 410 GLN A 441 GLN A 456 GLN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 GLN B 243 ASN ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS C 45 ASN C 112 ASN C 174 ASN C 399 ASN D 45 ASN D 140 ASN D 243 ASN ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 HIS E 427 ASN F 45 ASN F 118 ASN F 208 ASN F 267 GLN F 391 GLN F 399 ASN ** F 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.121116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.103828 restraints weight = 63364.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.103790 restraints weight = 50579.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.104677 restraints weight = 47232.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.104964 restraints weight = 35062.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.105172 restraints weight = 32534.254| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24256 Z= 0.129 Angle : 0.759 11.571 32940 Z= 0.372 Chirality : 0.045 0.191 3848 Planarity : 0.006 0.109 4404 Dihedral : 10.596 178.101 3585 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.86 % Favored : 91.02 % Rotamer: Outliers : 0.09 % Allowed : 5.24 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.35 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.04 (0.13), residues: 2640 helix: -3.54 (0.10), residues: 1176 sheet: -3.21 (0.26), residues: 268 loop : -3.04 (0.16), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 129 TYR 0.041 0.002 TYR C 344 PHE 0.016 0.001 PHE D 259 TRP 0.015 0.002 TRP E 294 HIS 0.006 0.001 HIS E 425 Details of bonding type rmsd covalent geometry : bond 0.00282 (24252) covalent geometry : angle 0.75947 (32940) hydrogen bonds : bond 0.03868 ( 678) hydrogen bonds : angle 6.09648 ( 1893) Misc. bond : bond 0.00140 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 381 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.6793 (mmp) cc_final: 0.6521 (tmm) REVERT: A 142 ILE cc_start: 0.8045 (mt) cc_final: 0.7842 (mm) REVERT: A 267 GLN cc_start: 0.7928 (mm-40) cc_final: 0.7701 (mm-40) REVERT: B 222 GLN cc_start: 0.8610 (mm-40) cc_final: 0.8210 (mp10) REVERT: B 291 ASP cc_start: 0.7034 (t70) cc_final: 0.6046 (t0) REVERT: B 294 TRP cc_start: 0.5173 (m100) cc_final: 0.4316 (t-100) REVERT: C 69 PHE cc_start: 0.7415 (t80) cc_final: 0.6702 (t80) REVERT: C 197 PHE cc_start: 0.6592 (m-80) cc_final: 0.6058 (p90) REVERT: C 316 SER cc_start: 0.8369 (m) cc_final: 0.7712 (t) REVERT: C 341 MET cc_start: 0.7881 (ttt) cc_final: 0.7635 (ttp) REVERT: C 357 ARG cc_start: 0.8065 (mmm160) cc_final: 0.7852 (tpp80) REVERT: C 383 SER cc_start: 0.7943 (m) cc_final: 0.7648 (t) REVERT: C 438 ILE cc_start: 0.7123 (pt) cc_final: 0.6875 (mm) REVERT: D 112 ASN cc_start: 0.8388 (m-40) cc_final: 0.7582 (t0) REVERT: D 328 ARG cc_start: 0.7892 (mtp-110) cc_final: 0.7482 (ttm-80) REVERT: D 366 ARG cc_start: 0.7920 (mpp80) cc_final: 0.7165 (mtt90) REVERT: E 150 GLN cc_start: 0.6273 (mp10) cc_final: 0.6055 (mp10) REVERT: E 222 GLN cc_start: 0.7712 (mm-40) cc_final: 0.7168 (mp10) REVERT: E 235 MET cc_start: 0.8693 (tpp) cc_final: 0.8346 (mmt) REVERT: E 237 LYS cc_start: 0.7874 (ttpt) cc_final: 0.7636 (ttpt) REVERT: E 349 ARG cc_start: 0.8409 (mtm110) cc_final: 0.7496 (ptm160) REVERT: E 443 ASN cc_start: 0.6922 (p0) cc_final: 0.6587 (p0) REVERT: F 119 ILE cc_start: 0.7437 (mm) cc_final: 0.6898 (mm) REVERT: F 366 ARG cc_start: 0.8299 (mtm-85) cc_final: 0.7811 (ttp-110) outliers start: 2 outliers final: 0 residues processed: 382 average time/residue: 0.1745 time to fit residues: 100.2889 Evaluate side-chains 250 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 98 optimal weight: 1.9990 chunk 276 optimal weight: 9.9990 chunk 58 optimal weight: 30.0000 chunk 0 optimal weight: 50.0000 chunk 109 optimal weight: 0.7980 chunk 309 optimal weight: 30.0000 chunk 92 optimal weight: 3.9990 chunk 315 optimal weight: 9.9990 chunk 313 optimal weight: 10.0000 chunk 290 optimal weight: 10.0000 chunk 171 optimal weight: 8.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 GLN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 ASN ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN C 441 GLN D 45 ASN D 140 ASN D 198 GLN ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 ASN E 456 GLN F 45 ASN F 399 ASN F 425 HIS ** F 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.115843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.098509 restraints weight = 65778.