Starting phenix.real_space_refine on Fri Mar 6 19:06:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7trg_26089/03_2026/7trg_26089.cif Found real_map, /net/cci-nas-00/data/ceres_data/7trg_26089/03_2026/7trg_26089.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7trg_26089/03_2026/7trg_26089.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7trg_26089/03_2026/7trg_26089.map" model { file = "/net/cci-nas-00/data/ceres_data/7trg_26089/03_2026/7trg_26089.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7trg_26089/03_2026/7trg_26089.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Al 8 5.89 5 P 16 5.49 5 Mg 8 5.21 5 S 203 5.16 5 C 21060 2.51 5 N 5865 2.21 5 O 6530 1.98 5 F 24 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33714 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 1316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1316 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 6, 'TRANS': 163} Chain breaks: 2 Chain: "B" Number of atoms: 4029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4029 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "C" Number of atoms: 4003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4003 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 15, 'TRANS': 505} Chain breaks: 1 Chain: "D" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4063 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 18, 'TRANS': 508} Chain: "E" Number of atoms: 3960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3960 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 11, 'TRANS': 514} Chain: "F" Number of atoms: 3924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3924 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 505} Chain: "G" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4063 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 14, 'TRANS': 520} Chain: "H" Number of atoms: 4064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4064 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 16, 'TRANS': 506} Chain: "I" Number of atoms: 4028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4028 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 14, 'TRANS': 511} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 7.36, per 1000 atoms: 0.22 Number of scatterers: 33714 At special positions: 0 Unit cell: (180.4, 183.7, 113.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 203 16.00 P 16 15.00 Al 8 13.00 Mg 8 11.99 F 24 9.00 O 6530 8.00 N 5865 7.00 C 21060 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 1.3 seconds 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8142 Finding SS restraints... Secondary structure from input PDB file: 182 helices and 49 sheets defined 55.7% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 46 through 49 removed outlier: 3.615A pdb=" N VAL A 49 " --> pdb=" O ARG A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 46 through 49' Processing helix chain 'A' and resid 71 through 79 Processing helix chain 'A' and resid 109 through 127 removed outlier: 3.742A pdb=" N SER A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 150 through 159 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 28 through 44 removed outlier: 3.655A pdb=" N THR B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 68 through 76 Processing helix chain 'B' and resid 80 through 97 Processing helix chain 'B' and resid 100 through 122 removed outlier: 3.603A pdb=" N VAL B 104 " --> pdb=" O GLY B 100 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 143 Processing helix chain 'B' and resid 144 through 147 Processing helix chain 'B' and resid 156 through 170 removed outlier: 4.978A pdb=" N THR B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N SER B 167 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 190 removed outlier: 3.798A pdb=" N ILE B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 200 No H-bonds generated for 'chain 'B' and resid 198 through 200' Processing helix chain 'B' and resid 211 through 215 Processing helix chain 'B' and resid 262 through 286 removed outlier: 5.017A pdb=" N SER B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LYS B 270 " --> pdb=" O MET B 266 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'B' and resid 319 through 329 Processing helix chain 'B' and resid 340 through 344 Processing helix chain 'B' and resid 381 through 405 Processing helix chain 'B' and resid 413 through 429 removed outlier: 4.057A pdb=" N THR B 429 " --> pdb=" O SER B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 444 Processing helix chain 'B' and resid 446 through 457 Processing helix chain 'B' and resid 459 through 472 Processing helix chain 'B' and resid 492 through 496 Processing helix chain 'B' and resid 501 through 520 Processing helix chain 'C' and resid 18 through 35 removed outlier: 3.608A pdb=" N LEU C 22 " --> pdb=" O GLY C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 40 removed outlier: 3.620A pdb=" N THR C 39 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU C 40 " --> pdb=" O ARG C 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 36 through 40' Processing helix chain 'C' and resid 61 through 69 Processing helix chain 'C' and resid 76 through 90 removed outlier: 3.658A pdb=" N VAL C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 114 removed outlier: 3.698A pdb=" N VAL C 97 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR C 98 " --> pdb=" O THR C 94 " (cutoff:3.500A) Proline residue: C 110 - end of helix Processing helix chain 'C' and resid 117 through 140 removed outlier: 3.918A pdb=" N ILE C 121 " --> pdb=" O HIS C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 163 removed outlier: 3.509A pdb=" N LYS C 153 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU C 154 " --> pdb=" O GLU C 150 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU C 155 " --> pdb=" O GLN C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 171 through 185 removed outlier: 4.048A pdb=" N LYS C 177 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N MET C 178 " --> pdb=" O PHE C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 193 No H-bonds generated for 'chain 'C' and resid 191 through 193' Processing helix chain 'C' and resid 204 through 208 Processing helix chain 'C' and resid 224 through 228 removed outlier: 3.943A pdb=" N GLN C 228 " --> pdb=" O PHE C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 283 removed outlier: 3.868A pdb=" N GLU C 270 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TRP C 271 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 305 Processing helix chain 'C' and resid 315 through 327 Processing helix chain 'C' and resid 378 through 402 removed outlier: 3.559A pdb=" N ALA C 392 " --> pdb=" O SER C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 425 removed outlier: 3.628A pdb=" N ARG C 425 " --> pdb=" O ARG C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 428 No H-bonds generated for 'chain 'C' and resid 426 through 428' Processing helix chain 'C' and resid 429 through 442 removed outlier: 3.918A pdb=" N LEU C 433 " --> pdb=" O GLY C 429 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU C 442 " --> pdb=" O TYR C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 454 removed outlier: 3.647A pdb=" N ARG C 447 " --> pdb=" O GLU C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 471 removed outlier: 3.554A pdb=" N GLN C 470 " --> pdb=" O ALA C 466 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY C 471 " --> pdb=" O ARG C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 526 Processing helix chain 'D' and resid 21 through 23 No H-bonds generated for 'chain 'D' and resid 21 through 23' Processing helix chain 'D' and resid 30 through 50 removed outlier: 3.902A pdb=" N LEU D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N THR D 50 " --> pdb=" O ASN D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 81 Processing helix chain 'D' and resid 85 through 102 Processing helix chain 'D' and resid 107 through 126 removed outlier: 3.681A pdb=" N GLU D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLN D 122 " --> pdb=" O GLU D 118 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU D 123 " --> pdb=" O GLU D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 149 removed outlier: 3.638A pdb=" N ASP D 149 " --> pdb=" O ILE D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 174 Processing helix chain 'D' and resid 176 through 180 removed outlier: 4.301A pdb=" N SER D 180 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 197 Processing helix chain 'D' and resid 218 through 222 Processing helix chain 'D' and resid 270 through 295 removed outlier: 3.759A pdb=" N LYS D 282 " --> pdb=" O GLN D 278 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE D 289 " --> pdb=" O PHE D 285 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR D 295 " --> pdb=" O GLN D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 317 Processing helix chain 'D' and resid 326 through 338 Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.810A pdb=" N LEU D 353 " --> pdb=" O ALA D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 415 Processing helix chain 'D' and resid 423 through 438 removed outlier: 3.708A pdb=" N ASP D 438 " --> pdb=" O SER D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 455 Processing helix chain 'D' and resid 456 through 467 removed outlier: 3.854A pdb=" N MET D 460 " --> pdb=" O GLU D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 484 