Starting phenix.real_space_refine on Sat Mar 7 00:18:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tub_26131/03_2026/7tub_26131.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tub_26131/03_2026/7tub_26131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tub_26131/03_2026/7tub_26131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tub_26131/03_2026/7tub_26131.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tub_26131/03_2026/7tub_26131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tub_26131/03_2026/7tub_26131.map" } resolution = 3.6 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= 1.000 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: 8 Type Number sf(0) Gaussians Al 8 5.89 5 P 16 5.49 5 Mg 8 5.21 5 S 220 5.16 5 C 22426 2.51 5 N 6233 2.21 5 O 6942 1.98 5 F 24 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35877 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 3442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3442 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 20, 'TRANS': 418} Chain breaks: 1 Chain: "B" Number of atoms: 4029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4029 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "C" Number of atoms: 4003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4003 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 15, 'TRANS': 505} Chain breaks: 1 Chain: "D" Number of atoms: 4072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4072 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 18, 'TRANS': 509} Chain: "E" Number of atoms: 3960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3960 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 11, 'TRANS': 514} Chain: "F" Number of atoms: 3924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3924 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 505} Chain: "G" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4063 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 14, 'TRANS': 520} Chain: "H" Number of atoms: 4064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4064 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 16, 'TRANS': 506} Chain: "I" Number of atoms: 4056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4056 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 14, 'TRANS': 514} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 7.92, per 1000 atoms: 0.22 Number of scatterers: 35877 At special positions: 0 Unit cell: (180.4, 183.7, 115.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 220 16.00 P 16 15.00 Al 8 13.00 Mg 8 11.99 F 24 9.00 O 6942 8.00 N 6233 7.00 C 22426 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 1.4 seconds 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8658 Finding SS restraints... Secondary structure from input PDB file: 194 helices and 50 sheets defined 55.1% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 10 through 26 removed outlier: 3.712A pdb=" N ASN A 14 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 49 Processing helix chain 'A' and resid 69 through 79 removed outlier: 4.106A pdb=" N MET A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 109 through 125 removed outlier: 4.336A pdb=" N ASP A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N SER A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP A 118 " --> pdb=" O ASP A 114 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 159 Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 181 through 194 removed outlier: 3.691A pdb=" N LEU A 187 " --> pdb=" O TYR A 183 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER A 188 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU A 194 " --> pdb=" O HIS A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 removed outlier: 4.215A pdb=" N CYS A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 242 removed outlier: 3.521A pdb=" N LEU A 225 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 236 " --> pdb=" O THR A 232 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 237 " --> pdb=" O MET A 233 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N CYS A 239 " --> pdb=" O GLY A 235 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG A 241 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE A 242 " --> pdb=" O THR A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 258 Processing helix chain 'A' and resid 275 through 282 Processing helix chain 'A' and resid 285 through 292 removed outlier: 3.571A pdb=" N GLN A 292 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 337 removed outlier: 4.286A pdb=" N VAL A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN A 337 " --> pdb=" O VAL A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 341 Processing helix chain 'A' and resid 374 through 390 removed outlier: 3.716A pdb=" N ARG A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 405 through 425 removed outlier: 3.753A pdb=" N THR A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN A 414 " --> pdb=" O GLU A 410 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 removed outlier: 3.940A pdb=" N MET B 14 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 15 " --> pdb=" O PHE B 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 10 through 15' Processing helix chain 'B' and resid 23 through 44 removed outlier: 3.856A pdb=" N GLU B 27 " --> pdb=" O SER B 23 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR B 30 " --> pdb=" O GLU B 26 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ARG B 31 " --> pdb=" O GLU B 27 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 42 " --> pdb=" O GLU B 38 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 68 through 76 Processing helix chain 'B' and resid 80 through 97 removed outlier: 3.849A pdb=" N ILE B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 122 removed outlier: 3.682A pdb=" N VAL B 104 " --> pdb=" O GLY B 100 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 143 Processing helix chain 'B' and resid 144 through 147 Processing helix chain 'B' and resid 156 through 170 removed outlier: 3.926A pdb=" N SER B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N THR B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N SER B 167 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER B 170 " --> pdb=" O THR B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 211 through 215 removed outlier: 3.566A pdb=" N SER B 214 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 286 removed outlier: 4.779A pdb=" N SER B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LYS B 270 " --> pdb=" O MET B 266 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'B' and resid 319 through 329 Processing helix chain 'B' and resid 340 through 344 removed outlier: 3.760A pdb=" N MET B 344 " --> pdb=" O LEU B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 405 Processing helix chain 'B' and resid 413 through 428 Processing helix chain 'B' and resid 434 through 444 removed outlier: 3.515A pdb=" N ILE B 438 " --> pdb=" O GLU B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 456 Processing helix chain 'B' and resid 459 through 473 removed outlier: 3.945A pdb=" N VAL B 463 " --> pdb=" O LYS B 459 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU B 473 " --> pdb=" O ALA B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 496 Processing helix chain 'B' and resid 501 through 520 removed outlier: 3.557A pdb=" N LYS B 509 " --> pdb=" O TYR B 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 36 removed outlier: 3.682A pdb=" N GLN C 30 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE C 32 " --> pdb=" O ALA C 28 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL C 36 " --> pdb=" O ILE C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 40 removed outlier: 3.754A pdb=" N LEU C 40 " --> pdb=" O ARG C 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 37 through 40' Processing helix chain 'C' and resid 61 through 69 Processing helix chain 'C' and resid 75 through 90 removed outlier: 4.304A pdb=" N LEU C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA C 83 " --> pdb=" O LEU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 114 removed outlier: 3.715A pdb=" N VAL C 108 " --> pdb=" O PHE C 104 " (cutoff:3.500A) Proline residue: C 110 - end of helix Processing helix chain 'C' and resid 117 through 140 removed outlier: 3.734A pdb=" N GLN C 130 " --> pdb=" O ARG C 126 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU C 138 " --> pdb=" O ASN C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 162 removed outlier: 3.522A pdb=" N ARG C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU C 156 " --> pdb=" O ARG C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 171 through 185 removed outlier: 3.847A pdb=" N LYS C 177 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET C 178 " --> pdb=" O PHE C 174 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N MET C 185 " --> pdb=" O ASP C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 193 No H-bonds generated for 'chain 'C' and resid 191 through 193' Processing helix chain 'C' and resid 204 through 208 Processing helix chain 'C' and resid 224 through 228 removed outlier: 3.857A pdb=" N MET C 227 " --> pdb=" O GLY C 224 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN C 228 " --> pdb=" O PHE C 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 224 through 228' Processing helix chain 'C' and resid 259 through 284 removed outlier: 3.512A pdb=" N GLU C 270 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TRP C 271 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 306 removed outlier: 3.847A pdb=" N ARG C 306 " --> pdb=" O TYR C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 327 Processing helix chain 'C' and resid 378 through 402 removed outlier: 3.502A pdb=" N MET C 382 " --> pdb=" O ALA C 378 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP C 391 " --> pdb=" O ARG C 387 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS C 401 " --> pdb=" O ARG C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 425 removed outlier: 3.517A pdb=" N MET C 414 " --> pdb=" O GLY C 410 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU C 415 " --> pdb=" O ALA C 411 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG C 425 " --> pdb=" O ARG C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 427 No H-bonds generated for 'chain 'C' and resid 426 through 427' Processing helix chain 'C' and resid 428 through 429 No H-bonds generated for 'chain 'C' and resid 428 through 429' Processing helix chain 'C' and resid 430 through 442 removed outlier: 3.591A pdb=" N ILE C 435 " --> pdb=" O GLN C 431 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU C 442 " --> pdb=" O TYR C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 454 Processing helix chain 'C' and resid 456 through 471 removed outlier: 3.759A pdb=" N GLY C 471 " --> pdb=" O ARG C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 525 removed outlier: 3.623A pdb=" N ALA C 515 " --> pdb=" O ASN C 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 48 removed outlier: 3.580A pdb=" N LEU D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 81 Processing helix chain 'D' and resid 85 through 102 Processing helix chain 'D' and resid 105 through 119 removed outlier: 3.689A pdb=" N VAL D 109 " --> pdb=" O GLY D 105 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL D 111 " --> pdb=" O THR D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 removed outlier: 4.222A pdb=" N LEU D 123 " --> pdb=" O GLU D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 149 removed outlier: 3.510A pdb=" N ASP D 149 " --> pdb=" O ILE D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 174 Processing helix chain 'D' and resid 175 through 180 removed outlier: 6.738A pdb=" N VAL D 178 " --> pdb=" O SER D 175 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER D 180 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 195 Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 218 through 222 Processing helix chain 'D' and resid 270 through 295 removed outlier: 3.537A pdb=" N LYS D 282 " --> pdb=" O GLN D 278 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU D 286 " --> pdb=" O LYS D 282 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET D 288 " --> pdb=" O LYS D 284 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE D 289 " --> pdb=" O PHE D 285 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR D 295 " --> pdb=" O GLN D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 317 removed outlier: 3.522A pdb=" N HIS D 312 " --> pdb=" O ASP D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 338 Processing helix chain 'D' and resid 391 through 415 Processing helix chain 'D' and resid 423 through 438 removed outlier: 3.775A pdb=" N ASP D 438 " --> pdb=" O SER D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 456 Processing helix chain 'D' and resid 456 through 467 removed outlier: 3.517A pdb=" N ASN D 465 " --> pdb=" O ALA D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 484 Processing helix chain 'D' and resid 500 through 505 Processing helix chain 'D' and resid 510 through 528 removed outlier: 3.712A pdb=" N MET D 526 " --> pdb=" O GLN D 522 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 40 removed outlier: 3.593A pdb=" N LEU E 26 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL E 39 " --> pdb=" O ILE E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 43 No H-bonds generated for 'chain 'E' and resid 41 through 43' Processing helix chain 'E' and resid 66 through 74 removed outlier: 3.645A pdb=" N ILE E 70 " --> pdb=" O ASP E 66 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU E 71 " --> pdb=" O GLY E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 95 removed outlier: 3.915A pdb=" N VAL E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU E 84 " --> pdb=" O ALA E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 118 removed outlier: 3.738A pdb=" N THR E 103 " --> pdb=" O THR E 99 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU E 110 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER E 115 " --> pdb=" O ARG E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 143 removed outlier: 3.575A pdb=" N ILE E 126 " --> pdb=" O HIS E 122 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU E 132 " --> pdb=" O ALA E 128 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS E 135 " --> pdb=" O ARG E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 167 Processing helix chain 'E' and resid 170 through 174 Processing helix chain 'E' and resid 175 through 189 removed outlier: 3.746A pdb=" N LYS E 181 " --> pdb=" O ASP E 177 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU E 182 " --> pdb=" O HIS E 178 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG E 189 " --> pdb=" O GLU E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 208 through 212 removed outlier: 3.696A pdb=" N SER E 212 " --> pdb=" O LEU E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 284 removed outlier: 3.639A pdb=" N LYS E 272 " --> pdb=" O GLU E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 308 removed outlier: 3.606A pdb=" N GLN E 302 " --> pdb=" O ASN E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 328 removed outlier: 3.653A pdb=" N LEU E 323 " --> pdb=" O GLY E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 403 removed outlier: 3.672A pdb=" N ASP E 392 " --> pdb=" O ARG E 388 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA E 393 " --> pdb=" O SER E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 426 removed outlier: 3.520A pdb=" N LEU E 416 " --> pdb=" O CYS E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 444 removed outlier: 3.530A pdb=" N ALA E 435 " --> pdb=" O LYS E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 455 removed outlier: 3.509A pdb=" N THR E 448 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA E 454 " --> pdb=" O ILE E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 457 through 471 Processing helix chain 'E' and resid 488 through 492 Processing helix chain 'E' and resid 497 through 516 removed outlier: 3.603A pdb=" N ALA E 511 " --> pdb=" O ALA E 507 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU E 512 " --> pdb=" O ALA E 508 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU E 515 " --> pdb=" O ALA E 511 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 48 removed outlier: 3.571A pdb=" N PHE F 35 " --> pdb=" O ALA F 31 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA F 45 " --> pdb=" O ALA F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 81 Processing helix chain 'F' and resid 85 through 89 Processing helix chain 'F' and resid 90 through 102 Processing helix chain 'F' and resid 107 through 119 Processing helix chain 'F' and resid 119 through 127 removed outlier: 3.988A pdb=" N LEU F 123 " --> pdb=" O SER F 119 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN F 125 " --> pdb=" O THR F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 152 Processing helix chain 'F' and resid 159 through 170 removed outlier: 3.817A pdb=" N LEU F 163 " --> pdb=" O ASP F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 178 removed outlier: 4.538A pdb=" N GLN F 178 " --> pdb=" O VAL F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 193 Proline residue: F 185 - end of helix removed outlier: 3.500A pdb=" N VAL F 188 " --> pdb=" O SER F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 206 No H-bonds generated for 'chain 'F' and resid 204 through 206' Processing helix chain 'F' and resid 217 through 221 Processing helix chain 'F' and resid 268 through 293 removed outlier: 4.134A pdb=" N MET F 272 " --> pdb=" O ASP F 268 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASP F 273 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU F 286 " --> pdb=" O TYR F 282 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR F 293 " --> pdb=" O GLN F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 320 Processing helix chain 'F' and resid 332 through 341 Processing helix chain 'F' and resid 347 through 351 Processing helix chain 'F' and resid 352 through 356 removed outlier: 3.750A pdb=" N MET F 355 " --> pdb=" O THR F 352 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU F 356 " --> pdb=" O ALA F 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 352 through 356' Processing helix chain 'F' and resid 394 through 418 Processing helix chain 'F' and resid 426 through 443 removed outlier: 3.583A pdb=" N ARG F 441 " --> pdb=" O THR F 437 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR F 442 " --> pdb=" O GLU F 438 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU F 443 " --> pdb=" O TYR F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 458 removed outlier: 3.944A pdb=" N CYS F 450 " --> pdb=" O MET F 446 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET F 458 " --> pdb=" O PHE F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 459 through 469 removed outlier: 3.593A pdb=" N ALA F 469 " --> pdb=" O LEU F 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 485 Processing helix chain 'F' and resid 504 through 507 Processing helix chain 'F' and resid 512 through 530 Processing helix chain 'G' and resid 14 through 33 removed outlier: 3.737A pdb=" N ARG G 18 " --> pdb=" O GLY G 14 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE G 28 " --> pdb=" O ALA G 24 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA G 29 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL G 32 " --> pdb=" O ILE G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 36 No H-bonds generated for 'chain 'G' and resid 34 through 36' Processing helix chain 'G' and resid 57 through 65 Processing helix chain 'G' and resid 69 through 86 removed outlier: 4.424A pdb=" N LEU G 75 " --> pdb=" O ALA G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 110 removed outlier: 3.591A pdb=" N VAL G 93 " --> pdb=" O GLY G 89 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL G 94 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU G 106 " --> pdb=" O LYS G 102 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU G 107 " --> pdb=" O ASN G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 132 Processing helix chain 'G' and resid 143 through 157 removed outlier: 3.510A pdb=" N LEU G 148 " --> pdb=" O GLY G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 178 Processing helix chain 'G' and resid 204 through 208 Processing helix chain 'G' and resid 256 through 258 No H-bonds generated for 'chain 'G' and resid 256 through 258' Processing helix chain 'G' and resid 259 through 280 removed outlier: 3.791A pdb=" N GLU G 267 " --> pdb=" O ILE G 263 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER G 268 " --> pdb=" O ARG G 264 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N THR G 271 " --> pdb=" O GLU G 267 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS G 272 " --> pdb=" O SER G 268 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 304 removed outlier: 3.942A pdb=" N LYS G 298 " --> pdb=" O ASP G 294 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR G 299 " --> pdb=" O MET G 295 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE G 300 " --> pdb=" O CYS G 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 324 Processing helix chain 'G' and resid 341 through 345 removed outlier: 3.968A pdb=" N MET G 344 " --> pdb=" O GLU G 341 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU G 345 " --> pdb=" O ALA G 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 341 through 345' Processing helix chain 'G' and resid 381 through 405 removed outlier: 3.573A pdb=" N MET G 388 " --> pdb=" O MET G 384 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP G 394 " --> pdb=" O ARG G 390 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA G 395 " --> pdb=" O SER G 391 " (cutoff:3.500A) Processing helix chain 'G' and resid 413 through 427 Processing helix chain 'G' and resid 428 through 430 No H-bonds generated for 'chain 'G' and resid 428 through 430' Processing helix chain 'G' and resid 433 through 446 removed outlier: 4.066A pdb=" N ALA G 437 " --> pdb=" O ARG G 433 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU G 446 " --> pdb=" O ALA G 442 " (cutoff:3.500A) Processing helix chain 'G' and resid 446 through 456 removed outlier: 3.693A pdb=" N ASN G 450 " --> pdb=" O LEU G 446 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA G 456 " --> pdb=" O LEU G 452 " (cutoff:3.500A) Processing helix chain 'G' and resid 459 through 476 removed outlier: 3.677A pdb=" N VAL G 464 " --> pdb=" O SER G 460 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 485 removed outlier: 4.615A pdb=" N ASN G 482 " --> pdb=" O GLU G 479 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP G 485 " --> pdb=" O ASN G 482 " (cutoff:3.500A) Processing helix chain 'G' and resid 497 through 502 Processing helix chain 'G' and resid 507 through 526 removed outlier: 3.583A pdb=" N ILE G 524 " --> pdb=" O ALA G 520 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 38 removed outlier: 3.781A pdb=" N GLN H 23 " --> pdb=" O GLY H 19 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE H 33 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE H 37 " --> pdb=" O ILE H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 68 removed outlier: 3.624A pdb=" N LEU H 67 " --> pdb=" O GLY H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 92 removed outlier: 3.707A pdb=" N SER H 79 " --> pdb=" O PRO H 75 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N MET H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG H 85 " --> pdb=" O ILE H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 108 Processing helix chain 'H' and resid 109 through 114 Processing helix chain 'H' and resid 118 through 140 removed outlier: 3.617A pdb=" N VAL H 122 " --> pdb=" O HIS H 118 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP H 131 " --> pdb=" O ARG H 127 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP H 132 " --> pdb=" O LYS H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 161 removed outlier: 3.628A pdb=" N ASN H 154 " --> pdb=" O ASP H 150 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER H 159 " --> pdb=" O ILE H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 167 removed outlier: 3.810A pdb=" N ARG H 167 " --> pdb=" O ALA H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 184 removed outlier: 3.980A pdb=" N ASN H 174 " --> pdb=" O SER H 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 212 removed outlier: 3.506A pdb=" N SER H 212 " --> pdb=" O ILE H 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 260 through 284 removed outlier: 4.485A pdb=" N PHE H 264 " --> pdb=" O ARG H 260 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N THR H 265 " --> pdb=" O GLU H 261 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG H 266 " --> pdb=" O GLU H 262 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU H 271 " --> pdb=" O ILE H 267 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU H 272 " --> pdb=" O LEU H 268 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 307 Processing helix chain 'H' and resid 316 through 328 removed outlier: 3.519A pdb=" N ASN H 321 " --> pdb=" O LYS H 317 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG H 322 " --> pdb=" O THR H 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 334 through 338 Processing helix chain 'H' and resid 380 through 404 removed outlier: 3.532A pdb=" N ASP H 393 " --> pdb=" O ARG H 389 " (cutoff:3.500A) Processing helix chain 'H' and resid 412 through 427 removed outlier: 3.847A pdb=" N LYS H 427 " --> pdb=" O THR H 423 " (cutoff:3.500A) Processing helix chain 'H' and resid 433 through 443 removed outlier: 4.007A pdb=" N ALA H 441 " --> pdb=" O TYR H 437 " (cutoff:3.500A) Processing helix chain 'H' and resid 445 through 456 Processing helix chain 'H' and resid 460 through 471 removed outlier: 3.521A pdb=" N THR H 464 " --> pdb=" O ILE H 460 " (cutoff:3.500A) Processing helix chain 'H' and resid 490 through 494 Processing helix chain 'H' and resid 499 through 517 Processing helix chain 'I' and resid 15 through 35 removed outlier: 3.575A pdb=" N GLY I 29 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU I 30 " --> pdb=" O ALA I 26 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN I 31 " --> pdb=" O ALA I 27 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL I 33 " --> pdb=" O GLY I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 67 removed outlier: 3.642A pdb=" N LEU I 63 " --> pdb=" O ASP I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 89 removed outlier: 3.857A pdb=" N ILE I 77 " --> pdb=" O THR I 73 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA I 78 " --> pdb=" O ALA I 74 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE I 87 " --> pdb=" O ALA I 83 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR I 88 " --> pdb=" O GLN I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 111 removed outlier: 3.506A pdb=" N VAL I 96 " --> pdb=" O THR I 92 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR I 109 " --> pdb=" O GLN I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 115 through 138 removed outlier: 4.019A pdb=" N ILE I 119 " --> pdb=" O HIS I 115 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU I 135 " --> pdb=" O LEU I 131 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU I 136 " --> pdb=" O GLN I 132 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL I 137 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS I 138 " --> pdb=" O LEU I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 157 Processing helix chain 'I' and resid 161 through 180 removed outlier: 3.601A pdb=" N ASP I 166 " --> pdb=" O ALA I 162 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL I 167 " --> pdb=" O GLU I 163 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU I 170 " --> pdb=" O ASP I 166 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA I 171 " --> pdb=" O VAL I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 200 through 204 removed outlier: 3.562A pdb=" N ASP I 203 " --> pdb=" O SER I 200 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR I 204 " --> pdb=" O GLU I 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 200 through 204' Processing helix chain 'I' and resid 252 through 263 Processing helix chain 'I' and resid 264 through 282 removed outlier: 3.772A pdb=" N ARG I 270 " --> pdb=" O PHE I 266 " (cutoff:3.500A) Processing helix chain 'I' and resid 298 through 307 Processing helix chain 'I' and resid 319 through 328 removed outlier: 4.480A pdb=" N THR I 325 " --> pdb=" O MET I 321 " (cutoff:3.500A) Processing helix chain 'I' and resid 340 through 344 Processing helix chain 'I' and resid 380 through 404 Processing helix chain 'I' and resid 412 through 424 removed outlier: 4.072A pdb=" N VAL I 416 " --> pdb=" O GLY I 412 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS I 424 " --> pdb=" O GLU I 420 " (cutoff:3.500A) Processing helix chain 'I' and resid 432 through 444 removed outlier: 4.126A pdb=" N GLY I 436 " --> pdb=" O ARG I 432 " (cutoff:3.500A) Processing helix chain 'I' and resid 445 through 456 removed outlier: 3.580A pdb=" N LYS I 449 " --> pdb=" O LEU I 445 " (cutoff:3.500A) Processing helix chain 'I' and resid 458 through 469 Processing helix chain 'I' and resid 489 through 493 Processing helix chain 'I' and resid 498 through 517 removed outlier: 3.554A pdb=" N THR I 509 " --> pdb=" O LEU I 505 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU I 517 " --> pdb=" O THR I 513 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 92 removed outlier: 8.264A pdb=" N VAL A 91 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU A 65 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N SER A 138 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N PHE A 133 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N PHE A 167 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU A 135 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N VAL A 169 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N HIS A 137 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU A 198 " --> pdb=" O MET A 164 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR A 166 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR A 199 " --> pdb=" O PHE A 266 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N CYS A 201 " --> pdb=" O PRO A 268 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N PHE A 265 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N SER A 371 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ALA A 364 " --> pdb=" O PHE A 317 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N PHE A 317 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N THR A 366 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ALA A 315 " --> pdb=" O THR A 366 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE A 368 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL A 313 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASN A 370 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A 350 " --> pdb=" O VAL A 313 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 22 removed outlier: 6.530A pdb=" N MET I 44 " --> pdb=" O VAL B 521 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLN B 523 " --> pdb=" O MET I 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 63 through 66 removed outlier: 6.340A pdb=" N ASN B 53 " --> pdb=" O VAL C 526 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU C 528 " --> pdb=" O ASN B 53 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 150 removed outlier: 3.771A pdb=" N CYS B 149 " --> pdb=" O LEU B 408 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 202 through 208 removed outlier: 6.489A pdb=" N ARG B 203 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LEU B 377 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N CYS B 205 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N GLY B 379 " --> pdb=" O CYS B 205 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE B 207 " --> pdb=" O GLY B 379 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 220 through 223 Processing sheet with id=AA8, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AA9, first strand: chain 'B' and resid 255 through 259 removed outlier: 3.649A pdb=" N ARG C 256 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N LYS D 265 " --> pdb=" O ALA C 253 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE C 255 " --> pdb=" O LYS D 265 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ASP D 267 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL C 257 " --> pdb=" O ASP D 267 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ARG E 255 " --> pdb=" O HIS D 264 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N LEU D 266 " --> pdb=" O ARG E 255 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ARG E 257 " --> pdb=" O LEU D 266 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N VAL D 268 " --> pdb=" O ARG E 257 " (cutoff:3.500A) removed outlier: 9.498A pdb=" N GLN F 263 " --> pdb=" O SER E 254 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL E 256 " --> pdb=" O GLN F 263 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL F 265 " --> pdb=" O VAL E 256 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL E 258 " --> pdb=" O VAL F 265 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N GLN G 251 " --> pdb=" O ASN F 262 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE F 264 " --> pdb=" O GLN G 251 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL G 253 " --> pdb=" O ILE F 264 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL F 266 " --> pdb=" O VAL G 253 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N ASP H 255 " --> pdb=" O VAL G 250 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL G 252 " --> pdb=" O ASP H 255 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N GLU H 257 " --> pdb=" O VAL G 252 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE G 254 " --> pdb=" O GLU H 257 " (cutoff:3.500A) removed outlier: 9.290A pdb=" N GLY I 247 " --> pdb=" O THR H 254 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE H 256 " --> pdb=" O GLY I 247 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N PHE I 249 " --> pdb=" O ILE H 256 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE H 258 " --> pdb=" O PHE I 249 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 478 through 480 Processing sheet with id=AB2, first strand: chain 'C' and resid 56 through 59 removed outlier: 7.527A pdb=" N ASP C 46 " --> pdb=" O ASP D 531 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE D 533 " --> pdb=" O ASP C 46 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU C 48 " --> pdb=" O ILE D 533 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LYS D 535 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N VAL C 50 " --> pdb=" O LYS D 535 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D 28 " --> pdb=" O ILE D 533 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS D 535 " --> pdb=" O SER D 26 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AB4, first strand: chain 'C' and resid 195 through 200 removed outlier: 6.739A pdb=" N GLY C 196 " --> pdb=" O PHE C 372 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU C 374 " --> pdb=" O GLY C 196 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS C 198 " --> pdb=" O LEU C 374 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 213 through 217 Processing sheet with id=AB6, first strand: chain 'C' and resid 309 through 312 Processing sheet with id=AB7, first strand: chain 'C' and resid 485 through 488 Processing sheet with id=AB8, first strand: chain 'D' and resid 68 through 71 removed outlier: 6.254A pdb=" N ASP D 58 " --> pdb=" O VAL E 517 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASN E 519 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE E 521 " --> pdb=" O MET D 60 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 153 through 154 Processing sheet with id=AC1, first strand: chain 'D' and resid 209 through 213 removed outlier: 6.435A pdb=" N LYS D 210 " --> pdb=" O ILE D 385 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE D 387 " --> pdb=" O LYS D 210 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLU D 212 " --> pdb=" O ILE D 387 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 228 through 230 Processing sheet with id=AC3, first strand: chain 'D' and resid 321 through 322 removed outlier: 6.898A pdb=" N ALA D 300 " --> pdb=" O VAL D 322 " (cutoff:3.500A) removed outlier: 8.883A pdb=" N VAL D 342 " --> pdb=" O ILE D 248 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE D 250 " --> pdb=" O VAL D 342 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 321 through 322 removed outlier: 6.898A pdb=" N ALA D 300 " --> pdb=" O VAL D 322 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 61 through 64 removed outlier: 7.428A pdb=" N ASP E 49 " --> pdb=" O ASP F 533 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL F 535 " --> pdb=" O ASP E 49 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE E 51 " --> pdb=" O VAL F 535 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ASN F 537 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU E 53 " --> pdb=" O ASN F 537 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 146 through 147 Processing sheet with id=AC7, first strand: chain 'E' and resid 199 through 203 Processing sheet with id=AC8, first strand: chain 'E' and resid 218 through 220 removed outlier: 3.567A pdb=" N ILE E 237 " --> pdb=" O GLY E 344 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS E 346 " --> pdb=" O ALA E 235 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU E 348 " --> pdb=" O GLU E 233 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLU E 233 " --> pdb=" O LEU E 348 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 218 through 220 removed outlier: 3.567A pdb=" N ILE E 237 " --> pdb=" O GLY E 344 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS E 346 " --> pdb=" O ALA E 235 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU E 348 " --> pdb=" O GLU E 233 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLU E 233 " --> pdb=" O LEU E 348 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N ALA E 332 " --> pdb=" O ILE E 237 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE E 239 " --> pdb=" O ALA E 332 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 476 through 479 removed outlier: 3.515A pdb=" N THR E 484 " --> pdb=" O ASP E 479 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 68 through 71 removed outlier: 6.640A pdb=" N ASP F 58 " --> pdb=" O ILE G 527 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP G 529 " --> pdb=" O ASP F 58 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AD4, first strand: chain 'F' and resid 208 through 212 removed outlier: 6.436A pdb=" N LYS F 209 " --> pdb=" O ILE F 388 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL F 390 " --> pdb=" O LYS F 209 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL F 211 " --> pdb=" O VAL F 390 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU F 222 " --> pdb=" O VAL F 389 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 226 through 229 removed outlier: 6.511A pdb=" N CYS F 379 " --> pdb=" O ALA F 359 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA F 359 " --> pdb=" O CYS F 379 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N SER F 358 " --> pdb=" O LYS F 245 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LYS F 245 " --> pdb=" O SER F 358 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLU F 360 " --> pdb=" O LYS F 243 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASP F 327 " --> pdb=" O ILE F 300 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 491 through 494 Processing sheet with id=AD7, first strand: chain 'G' and resid 54 through 55 removed outlier: 5.632A pdb=" N ASP G 42 " --> pdb=" O ILE H 519 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP H 521 " --> pdb=" O ASP G 42 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER H 524 " --> pdb=" O LYS H 15 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 137 through 138 Processing sheet with id=AD9, first strand: chain 'G' and resid 181 through 182 Processing sheet with id=AE1, first strand: chain 'G' and resid 196 through 199 removed outlier: 6.325A pdb=" N ASN G 196 " --> pdb=" O ILE G 375 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LEU G 377 " --> pdb=" O ASN G 196 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU G 198 " --> pdb=" O LEU G 377 " (cutoff:3.500A) removed outlier: 9.626A pdb=" N SER G 212 " --> pdb=" O ASN G 366 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP G 359 " --> pdb=" O ILE G 356 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR G 367 " --> pdb=" O ALA G 348 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ALA G 348 " --> pdb=" O THR G 367 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 196 through 199 removed outlier: 6.325A pdb=" N ASN G 196 " --> pdb=" O ILE G 375 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LEU G 377 " --> pdb=" O ASN G 196 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU G 198 " --> pdb=" O LEU G 377 " (cutoff:3.500A) removed outlier: 9.626A pdb=" N SER G 212 " --> pdb=" O ASN G 366 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP G 359 " --> pdb=" O ILE G 356 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR G 367 " --> pdb=" O ALA G 348 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ALA G 348 " --> pdb=" O THR G 367 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL G 285 " --> pdb=" O LYS G 233 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 57 through 60 removed outlier: 7.587A pdb=" N MET H 47 " --> pdb=" O ASP I 519 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE I 521 " --> pdb=" O MET H 47 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N MET H 49 " --> pdb=" O ILE I 521 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ARG I 523 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU H 51 " --> pdb=" O ARG I 523 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 142 through 143 Processing sheet with id=AE5, first strand: chain 'H' and resid 185 through 186 Processing sheet with id=AE6, first strand: chain 'H' and resid 199 through 205 removed outlier: 6.612A pdb=" N ARG H 200 " --> pdb=" O ILE H 374 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LEU H 376 " --> pdb=" O ARG H 200 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLU H 202 " --> pdb=" O LEU H 376 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N GLY H 378 " --> pdb=" O GLU H 202 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ILE H 204 " --> pdb=" O GLY H 378 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR H 373 " --> pdb=" O LEU H 215 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU H 215 " --> pdb=" O THR H 373 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 218 through 220 removed outlier: 3.608A pdb=" N THR H 364 " --> pdb=" O LEU H 349 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU H 349 " --> pdb=" O THR H 364 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 310 through 312 removed outlier: 9.294A pdb=" N VAL H 332 " --> pdb=" O ILE H 238 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU H 240 " --> pdb=" O VAL H 332 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 478 through 480 Processing sheet with id=AF1, first strand: chain 'I' and resid 139 through 140 Processing sheet with id=AF2, first strand: chain 'I' and resid 191 through 196 Processing sheet with id=AF3, first strand: chain 'I' and resid 210 through 212 Processing sheet with id=AF4, first strand: chain 'I' and resid 311 through 313 removed outlier: 5.976A pdb=" N TYR I 229 " --> pdb=" O VAL I 290 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE I 292 " --> pdb=" O TYR I 229 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU I 231 " --> pdb=" O ILE I 292 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 477 through 479 1963 hydrogen bonds defined for protein. 