Starting phenix.real_space_refine on Fri Mar 6 23:45:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e1y_30946/03_2026/7e1y_30946.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e1y_30946/03_2026/7e1y_30946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e1y_30946/03_2026/7e1y_30946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e1y_30946/03_2026/7e1y_30946.map" model { file = "/net/cci-nas-00/data/ceres_data/7e1y_30946/03_2026/7e1y_30946.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e1y_30946/03_2026/7e1y_30946.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 23248 2.51 5 N 5959 2.21 5 O 6440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.02s 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: 35743 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4468 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 538, 4458 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 511} Conformer: "B" Number of residues, atoms: 538, 4458 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 511} bond proxies already assigned to first conformer: 4579 Chain: "B" Number of atoms: 4468 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 538, 4458 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 511} Conformer: "B" Number of residues, atoms: 538, 4458 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 511} bond proxies already assigned to first conformer: 4579 Chain: "C" Number of atoms: 4468 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 538, 4458 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 511} Conformer: "B" Number of residues, atoms: 538, 4458 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 511} bond proxies already assigned to first conformer: 4579 Chain: "D" Number of atoms: 4468 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 538, 4458 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 511} Conformer: "B" Number of residues, atoms: 538, 4458 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 511} bond proxies already assigned to first conformer: 4579 Chain: "E" Number of atoms: 4468 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 538, 4458 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 511} Conformer: "B" Number of residues, atoms: 538, 4458 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 511} bond proxies already assigned to first conformer: 4579 Chain: "F" Number of atoms: 4468 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 538, 4458 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 511} Conformer: "B" Number of residues, atoms: 538, 4458 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 511} bond proxies already assigned to first conformer: 4579 Chain: "G" Number of atoms: 4468 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 538, 4458 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 511} Conformer: "B" Number of residues, atoms: 538, 4458 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 511} bond proxies already assigned to first conformer: 4579 Chain: "H" Number of atoms: 4467 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 538, 4458 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 511} Conformer: "B" Number of residues, atoms: 538, 4458 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 511} bond proxies already assigned to first conformer: 4580 Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N AHIS A 140 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 140 " occ=0.50 residue: pdb=" N AHIS B 140 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 140 " occ=0.50 residue: pdb=" N AHIS C 140 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS C 140 " occ=0.50 residue: pdb=" N AHIS D 140 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS D 140 " occ=0.50 residue: pdb=" N AHIS E 140 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS E 140 " occ=0.50 residue: pdb=" N AHIS F 140 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS F 140 " occ=0.50 residue: pdb=" N AHIS G 140 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS G 140 " occ=0.50 Time building chain proxies: 13.05, per 1000 atoms: 0.37 Number of scatterers: 35743 At special positions: 0 Unit cell: (189.618, 140.946, 193.674, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 6440 8.00 N 5959 7.00 C 23248 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 2.8 seconds 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8192 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 49 sheets defined 42.5% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 142 through 150 removed outlier: 3.620A pdb=" N ILE A 146 " --> pdb=" O PRO A 142 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR A 147 " --> pdb=" O TRP A 143 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N VAL A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 171 removed outlier: 3.543A pdb=" N ASN A 169 " --> pdb=" O SER A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.664A pdb=" N ALA A 191 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 227 removed outlier: 3.913A pdb=" N GLU A 216 " --> pdb=" O ARG A 212 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 252 through 271 removed outlier: 3.774A pdb=" N GLU A 256 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A 257 " --> pdb=" O ASN A 253 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU A 258 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 290 through 297 Processing helix chain 'A' and resid 341 through 351 Processing helix chain 'A' and resid 356 through 377 removed outlier: 3.639A pdb=" N TRP A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS A 374 " --> pdb=" O ARG A 370 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TRP A 375 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP A 377 " --> pdb=" O GLU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 419 removed outlier: 3.686A pdb=" N THR A 402 " --> pdb=" O ASN A 398 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A 403 " --> pdb=" O PRO A 399 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR A 404 " --> pdb=" O PRO A 400 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 