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.098150 restraints weight = 60728.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.099123 restraints weight = 54300.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.099413 restraints weight = 39538.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.099624 restraints weight = 37112.254| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 24256 Z= 0.246 Angle : 0.812 11.265 32940 Z= 0.401 Chirality : 0.048 0.200 3848 Planarity : 0.006 0.104 4404 Dihedral : 10.619 179.889 3585 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.20 % Favored : 87.65 % Rotamer: Outliers : 0.09 % Allowed : 4.62 % Favored : 95.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.35 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.63 (0.14), residues: 2640 helix: -3.00 (0.12), residues: 1184 sheet: -3.16 (0.27), residues: 270 loop : -3.02 (0.17), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 93 TYR 0.030 0.002 TYR D 344 PHE 0.023 0.002 PHE C 460 TRP 0.015 0.002 TRP B 48 HIS 0.006 0.001 HIS B 29 Details of bonding type rmsd covalent geometry : bond 0.00546 (24252) covalent geometry : angle 0.81248 (32940) hydrogen bonds : bond 0.03958 ( 678) hydrogen bonds : angle 5.86169 ( 1893) Misc. bond : bond 0.00160 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 286 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ILE cc_start: 0.8097 (mt) cc_final: 0.7750 (mm) REVERT: B 222 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8151 (mp10) REVERT: B 376 ASN cc_start: 0.8359 (m-40) cc_final: 0.8118 (m-40) REVERT: C 197 PHE cc_start: 0.6561 (m-80) cc_final: 0.6053 (p90) REVERT: C 237 LYS cc_start: 0.8551 (ttmt) cc_final: 0.8193 (ttmm) REVERT: C 269 MET cc_start: 0.7421 (mtm) cc_final: 0.7017 (mtt) REVERT: C 316 SER cc_start: 0.8360 (m) cc_final: 0.7821 (t) REVERT: C 357 ARG cc_start: 0.8204 (mmm160) cc_final: 0.7946 (tpp80) REVERT: D 42 MET cc_start: 0.7201 (mtm) cc_final: 0.6934 (mtm) REVERT: D 112 ASN cc_start: 0.8466 (m-40) cc_final: 0.7457 (t0) REVERT: D 192 ARG cc_start: 0.7161 (tpm170) cc_final: 0.6380 (tmt170) REVERT: D 366 ARG cc_start: 0.8092 (mpp80) cc_final: 0.7256 (mtt90) REVERT: E 150 GLN cc_start: 0.6666 (mp10) cc_final: 0.6400 (mp10) REVERT: E 222 GLN cc_start: 0.7740 (mm-40) cc_final: 0.7195 (mp10) REVERT: E 349 ARG cc_start: 0.8480 (mtm110) cc_final: 0.7645 (ptm160) REVERT: E 443 ASN cc_start: 0.7206 (p0) cc_final: 0.6992 (p0) REVERT: F 266 GLU cc_start: 0.8244 (tt0) cc_final: 0.7961 (mp0) REVERT: F 401 ASP cc_start: 0.6876 (m-30) cc_final: 0.6278 (t0) outliers start: 2 outliers final: 0 residues processed: 288 average time/residue: 0.1672 time to fit residues: 73.4890 Evaluate side-chains 221 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 154 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 308 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 312 optimal weight: 9.9990 chunk 305 optimal weight: 20.0000 chunk 232 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 GLN A 456 GLN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 ASN ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 386 ASN C 399 ASN C 425 HIS D 140 ASN ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN ** E 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 29 HIS F 76 GLN F 399 ASN ** F 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.114725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.097930 restraints weight = 65532.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.097249 restraints weight = 62446.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.098222 restraints weight = 57446.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.098781 restraints weight = 40246.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.098916 restraints weight = 36942.014| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 24256 Z= 0.243 Angle : 0.822 11.281 32940 Z= 0.405 Chirality : 0.048 0.215 3848 Planarity : 0.006 0.100 4404 Dihedral : 10.551 179.774 3585 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.58 % Favored : 87.31 % Rotamer: Outliers : 0.13 % Allowed : 5.15 % Favored : 94.