Starting phenix.real_space_refine on Tue May 5 18:33:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yil_39322/05_2026/8yil_39322.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yil_39322/05_2026/8yil_39322.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yil_39322/05_2026/8yil_39322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yil_39322/05_2026/8yil_39322.map" model { file = "/net/cci-nas-00/data/ceres_data/8yil_39322/05_2026/8yil_39322.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yil_39322/05_2026/8yil_39322.cif" } resolution = 2.58 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= 0.001 sd= 0.183 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: 7 Type Number sf(0) Gaussians Fe 6 7.16 5 P 11 5.49 5 S 110 5.16 5 Cl 2 4.86 5 C 20950 2.51 5 N 5327 2.21 5 O 5920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 167 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32326 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3344 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 12, 'TRANS': 418} Chain: "C" Number of atoms: 3090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3090 Classifications: {'peptide': 385} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 365} Chain: "B" Number of atoms: 2735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2735 Classifications: {'peptide': 352} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 339} Chain: "D" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1961 Classifications: {'peptide': 248} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 225} Chain: "E" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1411 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 173} Chain: "N" Number of atoms: 3090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3090 Classifications: {'peptide': 385} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 365} Chain: "F" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 624 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "G" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1019 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain: "H" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 773 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain: "I" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 442 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "L" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3344 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 12, 'TRANS': 418} Chain: "O" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1961 Classifications: {'peptide': 248} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 225} Chain: "M" Number of atoms: 2735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2735 Classifications: {'peptide': 352} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 339} Chain: "S" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 773 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain: "P" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1411 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 173} Chain: "Q" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 633 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "R" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1019 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain: "T" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 443 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "U" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 347 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain: "V" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 406 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "C" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 340 Unusual residues: {'86T': 1, '8PE': 1, '9PE': 1, 'CN3': 1, 'CN5': 1, 'HEM': 2, 'UQ6': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 252 Unusual residues: {'86T': 1, '9PE': 1, 'CN3': 1, 'HEM': 2, 'UQ6': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "O" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'6PH': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'8PE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.00, per 1000 atoms: 0.22 Number of scatterers: 32326 At special positions: 0 Unit cell: (141.12, 127.68, 166.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 6 26.01 Cl 2 17.00 S 110 16.00 P 11 15.00 O 5920 8.00 N 5327 7.00 C 20950 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.4 seconds 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7464 Finding SS restraints... Secondary structure from input PDB file: 178 helices and 20 sheets defined 52.5% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 70 through 78 removed outlier: 3.607A pdb=" N ASN A 75 " --> pdb=" O ASN A 71 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE A 77 " --> pdb=" O TRP A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 88 removed outlier: 3.981A pdb=" N VAL A 85 " --> pdb=" O GLU A 81 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA A 86 " --> pdb=" O ASN A 82 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 122 removed outlier: 3.716A pdb=" N SER A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP A 118 " --> pdb=" O ASP A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 155 removed outlier: 3.528A pdb=" N GLU A 138 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS A 146 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 153 " --> pdb=" O GLN A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 169 removed outlier: 3.904A pdb=" N LEU A 161 " --> pdb=" O PRO A 157 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N HIS A 163 " --> pdb=" O ARG A 159 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A 169 " --> pdb=" O HIS A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 176 removed outlier: 3.529A pdb=" N SER A 175 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 176 " --> pdb=" O PRO A 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 176' Processing helix chain 'A' and resid 190 through 201 removed outlier: 3.962A pdb=" N GLU A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 224 removed outlier: 3.696A pdb=" N LEU A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 286 removed outlier: 3.552A pdb=" N LYS A 279 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N PHE A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 removed outlier: 3.564A pdb=" N LEU A 297 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN A 298 " --> pdb=" O SER A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 310 removed outlier: 3.514A pdb=" N GLN A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TYR A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 352 removed outlier: 3.656A pdb=" N LEU A 343 " --> pdb=" O MET A 339 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.593A pdb=" N ILE A 356 " --> pdb=" O ASN A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 379 removed outlier: 3.527A pdb=" N VAL A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 368 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 377 " --> pdb=" O GLN A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 396 removed outlier: 3.653A pdb=" N ASN A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 411 Processing helix chain 'A' and resid 414 through 426 removed outlier: 3.597A pdb=" N VAL A 418 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 450 removed outlier: 3.619A pdb=" N ILE A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 9 through 18 removed outlier: 3.781A pdb=" N VAL C 13 " --> pdb=" O TYR C 9 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C 18 " --> pdb=" O ASN C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 30 Processing helix chain 'C' and resid 31 through 51 removed outlier: 3.519A pdb=" N LEU C 35 " --> pdb=" O ASN C 31 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY C 37 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 71 removed outlier: 3.561A pdb=" N VAL C 65 " --> pdb=" O ALA C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 103 removed outlier: 3.681A pdb=" N LEU C 78 " --> pdb=" O ASN C 74 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY C 100 " --> pdb=" O HIS C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 133 removed outlier: 3.594A pdb=" N GLY C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 149 removed outlier: 3.787A pdb=" N TRP C 142 " --> pdb=" O GLN C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 154 removed outlier: 3.602A pdb=" N ALA C 153 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE C 154 " --> pdb=" O PHE C 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 150 through 154' Processing helix chain 'C' and resid 161 through 167 Processing helix chain 'C' and resid 172 through 203 removed outlier: 3.658A pdb=" N ALA C 181 " --> pdb=" O GLN C 177 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) Proline residue: C 187 - end of helix removed outlier: 3.510A pdb=" N ALA C 192 " --> pdb=" O PHE C 188 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 200 " --> pdb=" O MET C 196 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE C 203 " --> pdb=" O MET C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 247 removed outlier: 3.956A pdb=" N VAL C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR C 232 " --> pdb=" O LYS C 228 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE C 243 " --> pdb=" O ILE C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 258 removed outlier: 3.574A pdb=" N ILE C 258 " --> pdb=" O ASP C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 283 removed outlier: 3.709A pdb=" N ILE C 281 " --> pdb=" O PRO C 277 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 282 " --> pdb=" O PHE C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 301 removed outlier: 3.596A pdb=" N VAL C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ILE C 299 " --> pdb=" O MET C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 309 removed outlier: 3.661A pdb=" N ASP C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 340 removed outlier: 4.038A pdb=" N PHE C 327 " --> pdb=" O LYS C 323 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE C 329 " --> pdb=" O PHE C 325 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY C 337 " --> pdb=" O PHE C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 365 removed outlier: 3.785A pdb=" N MET C 351 " --> pdb=" O PRO C 347 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN C 353 " --> pdb=" O VAL C 349 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR C 356 " --> pdb=" O GLY C 352 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR C 359 " --> pdb=" O ALA C 355 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE C 360 " --> pdb=" O THR C 356 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N PHE C 363 " --> pdb=" O TYR C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 381 removed outlier: 3.836A pdb=" N THR C 372 " --> pdb=" O PRO C 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 42 removed outlier: 3.557A pdb=" N ALA B 42 " --> pdb=" O SER B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 53 removed outlier: 3.557A pdb=" N LEU B 50 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 73 removed outlier: 3.521A pdb=" N VAL B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 112 removed outlier: 3.974A pdb=" N TYR B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN B 103 " --> pdb=" O PRO B 99 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 122 removed outlier: 3.589A pdb=" N LEU B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR B 120 " --> pdb=" O PRO B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 135 removed outlier: 3.524A pdb=" N ALA B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 151 removed outlier: 3.564A pdb=" N GLN B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 180 removed outlier: 3.501A pdb=" N ILE B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS B 178 " --> pdb=" O ASP B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 193 through 203 removed outlier: 3.607A pdb=" N ARG B 199 " --> pdb=" O ALA B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 293 through 309 removed outlier: 3.533A pdb=" N SER B 298 " --> pdb=" O SER B 294 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS B 303 " --> pdb=" O SER B 299 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 305 " --> pdb=" O ILE B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 318 through 329 removed outlier: 3.539A pdb=" N LEU B 323 " --> pdb=" O ASN B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 343 removed outlier: 3.772A pdb=" N ALA B 342 " --> pdb=" O ASN B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 362 removed outlier: 3.684A pdb=" N LEU B 362 " --> pdb=" O VAL B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'D' and resid 63 through 68 Processing helix chain 'D' and resid 86 through 100 removed outlier: 3.525A pdb=" N ARG D 92 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN D 95 " --> pdb=" O ARG D 91 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL D 96 " --> pdb=" O ARG D 92 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU D 99 " --> pdb=" O GLN D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 116 Processing helix chain 'D' and resid 121 through 130 removed outlier: 3.654A pdb=" N GLU D 130 " --> pdb=" O ARG D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 168 removed outlier: 3.630A pdb=" N ALA D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 196 removed outlier: 3.594A pdb=" N ILE D 191 " --> pdb=" O GLY D 187 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU D 195 " --> pdb=" O ILE D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 260 removed outlier: 3.821A pdb=" N THR D 252 " --> pdb=" O ALA D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 292 removed outlier: 3.520A