Processing helix chain 'D' and resid 500 through 505 Processing helix chain 'D' and resid 510 through 529 Processing helix chain 'E' and resid 20 through 40 removed outlier: 3.503A pdb=" N VAL E 39 " --> pdb=" O ILE E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 43 No H-bonds generated for 'chain 'E' and resid 41 through 43' Processing helix chain 'E' and resid 66 through 74 Processing helix chain 'E' and resid 78 through 95 removed outlier: 3.634A pdb=" N LYS E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU E 84 " --> pdb=" O ALA E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 119 removed outlier: 3.603A pdb=" N VAL E 102 " --> pdb=" O GLY E 98 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR E 103 " --> pdb=" O THR E 99 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER E 115 " --> pdb=" O ARG E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 144 removed outlier: 3.541A pdb=" N ILE E 126 " --> pdb=" O HIS E 122 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 167 Processing helix chain 'E' and resid 168 through 174 removed outlier: 5.893A pdb=" N LEU E 171 " --> pdb=" O SER E 168 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU E 172 " --> pdb=" O SER E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 189 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 208 through 212 removed outlier: 3.639A pdb=" N SER E 212 " --> pdb=" O LEU E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 284 removed outlier: 4.013A pdb=" N VAL E 264 " --> pdb=" O SER E 260 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET E 275 " --> pdb=" O GLU E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 308 Processing helix chain 'E' and resid 316 through 328 Processing helix chain 'E' and resid 337 through 341 removed outlier: 3.833A pdb=" N VAL E 341 " --> pdb=" O PRO E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 403 removed outlier: 3.812A pdb=" N ASP E 392 " --> pdb=" O ARG E 388 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA E 393 " --> pdb=" O SER E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 426 Processing helix chain 'E' and resid 431 through 444 removed outlier: 3.644A pdb=" N ALA E 435 " --> pdb=" O LYS E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 455 Processing helix chain 'E' and resid 457 through 472 Processing helix chain 'E' and resid 488 through 492 Processing helix chain 'E' and resid 497 through 516 Processing helix chain 'F' and resid 28 through 49 Processing helix chain 'F' and resid 73 through 81 Processing helix chain 'F' and resid 85 through 89 Processing helix chain 'F' and resid 90 through 102 Processing helix chain 'F' and resid 107 through 127 removed outlier: 3.954A pdb=" N THR F 121 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LYS F 122 " --> pdb=" O ASP F 118 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU F 123 " --> pdb=" O SER F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 152 Processing helix chain 'F' and resid 159 through 172 removed outlier: 3.645A pdb=" N LEU F 163 " --> pdb=" O ASP F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 178 removed outlier: 4.423A pdb=" N GLN F 178 " --> pdb=" O VAL F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 193 Proline residue: F 185 - end of helix Processing helix chain 'F' and resid 204 through 206 No H-bonds generated for 'chain 'F' and resid 204 through 206' Processing helix chain 'F' and resid 217 through 221 Processing helix chain 'F' and resid 268 through 293 removed outlier: 4.023A pdb=" N MET F 272 " --> pdb=" O ASP F 268 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASP F 273 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU F 276 " --> pdb=" O MET F 272 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU F 286 " --> pdb=" O TYR F 282 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR F 293 " --> pdb=" O GLN F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 320 Processing helix chain 'F' and resid 332 through 341 Processing helix chain 'F' and resid 347 through 351 Processing helix chain 'F' and resid 352 through 356 removed outlier: 3.922A pdb=" N LEU F 356 " --> pdb=" O ALA F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 418 Processing helix chain 'F' and resid 426 through 443 removed outlier: 3.896A pdb=" N ARG F 441 " --> pdb=" O THR F 437 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR F 442 " --> pdb=" O GLU F 438 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU F 443 " --> pdb=" O TYR F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 457 removed outlier: 4.042A pdb=" N TYR F 449 " --> pdb=" O GLY F 445 " (cutoff:3.500A) Processing helix chain 'F' and resid 459 through 470 Processing helix chain 'F' and resid 472 through 485 Processing helix chain 'F' and resid 512 through 530 Processing helix chain 'G' and resid 14 through 33 removed outlier: 3.810A pdb=" N ARG G 18 " --> pdb=" O GLY G 14 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL G 32 " --> pdb=" O ILE G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 36 No H-bonds generated for 'chain 'G' and resid 34 through 36' Processing helix chain 'G' and resid 57 through 65 Processing helix chain 'G' and resid 69 through 86 removed outlier: 3.830A pdb=" N LEU G 75 " --> pdb=" O ALA G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 110 removed outlier: 3.582A pdb=" N ILE G 95 " --> pdb=" O THR G 91 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU G 106 " --> pdb=" O LYS G 102 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU G 107 " --> pdb=" O ASN G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 133 removed outlier: 3.566A pdb=" N VAL G 117 " --> pdb=" O HIS G 113 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN G 133 " --> pdb=" O VAL G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 157 Processing helix chain 'G' and resid 164 through 179 Processing helix chain 'G' and resid 204 through 208 Processing helix chain 'G' and resid 256 through 258 No H-bonds generated for 'chain 'G' and resid 256 through 258' Processing helix chain 'G' and resid 259 through 280 removed outlier: 3.988A pdb=" N ILE G 263 " --> pdb=" O LYS G 259 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER G 268 " --> pdb=" O ARG G 264 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N THR G 271 " --> pdb=" O GLU G 267 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS G 272 " --> pdb=" O SER G 268 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 304 removed outlier: 3.843A pdb=" N LYS G 298 " --> pdb=" O ASP G 294 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N TYR G 299 " --> pdb=" O MET G 295 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE G 300 " --> pdb=" O CYS G 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 324 Processing helix chain 'G' and resid 381 through 405 removed outlier: 3.732A pdb=" N ASP G 394 " --> pdb=" O ARG G 390 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA G 395 " --> pdb=" O SER G 391 " (cutoff:3.500A) Processing helix chain 'G' and resid 413 through 427 Processing helix chain 'G' and resid 428 through 431 Processing helix chain 'G' and resid 433 through 445 removed outlier: 3.940A pdb=" N ALA G 437 " --> pdb=" O ARG G 433 " (cutoff:3.500A) Processing helix chain 'G' and resid 446 through 456 removed outlier: 3.826A pdb=" N ASN G 450 " --> pdb=" O LEU G 446 " (cutoff:3.500A) Processing helix chain 'G' and resid 459 through 476 Processing helix chain 'G' and resid 477 through 486 removed outlier: 5.468A pdb=" N ASN G 482 " --> pdb=" O GLU G 479 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU G 483 " --> pdb=" O ARG G 480 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TRP G 485 " --> pdb=" O ASN G 482 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE G 486 " --> pdb=" O LEU G 483 " (cutoff:3.500A) Processing helix chain 'G' and resid 497 through 502 Processing helix chain 'G' and resid 507 through 526 Processing helix chain 'H' and resid 19 through 38 removed outlier: 3.914A pdb=" N GLN H 23 " --> pdb=" O GLY H 19 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE H 37 " --> pdb=" O ILE H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 68 Processing helix chain 'H' and resid 74 through 91 Processing helix chain 'H' and resid 96 through 108 Processing helix chain 'H' and resid 109 through 114 Processing helix chain 'H' and resid 118 through 140 removed outlier: 3.817A pdb=" N VAL H 122 " --> pdb=" O HIS H 118 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASP H 131 " --> pdb=" O ARG H 127 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP H 132 " --> pdb=" O LYS H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 161 Processing helix chain 'H' and resid 163 through 167 removed outlier: 4.030A pdb=" N ARG H 167 " --> pdb=" O ALA H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 184 Processing helix chain 'H' and resid 208 through 212 Processing helix chain 'H' and resid 262 through 284 removed outlier: 3.752A pdb=" N GLU H 271 " --> pdb=" O ILE H 267 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU H 272 " --> pdb=" O LEU H 268 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 307 Processing helix chain 'H' and resid 316 through 328 Processing helix chain 'H' and resid 334 through 338 Processing helix chain 'H' and resid 380 through 404 Processing helix chain 'H' and resid 412 through 427 removed outlier: 3.893A pdb=" N LYS H 427 " --> pdb=" O THR H 423 " (cutoff:3.500A) Processing helix chain 