5616 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: 8.29 Time building geometry restraints manager: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 6246 1.29 - 1.42: 7856 1.42 - 1.56: 21801 1.56 - 1.69: 34 1.69 - 1.82: 379 Bond restraints: 36316 Sorted by residual: bond pdb=" F3 AF3 I 603 " pdb="AL AF3 I 603 " ideal model delta sigma weight residual 1.637 1.801 -0.164 2.00e-02 2.50e+03 6.68e+01 bond pdb=" F2 AF3 B 603 " pdb="AL AF3 B 603 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.67e+01 bond pdb=" F3 AF3 B 603 " pdb="AL AF3 B 603 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.67e+01 bond pdb=" F1 AF3 F 603 " pdb="AL AF3 F 603 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.67e+01 bond pdb=" F2 AF3 F 603 " pdb="AL AF3 F 603 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.67e+01 ... (remaining 36311 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 48425 2.62 - 5.23: 525 5.23 - 7.85: 94 7.85 - 10.47: 9 10.47 - 13.08: 4 Bond angle restraints: 49057 Sorted by residual: angle pdb=" N VAL A 236 " pdb=" CA VAL A 236 " pdb=" C VAL A 236 " ideal model delta sigma weight residual 110.62 100.96 9.66 1.02e+00 9.61e-01 8.98e+01 angle pdb=" CA HIS I 198 " pdb=" CB HIS I 198 " pdb=" CG HIS I 198 " ideal model delta sigma weight residual 113.80 122.07 -8.27 1.00e+00 1.00e+00 6.84e+01 angle pdb=" N GLY A 235 " pdb=" CA GLY A 235 " pdb=" C GLY A 235 " ideal model delta sigma weight residual 112.50 122.02 -9.52 1.16e+00 7.43e-01 6.74e+01 angle pdb=" CA ASP B 193 " pdb=" C ASP B 193 " pdb=" O ASP B 193 " ideal model delta sigma weight residual 120.54 111.61 8.93 1.13e+00 7.83e-01 6.24e+01 angle pdb=" N LYS A 174 " pdb=" CA LYS A 174 " pdb=" C LYS A 174 " ideal model delta sigma weight residual 111.28 103.29 7.99 1.09e+00 8.42e-01 5.37e+01 ... (remaining 49052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 21803 35.86 - 71.72: 534 71.72 - 107.58: 48 107.58 - 143.43: 5 143.43 - 179.29: 2 Dihedral angle restraints: 22392 sinusoidal: 9013 harmonic: 13379 Sorted by residual: dihedral pdb=" O2A ADP B 602 " pdb=" O3A ADP B 602 " pdb=" PA ADP B 602 " pdb=" PB ADP B 602 " ideal model delta sinusoidal sigma weight residual 300.00 120.71 179.29 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP F 602 " pdb=" O3A ADP F 602 " pdb=" PA ADP F 602 " pdb=" PB ADP F 602 " ideal model delta sinusoidal sigma weight residual 300.00 145.66 154.35 1 2.00e+01 2.50e-03 4.56e+01 dihedral pdb=" O2A ADP G 602 " pdb=" O3A ADP G 602 " pdb=" PA ADP G 602 " pdb=" PB ADP G 602 " ideal model delta sinusoidal sigma weight residual 300.00 158.41 141.59 1 2.00e+01 2.50e-03 4.28e+01 ... (remaining 22389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 5085 0.064 - 0.127: 670 0.127 - 0.191: 40 0.191 - 0.255: 7 0.255 - 0.318: 4 Chirality restraints: 5806 Sorted by residual: chirality pdb=" CA HIS F 406 " pdb=" N HIS F 406 " pdb=" C HIS F 406 " pdb=" CB HIS F 406 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA SER B 189 " pdb=" N SER B 189 " pdb=" C SER B 189 " pdb=" CB SER B 189 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CB VAL A 23 " pdb=" CA VAL A 23 " pdb=" CG1 VAL A 23 " pdb=" CG2 VAL A 23 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 5803 not shown) Planarity restraints: 6282 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 171 " 0.028 2.00e-02 2.50e+03 5.59e-02 3.12e+01 pdb=" C PRO A 171 " -0.097 2.00e-02 2.50e+03 pdb=" O PRO A 171 " 0.037 2.00e-02 2.50e+03 pdb=" N SER A 172 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 188 " -0.022 2.00e-02 2.50e+03 4.20e-02 1.76e+01 pdb=" C VAL B 188 " 0.073 2.00e-02 2.50e+03 pdb=" O VAL B 188 " -0.026 2.00e-02 2.50e+03 pdb=" N SER B 189 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS I 198 " 0.019 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C HIS I 198 " -0.070 2.00e-02 2.50e+03 pdb=" O HIS I 198 " 0.027 2.00e-02 2.50e+03 pdb=" N LYS I 199 " 0.024 2.00e-02 2.50e+03 ... (remaining 6279 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 117 2.42 - 3.04: 21185 3.04 - 3.66: 50797 3.66 - 4.28: 74091 4.28 - 4.90: 125783 Nonbonded interactions: 271973 Sorted by model distance: nonbonded pdb="MG MG G 601 " pdb="AL AF3 G 603 " model vdw 1.797 1.890 nonbonded pdb="MG MG D 601 " pdb="AL AF3 D 603 " model vdw 1.816 1.890 nonbonded pdb="MG MG D 601 " pdb=" F1 AF3 D 603 " model vdw 1.891 2.120 nonbonded pdb="MG MG G 601 " pdb=" O3B ADP G 602 " model vdw 1.900 2.170 nonbonded pdb=" OD2 ASP B 99 " pdb="MG MG B 601 " model vdw 1.903 2.170 ... (remaining 271968 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 32.870 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.164 36316 Z= 0.275 Angle : 0.701 13.083 49057 Z= 0.408 Chirality : 0.044 0.318 5806 Planarity : 0.004 0.099 6282 Dihedral : 15.999 179.293 13734 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.00 % Favored : 95.92 % Rotamer: Outliers : 0.49 % Allowed : 12.66 % Favored : 86.85 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.12), residues: 4628 helix: -0.30 (0.11), residues: 2244 sheet: 0.02 (0.21), residues: 653 loop : -1.19 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 516 TYR 0.016 0.001 TYR A 425 PHE 0.012 0.001 PHE I 123 TRP 0.010 0.001 TRP A 344 HIS 0.018 0.001 HIS I 198 Details of bonding type rmsd covalent geometry : bond 0.00532 (36316) covalent geometry : angle 0.70115 (49057) hydrogen bonds : bond 0.29716 ( 1931) hydrogen bonds : angle 7.70810 ( 5616) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 227 time to evaluate : 1.390 Fit side-chains REVERT: D 239 MET cc_start: 0.8928 (mtt) cc_final: 0.8435 (mtt) REVERT: F 407 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7768 (p0) outliers start: 19 outliers final: 6 residues processed: 243 average time/residue: 0.2009 time to fit residues: 84.3112 Evaluate side-chains 222 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 215 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain I residue 159 LYS Chi-restraints excluded: chain I residue 199 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 432 optimal weight: 0.9980 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 9.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN D 72 ASN D 298 ASN ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 347 GLN ** H 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 198 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.087269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.074041 restraints weight = 81265.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.076296 restraints weight = 41495.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.077810 restraints weight = 25572.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.078827 restraints weight = 17896.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.079493 restraints weight = 13823.696| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 36316 Z= 0.172 Angle : 0.637 9.042 49057 Z= 0.327 Chirality : 0.045 0.176 5806 Planarity : 0.004 0.076 6282 Dihedral : 7.669 164.796 5052 Min Nonbonded Distance : 1.609 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.67 % Favored : 96.31 % Rotamer: Outliers : 1.57 % Allowed : 13.46 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.12), residues: 4628 helix: 0.97 (0.11), residues: 2289 sheet: 0.23 (0.22), residues: 594 loop : -1.28 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 516 TYR 0.016 0.001 TYR A 208 PHE 0.014 0.001 PHE A 167 TRP 0.008 0.001 TRP D 324 HIS 0.008 0.001 HIS I 198 Details of bonding type rmsd covalent geometry : bond 0.00385 (36316) covalent geometry : angle 0.63660 (49057) hydrogen bonds : bond 0.06919 ( 1931) hydrogen bonds : angle 4.82717 ( 5616) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 245 time to evaluate : 1.416 Fit side-chains REVERT: A 226 ASN cc_start: 0.8082 (m110) cc_final: 0.7845 (m110) REVERT: A 363 MET cc_start: 0.5181 (mmm) cc_final: 0.4831 (mmm) REVERT: B 385 MET cc_start: 0.8233 (mtt) cc_final: 0.7726 (mtt) REVERT: B 446 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7685 (mp0) REVERT: C 414 MET cc_start: 0.8307 (mmt) cc_final: 0.7998 (mmt) REVERT: F 407 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.7722 (m-30) REVERT: H 54 MET cc_start: 0.7990 (mtt) cc_final: 0.7785 (mtt) REVERT: I 199 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8788 (mmmm) REVERT: I 426 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8234 (ttpt) outliers start: 61 outliers final: 25 residues processed: 291 average time/residue: 0.1912 time to fit residues: 97.4416 Evaluate side-chains 252 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 223 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain F residue 503 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain I residue 199 LYS Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 366 CYS Chi-restraints excluded: chain I residue 402 ILE Chi-restraints excluded: chain I residue 426 LYS Chi-restraints excluded: chain I residue 522 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 99 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 428 optimal weight: 0.0980 chunk 427 optimal weight: 9.9990 chunk 257 optimal weight: 8.9990 chunk 337 optimal weight: 8.9990 chunk 303 optimal weight: 8.9990 chunk 202 optimal weight: 9.9990 chunk 437 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 ASN B 383 ASN C 511 ASN ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 497 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.088002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.074954 restraints weight = 81126.