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.35 (0.14), residues: 2640 helix: -2.68 (0.13), residues: 1173 sheet: -3.07 (0.28), residues: 266 loop : -2.97 (0.17), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 420 TYR 0.025 0.002 TYR D 344 PHE 0.028 0.002 PHE A 69 TRP 0.026 0.002 TRP F 48 HIS 0.005 0.001 HIS E 67 Details of bonding type rmsd covalent geometry : bond 0.00539 (24252) covalent geometry : angle 0.82184 (32940) hydrogen bonds : bond 0.03732 ( 678) hydrogen bonds : angle 5.77848 ( 1893) Misc. bond : bond 0.00163 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 293 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ILE cc_start: 0.8062 (mt) cc_final: 0.7779 (mm) REVERT: A 267 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7341 (mm-40) REVERT: A 270 MET cc_start: 0.8174 (tpp) cc_final: 0.7962 (tpp) REVERT: A 291 ASP cc_start: 0.5259 (p0) cc_final: 0.5055 (p0) REVERT: A 387 ARG cc_start: 0.8075 (ptm160) cc_final: 0.7705 (ptm160) REVERT: B 222 GLN cc_start: 0.8676 (mm-40) cc_final: 0.8183 (mp10) REVERT: B 291 ASP cc_start: 0.7585 (t0) cc_final: 0.6029 (t0) REVERT: B 294 TRP cc_start: 0.5643 (m100) cc_final: 0.3887 (t-100) REVERT: C 180 LYS cc_start: 0.8133 (mtmt) cc_final: 0.7674 (mmtt) REVERT: C 197 PHE cc_start: 0.6705 (m-80) cc_final: 0.6129 (p90) REVERT: C 237 LYS cc_start: 0.8562 (ttmt) cc_final: 0.8205 (ttmm) REVERT: C 269 MET cc_start: 0.7352 (mtm) cc_final: 0.7083 (mtt) REVERT: C 316 SER cc_start: 0.8365 (m) cc_final: 0.7853 (t) REVERT: C 341 MET cc_start: 0.8153 (ttt) cc_final: 0.7947 (ttt) REVERT: D 112 ASN cc_start: 0.8517 (m-40) cc_final: 0.7334 (t0) REVERT: D 192 ARG cc_start: 0.7309 (tpm170) cc_final: 0.6441 (tmt170) REVERT: D 366 ARG cc_start: 0.8093 (mpp80) cc_final: 0.7697 (mtt90) REVERT: E 150 GLN cc_start: 0.6711 (mp10) cc_final: 0.6420 (mp10) REVERT: E 222 GLN cc_start: 0.7821 (mm-40) cc_final: 0.7147 (mp10) REVERT: E 348 MET cc_start: 0.7251 (ttt) cc_final: 0.7032 (mtp) REVERT: E 349 ARG cc_start: 0.8350 (mtm110) cc_final: 0.7954 (ptp-110) REVERT: F 68 ILE cc_start: 0.9404 (mt) cc_final: 0.8887 (mt) outliers start: 3 outliers final: 0 residues processed: 296 average time/residue: 0.1676 time to fit residues: 76.9399 Evaluate side-chains 217 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 167 optimal weight: 4.9990 chunk 257 optimal weight: 2.9990 chunk 274 optimal weight: 30.0000 chunk 233 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 109 optimal weight: 0.4980 chunk 87 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 282 optimal weight: 30.0000 chunk 187 optimal weight: 2.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 GLN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 ASN ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 ASN C 399 ASN ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN E 252 GLN ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.117617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.100647 restraints weight = 64255.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.100034 restraints weight = 57590.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.101152 restraints weight = 52089.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.101523 restraints weight = 37057.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.101741 restraints weight = 34355.065| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24256 Z= 0.155 Angle : 0.728 10.774 32940 Z= 0.356 Chirality : 0.045 0.170 3848 Planarity : 0.005 0.097 4404 Dihedral : 10.138 179.027 3585 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.76 % Favored : 89.17 % Rotamer: Outliers : 0.04 % Allowed : 2.75 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.96 (0.15), residues: 2640 helix: -2.30 (0.14), residues: 1182 sheet: -2.74 (0.29), residues: 268 loop : -2.86 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 392 TYR 0.019 0.001 TYR A 105 PHE 0.029 0.001 PHE D 259 TRP 0.037 0.002 TRP D 48 HIS 0.007 0.001 HIS F 65 Details of bonding type rmsd covalent geometry : bond 0.00350 (24252) covalent geometry : angle 0.72845 (32940) hydrogen bonds : bond 0.03125 ( 678) hydrogen bonds : angle 5.28370 ( 1893) Misc. bond : bond 0.00136 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 298 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 MET cc_start: 0.8318 (tpp) cc_final: 0.8075 (tpp) REVERT: A 341 MET cc_start: 0.7828 (tmm) cc_final: 0.6946 (tmm) REVERT: A 387 ARG cc_start: 0.8216 (ptm160) cc_final: 0.7483 (ptm160) REVERT: B 222 