'H' and resid 433 through 444 removed outlier: 3.770A pdb=" N ALA H 441 " --> pdb=" O TYR H 437 " (cutoff:3.500A) Processing helix chain 'H' and resid 445 through 456 Processing helix chain 'H' and resid 458 through 471 removed outlier: 3.769A pdb=" N THR H 464 " --> pdb=" O ILE H 460 " (cutoff:3.500A) Processing helix chain 'H' and resid 490 through 494 Processing helix chain 'H' and resid 499 through 517 Processing helix chain 'I' and resid 3 through 8 removed outlier: 3.754A pdb=" N LEU I 7 " --> pdb=" O ALA I 3 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 35 removed outlier: 3.640A pdb=" N LEU I 20 " --> pdb=" O ALA I 16 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL I 33 " --> pdb=" O GLY I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 67 Processing helix chain 'I' and resid 71 through 88 Processing helix chain 'I' and resid 91 through 111 removed outlier: 3.675A pdb=" N VAL I 96 " --> pdb=" O THR I 92 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR I 109 " --> pdb=" O GLN I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 115 through 138 removed outlier: 3.972A pdb=" N ILE I 119 " --> pdb=" O HIS I 115 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU I 136 " --> pdb=" O GLN I 132 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS I 138 " --> pdb=" O LEU I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 157 Processing helix chain 'I' and resid 161 through 179 removed outlier: 3.634A pdb=" N VAL I 167 " --> pdb=" O GLU I 163 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU I 170 " --> pdb=" O ASP I 166 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA I 171 " --> pdb=" O VAL I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 200 through 204 Processing helix chain 'I' and resid 252 through 263 Processing helix chain 'I' and resid 264 through 282 removed outlier: 3.821A pdb=" N ARG I 270 " --> pdb=" O PHE I 266 " (cutoff:3.500A) Processing helix chain 'I' and resid 298 through 307 Processing helix chain 'I' and resid 317 through 329 removed outlier: 3.747A pdb=" N MET I 321 " --> pdb=" O LYS I 317 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU I 322 " --> pdb=" O ARG I 318 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR I 325 " --> pdb=" O MET I 321 " (cutoff:3.500A) Processing helix chain 'I' and resid 340 through 344 Processing helix chain 'I' and resid 380 through 404 Processing helix chain 'I' and resid 412 through 426 Processing helix chain 'I' and resid 427 through 429 No H-bonds generated for 'chain 'I' and resid 427 through 429' Processing helix chain 'I' and resid 432 through 445 removed outlier: 4.089A pdb=" N GLY I 436 " --> pdb=" O ARG I 432 " (cutoff:3.500A) Processing helix chain 'I' and resid 445 through 456 removed outlier: 4.085A pdb=" N LYS I 449 " --> pdb=" O LEU I 445 " (cutoff:3.500A) Processing helix chain 'I' and resid 458 through 469 Processing helix chain 'I' and resid 489 through 493 Processing helix chain 'I' and resid 498 through 517 removed outlier: 3.682A pdb=" N LEU I 517 " --> pdb=" O THR I 513 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 91 removed outlier: 8.922A pdb=" N VAL A 91 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU A 65 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N ILE A 64 " --> pdb=" O ILE A 4 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N HIS A 6 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N VAL A 66 " --> pdb=" O HIS A 6 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N GLN A 8 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N PHE A 133 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N PHE A 167 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU A 135 " --> pdb=" O PHE A 167 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 53 Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 22 removed outlier: 5.156A pdb=" N VAL B 521 " --> pdb=" O MET I 44 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N MET I 46 " --> pdb=" O VAL B 521 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLN B 523 " --> pdb=" O MET I 46 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VAL I 48 " --> pdb=" O GLN B 523 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE B 525 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 63 through 66 removed outlier: 7.903A pdb=" N ASN B 53 " --> pdb=" O ASP C 528 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N THR C 530 " --> pdb=" O ASN B 53 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N MET B 55 " --> pdb=" O THR C 530 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N LYS C 532 " --> pdb=" O MET B 55 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE B 57 " --> pdb=" O LYS C 532 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 202 through 208 removed outlier: 3.808A pdb=" N GLY B 379 " --> pdb=" O ILE B 207 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 220 through 223 Processing sheet with id=AA7, first strand: chain 'B' and resid 311 through 314 removed outlier: 6.307A pdb=" N LYS B 238 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL B 292 " --> pdb=" O LYS B 238 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA B 240 " --> pdb=" O VAL B 292 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 255 through 259 removed outlier: 8.433A pdb=" N GLU C 254 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL B 257 " --> pdb=" O GLU C 254 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ARG C 256 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ILE B 259 " --> pdb=" O ARG C 256 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N LYS D 265 " --> pdb=" O ALA C 253 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE C 255 " --> pdb=" O LYS D 265 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ASP D 267 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL C 257 " --> pdb=" O ASP D 267 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ARG E 255 " --> pdb=" O HIS D 264 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU D 266 " --> pdb=" O ARG E 255 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ARG E 257 " --> pdb=" O LEU D 266 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL D 268 " --> pdb=" O ARG E 257 " (cutoff:3.500A) removed outlier: 9.444A pdb=" N GLN F 263 " --> pdb=" O SER E 254 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL E 256 " --> pdb=" O GLN F 263 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL F 265 " --> pdb=" O VAL E 256 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL E 258 " --> pdb=" O VAL F 265 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N GLN G 251 " --> pdb=" O ASN F 262 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE F 264 " --> pdb=" O GLN G 251 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL G 253 " --> pdb=" O ILE F 264 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N VAL F 266 " --> pdb=" O VAL G 253 " (cutoff:3.500A) removed outlier: 9.202A pdb=" N ASP H 255 " --> pdb=" O VAL G 250 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL G 252 " --> pdb=" O ASP H 255 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N GLU H 257 " --> pdb=" O VAL G 252 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ILE G 254 " --> pdb=" O GLU H 257 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 408 through 410 Processing sheet with id=AB1, first strand: chain 'B' and resid 478 through 480 Processing sheet with id=AB2, first strand: chain 'C' and resid 56 through 59 removed outlier: 7.283A pdb=" N ASP C 46 " --> pdb=" O ASP D 531 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE D 533 " --> pdb=" O ASP C 46 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU C 48 " --> pdb=" O ILE D 533 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LYS D 535 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL C 50 " --> pdb=" O LYS D 535 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 195 through 199 removed outlier: 6.483A pdb=" N GLY C 196 " --> pdb=" O PHE C 372 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N LEU C 374 " --> pdb=" O GLY C 196 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LYS C 198 " --> pdb=" O LEU C 374 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 213 through 217 Processing sheet with id=AB5, first strand: chain 'C' and resid 309 through 311 Processing sheet with id=AB6, first strand: chain 'C' and resid 405 through 407 Processing sheet with id=AB7, first strand: chain 'C' and resid 486 through 489 Processing sheet with id=AB8, first strand: chain 'D' and resid 68 through 71 removed outlier: 6.400A pdb=" N ASP D 58 " --> pdb=" O VAL E 517 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASN E 519 " --> pdb=" O ASP D 58 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 153 through 154 Processing sheet with id=AC1, first strand: chain 'D' and resid 209 through 215 removed outlier: 6.664A pdb=" N LYS D 210 " --> pdb=" O ILE D 385 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE D 387 " --> pdb=" O LYS D 210 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLU D 212 " --> pdb=" O ILE D 387 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N GLY D 389 " --> pdb=" O GLU D 212 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS D 214 " --> pdb=" O GLY D 389 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 228 through 230 Processing sheet with id=AC3, first strand: chain 'D' and resid 321 through 322 removed outlier: 6.863A pdb=" N ALA D 300 " --> pdb=" O VAL D 