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.077133 restraints weight = 42003.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.078594 restraints weight = 26161.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.079498 restraints weight = 18493.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.080214 restraints weight = 14527.096| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36316 Z= 0.147 Angle : 0.580 7.985 49057 Z= 0.290 Chirality : 0.043 0.197 5806 Planarity : 0.003 0.065 6282 Dihedral : 7.005 147.243 5041 Min Nonbonded Distance : 1.628 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.95 % Favored : 96.02 % Rotamer: Outliers : 2.19 % Allowed : 14.13 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.12), residues: 4628 helix: 1.42 (0.11), residues: 2304 sheet: 0.20 (0.22), residues: 596 loop : -1.28 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 516 TYR 0.016 0.001 TYR F 269 PHE 0.017 0.001 PHE E 252 TRP 0.007 0.001 TRP D 304 HIS 0.004 0.001 HIS D 182 Details of bonding type rmsd covalent geometry : bond 0.00336 (36316) covalent geometry : angle 0.57965 (49057) hydrogen bonds : bond 0.05397 ( 1931) hydrogen bonds : angle 4.29708 ( 5616) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 243 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: A 73 MET cc_start: 0.6969 (tmm) cc_final: 0.6687 (tmm) REVERT: A 226 ASN cc_start: 0.8176 (m110) cc_final: 0.7929 (m-40) REVERT: A 363 MET cc_start: 0.5166 (mmm) cc_final: 0.4802 (mmm) REVERT: B 385 MET cc_start: 0.8134 (mtt) cc_final: 0.7657 (mtt) REVERT: B 446 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: C 414 MET cc_start: 0.8261 (mmt) cc_final: 0.7978 (mmt) REVERT: D 523 MET cc_start: 0.8354 (tpt) cc_final: 0.8152 (tpt) REVERT: F 320 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8247 (mtt) REVERT: F 407 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.7719 (m-30) REVERT: I 64 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9073 (mm) REVERT: I 112 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.6766 (mp0) REVERT: I 426 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8289 (ttpt) outliers start: 85 outliers final: 36 residues processed: 306 average time/residue: 0.1902 time to fit residues: 101.3392 Evaluate side-chains 268 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 226 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 507 MET Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 MET Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain F residue 503 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 112 GLU Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 426 LYS Chi-restraints excluded: chain I residue 522 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 157 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 159 optimal weight: 0.7980 chunk 340 optimal weight: 9.9990 chunk 315 optimal weight: 10.0000 chunk 318 optimal weight: 10.0000 chunk 198 optimal weight: 2.9990 chunk 335 optimal weight: 6.9990 chunk 170 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 ASN E 399 GLN ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 320 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.085725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.072523 restraints weight = 82246.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.074729 restraints weight = 42217.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.076212 restraints weight = 26145.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.077204 restraints weight = 18442.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.077831 restraints weight = 14298.977| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 36316 Z= 0.211 Angle : 0.636 9.712 49057 Z= 0.317 Chirality : 0.045 0.218 5806 Planarity : 0.004 0.063 6282 Dihedral : 6.947 130.683 5037 Min Nonbonded Distance : 1.589 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.49 % Favored : 95.48 % Rotamer: Outliers : 2.37 % Allowed : 15.39 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.12), residues: 4628 helix: 1.40 (0.11), residues: 2303 sheet: 0.13 (0.21), residues: 604 loop : -1.38 (0.14), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 314 TYR 0.020 0.001 TYR C 438 PHE 0.015 0.001 PHE G 167 TRP 0.010 0.001 TRP D 304 HIS 0.006 0.001 HIS D 182 Details of bonding type rmsd covalent geometry : bond 0.00504 (36316) covalent geometry : angle 0.63557 (49057) hydrogen bonds : bond 0.05850 ( 1931) hydrogen bonds : angle 4.37597 ( 5616) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 236 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 ASN cc_start: 0.8248 (m110) cc_final: 0.7946 (m-40) REVERT: B 208 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8585 (tt) REVERT: B 249 MET cc_start: 0.7522 (OUTLIER) cc_final: 0.7071 (mpp) REVERT: B 446 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7675 (mp0) REVERT: C 414 MET cc_start: 0.8396 (mmt) cc_final: 0.8027 (mmt) REVERT: D 523 MET cc_start: 0.8540 (tpt) cc_final: 0.8191 (tpt) REVERT: G 44 MET cc_start: 0.8306 (mpp) cc_final: 0.8073 (mpp) REVERT: G 263 ILE cc_start: 0.9335 (mm) cc_final: 0.9099 (mm) REVERT: I 64 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9098 (mm) REVERT: I 112 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.6893 (mp0) REVERT: I 426 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8388 (ttpt) outliers start: 92 outliers final: 55 residues processed: 312 average time/residue: 0.1978 time to fit residues: 107.4541 Evaluate side-chains 291 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 230 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 MET Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain F residue 503 ILE Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 313 LYS Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 454 VAL Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain H residue 463 LEU Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 112 GLU Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 281 VAL Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 366 CYS Chi-restraints excluded: chain I residue 402 ILE Chi-restraints excluded: chain I residue 414 VAL Chi-restraints excluded: chain I residue 426 LYS Chi-restraints excluded: chain I residue 522 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 370 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 240 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 242 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 371 optimal weight: 0.7980 chunk 224 optimal weight: 9.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.087663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.074429 restraints weight = 81332.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.076668 restraints weight = 41547.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.078167 restraints weight = 25672.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.079102 restraints weight = 18051.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.079848 restraints weight = 14109.249| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 36316 Z= 0.134 Angle : 0.568 9.375 49057 Z= 0.281 Chirality : 0.043 0.237 5806 Planarity : 0.003 0.058 6282 Dihedral : 6.678 127.394 5037 Min Nonbonded Distance : 1.636 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.59 % Favored : 96.39 % Rotamer: Outliers : 2.14 % Allowed : 16.65 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.13), residues: 4628 helix: 1.65 (0.11), residues: 2306 sheet: 0.13 (0.21), residues: 592 loop : -1.28 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 306 TYR 0.017 0.001 TYR C 438 PHE 0.016 0.001 PHE E 252 TRP 0.005 0.001 TRP D 304 HIS 0.004 0.001 HIS D 182 Details of bonding type rmsd covalent geometry : bond 0.00308 (36316) covalent geometry : angle 0.56782 (49057) hydrogen bonds : bond 0.04759 ( 1931) hydrogen bonds : angle 4.07747 ( 5616) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 245 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.7044 (OUTLIER) cc_final: 0.6842 (tpt) REVERT: A 226 ASN cc_start: 0.8151 (m110) cc_final: 0.7796 (m-40) REVERT: A 355 ASP cc_start: 0.5563 (p0) cc_final: 0.5317 (p0) REVERT: B 208 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8510 (tt) REVERT: B 385 MET cc_start: 0.8112 (mtt) cc_final: 0.7784 (mtt) REVERT: B 446 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7732 (mp0) REVERT: C 45 MET cc_start: 0.8396 (mmt) cc_final: 0.7970 (mmt) REVERT: D 523 MET cc_start: 0.8464 (tpt) cc_final: 0.8065 (tpt) REVERT: E 252 PHE cc_start: 0.6635 (m-80) cc_final: 0.6425 (m-80) REVERT: G 44 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.8116 (mpp) REVERT: G 263 ILE cc_start: 0.9307 (mm) cc_final: 0.9080 (mm) REVERT: H 291 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8475 (mt) REVERT: I 64 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9050 (mm) REVERT: I 112 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.6842 (mp0) REVERT: I 426 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8453 (ttpt) outliers start: 83 outliers final: 53 residues processed: 309 average time/residue: 0.1951 time to fit residues: 105.0280 Evaluate side-chains 295 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 234 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 468 MET Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 186 MET Chi-restraints excluded: chain F residue 272 MET Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 503 ILE Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain G residue 8 PHE Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 112 GLU Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 402 ILE Chi-restraints excluded: chain I residue 426 LYS Chi-restraints excluded: chain I residue 522 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 286 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 417 optimal weight: 4.9990 chunk 183 optimal weight: 10.0000 chunk 213 optimal weight: 5.9990 chunk 344 optimal weight: 7.9990 chunk 314 optimal weight: 7.9990 chunk 442 optimal weight: 5.9990 chunk 155 optimal weight: 0.3980 chunk 214 optimal weight: 5.9990 chunk 161 optimal weight: 7.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 ASN D 391 ASN F 262 ASN I 386 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.085814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.072607 restraints weight = 82372.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.074843 restraints weight = 41362.