pdb=" N LYS D 267 " --> pdb=" O HIS D 263 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU D 271 " --> pdb=" O LYS D 267 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS D 272 " --> pdb=" O ARG D 268 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU D 283 " --> pdb=" O SER D 279 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE D 285 " --> pdb=" O TYR D 281 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 297 removed outlier: 3.595A pdb=" N LYS D 296 " --> pdb=" O TRP D 292 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR D 297 " --> pdb=" O ALA D 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 292 through 297' Processing helix chain 'E' and resid 48 through 80 removed outlier: 3.931A pdb=" N GLY E 52 " --> pdb=" O ASP E 48 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG E 53 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR E 55 " --> pdb=" O LYS E 51 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N TYR E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET E 59 " --> pdb=" O TYR E 55 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL E 60 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER E 67 " --> pdb=" O MET E 63 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER E 73 " --> pdb=" O ALA E 69 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR E 74 " --> pdb=" O GLY E 70 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL E 75 " --> pdb=" O ALA E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 88 through 92 removed outlier: 3.690A pdb=" N ALA E 92 " --> pdb=" O LEU E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 130 removed outlier: 4.039A pdb=" N ALA E 129 " --> pdb=" O GLU E 125 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN E 130 " --> pdb=" O ILE E 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 125 through 130' Processing helix chain 'N' and resid 2 through 7 Processing helix chain 'N' and resid 9 through 18 removed outlier: 3.781A pdb=" N VAL N 13 " --> pdb=" O TYR N 9 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE N 18 " --> pdb=" O ASN N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 27 through 30 Processing helix chain 'N' and resid 31 through 51 removed outlier: 3.519A pdb=" N LEU N 35 " --> pdb=" O ASN N 31 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY N 37 " --> pdb=" O GLY N 33 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL N 41 " --> pdb=" O GLY N 37 " (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 71 removed outlier: 3.561A pdb=" N VAL N 65 " --> pdb=" O ALA N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 74 through 103 removed outlier: 3.681A pdb=" N LEU N 78 " --> pdb=" O ASN N 74 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY N 100 " --> pdb=" O HIS N 96 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 133 removed outlier: 3.594A pdb=" N GLY N 117 " --> pdb=" O LEU N 113 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE N 119 " --> pdb=" O ASN N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 149 removed outlier: 3.787A pdb=" N TRP N 142 " --> pdb=" O GLN N 138 " (cutoff:3.500A) Processing helix chain 'N' and resid 150 through 154 removed outlier: 3.602A pdb=" N ALA N 153 " --> pdb=" O LEU N 150 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE N 154 " --> pdb=" O PHE N 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 150 through 154' Processing helix chain 'N' and resid 160 through 167 Processing helix chain 'N' and resid 172 through 203 removed outlier: 3.658A pdb=" N ALA N 181 " --> pdb=" O GLN N 177 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU N 185 " --> pdb=" O ALA N 181 " (cutoff:3.500A) Proline residue: N 187 - end of helix removed outlier: 3.509A pdb=" N ALA N 192 " --> pdb=" O PHE N 188 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA N 200 " --> pdb=" O MET N 196 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE N 203 " --> pdb=" O MET N 199 " (cutoff:3.500A) Processing helix chain 'N' and resid 225 through 247 removed outlier: 3.955A pdb=" N VAL N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N THR N 232 " --> pdb=" O LYS N 228 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE N 243 " --> pdb=" O ILE N 239 " (cutoff:3.500A) Processing helix chain 'N' and resid 253 through 258 removed outlier: 3.575A pdb=" N ILE N 258 " --> pdb=" O ASP N 255 " (cutoff:3.500A) Processing helix chain 'N' and resid 275 through 283 removed outlier: 3.709A pdb=" N ILE N 281 " --> pdb=" O PRO N 277 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU N 282 " --> pdb=" O PHE N 278 " (cutoff:3.500A) Processing helix chain 'N' and resid 288 through 301 removed outlier: 3.596A pdb=" N VAL N 292 " --> pdb=" O LYS N 288 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE N 296 " --> pdb=" O VAL N 292 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ILE N 299 " --> pdb=" O MET N 295 " (cutoff:3.500A) Processing helix chain 'N' and resid 304 through 309 removed outlier: 3.661A pdb=" N ASP N 309 " --> pdb=" O LEU N 305 " (cutoff:3.500A) Processing helix chain 'N' and resid 319 through 340 removed outlier: 4.038A pdb=" N PHE N 327 " --> pdb=" O LYS N 323 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE N 329 " --> pdb=" O PHE N 325 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY N 337 " --> pdb=" O PHE N 333 " (cutoff:3.500A) Processing helix chain 'N' and resid 347 through 365 removed outlier: 3.784A pdb=" N MET N 351 " --> pdb=" O PRO N 347 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN N 353 " --> pdb=" O VAL N 349 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR N 356 " --> pdb=" O GLY N 352 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR N 359 " --> pdb=" O ALA N 355 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE N 360 " --> pdb=" O THR N 356 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE N 363 " --> pdb=" O TYR N 359 " (cutoff:3.500A) Processing helix chain 'N' and resid 365 through 381 removed outlier: 3.836A pdb=" N THR N 372 " --> pdb=" O PRO N 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 85 removed outlier: 3.716A pdb=" N ASP F 80 " --> pdb=" O ASP F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 106 removed outlier: 4.257A pdb=" N LEU F 94 " --> pdb=" O GLU F 90 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS F 101 " --> pdb=" O HIS F 97 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU F 103 " --> pdb=" O GLU F 99 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG F 104 " --> pdb=" O GLU F 100 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL F 105 " --> pdb=" O CYS F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 139 removed outlier: 3.689A pdb=" N LEU F 130 " --> pdb=" O GLU F 126 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR F 133 " --> pdb=" O HIS F 129 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR F 138 " --> pdb=" O LEU F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 142 No H-bonds generated for 'chain 'F' and resid 140 through 142' Processing helix chain 'G' and resid 4 through 17 removed outlier: 3.803A pdb=" N TYR G 14 " --> pdb=" O ARG G 10 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE G 15 " --> pdb=" O ILE G 11 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU G 16 " --> pdb=" O GLY G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 35 removed outlier: 3.847A pdb=" N LEU G 24 " --> pdb=" O VAL G 20 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL G 26 " --> pdb=" O SER G 22 " (cutoff:3.500A) Proline residue: G 27 - end of helix removed outlier: 3.695A pdb=" N GLN G 31 " --> pdb=" O PRO G 27 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN G 34 " --> pdb=" O ASN G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 42 Processing helix chain 'G' and resid 53 through 62 removed outlier: 3.576A pdb=" N ARG G 61 " --> pdb=" O GLN G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 84 removed outlier: 3.543A pdb=" N ALA G 72 " --> pdb=" O SER G 68 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR G 73 " --> pdb=" O TYR G 69 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU G 82 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU G 83 " --> pdb=" O HIS G 79 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR G 84 " --> pdb=" O GLN G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 93 removed outlier: 3.845A pdb=" N TRP G 93 " --> pdb=" O ARG G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 119 removed outlier: 3.645A pdb=" N GLU G 109 " --> pdb=" O PRO G 105 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA G 110 " --> pdb=" O TYR G 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 34 Processing helix chain 'H' and resid 47 through 55 removed outlier: 3.836A pdb=" N LYS H 53 " --> pdb=" O PHE H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 81 removed outlier: 3.849A pdb=" N ILE H 61 " --> pdb=" O LEU H 57 " (cutoff:3.500A) Proline residue: H 62 - end of helix removed outlier: 3.547A pdb=" N TYR H 66 " --> pdb=" O PRO H 62 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR H 76 " --> pdb=" O ASN H 72 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN H 77 " --> pdb=" O GLY H 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 22 Processing helix chain 'I' and resid 23 through 44 removed outlier: 3.955A pdb=" N VAL I 27 " --> pdb=" O ALA I 23 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN I 29 " --> pdb=" O ALA I 25 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL I 31 " --> pdb=" O VAL I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 54 removed outlier: 3.764A pdb=" N ALA I 54 " --> pdb=" O LYS I 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 78 removed outlier: 3.550A pdb=" N ASN L 75 " --> pdb=" O ASN L 71 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE L 76 " --> pdb=" O LEU L 72 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE L 77 " --> pdb=" O TRP L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 88 removed outlier: 3.981A pdb=" N VAL L 85 " --> pdb=" O GLU L 81 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA L 86 " --> pdb=" O ASN L 82 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS L 88 " --> pdb=" O ALA L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 122 removed outlier: 3.716A pdb=" N SER L 116 " --> pdb=" O SER L 112 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP L 118 " --> pdb=" O ASP L 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 155 removed outlier: 3.529A pdb=" N GLU L 138 " --> pdb=" O SER L 134 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS L 142 " --> pdb=" O GLU L 138 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER L 143 " --> pdb=" O ALA L 139 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS L 146 " --> pdb=" O LYS L 142 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN L 149 " --> pdb=" O LEU L 145 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU L 153 " --> pdb=" O GLN L 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 155 through 169 removed outlier: 3.905A pdb=" N LEU L 161 " --> pdb=" O PRO L 157 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N HIS L 163 " --> pdb=" O ARG L 159 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE L 169 " --> pdb=" O HIS L 165 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 176 removed outlier: 3.529A pdb=" N SER L 175 " --> pdb=" O THR L 172 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU L 176 " --> pdb=" O PRO L 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 172 through 176' Processing helix chain 'L' and resid 190 through 201 removed outlier: 3.962A pdb=" N GLU L 194 " --> pdb=" O VAL L 190 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN L 199 " --> pdb=" O SER L 195 " (cutoff:3.500A) Processing helix chain 'L' and resid 215 through 224 removed outlier: 3.697A pdb=" N LEU L 219 " --> pdb=" O LYS L 215 " (cutoff:3.500A) Processing helix chain 'L' and resid 274 through 286 removed outlier: 3.552A pdb=" N LYS L 279 " --> pdb=" O TYR L 275 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA L 282 " --> pdb=" O ALA L 278 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N PHE L 285 " --> pdb=" O ALA L 281 " (cutoff:3.500A) Processing helix chain 'L' and resid 293 through 298 removed outlier: 3.563A pdb=" N LEU L 297 " --> pdb=" O ALA L 294 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN L 298 " --> pdb=" O SER L 295 " (cutoff:3.500A) Processing helix chain 'L' and resid 302 through 310 removed outlier: 3.514A pdb=" N GLN L 307 " --> pdb=" O LEU L 303 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU L 308 " --> pdb=" O ASP L 304 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR L 309 " --> pdb=" O ASN L 305 " (cutoff:3.500A) Processing helix chain 'L' and resid 339 through 352 removed outlier: 3.655A pdb=" N LEU L 343 " --> pdb=" O MET L 339 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN L 352 " --> pdb=" O LEU L 348 " (cutoff:3.500A) Processing helix chain 'L' and resid 352 through 357 removed outlier: 3.593A pdb=" N ILE L 356 " --> pdb=" O ASN L 352 " (cutoff:3.500A) Processing helix chain 'L' and resid 359 through 379 removed outlier: 3.528A pdb=" N VAL L 363 " --> pdb=" O THR L 359 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER L 368 " --> pdb=" O GLU L 364 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU L 377 " --> pdb=" O GLN L 373 " (cutoff:3.500A) Processing helix chain 'L' and resid 384 through 396 removed outlier: 3.653A pdb=" N ASN L 388 " --> pdb=" O VAL L 384 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU L 393 " --> pdb=" O LEU L 389 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL L 394 " --> pdb=" O LEU L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 402 through 411 Processing helix chain 'L' and resid 414 through 426 removed outlier: 3.596A pdb=" N VAL L 418 " --> pdb=" O THR L 414 