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8240 (mp10) REVERT: B 250 MET cc_start: 0.8313 (ptp) cc_final: 0.8097 (ptm) REVERT: B 291 ASP cc_start: 0.7688 (t0) cc_final: 0.6315 (t0) REVERT: B 294 TRP cc_start: 0.5375 (m100) cc_final: 0.3933 (t-100) REVERT: B 383 SER cc_start: 0.7969 (t) cc_final: 0.7577 (p) REVERT: C 180 LYS cc_start: 0.8180 (mtmt) cc_final: 0.7706 (mmtt) REVERT: C 197 PHE cc_start: 0.6602 (m-80) cc_final: 0.6117 (p90) REVERT: C 237 LYS cc_start: 0.8560 (ttmt) cc_final: 0.8205 (ttmm) REVERT: C 316 SER cc_start: 0.8233 (m) cc_final: 0.7764 (t) REVERT: D 42 MET cc_start: 0.7014 (mtm) cc_final: 0.6722 (mtm) REVERT: D 112 ASN cc_start: 0.8447 (m-40) cc_final: 0.7504 (t0) REVERT: D 192 ARG cc_start: 0.7042 (tpm170) cc_final: 0.6475 (tmt170) REVERT: D 237 LYS cc_start: 0.7701 (ttmt) cc_final: 0.7426 (ttmm) REVERT: E 150 GLN cc_start: 0.6574 (mp10) cc_final: 0.6282 (mp10) REVERT: E 222 GLN cc_start: 0.7718 (mm-40) cc_final: 0.7162 (mp10) REVERT: E 349 ARG cc_start: 0.8383 (mtm110) cc_final: 0.7834 (ptp-110) outliers start: 1 outliers final: 0 residues processed: 299 average time/residue: 0.1629 time to fit residues: 76.1458 Evaluate side-chains 223 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 22 optimal weight: 10.0000 chunk 236 optimal weight: 6.9990 chunk 322 optimal weight: 20.0000 chunk 136 optimal weight: 0.9980 chunk 287 optimal weight: 20.0000 chunk 33 optimal weight: 0.0040 chunk 177 optimal weight: 0.9990 chunk 9 optimal weight: 0.0470 chunk 182 optimal weight: 10.0000 chunk 313 optimal weight: 9.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.5292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 243 ASN ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 ASN ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 ASN C 399 ASN D 309 ASN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 ASN ** E 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.121061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.104008 restraints weight = 63679.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.103640 restraints weight = 54030.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.104783 restraints weight = 52614.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.105034 restraints weight = 37625.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.105302 restraints weight = 34679.632| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 24256 Z= 0.117 Angle : 0.687 10.603 32940 Z= 0.332 Chirality : 0.043 0.180 3848 Planarity : 0.005 0.091 4404 Dihedral : 9.566 172.461 3585 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.28 % Favored : 90.68 % Rotamer: Outliers : 0.04 % Allowed : 2.18 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.43 (0.15), residues: 2640 helix: -1.87 (0.14), residues: 1159 sheet: -2.54 (0.29), residues: 278 loop : -2.56 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 278 TYR 0.021 0.001 TYR A 105 PHE 0.016 0.001 PHE F 69 TRP 0.019 0.002 TRP F 457 HIS 0.004 0.001 HIS B 29 Details of bonding type rmsd covalent geometry : bond 0.00246 (24252) covalent geometry : angle 0.68733 (32940) hydrogen bonds : bond 0.02674 ( 678) hydrogen bonds : angle 4.78594 ( 1893) Misc. bond : bond 0.00119 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 322 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLN cc_start: 0.7946 (mm-40) cc_final: 0.7516 (mm-40) REVERT: A 270 MET cc_start: 0.8138 (tpp) cc_final: 0.7773 (tpp) REVERT: A 341 MET cc_start: 0.7817 (tmm) cc_final: 0.7039 (tmm) REVERT: A 387 ARG cc_start: 0.8047 (ptm160) cc_final: 0.7692 (ptm160) REVERT: B 222 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8226 (mp10) REVERT: B 229 VAL cc_start: 0.7840 (t) cc_final: 0.7627 (t) REVERT: B 243 ASN cc_start: 0.7750 (t160) cc_final: 0.7429 (t0) REVERT: B 250 MET cc_start: 0.8233 (ptp) cc_final: 0.7994 (ptm) REVERT: B 291 ASP cc_start: 0.7573 (t70) cc_final: 0.6191 (t0) REVERT: B 294 TRP cc_start: 0.5171 (m100) cc_final: 0.3957 (t-100) REVERT: B 382 LEU cc_start: 0.8136 (tp) cc_final: 0.7443 (tt) REVERT: B 383 SER cc_start: 0.7772 (t) cc_final: 0.7352 (p) REVERT: C 69 PHE cc_start: 0.7469 (t80) cc_final: 0.6603 (t80) REVERT: C 137 SER cc_start: 0.9038 (m) cc_final: 0.8769 (t) REVERT: C 180 LYS cc_start: 0.8135 (mtmt) cc_final: 0.7778 (mmtt) REVERT: C 197 PHE cc_start: 0.6498 (m-80) cc_final: 0.6131 (p90) REVERT: C 237 LYS cc_start: 0.8516 (ttmt) cc_final: 0.8154 (ttmm) REVERT: C 316 SER cc_start: 0.8171 (m) cc_final: 0.7673 (t) REVERT: C 359 LEU cc_start: 0.9195 (mm) cc_final: 0.8747 (tp) REVERT: D 42 MET cc_start: 0.6838 (mtm) cc_final: 0.6582 (mtm) REVERT: D 72 MET cc_start: 0.8168 (mtp) cc_final: 0.7962 (mtm) REVERT: D 112 ASN cc_start: 0.8483 (m-40) cc_final: 0.7851 (t0) REVERT: D 237 LYS cc_start: 0.7568 (ttmt) cc_final: 0.7300 (ttmm) REVERT: E 222 GLN cc_start: 0.7630 (mm-40) cc_final: 0.7079 (mp10) REVERT: E 235 MET cc_start: 0.8564 (tpp) cc_final: 0.8297 (mmt) REVERT: E 349 ARG cc_start: 0.8263 (mtm110) cc_final: 0.7815 (ptp-110) REVERT: E 443 ASN cc_start: 0.6977 (OUTLIER) cc_final: 0.6658 (p0) REVERT: F 270 MET cc_start: 0.8515 (mtt) cc_final: 0.8244 (tpp) REVERT: F 401 ASP cc_start: 0.6949 (m-30) cc_final: 0.6730 (t70) outliers start: 1 outliers final: 0 residues processed: 322 average time/residue: 0.1522 time to fit residues: 77.9618 Evaluate side-chains 238 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 237 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 76 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 246 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 209 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 189 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 157 optimal weight: 4.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN A 456 GLN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 ASN B 425 HIS ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 ASN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 GLN ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.118269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.101504 restraints weight = 64005.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.101141 restraints weight = 57758.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.102253 restraints weight = 50742.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.102527 restraints weight = 36731.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.102759 restraints weight = 34806.381| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24256 Z= 0.154 Angle : 0.713 11.579 32940 Z= 0.346 Chirality : 0.045 0.233 3848 Planarity : 0.005 0.086 4404 Dihedral : 9.552 167.547 3585 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.98 % Favored : 88.98 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.28 (0.16), residues: 2640 helix: -1.70 (0.15), residues: 1161 sheet: -2.38 (0.29), residues: 271 loop : -2.55 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 420 TYR 0.020 0.002 TYR A 105 PHE 0.013 0.002 PHE D 259 TRP 0.019 0.001 TRP F 48 HIS 0.006 0.001 HIS B 29 Details of bonding type rmsd covalent geometry : bond 0.00351 (24252) covalent geometry : angle 0.71253 (32940) hydrogen bonds : bond 0.02764 ( 678) hydrogen bonds : angle 4.82667 ( 1893) Misc. bond : bond 0.00145 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8020 (mm-40) cc_final: 0.7814 (tp40) REVERT: A 270 MET cc_start: 0.8129 (tpp) cc_final: 0.7824 (tpp) REVERT: A 341 MET cc_start: 0.7847 (tmm) cc_final: 0.7184 (tmm) REVERT: A 387 ARG cc_start: 0.8103 (ptm160) cc_final: 0.7620 (ptm160) REVERT: B 222 GLN cc_start: 0.8688 (mm-40) cc_final: 0.8245 (mp10) REVERT: B 243 ASN cc_start: 0.7728 (t160) cc_final: 0.7272 (t0) REVERT: B 291 ASP cc_start: 0.7615 (t70) cc_final: 0.6207 (t0) REVERT: B 294 TRP cc_start: 0.5323 (m100) cc_final: 0.3966 (t-100) REVERT: B 348 MET cc_start: 0.7603 (mtp) cc_final: 0.7334 (mtp) REVERT: B 376 ASN cc_start: 0.8364 (m-40) cc_final: 0.8120 (m-40) REVERT: B 382 LEU cc_start: 0.8133 (tp) cc_final: 0.7498 (tt) REVERT: B 383 SER cc_start: 0.7901 (t) cc_final: 0.7334 (p) REVERT: C 69 PHE cc_start: 0.7431 (t80) cc_final: 0.6703 (t80) REVERT: C 180 LYS cc_start: 0.8023 (mtmt) cc_final: 0.7677 (mmtt) REVERT: C 197 PHE cc_start: 0.6613 (m-80) cc_final: 0.6234 (p90) REVERT: C 237 LYS cc_start: 0.8568 (ttmt) cc_final: 0.8230 (ttmm) REVERT: C 316 SER cc_start: 0.8185 (m) cc_final: 0.7722 (t) REVERT: C 359 LEU cc_start: 0.9073 (mm) cc_final: 0.8449 (tt) REVERT: D 42 MET cc_start: 0.6840 (mtm) cc_final: 0.6619 (mtm) REVERT: D 237 LYS cc_start: 0.7677 (ttmt) cc_final: 0.7361 (ttmm) REVERT: E 222 GLN cc_start: 0.7557 (mm-40) cc_final: 0.7282 (mp10) REVERT: E 349 ARG cc_start: 0.8188 (mtm110) cc_final: 0.7784 (ptp-110) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.1471 time to fit residues: 68.5401 Evaluate side-chains 223 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 284 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 224 optimal weight: 7.9990 chunk 130 optimal weight: 0.0050 chunk 253 optimal weight: 0.9990 chunk 114 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 151 optimal weight: 0.8980 overall best weight: 2.