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.076350 restraints weight = 25226.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.077360 restraints weight = 17573.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.077987 restraints weight = 13506.516| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 36316 Z= 0.198 Angle : 0.620 9.741 49057 Z= 0.307 Chirality : 0.045 0.254 5806 Planarity : 0.004 0.058 6282 Dihedral : 6.740 125.976 5037 Min Nonbonded Distance : 1.596 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.50 % Allowed : 17.09 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.13), residues: 4628 helix: 1.60 (0.11), residues: 2304 sheet: 0.10 (0.22), residues: 583 loop : -1.36 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 306 TYR 0.013 0.001 TYR I 250 PHE 0.015 0.001 PHE G 167 TRP 0.008 0.001 TRP D 324 HIS 0.007 0.001 HIS A 190 Details of bonding type rmsd covalent geometry : bond 0.00473 (36316) covalent geometry : angle 0.61953 (49057) hydrogen bonds : bond 0.05488 ( 1931) hydrogen bonds : angle 4.20795 ( 5616) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 238 time to evaluate : 1.465 Fit side-chains revert: symmetry clash REVERT: A 73 MET cc_start: 0.7010 (tmm) cc_final: 0.6702 (tmm) REVERT: A 226 ASN cc_start: 0.8207 (m110) cc_final: 0.7829 (m-40) REVERT: A 299 MET cc_start: 0.7502 (ptm) cc_final: 0.7293 (ptm) REVERT: A 355 ASP cc_start: 0.5623 (p0) cc_final: 0.5391 (p0) REVERT: A 363 MET cc_start: 0.4809 (mmm) cc_final: 0.4534 (mmm) REVERT: A 422 TYR cc_start: 0.8252 (OUTLIER) cc_final: 0.7404 (t80) REVERT: B 208 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8648 (tt) REVERT: B 249 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.6959 (mpp) REVERT: B 446 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7743 (mp0) REVERT: D 523 MET cc_start: 0.8495 (tpt) cc_final: 0.8110 (tpt) REVERT: E 252 PHE cc_start: 0.6601 (m-80) cc_final: 0.6401 (m-80) REVERT: G 44 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8124 (mpp) REVERT: G 263 ILE cc_start: 0.9322 (mm) cc_final: 0.9077 (mm) REVERT: G 265 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8606 (tt0) REVERT: H 291 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8526 (mt) REVERT: I 64 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9091 (mm) REVERT: I 112 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.6680 (mp0) REVERT: I 159 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8025 (mtpt) REVERT: I 426 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8462 (ttpt) outliers start: 97 outliers final: 70 residues processed: 318 average time/residue: 0.1990 time to fit residues: 110.7728 Evaluate side-chains 316 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 235 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 468 MET Chi-restraints excluded: chain D residue 526 MET Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 186 MET Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain F residue 503 ILE Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 265 GLN Chi-restraints excluded: chain G residue 313 LYS Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 454 VAL Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 258 ILE Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 463 LEU Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 112 GLU Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 159 LYS Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 366 CYS Chi-restraints excluded: chain I residue 414 VAL Chi-restraints excluded: chain I residue 426 LYS Chi-restraints excluded: chain I residue 522 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 135 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 184 optimal weight: 7.9990 chunk 375 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 285 optimal weight: 20.0000 chunk 97 optimal weight: 0.9980 chunk 413 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 430 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN C 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.087462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.074195 restraints weight = 82069.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.076488 restraints weight = 41004.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.078004 restraints weight = 24912.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.079038 restraints weight = 17315.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.079737 restraints weight = 13278.314| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 36316 Z= 0.134 Angle : 0.567 10.378 49057 Z= 0.279 Chirality : 0.043 0.277 5806 Planarity : 0.003 0.056 6282 Dihedral : 6.603 126.671 5037 Min Nonbonded Distance : 1.632 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.29 % Allowed : 17.81 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.13), residues: 4628 helix: 1.79 (0.11), residues: 2305 sheet: 0.09 (0.21), residues: 592 loop : -1.28 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 306 TYR 0.012 0.001 TYR F 269 PHE 0.011 0.001 PHE G 167 TRP 0.005 0.001 TRP D 324 HIS 0.007 0.001 HIS A 190 Details of bonding type rmsd covalent geometry : bond 0.00311 (36316) covalent geometry : angle 0.56748 (49057) hydrogen bonds : bond 0.04648 ( 1931) hydrogen bonds : angle 4.00246 ( 5616) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 255 time to evaluate : 1.498 Fit side-chains revert: symmetry clash REVERT: A 73 MET cc_start: 0.7108 (tmm) cc_final: 0.6743 (tmm) REVERT: A 226 ASN cc_start: 0.8233 (m110) cc_final: 0.7779 (m110) REVERT: A 355 ASP cc_start: 0.5641 (p0) cc_final: 0.5407 (p0) REVERT: A 422 TYR cc_start: 0.8196 (OUTLIER) cc_final: 0.7381 (t80) REVERT: B 85 MET cc_start: 0.8751 (mmm) cc_final: 0.8350 (mmm) REVERT: B 208 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8508 (tt) REVERT: B 385 MET cc_start: 0.8300 (mtt) cc_final: 0.8026 (mtt) REVERT: B 446 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7720 (mp0) REVERT: C 45 MET cc_start: 0.8474 (mmt) cc_final: 0.8060 (mmt) REVERT: D 523 MET cc_start: 0.8448 (tpt) cc_final: 0.8065 (tpt) REVERT: E 252 PHE cc_start: 0.6556 (m-80) cc_final: 0.6351 (m-80) REVERT: G 44 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8085 (mpp) REVERT: G 263 ILE cc_start: 0.9295 (mm) cc_final: 0.9051 (mm) REVERT: G 265 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8579 (tt0) REVERT: I 44 MET cc_start: 0.8156 (tpp) cc_final: 0.7898 (ttm) REVERT: I 64 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9076 (mm) REVERT: I 112 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.6661 (mp0) REVERT: I 159 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.7995 (mtpt) REVERT: I 426 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8476 (ttpt) outliers start: 89 outliers final: 65 residues processed: 330 average time/residue: 0.2020 time to fit residues: 116.3393 Evaluate side-chains 314 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 240 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 468 MET Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 186 MET Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 503 ILE Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 265 GLN Chi-restraints excluded: chain G residue 313 LYS Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 258 ILE Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 463 LEU Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 112 GLU Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 159 LYS Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 402 ILE Chi-restraints excluded: chain I residue 414 VAL Chi-restraints excluded: chain I residue 426 LYS Chi-restraints excluded: chain I residue 522 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 352 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 309 optimal weight: 0.0470 chunk 354 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 20.0000 chunk 258 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 263 optimal weight: 0.6980 overall best weight: 1.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN G 164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.088803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.075410 restraints weight = 81106.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.077725 restraints weight = 40629.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.079272 restraints weight = 24692.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.080318 restraints weight = 17145.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.080996 restraints weight = 13144.326| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 36316 Z= 0.109 Angle : 0.549 12.027 49057 Z= 0.266 Chirality : 0.042 0.281 5806 Planarity : 0.003 0.053 6282 Dihedral : 6.411 126.085 5037 Min Nonbonded Distance : 1.667 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.06 % Allowed : 18.09 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.13), residues: 4628 helix: 1.99 (0.11), residues: 2309 sheet: 0.17 (0.22), residues: 582 loop : -1.21 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 481 TYR 0.011 0.001 TYR F 269 PHE 0.011 0.001 PHE E 252 TRP 0.004 0.000 TRP A 344 HIS 0.009 0.001 HIS A 190 Details of bonding type rmsd covalent geometry : bond 0.00243 (36316) covalent geometry : angle 0.54881 (49057) hydrogen bonds : bond 0.04013 ( 1931) hydrogen bonds : angle 3.82637 ( 5616) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 255 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.7023 (tmm) cc_final: 0.6683 (tmm) REVERT: A 147 MET cc_start: 0.7030 (tpt) cc_final: 0.6800 (tpt) REVERT: A 226 ASN cc_start: 0.8201 (m110) cc_final: 0.7769 (m110) REVERT: A 380 ARG cc_start: 0.8427 (ttp-110) cc_final: 0.8037 (ptm-80) REVERT: A 422 TYR cc_start: 0.8179 (OUTLIER) cc_final: 0.7407 (t80) REVERT: B 52 MET cc_start: 0.8414 (mmm) cc_final: 0.8180 (mmm) REVERT: B 85 MET cc_start: 0.8734 (mmm) cc_final: 0.8397 (mmm) REVERT: B 208 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8467 (tt) REVERT: B 249 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.7097 (mpp) REVERT: B 300 MET cc_start: 0.8385 (tpp) cc_final: 0.7704 (tpp) REVERT: B 385 MET cc_start: 0.8189 (mtt) cc_final: 0.7924 (mtt) REVERT: B 446 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: C 45 MET cc_start: 0.8464 (mmt) cc_final: 0.8023 (mmt) REVERT: D 523 MET cc_start: 0.8442 (tpt) cc_final: 0.8237 (tpt) REVERT: E 252 PHE cc_start: 0.6497 (m-80) cc_final: 0.6272 (m-80) REVERT: F 407 ASP cc_start: 0.8539 (OUTLIER) cc_final: 0.7655 (m-30) REVERT: G 44 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8083 (mpp) REVERT: G 263 ILE cc_start: 0.9270 (mm) cc_final: 0.9036 (mm) REVERT: I 44 MET cc_start: 0.8135 (tpp) cc_final: 0.7888 (ttm) REVERT: I 64 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9102 (mm) REVERT: I 426 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8487 (ttpt) outliers start: 80 outliers final: 58 residues processed: 321 average time/residue: 0.2031 time to fit residues: 113.3671 Evaluate side-chains 305 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 239 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 468 MET Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 186 MET Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain G residue 8 PHE Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 313 LYS Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 463 LEU Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 402 ILE Chi-restraints excluded: chain I residue 426 LYS Chi-restraints excluded: chain I residue 522 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 170 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 341 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 210 optimal weight: 0.8980 chunk 171 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 305 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 278 optimal weight: 9.