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS L 424 " --> pdb=" O ALA L 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 444 through 450 removed outlier: 3.618A pdb=" N ILE L 448 " --> pdb=" O ASP L 444 " (cutoff:3.500A) Processing helix chain 'L' and resid 451 through 453 No H-bonds generated for 'chain 'L' and resid 451 through 453' Processing helix chain 'O' and resid 63 through 68 Processing helix chain 'O' and resid 86 through 100 removed outlier: 3.525A pdb=" N ARG O 92 " --> pdb=" O ALA O 88 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN O 95 " --> pdb=" O ARG O 91 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL O 96 " --> pdb=" O ARG O 92 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU O 99 " --> pdb=" O GLN O 95 " (cutoff:3.500A) Processing helix chain 'O' and resid 112 through 116 Processing helix chain 'O' and resid 121 through 130 removed outlier: 3.654A pdb=" N GLU O 130 " --> pdb=" O ARG O 126 " (cutoff:3.500A) Processing helix chain 'O' and resid 161 through 168 removed outlier: 3.630A pdb=" N ALA O 168 " --> pdb=" O ALA O 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 187 through 196 removed outlier: 3.594A pdb=" N ILE O 191 " --> pdb=" O GLY O 187 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU O 195 " --> pdb=" O ILE O 191 " (cutoff:3.500A) Processing helix chain 'O' and resid 243 through 260 removed outlier: 3.820A pdb=" N THR O 252 " --> pdb=" O ALA O 248 " (cutoff:3.500A) Processing helix chain 'O' and resid 262 through 292 removed outlier: 3.521A pdb=" N LYS O 267 " --> pdb=" O HIS O 263 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG O 268 " --> pdb=" O ASP O 264 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU O 271 " --> pdb=" O LYS O 267 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS O 272 " --> pdb=" O ARG O 268 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU O 283 " --> pdb=" O SER O 279 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE O 285 " --> pdb=" O TYR O 281 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP O 286 " --> pdb=" O LEU O 282 " (cutoff:3.500A) Processing helix chain 'O' and resid 292 through 297 removed outlier: 3.595A pdb=" N LYS O 296 " --> pdb=" O TRP O 292 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR O 297 " --> pdb=" O ALA O 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 292 through 297' Processing helix chain 'M' and resid 38 through 42 removed outlier: 3.557A pdb=" N ALA M 42 " --> pdb=" O SER M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 53 removed outlier: 3.557A pdb=" N LEU M 50 " --> pdb=" O GLY M 46 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 73 removed outlier: 3.520A pdb=" N VAL M 68 " --> pdb=" O ALA M 64 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU M 73 " --> pdb=" O ARG M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 112 removed outlier: 3.975A pdb=" N TYR M 101 " --> pdb=" O ASP M 97 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN M 103 " --> pdb=" O PRO M 99 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL M 108 " --> pdb=" O ALA M 104 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU M 109 " --> pdb=" O LEU M 105 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR M 112 " --> pdb=" O VAL M 108 " (cutoff:3.500A) Processing helix chain 'M' and resid 115 through 122 removed outlier: 3.590A pdb=" N LEU M 119 " --> pdb=" O LYS M 115 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR M 120 " --> pdb=" O PRO M 116 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 135 removed outlier: 3.523A pdb=" N ALA M 134 " --> pdb=" O ASP M 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 151 removed outlier: 3.563A pdb=" N GLN M 145 " --> pdb=" O SER M 141 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR M 150 " --> pdb=" O LEU M 146 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 180 removed outlier: 3.500A pdb=" N ILE M 172 " --> pdb=" O SER M 168 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS M 178 " --> pdb=" O ASP M 174 " (cutoff:3.500A) Processing helix chain 'M' and resid 181 through 183 No H-bonds generated for 'chain 'M' and resid 181 through 183' Processing helix chain 'M' and resid 193 through 203 removed outlier: 3.607A pdb=" N ARG M 199 " --> pdb=" O ALA M 195 " (cutoff:3.500A) Processing helix chain 'M' and resid 204 through 208 Processing helix chain 'M' and resid 251 through 260 Processing helix chain 'M' and resid 293 through 309 removed outlier: 3.533A pdb=" N SER M 298 " --> pdb=" O SER M 294 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER M 299 " --> pdb=" O ALA M 295 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS M 303 " --> pdb=" O SER M 299 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL M 305 " --> pdb=" O ILE M 301 " (cutoff:3.500A) Processing helix chain 'M' and resid 315 through 317 No H-bonds generated for 'chain 'M' and resid 315 through 317' Processing helix chain 'M' and resid 318 through 329 removed outlier: 3.538A pdb=" N LEU M 323 " --> pdb=" O ASN M 319 " (cutoff:3.500A) Processing helix chain 'M' and resid 339 through 343 removed outlier: 3.771A pdb=" N ALA M 342 " --> pdb=" O ASN M 339 " (cutoff:3.500A) Processing helix chain 'M' and resid 358 through 362 removed outlier: 3.684A pdb=" N LEU M 362 " --> pdb=" O VAL M 359 " (cutoff:3.500A) Processing helix chain 'M' and resid 364 through 368 Processing helix chain 'S' and resid 31 through 34 Processing helix chain 'S' and resid 46 through 55 removed outlier: 3.836A pdb=" N LYS S 53 " --> pdb=" O PHE S 49 " (cutoff:3.500A) Processing helix chain 'S' and resid 56 through 81 removed outlier: 3.849A pdb=" N ILE S 61 " --> pdb=" O LEU S 57 " (cutoff:3.500A) Proline residue: S 62 - end of helix removed outlier: 3.545A pdb=" N TYR S 66 " --> pdb=" O PRO S 62 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR S 76 " --> pdb=" O ASN S 72 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN S 77 " --> pdb=" O GLY S 73 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 80 removed outlier: 3.910A pdb=" N GLY P 52 " --> pdb=" O ASP P 48 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG P 53 " --> pdb=" O ALA P 49 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR P 55 " --> pdb=" O LYS P 51 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA P 56 " --> pdb=" O GLY P 52 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N TYR P 57 " --> pdb=" O ARG P 53 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET P 59 " --> pdb=" O TYR P 55 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL P 60 " --> pdb=" O ALA P 56 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER P 67 " --> pdb=" O MET P 63 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER P 73 " --> pdb=" O ALA P 69 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR P 74 " --> pdb=" O GLY P 70 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL P 75 " --> pdb=" O ALA P 71 " (cutoff:3.500A) Processing helix chain 'P' and resid 81 through 83 No H-bonds generated for 'chain 'P' and resid 81 through 83' Processing helix chain 'P' and resid 88 through 92 removed outlier: 3.690A pdb=" N ALA P 92 " --> pdb=" O LEU P 89 " (cutoff:3.500A) Processing helix chain 'P' and resid 125 through 130 removed outlier: 4.039A pdb=" N ALA P 129 " --> pdb=" O GLU P 125 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN P 130 " --> pdb=" O ILE P 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 125 through 130' Processing helix chain 'Q' and resid 76 through 85 removed outlier: 3.570A pdb=" N ASP Q 80 " --> pdb=" O ASP Q 76 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU Q 83 " --> pdb=" O GLU Q 79 " (cutoff:3.500A) Processing helix chain 'Q' and resid 88 through 106 removed outlier: 4.012A pdb=" N LEU Q 94 " --> pdb=" O GLU Q 90 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS Q 97 " --> pdb=" O ALA Q 93 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS Q 101 " --> pdb=" O HIS Q 97 " (cutoff:3.500A) Processing helix chain 'Q' and resid 123 through 139 removed outlier: 3.671A pdb=" N LEU Q 130 " --> pdb=" O GLU Q 126 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR Q 133 " --> pdb=" O HIS Q 129 " (cutoff:3.500A) Processing helix chain 'Q' and resid 140 through 142 No H-bonds generated for 'chain 'Q' and resid 140 through 142' Processing helix chain 'R' and resid 4 through 17 removed outlier: 3.802A pdb=" N TYR R 14 " --> pdb=" O ARG R 10 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU R 16 " --> pdb=" O GLY R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 20 through 35 removed outlier: 3.846A pdb=" N LEU R 24 " --> pdb=" O VAL R 20 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL R 26 " --> pdb=" O SER R 22 " (cutoff:3.500A) Proline residue: R 27 - end of helix removed outlier: 3.695A pdb=" N GLN R 31 " --> pdb=" O PRO R 27 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN R 34 " --> pdb=" O ASN R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 42 Processing helix chain 'R' and resid 53 through 62 removed outlier: 3.576A pdb=" N ARG R 61 " --> pdb=" O GLN R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 84 removed outlier: 3.543A pdb=" N ALA R 72 " --> pdb=" O SER R 68 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR R 73 " --> pdb=" O TYR R 69 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU R 82 " --> pdb=" O ALA R 78 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU R 83 " --> pdb=" O HIS R 79 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR R 84 " --> pdb=" O GLN R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 93 removed outlier: 3.844A pdb=" N TRP R 93 " --> pdb=" O ARG R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 119 removed outlier: 3.646A pdb=" N GLU R 109 " --> pdb=" O PRO R 105 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA R 110 " --> pdb=" O TYR R 106 " (cutoff:3.500A) Processing helix chain 'T' and resid 6 through 11 Processing helix chain 'T' and resid 13 through 22 removed outlier: 3.880A pdb=" N ILE T 21 " --> pdb=" O PHE T 17 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 44 removed outlier: 3.860A pdb=" N VAL T 27 " --> pdb=" O ALA T 23 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN T 29 " --> pdb=" O ALA T 25 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL T 31 " --> pdb=" O VAL T 27 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP T 33 " --> pdb=" O GLN T 29 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN T 42 " --> pdb=" O SER T 38 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 54 removed outlier: 3.696A pdb=" N ALA T 54 " --> pdb=" O LYS T 50 " (cutoff:3.500A) Processing helix chain 'U' and resid 19 through 24 Processing helix chain 'U' and resid 28 through 32 removed outlier: 3.538A pdb=" N MET U 31 " --> pdb=" O PRO U 28 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU U 32 " --> pdb=" O ASN U 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 28 through 32' Processing helix chain 'U' and resid 34 through 45 removed outlier: 3.517A pdb=" N PHE U 44 " --> pdb=" O GLY U 40 " (cutoff:3.500A) Processing helix chain 'V' and resid 26 through 31 removed outlier: 4.428A pdb=" N MET V 31 " --> pdb=" O ALA V 27 " (cutoff:3.500A) Processing helix chain 'V' and resid 31 through 39 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.540A pdb=" N GLU A 41 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY A 212 " --> pdb=" O GLU A 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 287 through 289 removed outlier: 3.553A pdb=" N ASN A 314 " --> pdb=" O ALA A 333 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY A 437 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG A 252 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE H 24 " --> pdb=" O ARG A 252 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR H 27 " --> pdb=" O LYS D 299 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 22 through 23 Processing sheet with id=AA4, first strand: chain 'B' and resid 18 through 22 removed outlier: 6.215A pdb=" N THR B 18 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N GLY B 189 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N SER B 20 " --> pdb=" O GLY B 189 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 228 through 232 removed outlier: 6.529A pdb=" N ASN B 229 " --> pdb=" O ALA B 355 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N GLY B 357 " --> pdb=" O ASN B 229 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL B 231 " --> pdb=" O GLY B 357 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY B 282 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER B 273 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 312 through 313 removed outlier: 3.540A pdb=" N PHE B 346 " --> pdb=" O LYS B 312 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 133 through 135 Processing sheet with id=AA8, first strand: chain 'D' and resid 213 through 214 Processing sheet with id=AA9, first strand: chain 'E' and resid 94 through 97 removed outlier: 3.508A pdb=" N VAL E 94 " --> pdb=" O VAL E 214 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 116 through 120 Processing sheet with id=AB2, first strand: chain 'N' and resid 22 through 23 Processing sheet with id=AB3, first strand: chain 'L' and resid 29 through 31 removed outlier: 3.541A pdb=" N GLU L 41 " --> pdb=" O GLY L 210 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY L 212 " --> pdb=" O GLU L 41 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 287 through 289 removed outlier: 3.553A pdb=" N ASN L 314 " --> pdb=" O ALA L 333 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY L 437 " --> pdb=" O LEU L 251 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG L 252 " --> pdb=" O ILE S 24 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ILE S 24 " --> pdb=" O ARG L 252 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR S 27 " --> pdb=" O LYS O 299 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 133 through 135 Processing sheet with id=AB6, first strand: chain 'O' and resid 213 through 214 Processing sheet with id=AB7, first strand: chain 'M' and resid 18 through 22 removed outlier: 6.215A pdb=" N THR M 18 " --> pdb=" O VAL M 187 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N GLY M 189 " --> pdb=" O THR M 18 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER M 20 " --> pdb=" O GLY M 189 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 228 through 232 removed outlier: 6.529A pdb=" N ASN M 229 " --> pdb=" O ALA M 355 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N GLY M 357 " --> pdb=" O ASN M 229 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL M 231 " --> pdb=" O GLY M 357 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY M 282 " --> pdb=" O PHE M 279 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER M 273 " --> pdb=" O PHE M 288 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 312 through 313 removed outlier: 3.541A pdb=" N PHE M 346 " --> pdb=" O LYS M 312 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'P' and resid 94 through 97 removed outlier: 3.507A pdb=" N VAL P 94 " --> pdb=" O VAL P 214 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'P' and resid 116 through 120 1289 hydrogen bonds defined for protein. 