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN A 456 GLN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN B 456 GLN C 243 ASN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN C 467 GLN D 201 HIS D 410 GLN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 GLN ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.119070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.102152 restraints weight = 64088.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.101551 restraints weight = 58871.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.102724 restraints weight = 51590.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.102997 restraints weight = 37829.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.103176 restraints weight = 35854.609| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24256 Z= 0.137 Angle : 0.699 11.751 32940 Z= 0.338 Chirality : 0.044 0.199 3848 Planarity : 0.005 0.082 4404 Dihedral : 9.393 165.304 3585 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.23 % Favored : 89.73 % Rotamer: Outliers : 0.04 % Allowed : 1.60 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.11 (0.16), residues: 2640 helix: -1.57 (0.15), residues: 1159 sheet: -2.29 (0.30), residues: 269 loop : -2.45 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 329 TYR 0.028 0.001 TYR D 344 PHE 0.013 0.001 PHE E 147 TRP 0.016 0.001 TRP F 457 HIS 0.005 0.001 HIS B 29 Details of bonding type rmsd covalent geometry : bond 0.00313 (24252) covalent geometry : angle 0.69913 (32940) hydrogen bonds : bond 0.02721 ( 678) hydrogen bonds : angle 4.70757 ( 1893) Misc. bond : bond 0.00140 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 290 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLN cc_start: 0.7943 (mm-40) cc_final: 0.7175 (mm-40) REVERT: A 270 MET cc_start: 0.8178 (tpp) cc_final: 0.7802 (tpp) REVERT: A 341 MET cc_start: 0.7905 (tmm) cc_final: 0.7195 (tmm) REVERT: A 387 ARG cc_start: 0.8108 (ptm160) cc_final: 0.7603 (ptm160) REVERT: B 202 ASP cc_start: 0.6604 (m-30) cc_final: 0.5413 (t70) REVERT: B 222 GLN cc_start: 0.8652 (mm-40) cc_final: 0.8248 (mp10) REVERT: B 291 ASP cc_start: 0.7721 (t70) cc_final: 0.6381 (t0) REVERT: B 294 TRP cc_start: 0.5646 (m100) cc_final: 0.4238 (t-100) REVERT: B 382 LEU cc_start: 0.8137 (tp) cc_final: 0.7490 (tt) REVERT: C 69 PHE cc_start: 0.7463 (t80) cc_final: 0.6704 (t80) REVERT: C 137 SER cc_start: 0.9089 (m) cc_final: 0.8826 (t) REVERT: C 180 LYS cc_start: 0.7960 (mtmt) cc_final: 0.7605 (mmtt) REVERT: C 197 PHE cc_start: 0.6606 (m-80) cc_final: 0.6259 (p90) REVERT: C 235 MET cc_start: 0.7337 (tpt) cc_final: 0.7060 (tpt) REVERT: C 237 LYS cc_start: 0.8595 (ttmt) cc_final: 0.8195 (ttmm) REVERT: C 316 SER cc_start: 0.8117 (m) cc_final: 0.7658 (t) REVERT: C 359 LEU cc_start: 0.9094 (mm) cc_final: 0.8510 (tt) REVERT: D 42 MET cc_start: 0.6861 (mtm) cc_final: 0.6658 (mtm) REVERT: D 237 LYS cc_start: 0.7608 (ttmt) cc_final: 0.7339 (ttmm) REVERT: E 222 GLN cc_start: 0.7569 (mm-40) cc_final: 0.7145 (mp10) REVERT: E 322 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7171 (mt-10) REVERT: E 349 ARG cc_start: 0.8132 (mtm110) cc_final: 0.7763 (ptp-110) REVERT: E 411 ASP cc_start: 0.8010 (m-30) cc_final: 0.7009 (m-30) REVERT: F 401 ASP cc_start: 0.7068 (m-30) cc_final: 0.6629 (t0) outliers start: 1 outliers final: 0 residues processed: 291 average time/residue: 0.1557 time to fit residues: 71.9489 Evaluate side-chains 224 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 20 optimal weight: 0.9980 chunk 283 optimal weight: 40.0000 chunk 65 optimal weight: 10.0000 chunk 228 optimal weight: 10.0000 chunk 255 optimal weight: 6.9990 chunk 276 optimal weight: 9.9990 chunk 212 optimal weight: 10.0000 chunk 300 optimal weight: 10.0000 chunk 286 optimal weight: 20.0000 chunk 32 optimal weight: 7.9990 chunk 152 optimal weight: 0.0570 overall best weight: 5.