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.087905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.074611 restraints weight = 81734.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.076901 restraints weight = 40979.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.078424 restraints weight = 24948.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.079451 restraints weight = 17384.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.080151 restraints weight = 13348.885| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 36316 Z= 0.139 Angle : 0.570 13.361 49057 Z= 0.278 Chirality : 0.043 0.273 5806 Planarity : 0.003 0.051 6282 Dihedral : 6.418 126.172 5037 Min Nonbonded Distance : 1.627 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.26 % Allowed : 17.91 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.13), residues: 4628 helix: 1.97 (0.11), residues: 2308 sheet: 0.09 (0.21), residues: 594 loop : -1.21 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 306 TYR 0.012 0.001 TYR C 438 PHE 0.012 0.001 PHE G 167 TRP 0.005 0.001 TRP D 324 HIS 0.004 0.001 HIS H 526 Details of bonding type rmsd covalent geometry : bond 0.00326 (36316) covalent geometry : angle 0.57003 (49057) hydrogen bonds : bond 0.04432 ( 1931) hydrogen bonds : angle 3.88628 ( 5616) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 243 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.7014 (tmm) cc_final: 0.6684 (tmm) REVERT: A 147 MET cc_start: 0.7105 (tpt) cc_final: 0.6840 (tpt) REVERT: A 226 ASN cc_start: 0.8215 (m110) cc_final: 0.7780 (m110) REVERT: A 422 TYR cc_start: 0.8199 (OUTLIER) cc_final: 0.7397 (t80) REVERT: B 85 MET cc_start: 0.8759 (mmm) cc_final: 0.8408 (mmm) REVERT: B 208 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8507 (tt) REVERT: B 249 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.7144 (mpp) REVERT: B 300 MET cc_start: 0.8405 (tpp) cc_final: 0.7726 (tpp) REVERT: B 446 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7723 (mp0) REVERT: C 45 MET cc_start: 0.8487 (mmt) cc_final: 0.8039 (mmt) REVERT: D 199 MET cc_start: 0.7443 (mmp) cc_final: 0.7228 (mmp) REVERT: D 239 MET cc_start: 0.8938 (mtt) cc_final: 0.8370 (mtt) REVERT: D 523 MET cc_start: 0.8461 (tpt) cc_final: 0.8056 (tpt) REVERT: F 407 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.7761 (m-30) REVERT: G 44 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8119 (mpp) REVERT: G 263 ILE cc_start: 0.9276 (mm) cc_final: 0.9038 (mm) REVERT: I 44 MET cc_start: 0.8150 (tpp) cc_final: 0.7892 (ttm) REVERT: I 64 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9065 (mm) REVERT: I 112 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.6730 (mp0) REVERT: I 159 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.7930 (mtpt) REVERT: I 426 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8490 (ttpt) outliers start: 88 outliers final: 66 residues processed: 318 average time/residue: 0.2031 time to fit residues: 112.0395 Evaluate side-chains 318 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 242 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 468 MET Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 186 MET Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 503 ILE Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 313 LYS Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 463 LEU Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 112 GLU Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 159 LYS Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 414 VAL Chi-restraints excluded: chain I residue 426 LYS Chi-restraints excluded: chain I residue 496 ASP Chi-restraints excluded: chain I residue 522 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 159 optimal weight: 0.7980 chunk 446 optimal weight: 7.9990 chunk 236 optimal weight: 10.0000 chunk 95 optimal weight: 0.7980 chunk 148 optimal weight: 20.0000 chunk 32 optimal weight: 8.9990 chunk 405 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 354 optimal weight: 0.9990 chunk 321 optimal weight: 9.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 ASN C 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.086813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.073455 restraints weight = 82761.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.075715 restraints weight = 41757.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.077235 restraints weight = 25558.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.078260 restraints weight = 17874.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.078904 restraints weight = 13767.202| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 36316 Z= 0.162 Angle : 0.594 14.273 49057 Z= 0.291 Chirality : 0.044 0.239 5806 Planarity : 0.003 0.054 6282 Dihedral : 6.486 126.094 5037 Min Nonbonded Distance : 1.617 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.06 % Allowed : 18.22 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.13), residues: 4628 helix: 1.92 (0.11), residues: 2305 sheet: 0.05 (0.21), residues: 595 loop : -1.25 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 380 TYR 0.013 0.001 TYR I 250 PHE 0.013 0.001 PHE G 167 TRP 0.006 0.001 TRP C 484 HIS 0.005 0.001 HIS H 526 Details of bonding type rmsd covalent geometry : bond 0.00385 (36316) covalent geometry : angle 0.59431 (49057) hydrogen bonds : bond 0.04773 ( 1931) hydrogen bonds : angle 3.96416 ( 5616) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 236 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.6847 (tmm) cc_final: 0.6625 (tmm) REVERT: A 147 MET cc_start: 0.7073 (tpt) cc_final: 0.6814 (tpt) REVERT: A 226 ASN cc_start: 0.8243 (m110) cc_final: 0.7783 (m110) REVERT: B 208 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8500 (tt) REVERT: B 249 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7172 (mpp) REVERT: B 385 MET cc_start: 0.8332 (mtt) cc_final: 0.7977 (mtt) REVERT: B 446 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7729 (mp0) REVERT: D 239 MET cc_start: 0.8951 (mtt) cc_final: 0.8379 (mtt) REVERT: D 523 MET cc_start: 0.8428 (tpt) cc_final: 0.8019 (tpt) REVERT: F 407 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.7793 (m-30) REVERT: G 44 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8134 (mpp) REVERT: G 263 ILE cc_start: 0.9281 (mm) cc_final: 0.9025 (mm) REVERT: G 500 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8466 (mt0) REVERT: I 44 MET cc_start: 0.8158 (tpp) cc_final: 0.7897 (ttm) REVERT: I 64 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9084 (mm) REVERT: I 112 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.6638 (mp0) REVERT: I 159 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.7949 (mtpt) REVERT: I 426 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8502 (ttpt) outliers start: 80 outliers final: 67 residues processed: 304 average time/residue: 0.1914 time to fit residues: 101.8476 Evaluate side-chains 312 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 236 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 468 MET Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 186 MET Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 503 ILE Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 313 LYS Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 463 LEU Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 112 GLU Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 159 LYS Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 414 VAL Chi-restraints excluded: chain I residue 426 LYS Chi-restraints excluded: chain I residue 496 ASP Chi-restraints excluded: chain I residue 522 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 122 optimal weight: 10.0000 chunk 380 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 chunk 136 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 303 optimal weight: 8.9990 chunk 423 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 193 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 ASN C 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.085383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.072194 restraints weight = 82257.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.074427 restraints weight = 41501.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.075918 restraints weight = 25405.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.076924 restraints weight = 17773.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.077610 restraints weight = 13687.350| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 36316 Z= 0.207 Angle : 0.639 13.837 49057 Z= 0.316 Chirality : 0.045 0.201 5806 Planarity : 0.004 0.057 6282 Dihedral : 6.684 126.141 5037 Min Nonbonded Distance : 1.597 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.14 % Allowed : 18.43 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.13), residues: 4628 helix: 1.76 (0.11), residues: 2296 sheet: 0.00 (0.22), residues: 587 loop : -1.31 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 380 TYR 0.014 0.001 TYR I 250 PHE 0.015 0.001 PHE G 167 TRP 0.008 0.001 TRP C 484 HIS 0.006 0.001 HIS D 182 Details of bonding type rmsd covalent geometry : bond 0.00495 (36316) covalent geometry : angle 0.63919 (49057) hydrogen bonds : bond 0.05541 ( 1931) hydrogen bonds : angle 4.16527 ( 5616) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4864.75 seconds wall clock time: 85 minutes 35.82 seconds (5135.82 seconds total)