3687 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: 5.96 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.33: 7347 1.33 - 1.51: 15882 1.51 - 1.70: 9713 1.70 - 1.88: 188 1.88 - 2.07: 24 Bond restraints: 33154 Sorted by residual: bond pdb=" O11 6PH O 402 " pdb=" P 6PH O 402 " ideal model delta sigma weight residual 2.292 1.644 0.648 2.00e-02 2.50e+03 1.05e+03 bond pdb=" C GLY L 233 " pdb=" N THR L 234 " ideal model delta sigma weight residual 1.331 1.590 -0.260 1.23e-02 6.61e+03 4.46e+02 bond pdb=" C PRO P 102 " pdb=" N LEU P 103 " ideal model delta sigma weight residual 1.334 1.579 -0.245 1.27e-02 6.20e+03 3.71e+02 bond pdb=" C GLY A 233 " pdb=" N THR A 234 " ideal model delta sigma weight residual 1.331 1.534 -0.203 1.23e-02 6.61e+03 2.73e+02 bond pdb=" C PRO G 2 " pdb=" N GLN G 3 " ideal model delta sigma weight residual 1.333 1.502 -0.168 1.24e-02 6.50e+03 1.84e+02 ... (remaining 33149 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.26: 44949 9.26 - 18.52: 57 18.52 - 27.78: 4 27.78 - 37.04: 2 37.04 - 46.29: 1 Bond angle restraints: 45013 Sorted by residual: angle pdb=" O ASN H 43 " pdb=" C ASN H 43 " pdb=" N ALA H 44 " ideal model delta sigma weight residual 122.59 97.34 25.25 1.33e+00 5.65e-01 3.60e+02 angle pdb=" O11 6PH O 402 " pdb=" P 6PH O 402 " pdb=" O13 6PH O 402 " ideal model delta sigma weight residual 62.77 109.06 -46.29 3.00e+00 1.11e-01 2.38e+02 angle pdb=" CA ASN H 43 " pdb=" C ASN H 43 " pdb=" N ALA H 44 " ideal model delta sigma weight residual 116.84 139.48 -22.64 1.71e+00 3.42e-01 1.75e+02 angle pdb=" C ASN S 43 " pdb=" N ALA S 44 " pdb=" CA ALA S 44 " ideal model delta sigma weight residual 120.31 139.24 -18.93 1.52e+00 4.33e-01 1.55e+02 angle pdb=" C1 6PH O 402 " pdb=" O11 6PH O 402 " pdb=" P 6PH O 402 " ideal model delta sigma weight residual 81.98 117.63 -35.65 3.00e+00 1.11e-01 1.41e+02 ... (remaining 45008 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 19023 35.81 - 71.61: 501 71.61 - 107.42: 76 107.42 - 143.23: 9 143.23 - 179.03: 12 Dihedral angle restraints: 19621 sinusoidal: 8022 harmonic: 11599 Sorted by residual: dihedral pdb=" CA VAL C 346 " pdb=" C VAL C 346 " pdb=" N PRO C 347 " pdb=" CA PRO C 347 " ideal model delta harmonic sigma weight residual 180.00 125.45 54.55 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CA VAL N 346 " pdb=" C VAL N 346 " pdb=" N PRO N 347 " pdb=" CA PRO N 347 " ideal model delta harmonic sigma weight residual 180.00 125.45 54.55 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CA LEU I 6 " pdb=" C LEU I 6 " pdb=" N TYR I 7 " pdb=" CA TYR I 7 " ideal model delta harmonic sigma weight residual -180.00 -127.35 -52.65 0 5.00e+00 4.00e-02 1.11e+02 ... (remaining 19618 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3538 0.055 - 0.111: 1054 0.111 - 0.166: 253 0.166 - 0.222: 20 0.222 - 0.277: 11 Chirality restraints: 4876 Sorted by residual: chirality pdb=" CB VAL N 312 " pdb=" CA VAL N 312 " pdb=" CG1 VAL N 312 " pdb=" CG2 VAL N 312 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB VAL C 312 " pdb=" CA VAL C 312 " pdb=" CG1 VAL C 312 " pdb=" CG2 VAL C 312 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB THR A 172 " pdb=" CA THR A 172 " pdb=" OG1 THR A 172 " pdb=" CG2 THR A 172 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 4873 not shown) Planarity restraints: 5695 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG V 17 " 1.037 9.50e-02 1.11e+02 4.65e-01 1.31e+02 pdb=" NE ARG V 17 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG V 17 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG V 17 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG V 17 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN H 43 " 0.057 2.00e-02 2.50e+03 8.77e-02 7.69e+01 pdb=" C ASN H 43 " -0.152 2.00e-02 2.50e+03 pdb=" O ASN H 43 " 0.044 2.00e-02 2.50e+03 pdb=" N ALA H 44 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG T 13 " -0.633 9.50e-02 1.11e+02 2.84e-01 4.91e+01 pdb=" NE ARG T 13 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG T 13 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG T 13 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG T 13 " -0.021 2.00e-02 2.50e+03 ... (remaining 5692 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 9642 2.82 - 3.34: 25587 3.34 - 3.86: 49870 3.86 - 4.38: 61223 4.38 - 4.90: 104753 Nonbonded interactions: 251075 Sorted by model distance: nonbonded pdb=" O SER A 112 " pdb=" OG SER A 112 " model vdw 2.296 3.040 nonbonded pdb=" O TYR N 132 " pdb=" OG SER N 140 " model vdw 2.336 3.040 nonbonded pdb=" O TYR C 132 " pdb=" OG SER C 140 " model vdw 2.336 3.040 nonbonded pdb=" O LEU U 20 " pdb=" OG1 THR U 24 " model vdw 2.338 3.040 nonbonded pdb=" OG SER N 247 " pdb=" OG1 THR N 250 " model vdw 2.343 3.040 ... (remaining 251070 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'M' } ncs_group { reference = (chain 'C' and (resid 1 through 385 or resid 403 through 404)) selection = (chain 'N' and (resid 1 through 385 or resid 403 through 404)) } ncs_group { reference = chain 'D' selection = (chain 'O' and resid 62 through 401) } ncs_group { reference = chain 'E' selection = chain 'P' } ncs_group { reference = chain 'F' selection = (chain 'Q' and resid 74 through 147) } ncs_group { reference = chain 'G' selection = chain 'R' } ncs_group { reference = chain 'H' selection = (chain 'S' and resid 2 through 94) } ncs_group { reference = (chain 'I' and resid 5 through 57) selection = (chain 'T' and resid 5 through 57) } ncs_group { reference = (chain 'U' and resid 11 through 53) selection = (chain 'V' and resid 11 through 53) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.310 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 28.180 Find NCS groups from input model: 0.590 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:9.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 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 : 0.012 0.648 33160 Z= 0.480 Angle : 1.157 46.294 45013 Z= 0.585 Chirality : 0.056 0.277 4876 Planarity : 0.011 0.465 5695 Dihedral : 17.619 179.034 12157 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.81 % Favored : 93.04 % Rotamer: Outliers : 1.91 % Allowed : 5.20 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 1.07 % Twisted General : 0.11 % 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: -5.39 (0.09), residues: 3952 helix: -4.53 (0.04), residues: 1862 sheet: -0.92 (0.25), residues: 360 loop : -2.89 (0.12), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG P 146 TYR 0.032 0.002 TYR T 7 PHE 0.025 0.002 PHE N 89 TRP 0.069 0.002 TRP A 457 HIS 0.019 0.002 HIS E 181 Details of bonding type rmsd covalent geometry : bond 0.00927 (33154) covalent geometry : angle 1.15672 (45013) hydrogen bonds : bond 0.35113 ( 1289) hydrogen bonds : angle 9.36735 ( 3687) Misc. bond : bond 0.53783 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 435 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7286 (tm-30) REVERT: A 126 GLN cc_start: 0.6886 (tm-30) cc_final: 0.6105 (mp10) REVERT: A 127 GLN cc_start: 0.7857 (pt0) cc_final: 0.7547 (pt0) REVERT: A 408 LYS cc_start: 0.8093 (mttt) cc_final: 0.7643 (mtpp) REVERT: A 446 MET cc_start: 0.9036 (mmm) cc_final: 0.8816 (mmm) REVERT: A 454 MET cc_start: 0.6568 (ttm) cc_final: 0.5935 (tpp) REVERT: C 239 ILE cc_start: 0.8411 (mt) cc_final: 0.8195 (mm) REVERT: C 253 HIS cc_start: 0.8050 (t70) cc_final: 0.7735 (t-170) REVERT: B 83 ASP cc_start: 0.8135 (m-30) cc_final: 0.7873 (m-30) REVERT: B 223 PHE cc_start: 0.8772 (p90) cc_final: 0.8468 (p90) REVERT: D 141 GLN cc_start: 0.8616 (mp10) cc_final: 0.8356 (mp-120) REVERT: E 31 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7504 (pttm) REVERT: N 239 ILE cc_start: 0.8397 (mt) cc_final: 0.8172 (mm) REVERT: N 253 HIS cc_start: 0.8063 (t70) cc_final: 0.7747 (t-170) REVERT: L 41 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7356 (tm-30) REVERT: L 126 GLN cc_start: 0.6887 (tm-30) cc_final: 0.6054 (mp10) REVERT: L 127 GLN cc_start: 0.7832 (pt0) cc_final: 0.7563 (pt0) REVERT: L 446 MET cc_start: 0.9045 (mmm) cc_final: 0.8832 (mmm) REVERT: L 454 MET cc_start: 0.6434 (ttm) cc_final: 0.5795 (tpp) REVERT: M 83 ASP cc_start: 0.8184 (m-30) cc_final: 0.7927 (m-30) REVERT: M 223 PHE cc_start: 0.8767 (p90) cc_final: 0.8505 (p90) REVERT: P 31 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7455 (pttm) REVERT: P 82 MET cc_start: 0.8758 (mtp) cc_final: 0.8444 (mtm) REVERT: P 119 ARG cc_start: -0.1751 (OUTLIER) cc_final: -0.2620 (tmt-80) REVERT: P 134 MET cc_start: 0.2780 (tpt) cc_final: 0.2262 (tpt) REVERT: Q 76 ASP cc_start: 0.6730 (p0) cc_final: 0.6269 (p0) REVERT: R 90 ARG cc_start: 0.7597 (ttm-80) cc_final: 0.7382 (ttm-80) REVERT: R 119 GLU cc_start: 0.7843 (pp20) cc_final: 0.7640 (pp20) REVERT: U 38 MET cc_start: 0.2812 (mmm) cc_final: 0.0701 (ptp) REVERT: V 38 MET cc_start: 0.1571 (mmm) cc_final: 0.0631 (pmm) outliers start: 65 outliers final: 13 residues processed: 484 average time/residue: 0.7687 time to fit residues: 428.9457 Evaluate side-chains 348 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 330 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 119 ARG Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain G residue 34 ASN Chi-restraints excluded: chain I residue 13 ARG Chi-restraints excluded: chain L residue 41 GLU Chi-restraints excluded: chain L residue 235 LYS Chi-restraints excluded: chain O residue 276 ILE Chi-restraints excluded: chain P residue 31 LYS Chi-restraints excluded: chain P residue 119 ARG Chi-restraints excluded: chain P residue 128 GLU Chi-restraints excluded: chain P residue 211 LYS Chi-restraints excluded: chain R residue 34 ASN Chi-restraints excluded: chain T residue 13 ARG Chi-restraints excluded: chain V residue 32 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 102 GLN A 156 HIS A 170 GLN A 203 ASN A 274 ASN A 283 GLN A 317 HIS A 350 GLN A 352 ASN A 376 GLN A 388 ASN C 22 GLN C 208 ASN B 57 GLN B 191 ASN D 79 ASN D 127 ASN D 161 ASN E 161 HIS E 181 HIS N 22 GLN N 208 ASN F 77 GLN G 3 GLN G 30 ASN G 31 GLN G 79 HIS H 21 GLN H 74 ASN ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 102 GLN L 156 HIS L 170 GLN L 203 ASN L 274 ASN L 283 GLN L 317 HIS L 350 GLN L 352 ASN L 376 GLN L 388 ASN O 79 ASN O 127 ASN O 161 ASN O 215 ASN M 57 GLN M 191 ASN S 21 GLN S 74 ASN P 106 ASN P 161 HIS P 181 HIS P 184 HIS Q 109 GLN R 3 GLN R 30 ASN R 31 GLN R 79 HIS T 29 GLN T 44 ASN V 52 GLN Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.157862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.116608 restraints weight = 43321.133| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.17 r_work: 0.3324 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.190 33160 Z= 0.213 Angle : 0.733 16.897 45013 Z= 0.370 Chirality : 0.047 0.160 4876 Planarity : 0.006 0.079 5695 Dihedral : 15.246 166.282 4825 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.87 % Favored : 94.03 % Rotamer: Outliers : 2.17 % Allowed : 9.86 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 1.07 % Twisted General : 0.05 % 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: -3.29 (0.11), residues: 3952 helix: -2.21 (0.09), residues: 1939 sheet: -0.20 (0.26), residues: 352 loop : -2.47 (0.13), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 190 TYR 0.019 0.002 TYR C 136 PHE 0.022 0.002 PHE A 315 TRP 0.026 0.002 TRP L 457 HIS 0.010 0.001 HIS E 181 Details of bonding type rmsd covalent geometry : bond 0.00515 (33154) covalent geometry : angle 0.73256 (45013) hydrogen bonds : bond 0.07890 ( 1289) hydrogen bonds : angle 4.66093 ( 3687) Misc. bond : bond 0.11194 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 364 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7561 (tm-30) REVERT: A 126 GLN cc_start: 0.7161 (tm-30) cc_final: 0.6085 (mp10) REVERT: A 127 GLN cc_start: 0.7985 (pt0) cc_final: 0.7307 (pt0) REVERT: A 296 ARG cc_start: 0.8693 (mtm-85) cc_final: 0.8392 (mtt-85) REVERT: A 399 SER cc_start: 0.8028 (m) cc_final: 0.7714 (p) REVERT: A 454 MET cc_start: 0.7234 (ttm) cc_final: 0.6053 (tpt) REVERT: A 455 MET cc_start: 0.6036 (ttp) cc_final: 0.5791 (ttp) REVERT: C 1 MET cc_start: 0.6696 (OUTLIER) cc_final: 0.6358 (ptp) REVERT: C 5 LYS cc_start: 0.7784 (mtpt) cc_final: 0.7561 (mtpp) REVERT: C 253 HIS cc_start: 0.8247 (t70) cc_final: 0.7037 (m90) REVERT: C 338 GLN cc_start: 0.8581 (mm-40) cc_final: 0.8274 (tp40) REVERT: C 374 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8112 (mt-10) REVERT: B 83 ASP cc_start: 0.8605 (m-30) cc_final: 0.8316 (m-30) REVERT: B 90 LYS cc_start: 0.8850 (tttt) cc_final: 