322 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LYS D 247 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ILE D 301 " --> pdb=" O LYS D 247 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA D 249 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N VAL D 342 " --> pdb=" O ILE D 248 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE D 250 " --> pdb=" O VAL D 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'D' and resid 321 through 322 removed outlier: 6.863A pdb=" N ALA D 300 " --> pdb=" O VAL D 322 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LYS D 247 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ILE D 301 " --> pdb=" O LYS D 247 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA D 249 " --> pdb=" O ILE D 301 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 61 through 64 removed outlier: 7.094A pdb=" N ASP E 49 " --> pdb=" O ASP F 534 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N VAL F 536 " --> pdb=" O ASP E 49 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE E 51 " --> pdb=" O VAL F 536 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR F 538 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU E 53 " --> pdb=" O THR F 538 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 146 through 147 Processing sheet with id=AC7, first strand: chain 'E' and resid 199 through 205 removed outlier: 6.736A pdb=" N HIS E 200 " --> pdb=" O ILE E 373 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N LEU E 375 " --> pdb=" O HIS E 200 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE E 202 " --> pdb=" O LEU E 375 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N GLY E 377 " --> pdb=" O ILE E 202 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LYS E 204 " --> pdb=" O GLY E 377 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 218 through 220 removed outlier: 6.569A pdb=" N VAL E 365 " --> pdb=" O CYS E 346 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N CYS E 346 " --> pdb=" O VAL E 365 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LYS E 347 " --> pdb=" O ASN E 234 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 310 through 312 removed outlier: 6.624A pdb=" N PHE E 290 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N ALA E 332 " --> pdb=" O ILE E 237 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE E 239 " --> pdb=" O ALA E 332 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 476 through 479 Processing sheet with id=AD2, first strand: chain 'F' and resid 68 through 71 removed outlier: 5.979A pdb=" N ASP F 58 " --> pdb=" O ILE G 527 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP G 529 " --> pdb=" O ASP F 58 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AD4, first strand: chain 'F' and resid 208 through 212 removed outlier: 6.544A pdb=" N LYS F 209 " --> pdb=" O ILE F 388 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL F 390 " --> pdb=" O LYS F 209 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL F 211 " --> pdb=" O VAL F 390 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 226 through 229 removed outlier: 6.561A pdb=" N CYS F 379 " --> pdb=" O ALA F 359 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ALA F 359 " --> pdb=" O CYS F 379 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU F 361 " --> pdb=" O GLU F 242 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N GLU F 242 " --> pdb=" O LEU F 361 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLU F 363 " --> pdb=" O ARG F 240 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG F 240 " --> pdb=" O GLU F 363 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL F 297 " --> pdb=" O LYS F 243 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LYS F 245 " --> pdb=" O VAL F 297 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LEU F 299 " --> pdb=" O LYS F 245 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLY F 247 " --> pdb=" O LEU F 299 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N GLN F 301 " --> pdb=" O GLY F 247 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ILE F 249 " --> pdb=" O GLN F 301 " (cutoff:3.500A) removed outlier: 10.460A pdb=" N LEU F 298 " --> pdb=" O LYS F 326 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N ILE F 328 " --> pdb=" O LEU F 298 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE F 300 " --> pdb=" O ILE F 328 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 491 through 494 Processing sheet with id=AD7, first strand: chain 'G' and resid 52 through 55 removed outlier: 5.770A pdb=" N ASP G 42 " --> pdb=" O ILE H 519 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP H 521 " --> pdb=" O ASP G 42 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 137 through 138 Processing sheet with id=AD9, first strand: chain 'G' and resid 196 through 199 removed outlier: 6.263A pdb=" N ASN G 196 " --> pdb=" O ILE G 375 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU G 377 " --> pdb=" O ASN G 196 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU G 198 " --> pdb=" O LEU G 377 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N SER G 212 " --> pdb=" O ASN G 366 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N THR G 367 " --> pdb=" O ALA G 348 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ALA G 348 " --> pdb=" O THR G 367 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 196 through 199 removed outlier: 6.263A pdb=" N ASN G 196 " --> pdb=" O ILE G 375 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU G 377 " --> pdb=" O ASN G 196 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU G 198 " --> pdb=" O LEU G 377 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N SER G 212 " --> pdb=" O ASN G 366 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N THR G 367 " --> pdb=" O ALA G 348 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ALA G 348 " --> pdb=" O THR G 367 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LYS G 233 " --> pdb=" O VAL G 285 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU G 287 " --> pdb=" O LYS G 233 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ALA G 235 " --> pdb=" O LEU G 287 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 57 through 60 removed outlier: 7.555A pdb=" N MET H 47 " --> pdb=" O ASP I 519 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE I 521 " --> pdb=" O MET H 47 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N MET H 49 " --> pdb=" O ILE I 521 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ARG I 523 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU H 51 " --> pdb=" O ARG I 523 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 142 through 143 Processing sheet with id=AE4, first strand: chain 'H' and resid 185 through 186 Processing sheet with id=AE5, first strand: chain 'H' and resid 199 through 205 removed outlier: 6.552A pdb=" N ARG H 200 " --> pdb=" O ILE H 374 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N LEU H 376 " --> pdb=" O ARG H 200 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLU H 202 " --> pdb=" O LEU H 376 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N GLY H 378 " --> pdb=" O GLU H 202 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ILE H 204 " --> pdb=" O GLY H 378 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR H 373 " --> pdb=" O LEU H 215 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 218 through 220 Processing sheet with id=AE7, first strand: chain 'H' and resid 238 through 241 removed outlier: 6.435A pdb=" N VAL H 239 " --> pdb=" O ILE H 291 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 478 through 481 removed outlier: 3.882A pdb=" N THR H 486 " --> pdb=" O ASN H 481 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 139 through 140 Processing sheet with id=AF1, first strand: chain 'I' and resid 191 through 196 removed outlier: 6.296A pdb=" N GLU I 192 " --> pdb=" O LEU I 374 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ILE I 376 " --> pdb=" O GLU I 192 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N MET I 194 " --> pdb=" O ILE I 376 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 210 through 212 Processing sheet with id=AF3, first strand: chain 'I' and resid 310 through 314 Processing sheet with id=AF4, first strand: chain 'I' and resid 477 through 479 1943 hydrogen bonds defined for protein. 5556 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: 6.85 Time building geometry restraints manager: 3.