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN A 456 GLN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 ASN B 456 GLN C 243 ASN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 GLN ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 456 GLN F 243 ASN ** F 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.114792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.097998 restraints weight = 65420.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.097830 restraints weight = 59088.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.098646 restraints weight = 59103.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.099017 restraints weight = 40525.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.099272 restraints weight = 36727.262| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 24256 Z= 0.253 Angle : 0.824 11.632 32940 Z= 0.404 Chirality : 0.049 0.291 3848 Planarity : 0.005 0.081 4404 Dihedral : 9.837 163.715 3585 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.48 % Favored : 86.40 % Rotamer: Outliers : 0.04 % Allowed : 0.98 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.56 (0.15), residues: 2640 helix: -1.86 (0.14), residues: 1199 sheet: -2.76 (0.28), residues: 268 loop : -2.73 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 420 TYR 0.026 0.002 TYR D 344 PHE 0.019 0.002 PHE C 460 TRP 0.025 0.002 TRP F 457 HIS 0.006 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00570 (24252) covalent geometry : angle 0.82389 (32940) hydrogen bonds : bond 0.03317 ( 678) hydrogen bonds : angle 5.21143 ( 1893) Misc. bond : bond 0.00198 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 269 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7729 (mm-40) REVERT: A 270 MET cc_start: 0.8127 (tpp) cc_final: 0.7736 (tpp) REVERT: A 387 ARG cc_start: 0.8217 (ptm160) cc_final: 0.7745 (ptm160) REVERT: B 34 GLU cc_start: 0.8232 (tt0) cc_final: 0.7690 (tp30) REVERT: B 222 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8254 (mp10) REVERT: B 337 ILE cc_start: 0.7875 (mp) cc_final: 0.7580 (mp) REVERT: B 348 MET cc_start: 0.7635 (mtp) cc_final: 0.7424 (mtp) REVERT: B 456 GLN cc_start: 0.5757 (OUTLIER) cc_final: 0.5083 (tm-30) REVERT: C 180 LYS cc_start: 0.8197 (mtmt) cc_final: 0.7743 (mmtt) REVERT: C 197 PHE cc_start: 0.6628 (m-80) cc_final: 0.6207 (p90) REVERT: C 237 LYS cc_start: 0.8704 (ttmt) cc_final: 0.8274 (ttmm) REVERT: C 316 SER cc_start: 0.8218 (m) cc_final: 0.7794 (t) REVERT: C 359 LEU cc_start: 0.9122 (mm) cc_final: 0.8523 (tt) REVERT: D 237 LYS cc_start: 0.7935 (ttmt) cc_final: 0.7725 (ttmm) REVERT: D 382 LEU cc_start: 0.8911 (mt) cc_final: 0.8585 (mt) REVERT: E 222 GLN cc_start: 0.7722 (mm-40) cc_final: 0.7134 (mp10) REVERT: E 322 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7205 (mt-10) REVERT: E 349 ARG cc_start: 0.8117 (mtm110) cc_final: 0.7801 (ptp-110) REVERT: E 411 ASP cc_start: 0.8421 (m-30) cc_final: 0.7394 (m-30) REVERT: F 401 ASP cc_start: 0.7109 (m-30) cc_final: 0.6503 (t0) outliers start: 1 outliers final: 0 residues processed: 270 average time/residue: 0.1498 time to fit residues: 65.0337 Evaluate side-chains 213 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 65 optimal weight: 20.0000 chunk 270 optimal weight: 40.0000 chunk 138 optimal weight: 0.0060 chunk 267 optimal weight: 20.0000 chunk 73 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 313 optimal weight: 10.0000 chunk 272 optimal weight: 30.0000 chunk 152 optimal weight: 5.9990 chunk 232 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 overall best weight: 5.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN A 456 GLN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 ASN ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 GLN C 243 ASN C 399 ASN ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 ASN ** E 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 HIS ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.113796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.096935 restraints weight = 65408.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.096216 restraints weight = 59360.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.097239 restraints weight = 56246.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.097775 restraints weight = 39684.