0.8529 (tttp) REVERT: B 223 PHE cc_start: 0.8945 (p90) cc_final: 0.8557 (p90) REVERT: B 291 ASP cc_start: 0.8625 (t70) cc_final: 0.7974 (t0) REVERT: D 135 ASP cc_start: 0.8298 (m-30) cc_final: 0.8068 (m-30) REVERT: D 141 GLN cc_start: 0.8426 (mp10) cc_final: 0.8104 (mp-120) REVERT: E 31 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.7437 (pttm) REVERT: E 55 TYR cc_start: 0.7620 (t80) cc_final: 0.7222 (t80) REVERT: E 57 TYR cc_start: 0.6025 (m-80) cc_final: 0.5568 (m-80) REVERT: N 1 MET cc_start: 0.6733 (OUTLIER) cc_final: 0.6380 (ptp) REVERT: N 5 LYS cc_start: 0.7855 (mtpt) cc_final: 0.7634 (mtpp) REVERT: N 253 HIS cc_start: 0.8223 (t70) cc_final: 0.7027 (m90) REVERT: N 338 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8291 (tp40) REVERT: F 76 ASP cc_start: 0.6892 (p0) cc_final: 0.6364 (p0) REVERT: F 92 LYS cc_start: 0.7370 (mttm) cc_final: 0.7123 (mptp) REVERT: F 103 GLU cc_start: 0.8219 (mp0) cc_final: 0.7935 (mt-10) REVERT: G 82 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8082 (mt-10) REVERT: H 71 LYS cc_start: 0.7286 (tmmt) cc_final: 0.6857 (mtpp) REVERT: L 41 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7575 (tm-30) REVERT: L 126 GLN cc_start: 0.7199 (tm-30) cc_final: 0.6831 (tm-30) REVERT: L 127 GLN cc_start: 0.7943 (pt0) cc_final: 0.7306 (pt0) REVERT: L 296 ARG cc_start: 0.8678 (mtm-85) cc_final: 0.8367 (mtp85) REVERT: L 378 TYR cc_start: 0.8781 (m-80) cc_final: 0.8509 (m-80) REVERT: L 399 SER cc_start: 0.8057 (m) cc_final: 0.7738 (p) REVERT: L 454 MET cc_start: 0.7268 (ttm) cc_final: 0.6014 (tpt) REVERT: L 455 MET cc_start: 0.6226 (ttp) cc_final: 0.5932 (ttp) REVERT: O 135 ASP cc_start: 0.8245 (m-30) cc_final: 0.8043 (m-30) REVERT: M 83 ASP cc_start: 0.8612 (m-30) cc_final: 0.8327 (m-30) REVERT: M 90 LYS cc_start: 0.8836 (tttt) cc_final: 0.8517 (tttp) REVERT: M 223 PHE cc_start: 0.8961 (p90) cc_final: 0.8575 (p90) REVERT: S 71 LYS cc_start: 0.7109 (tmmt) cc_final: 0.6733 (mtpp) REVERT: S 87 GLU cc_start: 0.7695 (tt0) cc_final: 0.7454 (mp0) REVERT: S 91 ARG cc_start: 0.7273 (ptt90) cc_final: 0.7025 (ppt170) REVERT: P 31 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7264 (pttm) REVERT: P 134 MET cc_start: 0.3211 (tpt) cc_final: 0.2569 (tpt) REVERT: Q 92 LYS cc_start: 0.7087 (mtmm) cc_final: 0.6867 (mtmm) REVERT: R 82 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8290 (mt-10) REVERT: V 38 MET cc_start: 0.0929 (mmm) cc_final: 0.0397 (ppp) outliers start: 74 outliers final: 28 residues processed: 409 average time/residue: 0.7501 time to fit residues: 355.3325 Evaluate side-chains 377 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 341 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain G residue 34 ASN Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain I residue 13 ARG Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain L residue 41 GLU Chi-restraints excluded: chain L residue 183 GLU Chi-restraints excluded: chain O residue 162 GLU Chi-restraints excluded: chain O residue 306 LYS Chi-restraints excluded: chain M residue 22 ARG Chi-restraints excluded: chain M residue 266 GLU Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain P residue 31 LYS Chi-restraints excluded: chain P residue 103 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 128 GLU Chi-restraints excluded: chain P residue 211 LYS Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain R residue 34 ASN Chi-restraints excluded: chain R residue 82 GLU Chi-restraints excluded: chain T residue 13 ARG Chi-restraints excluded: chain V residue 32 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 21 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 186 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 123 optimal weight: 0.8980 chunk 276 optimal weight: 0.6980 chunk 333 optimal weight: 5.9990 chunk 235 optimal weight: 7.9990 chunk 273 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 HIS E 106 ASN G 31 GLN H 34 GLN H 74 ASN I 14 ASN O 141 GLN M 117 HIS S 34 GLN S 74 ASN P 46 ASN R 31 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.162198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.121401 restraints weight = 43239.839| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.16 r_work: 0.3391 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.136 33160 Z= 0.114 Angle : 0.576 15.260 45013 Z= 0.290 Chirality : 0.042 0.150 4876 Planarity : 0.004 0.070 5695 Dihedral : 13.548 156.595 4805 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.03 % Allowed : 11.51 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 1.07 % 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: -1.88 (0.12), residues: 3952 helix: -0.76 (0.11), residues: 1938 sheet: 0.14 (0.25), residues: 382 loop : -2.14 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 190 TYR 0.012 0.001 TYR Q 114 PHE 0.014 0.001 PHE L 315 TRP 0.020 0.001 TRP L 457 HIS 0.004 0.001 HIS D 263 Details of bonding type rmsd covalent geometry : bond 0.00256 (33154) covalent geometry : angle 0.57553 (45013) hydrogen bonds : bond 0.05161 ( 1289) hydrogen bonds : angle 4.03240 ( 3687) Misc. bond : bond 0.08232 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 378 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7600 (tm-30) REVERT: A 127 GLN cc_start: 0.7870 (pt0) cc_final: 0.7667 (pt0) REVERT: A 147 GLN cc_start: 0.8570 (mt0) cc_final: 0.8285 (mt0) REVERT: A 252 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7417 (ttm170) REVERT: A 296 ARG cc_start: 0.8645 (mtm-85) cc_final: 0.8384 (mtp85) REVERT: A 399 SER cc_start: 0.7997 (m) cc_final: 0.7659 (p) REVERT: A 454 MET cc_start: 0.7230 (ttm) cc_final: 0.5969 (tpt) REVERT: C 1 MET cc_start: 0.6593 (ptp) cc_final: 0.6232 (ptp) REVERT: C 5 LYS cc_start: 0.7875 (mtpt) cc_final: 0.7660 (mtpp) REVERT: C 253 HIS cc_start: 0.8192 (t70) cc_final: 0.7015 (m90) REVERT: B 90 LYS cc_start: 0.8832 (tttt) cc_final: 0.8565 (ttmm) REVERT: B 223 PHE cc_start: 0.8964 (p90) cc_final: 0.8607 (p90) REVERT: B 291 ASP cc_start: 0.8555 (t70) cc_final: 0.7907 (t0) REVERT: D 135 ASP cc_start: 0.8391 (m-30) cc_final: 0.8189 (m-30) REVERT: D 222 SER cc_start: 0.8712 (p) cc_final: 0.8475 (m) REVERT: E 31 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7499 (mtmm) REVERT: E 68 SER cc_start: 0.7189 (m) cc_final: 0.6938 (p) REVERT: N 1 MET cc_start: 0.6632 (ptp) cc_final: 0.6264 (ptp) REVERT: N 5 LYS cc_start: 0.7880 (mtpt) cc_final: 0.7668 (mtpp) REVERT: N 253 HIS cc_start: 0.8148 (t70) cc_final: 0.6995 (m90) REVERT: F 76 ASP cc_start: 0.8168 (p0) cc_final: 0.7846 (p0) REVERT: F 103 GLU cc_start: 0.8106 (mp0) cc_final: 0.7799 (mt-10) REVERT: H 71 LYS cc_start: 0.6924 (tmmt) cc_final: 0.6635 (mtpp) REVERT: L 41 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7581 (tm-30) REVERT: L 147 GLN cc_start: 0.8537 (mt0) cc_final: 0.8254 (mt0) REVERT: L 252 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7338 (ttm170) REVERT: L 296 ARG cc_start: 0.8632 (mtm-85) cc_final: 0.8358 (mtp85) REVERT: L 378 TYR cc_start: 0.8642 (m-80) cc_final: 0.8417 (m-80) REVERT: L 399 SER cc_start: 0.8002 (m) cc_final: 0.7700 (p) REVERT: L 454 MET cc_start: 0.7182 (ttm) cc_final: 0.5965 (tpt) REVERT: L 455 MET cc_start: 0.6025 (ttp) cc_final: 0.5723 (ttp) REVERT: O 135 ASP cc_start: 0.8366 (m-30) cc_final: 0.8139 (m-30) REVERT: O 222 SER cc_start: 0.8729 (p) cc_final: 0.8499 (m) REVERT: O 233 MET cc_start: 0.8139 (ptm) cc_final: 0.7904 (ptp) REVERT: M 90 LYS cc_start: 0.8809 (tttt) cc_final: 0.8545 (ttmm) REVERT: M 223 PHE cc_start: 0.8954 (p90) cc_final: 0.8595 (p90) REVERT: M 291 ASP cc_start: 0.8553 (t70) cc_final: 0.7928 (t0) REVERT: S 71 LYS cc_start: 0.6938 (tmmt) cc_final: 0.6630 (mtpp) REVERT: S 87 GLU cc_start: 0.7861 (tt0) cc_final: 0.7623 (mp0) REVERT: P 31 LYS cc_start: 0.8241 (mtpt) cc_final: 0.7426 (mtmm) REVERT: P 55 TYR cc_start: 0.7504 (t80) cc_final: 0.7098 (t80) REVERT: P 68 SER cc_start: 0.7207 (m) cc_final: 0.6881 (p) REVERT: Q 76 ASP cc_start: 0.7798 (p0) cc_final: 0.7591 (p0) REVERT: Q 92 LYS cc_start: 0.7040 (mtmm) cc_final: 0.6838 (mtmm) REVERT: Q 108 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7782 (mt0) REVERT: Q 131 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7675 (mp10) REVERT: U 30 LEU cc_start: -0.2239 (OUTLIER) cc_final: -0.2862 (pp) outliers start: 69 outliers final: 18 residues processed: 417 average time/residue: 0.7312 time to fit residues: 354.4162 Evaluate side-chains 379 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 355 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain G residue 34 ASN Chi-restraints excluded: chain I residue 13 ARG Chi-restraints excluded: chain L residue 226 LYS Chi-restraints excluded: chain L residue 252 ARG Chi-restraints excluded: chain M residue 22 ARG Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 128 GLU Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 108 GLN Chi-restraints excluded: chain Q residue 131 GLN Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain R residue 34 ASN Chi-restraints excluded: chain T residue 13 ARG Chi-restraints excluded: chain U residue 30 LEU Chi-restraints excluded: chain V residue 32 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 231 optimal weight: 10.0000 chunk 266 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 308 optimal weight: 0.9990 chunk 71 optimal weight: 0.0980 chunk 343 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 268 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 279 optimal weight: 9.9990 chunk 252 optimal weight: 0.0170 overall best weight: 1.0224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 253 HIS D 161 ASN D 215 ASN E 184 HIS G 31 GLN G 57 GLN H 74 ASN O 141 GLN O 161 ASN S 74 ASN R 31 GLN R 57 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.162568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.121903 restraints weight = 43219.505| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.16 r_work: 0.3428 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.144 33160 Z= 0.111 Angle : 0.566 14.693 45013 Z= 0.282 Chirality : 0.042 0.153 4876 Planarity : 0.004 0.071 5695 Dihedral : 12.797 156.455 4791 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.88 % Allowed : 13.00 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 1.07 % 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: -1.24 (0.13), residues: 3952 helix: -0.13 (0.12), residues: 1950 sheet: 0.27 (0.26), residues: 374 loop : -1.91 (0.14), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 190 TYR 0.012 0.001 TYR F 133 PHE 0.014 0.001 PHE A 315 TRP 0.015 0.001 TRP L 457 HIS 0.004 0.001 HIS N 197 Details of bonding type rmsd covalent geometry : bond 0.00254 (33154) covalent geometry : angle 0.56617 (45013) hydrogen bonds : bond 0.04779 ( 1289) hydrogen bonds : angle 3.86772 ( 3687) Misc. bond : bond 0.08388 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 366 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7553 (tm-30) REVERT: A 248 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8307 (pp20) REVERT: A 252 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.7375 (ttm170) REVERT: A 296 ARG cc_start: 0.8604 (mtm-85) cc_final: 0.8222 (mtp-110) REVERT: A 399 SER cc_start: 0.7925 (m) cc_final: 0.7658 (p) REVERT: A 454 MET cc_start: 0.7239 (ttm) cc_final: 0.6037 (tpp) REVERT: A 455 MET cc_start: 0.6136 (ttp) cc_final: 0.5635 (tmm) REVERT: C 1 MET cc_start: 0.6465 (ptp) cc_final: 0.6101 (ptp) REVERT: C 253 HIS cc_start: 0.7958 (t-170) cc_final: 0.6932 (m90) REVERT: B 90 LYS cc_start: 0.8762 (tttt) cc_final: 0.8462 (ttmm) REVERT: B 223 PHE cc_start: 0.8920 (p90) cc_final: 0.8549 (p90) REVERT: B 291 ASP cc_start: 0.8474 (t70) cc_final: 0.7778 (t0) REVERT: D 222 SER cc_start: 0.8674 (p) cc_final: 0.8455 (m) REVERT: E 31 LYS cc_start: 0.8043 (mtpt) cc_final: 0.7108 (mtmm) REVERT: E 68 SER cc_start: 0.6956 (m) cc_final: 0.6754 (p) REVERT: N 1 MET cc_start: 0.6458 (ptp) cc_final: 0.6074 (ptp) REVERT: N 253 HIS cc_start: 0.8051 (t70) cc_final: 0.6857 (m90) REVERT: F 79 GLU cc_start: 0.6063 (mp0) cc_final: 0.5837 (mp0) REVERT: F 103 GLU cc_start: 0.8037 (mp0) cc_final: 0.7707 (mt-10) REVERT: G 82 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8195 (mt-10) REVERT: H 71 LYS cc_start: 0.6702 (OUTLIER) cc_final: 0.6441 (mtpp) REVERT: H 78 GLU cc_start: 0.7523 (tp30) cc_final: 0.7272 (tm-30) REVERT: L 41 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7607 (tm-30) REVERT: L 248 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8312 (pp20) REVERT: L 252 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7338 (ttm170) REVERT: L 296 ARG cc_start: 0.8588 (mtm-85) cc_final: 0.8192 (mtp-110) REVERT: L 399 SER cc_start: 0.8027 (m) cc_final: 0.7727 (p) REVERT: L 454 MET cc_start: 0.7137 (ttm) cc_final: 0.5926 (tpp) REVERT: O 135 ASP cc_start: 0.8377 (m-30) cc_final: 0.8169 (m-30) REVERT: O 222 SER cc_start: 0.8700 (p) cc_final: 0.8484 (m) REVERT: O 233 MET cc_start: 0.8045 (ptm) cc_final: 0.7810 (ptp) REVERT: M 90 LYS cc_start: 0.8756 (tttt) cc_final: 0.8464 (ttmm) REVERT: M 223 PHE cc_start: 0.8919 (p90) cc_final: 0.8547 (p90) REVERT: M 291 ASP cc_start: 0.8440 (t70) cc_final: 0.7741 (t0) REVERT: S 71 LYS cc_start: 0.6685 (OUTLIER) cc_final: 0.6408 (mtpp) REVERT: S 78 GLU cc_start: 0.7496 (tp30) cc_final: 0.7185 (tm-30) REVERT: P 31 LYS cc_start: 0.8284 (mtpt) cc_final: 0.7544 (mtmm) REVERT: P 68 SER cc_start: 0.7118 (m) cc_final: 0.6818 (p) REVERT: P 105 LYS cc_start: 0.3015 (OUTLIER) cc_final: 0.0936 (ptpp) REVERT: Q 106 LYS cc_start: 0.8046 (tppp) cc_final: 0.7716 (ttpm) REVERT: Q 108 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7955 (mm-40) REVERT: R 82 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8255 (mt-10) REVERT: V 32 LEU cc_start: 0.3536 (OUTLIER) cc_final: 0.2577 (pp) outliers start: 64 outliers final: 24 residues processed: 406 average time/residue: 0.7392 time to fit residues: 347.9402 Evaluate side-chains 379 