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 5881 1.28 - 1.41: 7046 1.41 - 1.55: 20787 1.55 - 1.69: 38 1.69 - 1.82: 350 Bond restraints: 34102 Sorted by residual: bond pdb=" F2 AF3 F 603 " pdb="AL AF3 F 603 " ideal model delta sigma weight residual 1.637 1.801 -0.164 2.00e-02 2.50e+03 6.70e+01 bond pdb=" F3 AF3 E 603 " pdb="AL AF3 E 603 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.68e+01 bond pdb=" F3 AF3 G 603 " pdb="AL AF3 G 603 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.68e+01 bond pdb=" F1 AF3 D 603 " pdb="AL AF3 D 603 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.68e+01 bond pdb=" F1 AF3 G 603 " pdb="AL AF3 G 603 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.67e+01 ... (remaining 34097 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 45395 2.31 - 4.62: 526 4.62 - 6.94: 102 6.94 - 9.25: 20 9.25 - 11.56: 9 Bond angle restraints: 46052 Sorted by residual: angle pdb=" CA ASP E 66 " pdb=" CB ASP E 66 " pdb=" CG ASP E 66 " ideal model delta sigma weight residual 112.60 120.65 -8.05 1.00e+00 1.00e+00 6.48e+01 angle pdb=" CA ASP E 245 " pdb=" CB ASP E 245 " pdb=" CG ASP E 245 " ideal model delta sigma weight residual 112.60 119.70 -7.10 1.00e+00 1.00e+00 5.04e+01 angle pdb=" C ASP G 57 " pdb=" N GLY G 58 " pdb=" CA GLY G 58 " ideal model delta sigma weight residual 119.98 126.99 -7.01 1.11e+00 8.12e-01 3.98e+01 angle pdb=" N THR E 246 " pdb=" CA THR E 246 " pdb=" C THR E 246 " ideal model delta sigma weight residual 111.90 103.80 8.10 1.32e+00 5.74e-01 3.77e+01 angle pdb=" C ASP E 66 " pdb=" CA ASP E 66 " pdb=" CB ASP E 66 " ideal model delta sigma weight residual 109.54 119.96 -10.42 1.84e+00 2.95e-01 3.20e+01 ... (remaining 46047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 20564 35.73 - 71.46: 444 71.46 - 107.19: 42 107.19 - 142.92: 4 142.92 - 178.65: 4 Dihedral angle restraints: 21058 sinusoidal: 8479 harmonic: 12579 Sorted by residual: dihedral pdb=" O1B ADP G 602 " pdb=" O3A ADP G 602 " pdb=" PB ADP G 602 " pdb=" PA ADP G 602 " ideal model delta sinusoidal sigma weight residual -60.00 118.65 -178.65 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP E 602 " pdb=" O3A ADP E 602 " pdb=" PB ADP E 602 " pdb=" PA ADP E 602 " ideal model delta sinusoidal sigma weight residual 300.00 126.13 173.86 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP F 602 " pdb=" O3A ADP F 602 " pdb=" PA ADP F 602 " pdb=" PB ADP F 602 " ideal model delta sinusoidal sigma weight residual -60.00 111.18 -171.18 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 21055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 5326 0.111 - 0.223: 149 0.223 - 0.334: 1 0.334 - 0.446: 0 0.446 - 0.557: 1 Chirality restraints: 5477 Sorted by residual: chirality pdb=" CA ASP E 66 " pdb=" N ASP E 66 " pdb=" C ASP E 66 " pdb=" CB ASP E 66 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.77e+00 chirality pdb=" CA ASP E 245 " pdb=" N ASP E 245 " pdb=" C ASP E 245 " pdb=" CB ASP E 245 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" C3' ADP F 602 " pdb=" C2' ADP F 602 " pdb=" C4' ADP F 602 " pdb=" O3' ADP F 602 " both_signs ideal model delta sigma weight residual False -2.51 -2.73 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 5474 not shown) Planarity restraints: 5885 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS C 468 " 0.022 2.00e-02 2.50e+03 4.19e-02 1.75e+01 pdb=" C HIS C 468 " -0.072 2.00e-02 2.50e+03 pdb=" O HIS C 468 " 0.025 2.00e-02 2.50e+03 pdb=" N ALA C 469 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP G 57 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.73e+00 pdb=" C ASP G 57 " 0.045 2.00e-02 2.50e+03 pdb=" O ASP G 57 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY G 58 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADP E 602 " 0.031 2.00e-02 2.50e+03 1.50e-02 6.22e+00 pdb=" C2 ADP E 602 " -0.003 2.00e-02 2.50e+03 pdb=" C4 ADP E 602 " -0.013 2.00e-02 2.50e+03 pdb=" C5 ADP E 602 " -0.013 2.00e-02 2.50e+03 pdb=" C6 ADP E 602 " -0.009 2.00e-02 2.50e+03 pdb=" C8 ADP E 602 " 0.003 2.00e-02 2.50e+03 pdb=" N1 ADP E 602 " 0.015 2.00e-02 2.50e+03 pdb=" N3 ADP E 602 " -0.011 2.00e-02 2.50e+03 pdb=" N6 ADP E 602 " 0.022 2.00e-02 2.50e+03 pdb=" N7 ADP E 602 " -0.011 2.00e-02 2.50e+03 pdb=" N9 ADP E 602 " -0.011 2.00e-02 2.50e+03 ... (remaining 5882 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 149 2.53 - 3.12: 24379 3.12 - 3.71: 48952 3.71 - 4.31: 67113 4.31 - 4.90: 119357 Nonbonded interactions: 259950 Sorted by model distance: nonbonded pdb="MG MG C 601 " pdb=" O3A ADP C 602 " model vdw 1.932 2.170 nonbonded pdb="MG MG D 601 " pdb=" O1B ADP D 602 " model vdw 1.946 2.170 nonbonded pdb="MG MG B 601 " pdb=" F1 AF3 B 603 " model vdw 1.955 2.120 nonbonded pdb="MG MG I 601 " pdb=" F1 AF3 I 603 " model vdw 1.971 2.120 nonbonded pdb="MG MG B 601 " pdb=" O1B ADP B 602 " model vdw 1.994 2.170 ... (remaining 259945 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 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: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 30.070 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 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:6.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.641 34106 Z= 0.618 Angle : 0.678 11.561 46052 Z= 0.366 Chirality : 0.044 0.557 5477 Planarity : 0.004 0.045 5885 Dihedral : 15.522 178.654 12916 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.77 % Favored : 96.19 % Rotamer: Outliers : 0.19 % Allowed : 9.48 % Favored : 90.33 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.13), residues: 4353 helix: 2.20 (0.11), residues: 2205 sheet: 0.70 (0.22), residues: 592 loop : -1.18 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 535 TYR 0.011 0.001 TYR G 131 PHE 0.024 0.001 PHE G 8 TRP 0.011 0.001 TRP A 21 HIS 0.004 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00533 (34102) covalent geometry : angle 0.67768 (46052) hydrogen bonds : bond 0.09239 ( 1926) hydrogen bonds : angle 4.10922 ( 5556) Misc. bond : bond 0.51287 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 247 time to evaluate : 1.222 Fit side-chains REVERT: A 42 LEU cc_start: 0.7751 (mm) cc_final: 0.7139 (tt) REVERT: C 252 ASN cc_start: 0.7651 (t0) cc_final: 0.7088 (t0) REVERT: C 470 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.7308 (pt0) REVERT: E 48 MET cc_start: 0.8897 (mmm) cc_final: 0.8681 (mmt) REVERT: G 225 MET cc_start: 0.9550 (mtt) cc_final: 0.9331 (mtt) REVERT: G 430 MET cc_start: 0.7023 (mmm) cc_final: 0.6786 (mmm) REVERT: H 182 MET cc_start: 0.8808 (ttm) cc_final: 0.8608 (ptm) outliers start: 7 outliers final: 1 residues processed: 250 average time/residue: 0.6945 time to fit residues: 207.4177 Evaluate side-chains 222 residues out of total 3649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 220 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain C residue 470 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 0.4980 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 9.9990 chunk 424 optimal weight: 5.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 HIS A 134 GLN H 111 HIS H 284 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.095961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.080100 restraints weight = 59354.632| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.49 r_work: 0.3030 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.0573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 34106 Z= 0.167 Angle : 0.602 8.209 46052 Z= 0.302 Chirality : 0.044 0.175 5477 Planarity : 0.004 0.058 5885 Dihedral : 8.240 177.824 4741 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.18 % Favored : 95.77 % Rotamer: Outliers : 1.43 % Allowed : 10.82 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.13), residues: 4353 helix: 2.22 (0.11), residues: 2216 sheet: 0.75 (0.22), residues: 575 loop : -1.22 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 535 TYR 0.017 0.001 TYR A 50 PHE 0.017 0.001 PHE G 167 TRP 0.010 0.001 TRP A 21 HIS 0.008 0.001 HIS H 111 Details of bonding type rmsd covalent geometry : bond 0.00400 (34102) covalent geometry : angle 0.60186 (46052) hydrogen bonds : bond 0.05838 ( 1926) hydrogen bonds : angle 3.86453 ( 5556) Misc. bond : bond 0.00272 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 234 time to evaluate : 1.247 Fit side-chains REVERT: A 6 HIS cc_start: 0.7813 (m-70) cc_final: 0.7428 (m90) REVERT: A 64 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7645 (mp) REVERT: A 131 GLN cc_start: 0.8456 (pt0) cc_final: 0.8098 (pt0) REVERT: B 522 ASP cc_start: 0.8750 (t0) cc_final: 0.8473 (t0) REVERT: C 252 ASN cc_start: 0.7749 (t0) cc_final: 0.7113 (t0) REVERT: C 470 GLN cc_start: 0.7179 (OUTLIER) cc_final: 0.6922 (pt0) REVERT: C 512 ASN cc_start: 0.8754 (OUTLIER) cc_final: 0.8542 (t0) REVERT: D 39 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8207 (mtm) REVERT: D 290 GLN cc_start: 0.8270 (tp-100) cc_final: 0.7915 (tp-100) REVERT: F 27 ARG cc_start: 0.5117 (mmm160) cc_final: 0.4695 (mtp180) REVERT: F 458 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8437 (mtp) REVERT: G 156 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8458 (mtm) REVERT: G 430 MET cc_start: 0.7337 (mmm) cc_final: 0.7010 (mmm) REVERT: I 44 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8923 (mmt) outliers start: 52 outliers final: 15 residues processed: 267 average time/residue: 0.6533 time to fit residues: 209.7710 Evaluate side-chains 240 residues out of total 3649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 218 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 470 GLN Chi-restraints excluded: chain C residue 512 ASN Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 458 MET Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain H residue 373 THR Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 333 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 85 optimal weight: 0.5980 chunk 196 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 230 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 237 optimal weight: 5.9990 chunk 323 optimal weight: 7.9990 chunk 127 optimal weight: 0.9980 chunk 316 optimal weight: 0.9980 chunk 411 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN H 111 HIS H 284 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.098288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.082503 restraints weight = 59094.543| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.49 r_work: 0.3071 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.0712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 