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.097930 restraints weight = 36963.276| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 24256 Z= 0.266 Angle : 0.856 11.436 32940 Z= 0.420 Chirality : 0.049 0.290 3848 Planarity : 0.005 0.079 4404 Dihedral : 10.024 164.553 3585 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.41 % Favored : 86.52 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.66 (0.15), residues: 2640 helix: -1.92 (0.14), residues: 1180 sheet: -2.83 (0.27), residues: 269 loop : -2.79 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 192 TYR 0.039 0.002 TYR D 344 PHE 0.022 0.002 PHE C 460 TRP 0.025 0.002 TRP F 457 HIS 0.006 0.001 HIS E 67 Details of bonding type rmsd covalent geometry : bond 0.00597 (24252) covalent geometry : angle 0.85597 (32940) hydrogen bonds : bond 0.03411 ( 678) hydrogen bonds : angle 5.44071 ( 1893) Misc. bond : bond 0.00177 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 PHE cc_start: 0.7169 (m-10) cc_final: 0.6953 (m-10) REVERT: A 267 GLN cc_start: 0.8206 (mm-40) cc_final: 0.7784 (mm-40) REVERT: A 270 MET cc_start: 0.8133 (tpp) cc_final: 0.7693 (tpp) REVERT: A 341 MET cc_start: 0.7766 (tmm) cc_final: 0.6969 (tmm) REVERT: A 387 ARG cc_start: 0.8183 (ptm160) cc_final: 0.7737 (ptm160) REVERT: B 34 GLU cc_start: 0.8247 (tt0) cc_final: 0.8037 (tt0) REVERT: B 235 MET cc_start: 0.6880 (mmt) cc_final: 0.6503 (mmt) REVERT: B 337 ILE cc_start: 0.7933 (mp) cc_final: 0.7591 (mp) REVERT: B 376 ASN cc_start: 0.8384 (m-40) cc_final: 0.8100 (m-40) REVERT: C 180 LYS cc_start: 0.8212 (mtmt) cc_final: 0.7766 (mmtt) REVERT: C 197 PHE cc_start: 0.6599 (m-80) cc_final: 0.6178 (p90) REVERT: C 237 LYS cc_start: 0.8681 (ttmt) cc_final: 0.8314 (ttmm) REVERT: C 316 SER cc_start: 0.8301 (m) cc_final: 0.7854 (t) REVERT: C 359 LEU cc_start: 0.9135 (mm) cc_final: 0.8537 (tt) REVERT: D 42 MET cc_start: 0.7024 (mtm) cc_final: 0.6762 (mtm) REVERT: D 382 LEU cc_start: 0.8712 (mt) cc_final: 0.8303 (mt) REVERT: E 222 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7171 (mp10) REVERT: E 322 GLU cc_start: 0.7516 (mt-10) cc_final: 0.7244 (mt-10) REVERT: E 435 GLU cc_start: 0.7664 (mp0) cc_final: 0.7414 (mp0) REVERT: F 401 ASP cc_start: 0.7075 (m-30) cc_final: 0.6432 (t0) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.1407 time to fit residues: 58.6377 Evaluate side-chains 207 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 42 optimal weight: 0.9980 chunk 253 optimal weight: 0.6980 chunk 190 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 267 optimal weight: 20.0000 chunk 16 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 chunk 198 optimal weight: 0.9990 chunk 284 optimal weight: 30.0000 chunk 204 optimal weight: 5.9990 chunk 298 optimal weight: 20.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 ASN B 456 GLN C 243 ASN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN D 410 GLN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 ASN E 252 GLN E 346 GLN ** F 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.119271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.101942 restraints weight = 63719.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.101761 restraints weight = 54338.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.102829 restraints weight = 51843.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.103119 restraints weight = 36512.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.103632 restraints weight = 34014.849| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24256 Z= 0.123 Angle : 0.719 11.732 32940 Z= 0.347 Chirality : 0.044 0.295 3848 Planarity : 0.005 0.072 4404 Dihedral : 9.295 164.660 3585 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.58 % Favored : 90.38 % Rotamer: Outliers : 0.04 % Allowed : 0.44 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.14 (0.16), residues: 2640 helix: -1.52 (0.15), residues: 1165 sheet: -2.52 (0.29), residues: 266 loop : -2.50 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 192 TYR 0.024 0.001 TYR D 344 PHE 0.024 0.002 PHE D 259 TRP 0.013 0.001 TRP F 294 HIS 0.005 0.001 HIS B 29 Details of bonding type rmsd covalent geometry : bond 0.00280 (24252) covalent geometry : angle 0.71899 (32940) hydrogen bonds : bond 0.02698 ( 678) hydrogen bonds : angle 4.83388 ( 1893) Misc. bond : bond 0.00135 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2906.08 seconds wall clock time: 51 minutes 22.28 seconds (3082.28 seconds total)