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 344 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain D residue 67 HIS Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain G residue 34 ASN Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain H residue 71 LYS Chi-restraints excluded: chain I residue 13 ARG Chi-restraints excluded: chain L residue 226 LYS Chi-restraints excluded: chain L residue 248 GLU Chi-restraints excluded: chain L residue 252 ARG Chi-restraints excluded: chain L residue 396 ILE Chi-restraints excluded: chain M residue 22 ARG Chi-restraints excluded: chain M residue 294 SER Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain P residue 103 LEU Chi-restraints excluded: chain P residue 105 LYS Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 211 LYS Chi-restraints excluded: chain Q residue 108 GLN Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain R residue 34 ASN Chi-restraints excluded: chain R residue 82 GLU Chi-restraints excluded: chain T residue 13 ARG Chi-restraints excluded: chain V residue 32 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 232 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 199 optimal weight: 7.9990 chunk 373 optimal weight: 4.9990 chunk 348 optimal weight: 9.9990 chunk 216 optimal weight: 3.9990 chunk 221 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 197 optimal weight: 6.9990 chunk 250 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 141 GLN G 31 GLN H 74 ASN O 141 GLN O 215 ASN S 74 ASN R 31 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.157560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.116513 restraints weight = 43393.772| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.15 r_work: 0.3353 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.191 33160 Z= 0.219 Angle : 0.696 14.025 45013 Z= 0.348 Chirality : 0.047 0.163 4876 Planarity : 0.005 0.078 5695 Dihedral : 13.096 161.863 4784 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.74 % Favored : 94.21 % Rotamer: Outliers : 2.79 % Allowed : 13.15 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 1.07 % 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: -1.38 (0.13), residues: 3952 helix: -0.30 (0.12), residues: 1961 sheet: 0.66 (0.28), residues: 338 loop : -1.99 (0.14), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 107 TYR 0.018 0.002 TYR F 133 PHE 0.021 0.002 PHE G 45 TRP 0.016 0.002 TRP L 457 HIS 0.008 0.001 HIS N 197 Details of bonding type rmsd covalent geometry : bond 0.00541 (33154) covalent geometry : angle 0.69644 (45013) hydrogen bonds : bond 0.07287 ( 1289) hydrogen bonds : angle 4.29021 ( 3687) Misc. bond : bond 0.11008 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 359 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7503 (tm-30) REVERT: A 126 GLN cc_start: 0.7176 (tm-30) cc_final: 0.6908 (tm-30) REVERT: A 194 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7346 (mp0) REVERT: A 252 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.7399 (ttm170) REVERT: A 296 ARG cc_start: 0.8616 (mtm-85) cc_final: 0.8256 (mtt-85) REVERT: A 399 SER cc_start: 0.8047 (m) cc_final: 0.7709 (p) REVERT: A 454 MET cc_start: 0.7276 (ttm) cc_final: 0.6087 (tpt) REVERT: A 455 MET cc_start: 0.6340 (ttp) cc_final: 0.5699 (tmm) REVERT: C 253 HIS cc_start: 0.8148 (t-170) cc_final: 0.7016 (m90) REVERT: B 90 LYS cc_start: 0.8761 (tttt) cc_final: 0.8416 (tttp) REVERT: B 223 PHE cc_start: 0.8849 (p90) cc_final: 0.8475 (p90) REVERT: E 31 LYS cc_start: 0.8307 (mtpt) cc_final: 0.7388 (mtmm) REVERT: E 57 TYR cc_start: 0.5940 (m-80) cc_final: 0.5469 (m-80) REVERT: E 68 SER cc_start: 0.7301 (m) cc_final: 0.7033 (p) REVERT: E 139 ASP cc_start: 0.3864 (OUTLIER) cc_final: 0.3646 (m-30) REVERT: N 253 HIS cc_start: 0.8106 (t70) cc_final: 0.6892 (m90) REVERT: F 131 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7452 (mp10) REVERT: F 145 LYS cc_start: 0.7394 (ptpt) cc_final: 0.7154 (ptpt) REVERT: G 82 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8140 (mt-10) REVERT: H 71 LYS cc_start: 0.7163 (OUTLIER) cc_final: 0.6746 (mtpp) REVERT: H 78 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7413 (tm-30) REVERT: L 41 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7465 (tm-30) REVERT: L 122 GLN cc_start: 0.6513 (OUTLIER) cc_final: 0.5766 (mp-120) REVERT: L 126 GLN cc_start: 0.7279 (tm-30) cc_final: 0.7031 (tm-30) REVERT: L 194 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7360 (mp0) REVERT: L 252 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7300 (ttm170) REVERT: L 296 ARG cc_start: 0.8597 (mtm-85) cc_final: 0.8156 (mtp-110) REVERT: L 399 SER cc_start: 0.8060 (m) cc_final: 0.7731 (p) REVERT: L 454 MET cc_start: 0.7392 (ttm) cc_final: 0.6219 (tpt) REVERT: O 135 ASP cc_start: 0.8511 (m-30) cc_final: 0.8307 (m-30) REVERT: O 233 MET cc_start: 0.8313 (ptm) cc_final: 0.8110 (ptp) REVERT: M 90 LYS cc_start: 0.8767 (tttt) cc_final: 0.8420 (tttp) REVERT: M 223 PHE cc_start: 0.8852 (p90) cc_final: 0.8480 (p90) REVERT: S 71 LYS cc_start: 0.7081 (OUTLIER) cc_final: 0.6653 (mtpp) REVERT: S 78 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7312 (tm-30) REVERT: P 31 LYS cc_start: 0.8268 (mtpt) cc_final: 0.7410 (mttp) REVERT: P 68 SER cc_start: 0.7032 (m) cc_final: 0.6694 (p) REVERT: P 105 LYS cc_start: 0.2759 (OUTLIER) cc_final: 0.1792 (mtmm) REVERT: Q 76 ASP cc_start: 0.7860 (p0) cc_final: 0.7535 (p0) REVERT: Q 92 LYS cc_start: 0.7209 (OUTLIER) cc_final: 0.6953 (mtmm) REVERT: R 82 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8228 (mt-10) REVERT: T 16 VAL cc_start: 0.4599 (OUTLIER) cc_final: 0.4370 (t) REVERT: U 31 MET cc_start: 0.5991 (tmt) cc_final: 0.5365 (tmm) outliers start: 95 outliers final: 38 residues processed: 422 average time/residue: 0.7653 time to fit residues: 373.6670 Evaluate side-chains 400 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 346 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain D residue 145 LYS Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 139 ASP Chi-restraints excluded: chain N residue 304 VAL Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain G residue 34 ASN Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain H residue 71 LYS Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 78 GLU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain I residue 13 ARG Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain L residue 122 GLN Chi-restraints excluded: chain L residue 160 VAL Chi-restraints excluded: chain L residue 194 GLU Chi-restraints excluded: chain L residue 226 LYS Chi-restraints excluded: chain L residue 252 ARG Chi-restraints excluded: chain L residue 396 ILE Chi-restraints excluded: chain O residue 145 LYS Chi-restraints excluded: chain O residue 162 GLU Chi-restraints excluded: chain O residue 276 ILE Chi-restraints excluded: chain M residue 22 ARG Chi-restraints excluded: chain M residue 294 SER Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain S residue 75 GLU Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 80 LEU Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain P residue 103 LEU Chi-restraints excluded: chain P residue 105 LYS Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 139 ASP Chi-restraints excluded: chain P residue 177 PHE Chi-restraints excluded: chain P residue 211 LYS Chi-restraints excluded: chain Q residue 92 LYS Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain R residue 34 ASN Chi-restraints excluded: chain R residue 82 GLU Chi-restraints excluded: chain T residue 13 ARG Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 50 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 158 optimal weight: 4.9990 chunk 287 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 171 optimal weight: 0.9980 chunk 199 optimal weight: 6.9990 chunk 170 optimal weight: 1.9990 chunk 354 optimal weight: 20.0000 chunk 149 optimal weight: 20.0000 chunk 187 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 141 GLN D 161 ASN D 215 ASN G 31 GLN H 74 ASN O 141 GLN O 161 ASN O 215 ASN S 47 ASN S 74 ASN R 31 GLN V 52 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.158311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.117089 restraints weight = 43292.229| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.17 r_work: 0.3354 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.179 33160 Z= 0.183 Angle : 0.657 13.666 45013 Z= 0.328 Chirality : 0.046 0.157 4876 Planarity : 0.005 0.076 5695 Dihedral : 12.831 159.774 4779 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.16 % Favored : 94.79 % Rotamer: Outliers : 2.70 % Allowed : 13.77 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 1.07 % 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: -1.21 (0.13), residues: 3952 helix: -0.13 (0.12), residues: 1959 sheet: 0.60 (0.28), residues: 342 loop : -1.92 (0.14), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 107 TYR 0.018 0.002 TYR F 133 PHE 0.018 0.002 PHE R 45 TRP 0.017 0.001 TRP L 457 HIS 0.007 0.001 HIS N 197 Details of bonding type rmsd covalent geometry : bond 0.00448 (33154) covalent geometry : angle 0.65698 (45013) hydrogen bonds : bond 0.06482 ( 1289) hydrogen bonds : angle 4.17831 ( 3687) Misc. bond : bond 0.10240 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 349 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7624 (tm-30) REVERT: A 126 GLN cc_start: 0.7361 (tm-30) cc_final: 0.7020 (tm-30) REVERT: A 127 GLN cc_start: 0.7802 (pt0) cc_final: 0.7148 (pt0) REVERT: A 194 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7328 (mp0) REVERT: A 252 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7461 (ttm170) REVERT: A 296 ARG cc_start: 0.8656 (mtm-85) cc_final: 0.8363 (mtt-85) REVERT: A 399 SER cc_start: 0.8075 (m) cc_final: 0.7765 (p) REVERT: A 454 MET cc_start: 0.7304 (ttm) cc_final: 0.6219 (tpt) REVERT: A 455 MET cc_start: 0.6406 (ttp) cc_final: 0.5791 (tmm) REVERT: C 253 HIS cc_start: 0.8200 (t-170) cc_final: 0.7106 (m90) REVERT: B 90 LYS cc_start: 0.8824 (tttt) cc_final: 0.8507 (tttp) REVERT: B 223 PHE cc_start: 0.8926 (p90) cc_final: 0.8511 (p90) REVERT: B 291 ASP cc_start: 0.8574 (t70) cc_final: 0.7999 (t0) REVERT: D 62 MET cc_start: 0.8045 (mtm) cc_final: 0.7737 (ptp) REVERT: E 31 LYS cc_start: 0.8319 (mtpt) cc_final: 0.7436 (mtmm) REVERT: E 57 TYR cc_start: 0.5916 (m-80) cc_final: 0.5435 (m-80) REVERT: E 68 SER cc_start: 0.7315 (m) cc_final: 0.7073 (p) REVERT: E 139 ASP cc_start: 0.3879 (OUTLIER) cc_final: 0.3656 (m-30) REVERT: E 156 LEU cc_start: 0.6484 (OUTLIER) cc_final: 0.6266 (mp) REVERT: N 253 HIS cc_start: 0.8152 (t70) cc_final: 0.7005 (m90) REVERT: F 90 GLU cc_start: 0.7357 (tp30) cc_final: 0.7132 (tt0) REVERT: F 131 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7435 (mp10) REVERT: F 145 LYS cc_start: 0.7517 (ptpt) cc_final: 0.7219 (ptpt) REVERT: G 82 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8158 (mt-10) REVERT: G 90 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7441 (ttt90) REVERT: H 71 LYS cc_start: 0.7214 (OUTLIER) cc_final: 0.6803 (mtpp) REVERT: L 41 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7631 (tm-30) REVERT: L 122 GLN cc_start: 0.6494 (OUTLIER) cc_final: 0.5722 (mp-120) REVERT: L 126 GLN cc_start: 0.7392 (tm-30) cc_final: 0.7150 (tm-30) REVERT: L 194 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7326 (mp0) REVERT: L 252 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.7426 (ttm170) REVERT: L 296 ARG cc_start: 0.8656 (mtm-85) cc_final: 0.8273 (mtp-110) REVERT: L 399 SER cc_start: 0.8082 (m) cc_final: 0.7768 (p) REVERT: L 454 MET cc_start: 0.7413 (ttm) cc_final: 0.6302 (tpt) REVERT: O 135 ASP cc_start: 0.8597 (m-30) cc_final: 0.8376 (m-30) REVERT: O 233 MET cc_start: 0.8365 (ptm) cc_final: 0.8125 (ptp) REVERT: M 90 LYS cc_start: 0.8822 (tttt) cc_final: 0.8503 (tttp) REVERT: M 223 PHE cc_start: 0.8930 (p90) cc_final: 0.8516 (p90) REVERT: M 291 ASP cc_start: 0.8564 (t70) cc_final: 0.8012 (t0) REVERT: S 71 LYS cc_start: 0.7252 (OUTLIER) cc_final: 0.6833 (mtpp) REVERT: S 78 GLU cc_start: 0.7692 (tp30) cc_final: 0.7473 (tm-30) REVERT: P 31 LYS cc_start: 0.8318 (mtpt) cc_final: 0.7512 (mttp) REVERT: P 57 TYR cc_start: 0.5918 (m-80) cc_final: 0.5411 (m-80) REVERT: P 68 SER cc_start: 0.7220 (m) cc_final: 0.6916 (p) REVERT: P 105 LYS cc_start: 0.2905 (OUTLIER) cc_final: 0.0666 (ptpp) REVERT: P 146 ARG cc_start: 0.3655 (OUTLIER) cc_final: 0.3442 (tpp-160) REVERT: Q 76 ASP cc_start: 0.7810 (p0) cc_final: 0.7479 (p0) REVERT: Q 92 LYS cc_start: 0.7359 (mtmm) cc_final: 0.7096 (mtmm) REVERT: R 82 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8207 (mt-10) REVERT: T 16 VAL cc_start: 0.4346 (OUTLIER) cc_final: 0.4113 (t) REVERT: U 31 MET cc_start: 0.5995 (tmt) cc_final: 0.5398 (tmm) outliers start: 92 outliers final: 43 residues processed: 410 average time/residue: 0.7426 time to fit residues: 352.7273 Evaluate side-chains 403 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 344 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain D residue 67 HIS Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 139 ASP Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain N residue 304 VAL Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain G residue 34 ASN Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 71 LYS Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain I residue 13 ARG Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain L residue 122 GLN Chi-restraints excluded: chain L residue 160 VAL Chi-restraints excluded: chain L residue 194 GLU Chi-restraints excluded: chain L residue 226 LYS Chi-restraints excluded: chain L residue 252 ARG Chi-restraints excluded: chain L residue 341 ASP Chi-restraints excluded: chain L residue 396 ILE Chi-restraints excluded: chain O residue 145 LYS Chi-restraints excluded: chain O residue 162 GLU Chi-restraints excluded: chain O residue 276 ILE Chi-restraints excluded: chain M