34106 Z= 0.109 Angle : 0.540 7.416 46052 Z= 0.269 Chirality : 0.042 0.176 5477 Planarity : 0.003 0.046 5885 Dihedral : 7.760 168.723 4739 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.32 % Allowed : 11.92 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.54 (0.13), residues: 4353 helix: 2.46 (0.11), residues: 2213 sheet: 0.86 (0.22), residues: 573 loop : -1.11 (0.15), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 86 TYR 0.013 0.001 TYR A 50 PHE 0.013 0.001 PHE G 167 TRP 0.009 0.001 TRP A 21 HIS 0.009 0.001 HIS H 111 Details of bonding type rmsd covalent geometry : bond 0.00231 (34102) covalent geometry : angle 0.53968 (46052) hydrogen bonds : bond 0.04596 ( 1926) hydrogen bonds : angle 3.67027 ( 5556) Misc. bond : bond 0.00038 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 240 time to evaluate : 1.325 Fit side-chains revert: symmetry clash REVERT: A 6 HIS cc_start: 0.7836 (m-70) cc_final: 0.7481 (m90) REVERT: A 64 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7707 (mp) REVERT: A 89 ASN cc_start: 0.7725 (m110) cc_final: 0.7469 (m110) REVERT: A 131 GLN cc_start: 0.8403 (pt0) cc_final: 0.7985 (pt0) REVERT: A 147 MET cc_start: -0.1372 (tpp) cc_final: -0.2078 (mpt) REVERT: B 522 ASP cc_start: 0.8752 (t0) cc_final: 0.8476 (t0) REVERT: C 153 LYS cc_start: 0.8176 (mtmm) cc_final: 0.7924 (mttp) REVERT: C 252 ASN cc_start: 0.7725 (t0) cc_final: 0.7084 (t0) REVERT: C 512 ASN cc_start: 0.8621 (OUTLIER) cc_final: 0.8392 (t0) REVERT: D 290 GLN cc_start: 0.8279 (tp-100) cc_final: 0.7980 (tp-100) REVERT: F 446 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.6761 (mmt) REVERT: G 156 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8393 (mtm) REVERT: G 302 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7856 (mp0) REVERT: G 430 MET cc_start: 0.7329 (mmm) cc_final: 0.7051 (mmm) outliers start: 48 outliers final: 21 residues processed: 272 average time/residue: 0.6632 time to fit residues: 217.3977 Evaluate side-chains 247 residues out of total 3649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 221 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 512 ASN Chi-restraints excluded: chain E residue 252 PHE Chi-restraints excluded: chain E residue 445 MET Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 399 GLU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 446 MET Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 302 GLU Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain I residue 333 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 5 optimal weight: 0.0000 chunk 308 optimal weight: 0.9980 chunk 339 optimal weight: 0.4980 chunk 161 optimal weight: 9.9990 chunk 222 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 216 optimal weight: 4.9990 chunk 178 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 chunk 224 optimal weight: 9.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN D 278 GLN F 296 ASN ** G 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 284 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.095938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.080082 restraints weight = 59549.233| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.49 r_work: 0.3028 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 34106 Z= 0.151 Angle : 0.571 8.615 46052 Z= 0.285 Chirality : 0.043 0.202 5477 Planarity : 0.003 0.042 5885 Dihedral : 7.615 171.239 4736 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.78 % Allowed : 12.36 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.13), residues: 4353 helix: 2.38 (0.11), residues: 2223 sheet: 0.82 (0.22), residues: 580 loop : -1.17 (0.15), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 321 TYR 0.011 0.001 TYR B 505 PHE 0.023 0.001 PHE A 20 TRP 0.007 0.001 TRP C 485 HIS 0.008 0.001 HIS H 111 Details of bonding type rmsd covalent geometry : bond 0.00358 (34102) covalent geometry : angle 0.57148 (46052) hydrogen bonds : bond 0.05419 ( 1926) hydrogen bonds : angle 3.73328 ( 5556) Misc. bond : bond 0.00083 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 235 time to evaluate : 1.115 Fit side-chains REVERT: A 6 HIS cc_start: 0.7761 (m-70) cc_final: 0.7387 (m90) REVERT: A 20 PHE cc_start: 0.8145 (t80) cc_final: 0.7583 (t80) REVERT: A 64 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7738 (mp) REVERT: B 249 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7636 (mpp) REVERT: B 522 ASP cc_start: 0.8785 (t0) cc_final: 0.8529 (t0) REVERT: C 252 ASN cc_start: 0.7680 (t0) cc_final: 0.7098 (t0) REVERT: C 512 ASN cc_start: 0.8673 (OUTLIER) cc_final: 0.8441 (t0) REVERT: D 290 GLN cc_start: 0.8353 (tp-100) cc_final: 0.8063 (tp-100) REVERT: F 27 ARG cc_start: 0.4419 (mmm160) cc_final: 0.4085 (mtp180) REVERT: F 399 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7636 (mp0) REVERT: G 156 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8409 (mtm) REVERT: G 302 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7879 (mp0) REVERT: G 409 VAL cc_start: 0.8976 (OUTLIER) cc_final: 0.8664 (m) REVERT: G 430 MET cc_start: 0.7368 (mmm) cc_final: 0.7090 (mmm) REVERT: I 44 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8926 (mmt) outliers start: 65 outliers final: 30 residues processed: 283 average time/residue: 0.6255 time to fit residues: 214.0333 Evaluate side-chains 265 residues out of total 3649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 227 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 512 ASN Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 445 MET Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 399 GLU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 302 GLU Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 336 GLU Chi-restraints excluded: chain H residue 373 THR Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 333 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 303 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 373 optimal weight: 8.9990 chunk 231 optimal weight: 8.9990 chunk 225 optimal weight: 1.9990 chunk 338 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 218 optimal weight: 2.9990 chunk 154 optimal weight: 10.0000 chunk 259 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN ** G 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 284 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.096178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.080256 restraints weight = 59776.061| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.50 r_work: 0.2984 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 34106 Z= 0.103 Angle : 0.531 14.514 46052 Z= 0.261 Chirality : 0.041 0.180 5477 Planarity : 0.003 0.038 5885 Dihedral : 7.264 172.580 4736 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.73 % Allowed : 12.99 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.66 (0.13), residues: 4353 helix: 2.56 (0.11), residues: 2225 sheet: 0.85 (0.22), residues: 580 loop : -1.06 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 535 TYR 0.012 0.001 TYR B 505 PHE 0.018 0.001 PHE A 20 TRP 0.006 0.001 TRP H 435 HIS 0.008 0.001 HIS H 111 Details of bonding type rmsd covalent geometry : bond 0.00211 (34102) covalent geometry : angle 0.53091 (46052) hydrogen bonds : bond 0.04185 ( 1926) hydrogen bonds : angle 3.56524 ( 5556) Misc. bond : bond 0.00026 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 246 time to evaluate : 1.412 Fit side-chains REVERT: A 2 ARG cc_start: 0.7932 (mmm160) cc_final: 0.7428 (mmm-85) REVERT: A 20 PHE cc_start: 0.8103 (t80) cc_final: 0.7480 (t80) REVERT: A 42 LEU cc_start: 0.7611 (mm) cc_final: 0.7122 (tt) REVERT: A 89 ASN cc_start: 0.7500 (m110) cc_final: 0.7260 (m110) REVERT: A 147 MET cc_start: -0.1641 (tpp) cc_final: -0.2219 (mpt) REVERT: B 249 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7708 (mpp) REVERT: B 416 GLU cc_start: 0.8731 (mp0) cc_final: 0.8428 (mp0) REVERT: B 522 ASP cc_start: 0.8842 (t0) cc_final: 0.8572 (t0) REVERT: C 252 ASN cc_start: 0.7549 (t0) cc_final: 0.6984 (t0) REVERT: C 512 ASN cc_start: 0.8325 (OUTLIER) cc_final: 0.8057 (t0) REVERT: D 290 GLN cc_start: 0.8166 (tp-100) cc_final: 0.7864 (tp-100) REVERT: E 284 LYS cc_start: 0.8564 (ttpt) cc_final: 0.8201 (tppp) REVERT: F 399 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7288 (mp0) REVERT: G 156 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8299 (mtm) REVERT: G 302 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7724 (mp0) REVERT: G 409 VAL cc_start: 0.8837 (OUTLIER) cc_final: 0.8613 (m) REVERT: G 430 MET cc_start: 0.7269 (mmm) cc_final: 0.6955 (mmm) REVERT: G 529 ASP cc_start: 0.8872 (p0) cc_final: 0.8653 (p0) REVERT: H 111 HIS cc_start: 0.8456 (t70) cc_final: 0.8252 (t-90) REVERT: I 522 MET cc_start: 0.8399 (ttm) cc_final: 0.8102 (ttm) outliers start: 63 outliers final: 28 residues processed: 287 average time/residue: 0.6495 time to fit residues: 225.4679 Evaluate side-chains 257 residues out of total 3649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 223 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 512 ASN Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 252 PHE Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 445 MET Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 399 GLU Chi-restraints excluded: chain F residue 503 ILE Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 302 GLU Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain H residue 193 ILE Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain H residue 336 GLU Chi-restraints excluded: chain I residue 333 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 403 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 235 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 chunk 345 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 HIS A 131 GLN A 134 GLN B 435 GLN B 471 HIS C 233 HIS E 294 GLN ** G 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.089729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.073726 restraints weight = 60890.561| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.55 r_work: 0.2869 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 34106 Z= 0.266 Angle : 0.680 17.496 46052 Z= 0.339 Chirality : 0.047 0.191 5477 Planarity : 0.004 0.042 5885 Dihedral : 7.582 174.703 4736 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.62 % Favored : 95.36 % Rotamer: Outliers : 2.16 % Allowed : 13.73 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.13), residues: 4353 helix: 2.11 (0.11), residues: 2231 sheet: 0.68 (0.22), residues: 592 loop : -1.26 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 321 TYR 0.014 0.002 TYR D 280 PHE 0.024 0.002 PHE D 16 TRP 0.012 0.002 TRP C 485 HIS 0.007 0.001 HIS I 382 Details of bonding type rmsd covalent geometry : bond 0.00665 (34102) covalent geometry : angle 0.68048 (46052) hydrogen bonds : bond 0.07171 ( 1926) hydrogen bonds : angle 3.97149 ( 5556) Misc. bond : bond 0.00124 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 226 time to evaluate : 1.320 Fit side-chains REVERT: A 2 ARG cc_start: 0.7997 (mmm160) cc_final: 0.7616 (mmm-85) REVERT: A 20 PHE cc_start: 0.8044 (t80) cc_final: 0.7338 (t80) REVERT: A 89 ASN cc_start: 0.7706 (m110) cc_final: 0.7431 (m110) REVERT: A 147 MET cc_start: -0.1327 (tpp) cc_final: -0.2160 (mpt) REVERT: B 315 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8614 (pp) REVERT: B 416 GLU cc_start: 0.8925 (mp0) cc_final: 0.8612 (mp0) REVERT: C 252 ASN cc_start: 0.7660 (t0) cc_final: 0.6994 (t0) REVERT: C 512 ASN cc_start: 0.8663 (OUTLIER) cc_final: 0.8432 (t0) REVERT: D 290 GLN cc_start: 0.8279 (tp-100) cc_final: 0.8007 (tp-100) REVERT: F 399 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7559 (mp0) REVERT: G 156 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8439 (mtm) REVERT: G 302 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7736 (mp0) REVERT: G 349 GLU cc_start: 0.8252 (tt0) cc_final: 0.8050 (tt0) REVERT: G 409 VAL cc_start: 0.8817 (OUTLIER) cc_final: 0.8601 (m) REVERT: G 430 MET cc_start: 0.7387 (mmm) cc_final: 0.7127 (mmm) REVERT: G 529 ASP cc_start: 0.9034 (p0) cc_final: 0.8798 (p0) REVERT: H 7 VAL cc_start: 0.7354 (t) cc_final: 0.7087 (p) REVERT: H 15 LYS cc_start: 0.7777 (tttp) cc_final: 0.7359 (mmmt) outliers start: 79 outliers final: 35 residues processed: 284 average time/residue: 0.6587 time to fit residues: 226.5596 Evaluate side-chains 261 residues out of total 3649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 220 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 512 ASN Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 445 MET Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 399 GLU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 302 GLU Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 193 ILE Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 336 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 19 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 chunk 166 optimal weight: 0.8980 chunk 370 optimal weight: 3.9990 chunk 337 optimal weight: 5.9990 chunk 244 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 218 optimal weight: 2.9990 chunk 296 optimal weight: 0.9990 chunk 372 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 131 GLN ** G 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 386 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.091832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.075800 restraints weight = 60725.390| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.57 r_work: 0.2905 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 34106 Z= 0.160 Angle : 0.598 16.153 46052 Z= 0.296 Chirality : 0.043 0.182 5477 Planarity : 0.003 0.045 5885 Dihedral : 7.295 176.156 4736 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.70 % Favored : 96.28 % Rotamer: Outliers : 1.84 % Allowed : 14.36 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.13), residues: 4353 helix: 2.22 (0.11), residues: 2228 sheet: 0.73 (0.22), residues: 579 loop : -1.24 (0.15), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 228 TYR 0.014 0.001 TYR B 505 PHE 0.017 0.001 PHE A 20 TRP 0.010 0.001 TRP A 21 HIS 0.004 0.001 HIS E 178 Details of bonding type rmsd covalent geometry : bond 0.00378 (34102) covalent geometry : angle 0.59848 (46052) hydrogen bonds : bond 0.05862 ( 1926) hydrogen bonds : angle 3.82957 ( 5556) Misc. bond : bond 0.00074 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 229 time to evaluate : 1.369 Fit side-chains revert: symmetry clash REVERT: A 2 ARG cc_start: 0.7812 (mmm160) cc_final: 0.7238 (mmm-85) REVERT: A 20 PHE cc_start: 0.8123 (t80) cc_final: 0.7382 (t80) REVERT: B 86 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8408 (tp) REVERT: B 249 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7835 (mpp) REVERT: B 315 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8609 (pp) REVERT: B 522 ASP cc_start: 0.8971 (t0) cc_final: 0.8690 (t0) REVERT: C 153 LYS cc_start: 0.8179 (mttp) cc_final: 0.7977 (mtmm) REVERT: C 252 ASN cc_start: 0.7597 (t0) cc_final: 0.6956 (t0) REVERT: C 512 ASN cc_start: 0.8546 (OUTLIER) cc_final: 0.8316 (t0) REVERT: D 290 GLN cc_start: 0.8266 (tp-100) cc_final: 0.8008 (tp-100) REVERT: F 399 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7428 (mp0) REVERT: F 446 MET cc_start: 0.7479 (OUTLIER) cc_final: 0.6309 (mmt) REVERT: G 156 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8384 (mtm) REVERT: G 302 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7747 (mp0) REVERT: G 349 GLU cc_start: 0.8283 (tt0) cc_final: 0.8061 (tt0) REVERT: G 486 ILE cc_start: 0.7539 (pp) cc_final: 0.7338 (mm) REVERT: G 529 ASP cc_start: 0.9035 (p0) cc_final: 0.8814 (p0) REVERT: H 15 LYS cc_start: 0.7753 (tttp) cc_final: 0.7329 (mmmt) REVERT: I 190 MET cc_start: 0.8762 (mmp) cc_final: 0.8508 (mmp) outliers start: 67 outliers final: 39 residues processed: 278 average time/residue: 0.6527 time to fit residues: 219.9211 Evaluate side-chains 270 residues out of total 3649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 223 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 512 ASN Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 445 MET Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 399 GLU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 446 MET Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 302 GLU Chi-restraints excluded: chain H residue 193 ILE Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 336 GLU Chi-restraints excluded: chain H residue 373 THR Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 333 LEU Chi-restraints excluded: chain I residue 514 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 372 optimal weight: 10.0000 chunk 347 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 336 optimal weight: 0.5980 chunk 39 optimal weight: 7.9990 chunk 138 optimal weight: 7.9990 chunk 315 optimal weight: 0.9990 chunk 323 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 306 optimal weight: 7.9990 chunk 391 optimal weight: 0.6980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 14 ASN A 131 GLN ** G 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.094978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.078963 restraints weight = 59899.582| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.56 r_work: 0.2959 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 34106 Z= 0.110 Angle : 0.550 15.609 46052 Z= 0.270 Chirality : 0.041 0.186 5477 Planarity : 0.003 0.039 5885 Dihedral : 6.842 178.429 4736 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.56 % Allowed : 14.88 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.13), residues: 4353 helix: 2.47 (0.11), residues: 2230 sheet: 0.76 (0.22), residues: 583 loop : -1.11 (0.15), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.013 0.001 TYR A 36 PHE 0.017 0.001 PHE G 8 TRP 0.009 0.001 TRP A 21 HIS 0.007 0.001 HIS H 111 Details of bonding type rmsd covalent geometry : bond 0.00239 (34102) covalent geometry : angle 0.55008 (46052) hydrogen bonds : bond 0.04377 ( 1926) hydrogen bonds : angle 3.60511 ( 5556) Misc. bond : bond 0.00039 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 234 time to evaluate : 1.371 Fit side-chains revert: symmetry clash REVERT: A 2 ARG cc_start: 0.7609 (mmm160) cc_final: 0.7101 (mmm-85) REVERT: A 20 PHE cc_start: 0.8123 (t80) cc_final: 0.7395 (t80) REVERT: A 42 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.6875 (tt) REVERT: A 147 MET cc_start: -0.1109 (tpp) cc_final: -0.1968 (mpt) REVERT: B 249 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7776 (mpp) REVERT: B 522 ASP cc_start: 0.8940 (t0) cc_final: 0.8724 (t0) REVERT: C 251 ASP cc_start: 0.8608 (p0) cc_final: 0.8320 (p0) REVERT: C 252 ASN cc_start: 0.7499 (t0) cc_final: 0.6907 (t0) REVERT: C 512 ASN cc_start: 0.8379 (OUTLIER) cc_final: 0.8109 (t0) REVERT: D 290 GLN cc_start: 0.8220 (tp-100) cc_final: 0.7963 (tp-100) REVERT: E 284 LYS cc_start: 0.8642 (ttpt) cc_final: 0.8284 (tppp) REVERT: F 