residue 22 ARG Chi-restraints excluded: chain M residue 294 SER Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain S residue 75 GLU Chi-restraints excluded: chain S residue 80 LEU Chi-restraints excluded: chain P residue 105 LYS Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 146 ARG Chi-restraints excluded: chain P residue 198 LEU Chi-restraints excluded: chain P residue 211 LYS Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 145 LYS Chi-restraints excluded: chain R residue 34 ASN Chi-restraints excluded: chain R residue 82 GLU Chi-restraints excluded: chain T residue 13 ARG Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain U residue 38 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 264 optimal weight: 0.0000 chunk 266 optimal weight: 7.9990 chunk 259 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 258 optimal weight: 0.8980 chunk 265 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 288 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 219 optimal weight: 30.0000 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 43 GLN D 141 GLN D 215 ASN E 46 ASN G 31 GLN H 74 ASN I 14 ASN O 141 GLN O 215 ASN S 74 ASN R 31 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.163203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.122926 restraints weight = 43344.758| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.17 r_work: 0.3410 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.140 33160 Z= 0.103 Angle : 0.553 13.555 45013 Z= 0.277 Chirality : 0.042 0.154 4876 Planarity : 0.004 0.069 5695 Dihedral : 11.983 154.505 4779 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.85 % Allowed : 15.06 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 1.07 % 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: -0.61 (0.13), residues: 3952 helix: 0.44 (0.12), residues: 1937 sheet: 0.49 (0.26), residues: 382 loop : -1.65 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 104 TYR 0.012 0.001 TYR Q 114 PHE 0.012 0.001 PHE L 315 TRP 0.015 0.001 TRP L 457 HIS 0.005 0.001 HIS O 263 Details of bonding type rmsd covalent geometry : bond 0.00235 (33154) covalent geometry : angle 0.55315 (45013) hydrogen bonds : bond 0.04143 ( 1289) hydrogen bonds : angle 3.79962 ( 3687) Misc. bond : bond 0.08221 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 368 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7644 (tm-30) REVERT: A 194 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7204 (mp0) REVERT: A 296 ARG cc_start: 0.8599 (mtm-85) cc_final: 0.8341 (mtp85) REVERT: A 399 SER cc_start: 0.8094 (m) cc_final: 0.7775 (p) REVERT: A 409 LYS cc_start: 0.8705 (mttp) cc_final: 0.8380 (mtmt) REVERT: A 454 MET cc_start: 0.7501 (ttm) cc_final: 0.6242 (tpt) REVERT: A 455 MET cc_start: 0.6249 (ttp) cc_final: 0.5630 (tmm) REVERT: C 253 HIS cc_start: 0.8097 (t-170) cc_final: 0.7031 (m90) REVERT: B 54 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.8224 (t80) REVERT: B 90 LYS cc_start: 0.8809 (tttt) cc_final: 0.8533 (ttmm) REVERT: B 223 PHE cc_start: 0.8964 (p90) cc_final: 0.8625 (p90) REVERT: B 291 ASP cc_start: 0.8499 (t70) cc_final: 0.7941 (t0) REVERT: D 62 MET cc_start: 0.8017 (mtm) cc_final: 0.7798 (ptp) REVERT: E 31 LYS cc_start: 0.8247 (mtpt) cc_final: 0.7374 (mtmm) REVERT: E 55 TYR cc_start: 0.7523 (t80) cc_final: 0.7036 (t80) REVERT: E 57 TYR cc_start: 0.5802 (m-80) cc_final: 0.5295 (m-80) REVERT: E 156 LEU cc_start: 0.6513 (OUTLIER) cc_final: 0.6264 (mp) REVERT: N 253 HIS cc_start: 0.8130 (t70) cc_final: 0.6993 (m-70) REVERT: G 82 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8124 (mt-10) REVERT: H 71 LYS cc_start: 0.6863 (OUTLIER) cc_final: 0.6572 (mtpp) REVERT: L 41 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7593 (tm-30) REVERT: L 122 GLN cc_start: 0.6319 (OUTLIER) cc_final: 0.5626 (mp-120) REVERT: L 194 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: L 296 ARG cc_start: 0.8574 (mtm-85) cc_final: 0.8244 (mtp-110) REVERT: L 399 SER cc_start: 0.8066 (m) cc_final: 0.7789 (p) REVERT: L 454 MET cc_start: 0.7331 (ttm) cc_final: 0.6156 (tpt) REVERT: O 135 ASP cc_start: 0.8631 (m-30) cc_final: 0.8399 (m-30) REVERT: O 233 MET cc_start: 0.8132 (ptm) cc_final: 0.7857 (ptp) REVERT: M 54 PHE cc_start: 0.9081 (OUTLIER) cc_final: 0.8201 (t80) REVERT: M 90 LYS cc_start: 0.8785 (tttt) cc_final: 0.8509 (ttmm) REVERT: M 223 PHE cc_start: 0.8950 (p90) cc_final: 0.8618 (p90) REVERT: M 291 ASP cc_start: 0.8459 (t70) cc_final: 0.7929 (t0) REVERT: S 71 LYS cc_start: 0.7043 (OUTLIER) cc_final: 0.6700 (mtpp) REVERT: S 78 GLU cc_start: 0.7575 (tp30) cc_final: 0.7373 (tm-30) REVERT: P 31 LYS cc_start: 0.8142 (mtpt) cc_final: 0.7347 (mttp) REVERT: P 55 TYR cc_start: 0.7614 (t80) cc_final: 0.7184 (t80) REVERT: P 68 SER cc_start: 0.7072 (m) cc_final: 0.6868 (p) REVERT: P 105 LYS cc_start: 0.2976 (OUTLIER) cc_final: 0.0921 (ptpp) REVERT: P 146 ARG cc_start: 0.3539 (OUTLIER) cc_final: 0.3244 (tpp-160) REVERT: Q 108 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7628 (mt0) REVERT: Q 131 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7532 (mp10) REVERT: Q 145 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.6941 (ptpt) REVERT: R 82 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8191 (mt-10) REVERT: T 16 VAL cc_start: 0.4523 (OUTLIER) cc_final: 0.4295 (t) REVERT: U 31 MET cc_start: 0.5867 (tmt) cc_final: 0.5283 (tmm) outliers start: 63 outliers final: 25 residues processed: 406 average time/residue: 0.7226 time to fit residues: 341.4984 Evaluate side-chains 396 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 355 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain D residue 67 HIS Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain G residue 34 ASN Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 71 LYS Chi-restraints excluded: chain I residue 13 ARG Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain L residue 122 GLN Chi-restraints excluded: chain L residue 194 GLU Chi-restraints excluded: chain L residue 396 ILE Chi-restraints excluded: chain O residue 67 HIS Chi-restraints excluded: chain O residue 162 GLU Chi-restraints excluded: chain M residue 22 ARG Chi-restraints excluded: chain M residue 54 PHE Chi-restraints excluded: chain M residue 294 SER Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain P residue 103 LEU Chi-restraints excluded: chain P residue 105 LYS Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 146 ARG Chi-restraints excluded: chain P residue 211 LYS Chi-restraints excluded: chain Q residue 108 GLN Chi-restraints excluded: chain Q residue 131 GLN Chi-restraints excluded: chain Q residue 145 LYS Chi-restraints excluded: chain R residue 34 ASN Chi-restraints excluded: chain R residue 82 GLU Chi-restraints excluded: chain T residue 13 ARG Chi-restraints excluded: chain T residue 16 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 152 optimal weight: 30.0000 chunk 68 optimal weight: 0.8980 chunk 71 optimal weight: 9.9990 chunk 362 optimal weight: 0.9990 chunk 148 optimal weight: 8.9990 chunk 313 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 206 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 267 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 141 GLN D 161 ASN D 215 ASN G 31 GLN H 74 ASN O 141 GLN O 161 ASN O 215 ASN S 74 ASN R 31 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.160120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.120497 restraints weight = 43234.030| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.36 r_work: 0.3363 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.164 33160 Z= 0.140 Angle : 0.608 13.432 45013 Z= 0.302 Chirality : 0.044 0.153 4876 Planarity : 0.004 0.074 5695 Dihedral : 11.999 156.113 4779 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.79 % Allowed : 15.53 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 1.07 % 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: -0.63 (0.13), residues: 3952 helix: 0.42 (0.12), residues: 1935 sheet: 0.76 (0.28), residues: 342 loop : -1.68 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 107 TYR 0.014 0.001 TYR C 136 PHE 0.017 0.001 PHE L 315 TRP 0.013 0.001 TRP L 457 HIS 0.005 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00334 (33154) covalent geometry : angle 0.60820 (45013) hydrogen bonds : bond 0.05593 ( 1289) hydrogen bonds : angle 3.98921 ( 3687) Misc. bond : bond 0.09403 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 354 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7598 (tm-30) REVERT: A 194 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7297 (mp0) REVERT: A 252 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.7428 (ttm170) REVERT: A 296 ARG cc_start: 0.8614 (mtm-85) cc_final: 0.8297 (mtt-85) REVERT: A 399 SER cc_start: 0.8059 (m) cc_final: 0.7739 (p) REVERT: A 454 MET cc_start: 0.7403 (ttm) cc_final: 0.6181 (tpt) REVERT: A 455 MET cc_start: 0.6456 (ttp) cc_final: 0.5797 (tmm) REVERT: C 253 HIS cc_start: 0.8134 (t-170) cc_final: 0.7028 (m90) REVERT: B 90 LYS cc_start: 0.8770 (tttt) cc_final: 0.8489 (ttmm) REVERT: B 223 PHE cc_start: 0.8910 (p90) cc_final: 0.8670 (p90) REVERT: B 291 ASP cc_start: 0.8515 (t70) cc_final: 0.7843 (t0) REVERT: D 62 MET cc_start: 0.8025 (mtm) cc_final: 0.7730 (ptp) REVERT: D 137 GLU cc_start: 0.8547 (pt0) cc_final: 0.8331 (mt-10) REVERT: E 31 LYS cc_start: 0.8316 (mtpt) cc_final: 0.7423 (mtmm) REVERT: E 57 TYR cc_start: 0.5875 (m-80) cc_final: 0.5384 (m-80) REVERT: E 156 LEU cc_start: 0.6346 (OUTLIER) cc_final: 0.6144 (mp) REVERT: N 253 HIS cc_start: 0.8102 (t70) cc_final: 0.6913 (m90) REVERT: F 107 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8408 (pp) REVERT: G 82 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8104 (mt-10) REVERT: H 71 LYS cc_start: 0.6860 (OUTLIER) cc_final: 0.6525 (mtpp) REVERT: L 41 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7649 (tm-30) REVERT: L 122 GLN cc_start: 0.6351 (OUTLIER) cc_final: 0.5648 (mp-120) REVERT: L 126 GLN cc_start: 0.7345 (tm-30) cc_final: 0.7075 (tm-30) REVERT: L 194 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7347 (mp0) REVERT: L 252 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7400 (ttm170) REVERT: L 296 ARG cc_start: 0.8582 (mtm-85) cc_final: 0.8183 (mtp-110) REVERT: L 399 SER cc_start: 0.8080 (m) cc_final: 0.7769 (p) REVERT: L 454 MET cc_start: 0.7489 (ttm) cc_final: 0.6289 (tpt) REVERT: O 135 ASP cc_start: 0.8605 (m-30) cc_final: 0.8361 (m-30) REVERT: O 233 MET cc_start: 0.8169 (ptm) cc_final: 0.7927 (ptp) REVERT: M 90 LYS cc_start: 0.8743 (tttt) cc_final: 0.8464 (ttmm) REVERT: M 223 PHE cc_start: 0.8916 (p90) cc_final: 0.8683 (p90) REVERT: M 291 ASP cc_start: 0.8475 (t70) cc_final: 0.7824 (t0) REVERT: S 71 LYS cc_start: 0.6952 (OUTLIER) cc_final: 0.6585 (mtpp) REVERT: S 78 GLU cc_start: 0.7635 (tp30) cc_final: 0.7400 (tm-30) REVERT: P 31 LYS cc_start: 0.8199 (mtpt) cc_final: 0.7372 (mttp) REVERT: P 68 SER cc_start: 0.7049 (m) cc_final: 0.6784 (p) REVERT: P 105 LYS cc_start: 0.2927 (OUTLIER) cc_final: 0.0860 (ptpp) REVERT: P 146 ARG cc_start: 0.3535 (OUTLIER) cc_final: 0.3214 (tpp-160) REVERT: Q 76 ASP cc_start: 0.7738 (p0) cc_final: 0.7193 (p0) REVERT: Q 92 LYS cc_start: 0.7304 (mtmm) cc_final: 0.7071 (mtmm) REVERT: Q 108 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7546 (mt0) REVERT: Q 145 LYS cc_start: 0.7267 (ptpt) cc_final: 0.7005 (ptpt) REVERT: R 82 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8167 (mt-10) REVERT: T 16 VAL cc_start: 0.4229 (OUTLIER) cc_final: 0.4019 (t) REVERT: U 31 MET cc_start: 0.5752 (tmt) cc_final: 0.5233 (tmm) outliers start: 61 outliers final: 30 residues processed: 395 average time/residue: 0.7709 time to fit residues: 351.2179 Evaluate side-chains 392 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 347 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain G residue 34 ASN Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 71 LYS Chi-restraints excluded: chain I residue 13 ARG Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain L residue 122 GLN Chi-restraints excluded: chain L residue 194 GLU Chi-restraints excluded: chain L residue 252 ARG Chi-restraints excluded: chain L residue 396 ILE Chi-restraints excluded: chain L residue 424 LYS Chi-restraints excluded: chain O residue 67 HIS Chi-restraints excluded: chain O residue 145 LYS Chi-restraints excluded: chain O residue 162 GLU Chi-restraints excluded: chain M residue 22 ARG Chi-restraints excluded: chain M residue 294 SER Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain P residue 103 LEU Chi-restraints excluded: chain P residue 105 LYS Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 146 ARG Chi-restraints excluded: chain P residue 211 LYS Chi-restraints excluded: chain Q residue 108 GLN Chi-restraints excluded: chain R residue 34 ASN Chi-restraints excluded: chain R residue 82 GLU Chi-restraints excluded: chain T residue 9 THR Chi-restraints excluded: chain T residue 13 ARG Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain U residue 32 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 269 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 347 optimal weight: 20.0000 chunk 255 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 387 optimal weight: 0.0270 chunk 339 optimal weight: 1.9990 chunk 276 optimal weight: 4.9990 chunk 311 optimal weight: 2.9990 chunk 386 optimal weight: 6.9990 chunk 172 optimal weight: 8.9990 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN D 67 HIS D 141 GLN D 215 ASN G 31 GLN H 74 ASN L 102 GLN O 141 GLN O 215 ASN S 74 ASN R 31 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.158244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.117344 restraints weight = 43165.661| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.15 r_work: 0.3341 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.176 33160 Z= 0.187 Angle : 0.664 13.238 45013 Z= 0.331 Chirality : 0.046 0.158 4876 Planarity : 0.004 0.077 5695 Dihedral : 12.242 157.626 4779 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.91 % Allowed : 16.00 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 1.07 % 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: -0.84 (0.13), residues: 3952 helix: 0.18 (0.12), residues: 1959 sheet: 0.94 (0.28), residues: 320 loop : -1.75 (0.14), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 107 TYR 0.016 0.002 TYR Q 133 PHE 0.018 0.002 PHE L 315 TRP 0.013 0.001 TRP C 142 HIS 0.007 0.001 HIS N 197 Details of bonding type rmsd covalent geometry : bond 0.00458 (33154) covalent geometry : angle 0.66428 (45013) hydrogen bonds : bond 0.06565 ( 1289) hydrogen bonds : angle 4.17249 ( 3687) Misc. bond : bond 0.10146 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 353 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7636 (tm-30) REVERT: A 126 GLN cc_start: 0.7378 (tm-30) cc_final: 0.7167 (tm-30) REVERT: A 194 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7392 (mp0) REVERT: A 252 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.7491 (ttm170) REVERT: A 296 ARG cc_start: 0.8645 (mtm-85) cc_final: 0.8337 (mtt-85) REVERT: A 399 SER cc_start: 0.8080 (m) cc_final: 0.7794 (p) REVERT: A 454 MET cc_start: 0.7340 (ttm) cc_final: 0.6192 (tpt) REVERT: A 455 MET cc_start: 0.6474 (ttp) cc_final: 0.5816 (tmm) REVERT: C 253 HIS cc_start: 0.8186 (t-170) cc_final: 0.7085 (m90) REVERT: B 90 LYS cc_start: 0.8794 (tttt) cc_final: 0.8468 (tttp) REVERT: B 194 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7412 (tt0) REVERT: B 223 PHE cc_start: 0.8922 (p90) cc_final: 0.8552 (p90) REVERT: B 247 LYS cc_start: 0.9044 (tttt) cc_final: 0.8742 (ttmp) REVERT: B 291 ASP cc_start: 0.8610 (t70) cc_final: 0.7904 (t0) REVERT: E 31 LYS cc_start: 0.8304 (mtpt) cc_final: 0.7399 (mtmm) REVERT: E 57 TYR cc_start: 0.5939 (m-80) cc_final: 0.5502 (m-80) REVERT: E 156 LEU cc_start: 0.6388 (OUTLIER) cc_final: 0.6181 (mp) REVERT: N 253 HIS cc_start: 0.8178 (t70) cc_final: 0.7001 (m90) REVERT: F 107 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8389 (pp) REVERT: F 131 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7474 (mp10) REVERT: F 145 LYS cc_start: 0.7487 (ptpt) cc_final: 0.7261 (ptpt) REVERT: G 82 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8132 (mt-10) REVERT: H 71 LYS cc_start: 0.7155 (OUTLIER) cc_final: 0.6767 (mtpp) REVERT: L 41 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7629 (tm-30) REVERT: L 122 GLN cc_start: 0.6433 (OUTLIER) cc_final: 0.5650 (mp-120) REVERT: L 126 GLN cc_start: 0.7402 (tm-30) cc_final: 0.7165 (tm-30) REVERT: L 194 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7420 (mp0) REVERT: L 252 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.7417 (ttm170) REVERT: L 296 ARG cc_start: 0.8625 (mtm-85) cc_final: 0.8317 (mtt-85) REVERT: L 399 SER cc_start: 0.8081 (m) cc_final: 0.7800 (p) REVERT: L 454 MET cc_start: 0.7442 (ttm) cc_final: 0.6259 (tpt) REVERT: L 455 MET cc_start: 0.6393 (ttp) cc_final: 0.5768 (tmm) REVERT: O 135 ASP cc_start: 0.8634 (m-30) cc_final: 0.8395 (m-30) REVERT: O 137 GLU cc_start: 0.8547 (pt0) cc_final: 0.8304 (mt-10) REVERT: O 233 MET cc_start: 0.8293 (ptm) cc_final: 0.8062 (ptp) REVERT: M 90 LYS cc_start: 0.8793 (tttt) cc_final: 0.8467 (tttp) REVERT: M 194 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7385 (tt0) REVERT: M 223 PHE cc_start: 0.8928 (p90) cc_final: 0.8561 (p90) REVERT: M 247 LYS cc_start: 0.9031 (tttt) cc_final: 0.8742 (ttmp) REVERT: M 291 ASP cc_start: 0.8587 (t70) cc_final: 0.7908 (t0) REVERT: S 71 LYS cc_start: 0.7162 (OUTLIER) cc_final: 0.6737 (mtpp) REVERT: P 31 LYS cc_start: 0.8203 (mtpt) cc_final: 0.7384 (mttp) REVERT: P 68 SER cc_start: 0.7202 (m) cc_final: 0.6925 (p) REVERT: P 105 LYS cc_start: 0.2855 (OUTLIER) cc_final: 0.0611 (ptpp) REVERT: P 146 ARG cc_start: 0.3517 (OUTLIER) cc_final: 0.3123 (tpp-160) REVERT: Q 76 ASP cc_start: 0.7879 (p0) cc_final: 0.7376 (p0) REVERT: Q 92 LYS cc_start: 0.7476 (mtmm) cc_final: 0.7275 (mtmm) REVERT: Q 108 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7609 (mt0) REVERT: R 82 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8161 (mt-10) REVERT: T 16 VAL cc_start: 0.4112 (OUTLIER) cc_final: 0.3903 (t) REVERT: U 31 MET cc_start: 0.5561 (tmt) cc_final: 0.4994 (tmm) outliers start: 65 outliers final: 29 residues processed: 395 average time/residue: 0.7722 time to fit residues: 351.0635 Evaluate side-chains 397 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 350 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain D residue 145 LYS Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain G residue 34 ASN Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 71 LYS Chi-restraints excluded: chain I residue 13 ARG Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain L residue 122 GLN Chi-restraints excluded: chain L residue 194 GLU Chi-restraints excluded: chain L residue 252 ARG Chi-restraints excluded: chain L residue 368 SER Chi-restraints excluded: chain L residue 396 ILE Chi-restraints excluded: chain O residue 145 LYS Chi-restraints excluded: chain O residue 162 GLU Chi-restraints excluded: chain M residue 22 ARG Chi-restraints excluded: chain M residue 194 GLU Chi-restraints excluded: chain M residue 294 SER Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain P residue 103 LEU Chi-restraints excluded: chain P residue 105 LYS Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 146 ARG Chi-restraints excluded: chain P residue 211 LYS Chi-restraints excluded: chain Q residue 108 GLN Chi-restraints excluded: chain R residue 82 GLU Chi-restraints excluded: chain T residue 9 THR Chi-restraints excluded: chain T residue 13 ARG Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain U residue 38 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 103 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 chunk 182 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 149 optimal weight: 30.0000 chunk 64 optimal weight: 0.0010 chunk 307 optimal weight: 2.9990 chunk 196 optimal weight: 0.8980 chunk 295 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 263 optimal weight: 3.9990 overall best weight: 1.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 141 GLN D 161 ASN D 215 ASN G 31 GLN H 74 ASN O 141 GLN O 161 ASN O 215 ASN S 74 ASN R 31 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.160964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.121116 restraints weight = 43238.801| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.43 r_work: 0.3376 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.148 33160 Z= 0.124 Angle : 0.590 13.386 45013 Z= 0.295 Chirality : 0.043 0.168 4876 Planarity : 0.004 0.073 5695 Dihedral : 11.872 154.267 4777 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.35 % Allowed : 16.44 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 1.07 % 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: -0.56 (0.13), residues: 3952 helix: 0.47 (0.12), residues: 1941 sheet: 0.66 (0.27), residues: 348 loop : -1.61 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 107 TYR 0.012 0.001 TYR C 136 PHE 0.014 0.001 PHE A 315 TRP 0.013 0.001 TRP L 457 HIS 0.004 0.001 HIS N 197 Details of bonding type rmsd covalent geometry : bond 0.00291 (33154) covalent geometry : angle 0.58976 (45013) hydrogen bonds : bond 0.05020 ( 1289) hydrogen bonds : angle 3.93916 ( 3687) Misc. bond : bond 0.08529 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 351 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7604 (tm-30) REVERT: A 194 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: A 252 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7376 (ttm170) REVERT: A 296 ARG cc_start: 0.8598 (mtm-85) cc_final: 0.8271 (mtt-85) REVERT: A 399 SER cc_start: 0.8100 (m) cc_final: 0.7783 (p) REVERT: A 454 MET cc_start: 0.7402 (ttm) cc_final: 0.6153 (tpt) REVERT: A 455 MET cc_start: 0.6421 (ttp) cc_final: 0.5723 (tmm) REVERT: C 253 HIS cc_start: 0.8103 (t-170) cc_final: 0.6994 (m90) REVERT: C 288 LYS cc_start: 0.8538 (ttmt) cc_final: 0.8298 (mtpt) REVERT: B 90 LYS cc_start: 0.8793 (tttt) cc_final: 0.8492 (ttmm) REVERT: B 223 PHE cc_start: 0.8902 (p90) cc_final: 0.8521 (p90) REVERT: B 291 ASP cc_start: 0.8527 (t70) cc_final: 0.7879 (t0) REVERT: E 31 LYS cc_start: 0.8281 (mtpt) cc_final: 0.7376 (mtmm) REVERT: E 55 TYR cc_start: 0.7449 (t80) cc_final: 0.6957 (t80) REVERT: E 57 TYR cc_start: 0.5762 (m-80) cc_final: 0.5397 (m-80) REVERT: E 156 LEU cc_start: 0.6334 (OUTLIER) cc_final: 0.6131 (mp) REVERT: N 253 HIS cc_start: 0.8073 (t70) cc_final: 0.6879 (m-70) REVERT: N 288 LYS cc_start: 0.8561 (ttmt) cc_final: 0.8332 (mtpt) REVERT: F 145 LYS cc_start: 0.7390 (ptpt) cc_final: 0.7187 (ptpt) REVERT: G 82 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8087 (mt-10) REVERT: H 71 LYS cc_start: 0.6858 (OUTLIER) cc_final: 0.6531 (mtpp) REVERT: L 41 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7636 (tm-30) REVERT: L 122 GLN cc_start: 0.6292 (OUTLIER) cc_final: 0.5596 (mp-120) REVERT: L 194 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: L 252 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7340 (ttm170) REVERT: L 296 ARG cc_start: 0.8562 (mtm-85) cc_final: 0.8235 (mtt-85) REVERT: L 399 SER cc_start: 0.8093 (m) cc_final: 0.7842 (p) REVERT: L 454 MET cc_start: 0.7470 (ttm) cc_final: 0.6194 (tpt) REVERT: L 455 MET cc_start: 0.6440 (ttp) cc_final: 0.5825 (tmm) REVERT: O 135 ASP cc_start: 0.8656 (m-30) cc_final: 0.8405 (m-30) REVERT: O 137 GLU cc_start: 0.8506 (pt0) cc_final: 0.8271 (mt-10) REVERT: O 233 MET cc_start: 0.8173 (ptm) cc_final: 0.7933 (ptp) REVERT: M 90 LYS cc_start: 0.8746 (tttt) cc_final: 0.8462 (ttmm) REVERT: M 223 PHE cc_start: 0.8913 (p90) cc_final: 0.8539 (p90) REVERT: M 291 ASP cc_start: 0.8515 (t70) cc_final: 0.7894 (t0) REVERT: S 71 LYS cc_start: 0.6926 (OUTLIER) cc_final: 0.6541 (mtpp) REVERT: P 31 LYS cc_start: 0.8157 (mtpt) cc_final: 0.7341 (mttp) REVERT: P 55 TYR cc_start: 0.7574 (t80) cc_final: 0.7061 (t80) REVERT: P 68 SER cc_start: 0.6962 (m) cc_final: 0.6713 (p) REVERT: P 105 LYS cc_start: 0.2721 (OUTLIER) cc_final: 0.0580 (ptpp) REVERT: P 146 ARG cc_start: 0.3516 (OUTLIER) cc_final: 0.3222 (tpp-160) REVERT: Q 76 ASP cc_start: 0.7833 (p0) cc_final: 0.7333 (p0) REVERT: Q 92 LYS cc_start: 0.7406 (mtmm) cc_final: 0.7206 (mtmm) REVERT: Q 108 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7555 (mm-40) REVERT: Q 145 LYS cc_start: 0.7254 (OUTLIER) cc_final: 0.6988 (ptpt) REVERT: R 82 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8125 (mt-10) REVERT: T 16 VAL cc_start: 0.4114 (OUTLIER) cc_final: 0.3904 (t) REVERT: U 31 MET cc_start: 0.5518 (tmt) cc_final: 0.5007 (tmm) outliers start: 46 outliers final: 26 residues processed: 383 average time/residue: 0.7883 time to fit residues: 347.6600 Evaluate side-chains 388 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 347 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain G residue 34 ASN Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 71 LYS Chi-restraints excluded: chain I residue 13 ARG Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain L residue 122 GLN Chi-restraints excluded: chain L residue 194 GLU Chi-restraints excluded: chain L residue 252 ARG Chi-restraints excluded: chain L residue 396 ILE Chi-restraints excluded: chain O residue 162 GLU Chi-restraints excluded: chain M residue 22 ARG Chi-restraints excluded: chain M residue 294 SER Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain P residue 103 LEU Chi-restraints excluded: chain P residue 105 LYS Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 146 ARG Chi-restraints excluded: chain P residue 211 LYS Chi-restraints excluded: chain Q residue 108 GLN Chi-restraints excluded: chain Q residue 145 LYS Chi-restraints excluded: chain R residue 34 ASN Chi-restraints excluded: chain R residue 82 GLU Chi-restraints excluded: chain T residue 13 ARG Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain U residue 32 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 107 optimal weight: 7.9990 chunk 112 optimal weight: 0.0040 chunk 371 optimal weight: 4.9990 chunk 328 optimal weight: 0.7980 chunk 375 optimal weight: 0.9990 chunk 68 optimal weight: 0.3980 chunk 114 optimal weight: 0.5980 chunk 337 optimal weight: 0.8980 chunk 278 optimal weight: 3.9990 chunk 194 optimal weight: 0.8980 chunk 359 optimal weight: 10.0000 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN B 258 ASN D 67 HIS D 141 GLN D 161 ASN D 215 ASN ** E 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 43 GLN G 31 GLN H 74 ASN L 67 ASN O 141 GLN O 161 ASN O 215 ASN M 258 ASN S 74 ASN R 31 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.164540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.124452 restraints weight = 43377.023| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.18 r_work: 0.3428 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.138 33160 Z= 0.099 Angle : 0.541 13.311 45013 Z= 0.270 Chirality : 0.041 0.172 4876 Planarity : 0.004 0.068 5695 Dihedral : 11.449 154.666 4777 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.12 % Allowed : 16.76 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 1.07 % 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: -0.14 (0.14), residues: 3952 helix: 0.87 (0.12), residues: 1922 sheet: 0.58 (0.26), residues: 384 loop : -1.43 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 104 TYR 0.011 0.001 TYR Q 114 PHE 0.011 0.001 PHE L 315 TRP 0.013 0.001 TRP D 257 HIS 0.004 0.001 HIS O 263 Details of bonding type rmsd covalent geometry : bond 0.00224 (33154) covalent geometry : angle 0.54096 (45013) hydrogen bonds : bond 0.03804 ( 1289) hydrogen bonds : angle 3.73242 ( 3687) Misc. bond : bond 0.08328 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13452.65 seconds wall clock time: 228 minutes 47.46 seconds (13727.46 seconds total)