399 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7363 (mp0) REVERT: G 139 ASN cc_start: 0.8690 (p0) cc_final: 0.8306 (p0) REVERT: G 156 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8353 (mtm) REVERT: G 302 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7802 (mp0) REVERT: G 486 ILE cc_start: 0.7569 (pp) cc_final: 0.7337 (mm) REVERT: H 15 LYS cc_start: 0.7718 (tttp) cc_final: 0.7297 (mmmt) REVERT: I 190 MET cc_start: 0.8759 (mmp) cc_final: 0.8508 (mmp) outliers start: 57 outliers final: 31 residues processed: 277 average time/residue: 0.6924 time to fit residues: 230.3203 Evaluate side-chains 258 residues out of total 3649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 221 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 364 CYS Chi-restraints excluded: chain C residue 512 ASN Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 399 GLU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 503 ILE Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 302 GLU Chi-restraints excluded: chain H residue 193 ILE Chi-restraints excluded: chain H residue 336 GLU Chi-restraints excluded: chain H residue 373 THR Chi-restraints excluded: chain I residue 333 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 325 optimal weight: 5.9990 chunk 160 optimal weight: 8.9990 chunk 52 optimal weight: 8.9990 chunk 198 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 232 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 288 optimal weight: 6.9990 chunk 256 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 HIS A 14 ASN A 131 GLN ** G 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.092877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.076823 restraints weight = 60242.276| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.56 r_work: 0.2925 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 34106 Z= 0.152 Angle : 0.581 15.152 46052 Z= 0.286 Chirality : 0.043 0.186 5477 Planarity : 0.003 0.039 5885 Dihedral : 6.920 179.089 4736 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.00 % Favored : 95.98 % Rotamer: Outliers : 1.32 % Allowed : 15.46 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.13), residues: 4353 helix: 2.40 (0.11), residues: 2230 sheet: 0.77 (0.22), residues: 579 loop : -1.15 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 228 TYR 0.013 0.001 TYR G 181 PHE 0.016 0.001 PHE A 20 TRP 0.008 0.001 TRP A 21 HIS 0.007 0.001 HIS H 111 Details of bonding type rmsd covalent geometry : bond 0.00362 (34102) covalent geometry : angle 0.58093 (46052) hydrogen bonds : bond 0.05321 ( 1926) hydrogen bonds : angle 3.68493 ( 5556) Misc. bond : bond 0.00074 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 219 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 ARG cc_start: 0.7697 (mmm160) cc_final: 0.7138 (mmm-85) REVERT: A 20 PHE cc_start: 0.8061 (t80) cc_final: 0.7352 (t80) REVERT: A 42 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7085 (tt) REVERT: A 89 ASN cc_start: 0.7164 (m110) cc_final: 0.6816 (m-40) REVERT: B 155 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8240 (ttm110) REVERT: B 522 ASP cc_start: 0.8953 (t0) cc_final: 0.8716 (t0) REVERT: C 153 LYS cc_start: 0.8104 (mtmm) cc_final: 0.7868 (mttp) REVERT: C 252 ASN cc_start: 0.7528 (t0) cc_final: 0.6932 (t0) REVERT: C 512 ASN cc_start: 0.8487 (OUTLIER) cc_final: 0.8259 (t0) REVERT: D 290 GLN cc_start: 0.8251 (tp-100) cc_final: 0.7989 (tp-100) REVERT: F 399 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: G 156 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8361 (mtm) REVERT: G 302 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7749 (mp0) REVERT: I 190 MET cc_start: 0.8744 (mmp) cc_final: 0.8505 (mmp) REVERT: I 522 MET cc_start: 0.8512 (ttm) cc_final: 0.8277 (ptp) outliers start: 48 outliers final: 34 residues processed: 257 average time/residue: 0.6615 time to fit residues: 203.8923 Evaluate side-chains 253 residues out of total 3649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 213 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 364 CYS Chi-restraints excluded: chain C residue 512 ASN Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 399 GLU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 302 GLU Chi-restraints excluded: chain H residue 111 HIS Chi-restraints excluded: chain H residue 193 ILE Chi-restraints excluded: chain H residue 336 GLU Chi-restraints excluded: chain H residue 373 THR Chi-restraints excluded: chain I residue 333 LEU Chi-restraints excluded: chain I residue 514 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 146 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 348 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 chunk 273 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 264 optimal weight: 2.9990 chunk 291 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 356 optimal weight: 0.9980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 HIS H 111 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.093804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.077712 restraints weight = 60438.285| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.57 r_work: 0.2938 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34106 Z= 0.125 Angle : 0.565 15.606 46052 Z= 0.277 Chirality : 0.042 0.192 5477 Planarity : 0.003 0.039 5885 Dihedral : 6.831 179.003 4736 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.29 % Allowed : 15.54 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.13), residues: 4353 helix: 2.47 (0.11), residues: 2223 sheet: 0.78 (0.22), residues: 581 loop : -1.11 (0.15), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 162 TYR 0.013 0.001 TYR G 181 PHE 0.022 0.001 PHE G 8 TRP 0.009 0.001 TRP A 21 HIS 0.035 0.001 HIS H 111 Details of bonding type rmsd covalent geometry : bond 0.00283 (34102) covalent geometry : angle 0.56509 (46052) hydrogen bonds : bond 0.04892 ( 1926) hydrogen bonds : angle 3.63326 ( 5556) Misc. bond : bond 0.00055 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 219 time to evaluate : 1.393 Fit side-chains revert: symmetry clash REVERT: A 2 ARG cc_start: 0.7834 (mmm160) cc_final: 0.7271 (mmm-85) REVERT: A 20 PHE cc_start: 0.8067 (t80) cc_final: 0.7384 (t80) REVERT: A 42 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7086 (tt) REVERT: A 89 ASN cc_start: 0.7108 (m110) cc_final: 0.6771 (m110) REVERT: B 155 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8226 (ttm110) REVERT: B 249 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7782 (mpp) REVERT: B 522 ASP cc_start: 0.8919 (t0) cc_final: 0.8689 (t0) REVERT: C 252 ASN cc_start: 0.7502 (t0) cc_final: 0.7003 (t0) REVERT: C 512 ASN cc_start: 0.8452 (OUTLIER) cc_final: 0.8198 (t0) REVERT: D 290 GLN cc_start: 0.8234 (tp-100) cc_final: 0.7977 (tp-100) REVERT: E 284 LYS cc_start: 0.8653 (ttpt) cc_final: 0.8314 (tppp) REVERT: F 399 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: G 156 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8358 (mtm) REVERT: G 302 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7750 (mp0) outliers start: 47 outliers final: 36 residues processed: 255 average time/residue: 0.6665 time to fit residues: 204.5538 Evaluate side-chains 259 residues out of total 3649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 216 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 364 CYS Chi-restraints excluded: chain C residue 512 ASN Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 399 GLU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 302 GLU Chi-restraints excluded: chain H residue 193 ILE Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 336 GLU Chi-restraints excluded: chain H residue 373 THR Chi-restraints excluded: chain I residue 333 LEU Chi-restraints excluded: chain I residue 426 LYS Chi-restraints excluded: chain I residue 514 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 133 optimal weight: 0.8980 chunk 155 optimal weight: 10.0000 chunk 319 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 338 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 98 optimal weight: 9.9990 chunk 327 optimal weight: 0.8980 chunk 412 optimal weight: 2.9990 chunk 342 optimal weight: 8.9990 chunk 123 optimal weight: 8.9990 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 HIS A 14 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.090853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.074827 restraints weight = 60799.683| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.56 r_work: 0.2888 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 34106 Z= 0.214 Angle : 0.636 14.896 46052 Z= 0.316 Chirality : 0.045 0.186 5477 Planarity : 0.004 0.039 5885 Dihedral : 7.067 179.543 4736 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.27 % Favored : 95.70 % Rotamer: Outliers : 1.29 % Allowed : 15.65 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.13), residues: 4353 helix: 2.22 (0.11), residues: 2230 sheet: 0.70 (0.22), residues: 581 loop : -1.23 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 321 TYR 0.015 0.001 TYR G 181 PHE 0.019 0.002 PHE D 16 TRP 0.010 0.001 TRP C 485 HIS 0.006 0.001 HIS I 382 Details of bonding type rmsd covalent geometry : bond 0.00527 (34102) covalent geometry : angle 0.63562 (46052) hydrogen bonds : bond 0.06357 ( 1926) hydrogen bonds : angle 3.84712 ( 5556) Misc. bond : bond 0.00107 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8641.25 seconds wall clock time: 148 minutes 13.35 seconds (8893.35 seconds total)