416 " --> pdb=" O TYR A 412 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 434 Processing helix chain 'A' and resid 461 through 483 removed outlier: 3.521A pdb=" N LYS A 468 " --> pdb=" O GLU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 501 removed outlier: 3.641A pdb=" N ALA A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N HIS A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 500 " --> pdb=" O ALA A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 532 removed outlier: 3.697A pdb=" N ILE A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 522 " --> pdb=" O THR A 518 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 523 " --> pdb=" O TRP A 519 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 527 " --> pdb=" O ALA A 523 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG A 530 " --> pdb=" O ILE A 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 150 removed outlier: 3.674A pdb=" N ILE B 146 " --> pdb=" O PRO B 142 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR B 147 " --> pdb=" O TRP B 143 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N VAL B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 171 removed outlier: 3.610A pdb=" N ASN B 169 " --> pdb=" O SER B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 193 removed outlier: 4.168A pdb=" N GLN B 187 " --> pdb=" O SER B 183 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA B 191 " --> pdb=" O GLN B 187 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU B 193 " --> pdb=" O GLN B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 227 removed outlier: 3.707A pdb=" N THR B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 248 Processing helix chain 'B' and resid 251 through 271 removed outlier: 3.821A pdb=" N VAL B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU B 257 " --> pdb=" O ASN B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 285 Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 290 through 297 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 341 through 351 removed outlier: 3.812A pdb=" N LEU B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 377 removed outlier: 3.784A pdb=" N TRP B 361 " --> pdb=" O GLU B 357 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 374 " --> pdb=" O ARG B 370 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TRP B 375 " --> pdb=" O VAL B 371 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP B 377 " --> pdb=" O GLU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 395 Processing helix chain 'B' and resid 398 through 419 removed outlier: 3.842A pdb=" N THR B 402 " --> pdb=" O ASN B 398 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B 403 " --> pdb=" O PRO B 399 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR B 404 " --> pdb=" O PRO B 400 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 416 " --> pdb=" O TYR B 412 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN B 419 " --> pdb=" O THR B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 434 Processing helix chain 'B' and resid 459 through 461 No H-bonds generated for 'chain 'B' and resid 459 through 461' Processing helix chain 'B' and resid 462 through 483 Processing helix chain 'B' and resid 487 through 501 removed outlier: 3.757A pdb=" N HIS B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA B 500 " --> pdb=" O ALA B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 507 removed outlier: 3.754A pdb=" N TRP B 506 " --> pdb=" O ASP B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 532 removed outlier: 3.598A pdb=" N ILE B 516 " --> pdb=" O LEU B 512 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG B 530 " --> pdb=" O ILE B 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 150 Processing helix chain 'C' and resid 159 through 171 removed outlier: 3.774A pdb=" N ASN C 169 " --> pdb=" O SER C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 193 removed outlier: 3.818A pdb=" N ALA C 191 " --> pdb=" O GLN C 187 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU C 193 " --> pdb=" O GLN C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 213 Processing helix chain 'C' and resid 214 through 227 removed outlier: 3.547A pdb=" N ASN C 219 " --> pdb=" O GLU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 248 Processing helix chain 'C' and resid 251 through 270 removed outlier: 3.770A pdb=" N VAL C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 285 Processing helix chain 'C' and resid 289 through 297 removed outlier: 4.304A pdb=" N ILE C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 350 removed outlier: 4.040A pdb=" N LEU C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 377 removed outlier: 3.969A pdb=" N TRP C 361 " --> pdb=" O GLU C 357 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS C 374 " --> pdb=" O ARG C 370 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TRP C 375 " --> pdb=" O VAL C 371 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASP C 377 " --> pdb=" O GLU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 395 Processing helix chain 'C' and resid 398 through 419 removed outlier: 3.786A pdb=" N THR C 402 " --> pdb=" O ASN C 398 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA C 403 " --> pdb=" O PRO C 399 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR C 404 " --> pdb=" O PRO C 400 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR C 415 " --> pdb=" O ILE C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 434 Processing helix chain 'C' and resid 462 through 483 Processing helix chain 'C' and resid 487 through 501 removed outlier: 3.571A pdb=" N ALA C 496 " --> pdb=" O GLU C 492 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA C 500 " --> pdb=" O ALA C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 507 removed outlier: 3.877A pdb=" N TRP C 506 " --> pdb=" O ASP C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 532 removed outlier: 3.639A pdb=" N ILE C 516 " --> pdb=" O LEU C 512 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR C 518 " --> pdb=" O LYS C 514 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL C 522 " --> pdb=" O THR C 518 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG C 530 " --> pdb=" O ILE C 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 150 removed outlier: 3.521A pdb=" N TYR D 147 " --> pdb=" O TRP D 143 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL D 148 " --> pdb=" O ALA D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 171 removed outlier: 3.673A pdb=" N ASN D 169 " --> pdb=" O SER D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 193 removed outlier: 3.559A pdb=" N ALA D 191 " --> pdb=" O GLN D 187 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 192 " --> pdb=" O TRP D 188 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU D 193 " --> pdb=" O GLN D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 227 removed outlier: 3.522A pdb=" N GLU D 216 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 248 Processing helix chain 'D' and resid 252 through 271 removed outlier: 3.748A pdb=" N GLU D 257 " --> pdb=" O ASN D 253 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY D 271 " --> pdb=" O SER D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 285 Processing helix chain 'D' and resid 289 through 297 removed outlier: 4.491A pdb=" N ILE D 293 " --> pdb=" O LYS D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 350 removed outlier: 4.140A pdb=" N LEU D 348 " --> pdb=" O LEU D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 377 removed outlier: 4.035A pdb=" N TRP D 361 " --> pdb=" O GLU D 357 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS D 374 " --> pdb=" O ARG D 370 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TRP D 375 " --> pdb=" O VAL D 371 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE D 376 " --> pdb=" O ALA D 372 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP D 377 " --> pdb=" O GLU D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 419 removed outlier: 3.880A pdb=" N THR D 402 " --> pdb=" O ASN D 398 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA D 403 " --> pdb=" O PRO D 399 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR D 404 " --> pdb=" O PRO D 400 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR D 415 " --> pdb=" O ILE D 411 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU D 416 " --> pdb=" O TYR D 412 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER D 417 " --> pdb=" O LEU D 413 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP D 418 " --> pdb=" O GLU D 414 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN D 419 " --> pdb=" O THR D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 434 Processing helix chain 'D' and resid 459 through 461 No H-bonds generated for 'chain 'D' and resid 459 through 461' Processing helix chain 'D' and resid 462 through 483 removed outlier: 3.602A pdb=" N LYS D 468 " --> pdb=" O GLU D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 501 removed outlier: 3.747A pdb=" N HIS D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA D 500 " --> pdb=" O ALA D 496 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU D 501 " --> pdb=" O LEU D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 507 removed outlier: 3.772A pdb=" N TRP D 506 " --> pdb=" O ASP D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 532 removed outlier: 3.538A pdb=" N ILE D 516 " --> pdb=" O LEU D 512 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG D 530 " --> pdb=" O ILE D 526 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 150 Processing helix chain 'E' and resid 159 through 171 removed outlier: 3.524A pdb=" N SER E 165 " --> pdb=" O TYR E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 193 removed outlier: 3.746A pdb=" N ALA E 191 " --> pdb=" O GLN E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 227 removed outlier: 3.527A pdb=" N GLU E 216 " --> pdb=" O ARG E 212 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR E 217 " --> pdb=" O LEU E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 248 Processing helix chain 'E' and resid 251 through 270 removed outlier: 3.875A pdb=" N VAL E 255 " --> pdb=" O ALA E 251 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU E 257 " --> pdb=" O ASN E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 285 Processing helix chain 'E' and resid 289 through 297 removed outlier: 4.368A pdb=" N ILE E 293 " --> pdb=" O LYS E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 350 removed outlier: 3.958A pdb=" N LEU E 348 " --> pdb=" O LEU E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 377 removed outlier: 3.886A pdb=" N TRP E 361 " --> pdb=" O GLU E 357 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS E 374 " --> pdb=" O ARG E 370 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TRP E 375 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE E 376 " --> pdb=" O ALA E 372 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP E 377 " --> pdb=" O GLU E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 395 Processing helix chain 'E' and resid 398 through 419 removed outlier: 3.535A pdb=" N THR E 402 " --> pdb=" O ASN E 398 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA E 403 " --> pdb=" O PRO E 399 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR E 404 " --> pdb=" O PRO E 400 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU E 416 " --> pdb=" O TYR E 412 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN E 419 " --> pdb=" O THR E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 434 Processing helix chain 'E' and resid 461 through 483 removed outlier: 3.533A pdb=" N TYR E 465 " --> pdb=" O GLN E 461 " (cutoff:3.500A) Processing helix chain 'E' and resid 487 through 501 removed outlier: 3.972A pdb=" N ALA E 496 " --> pdb=" O GLU E 492 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS E 499 " --> pdb=" O TRP E 495 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA E 500 " --> pdb=" O ALA E 496 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 507 removed outlier: 3.681A pdb=" N TRP E 506 " --> pdb=" O ASP E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 512 through 532 removed outlier: 3.505A pdb=" N ILE E 516 " --> pdb=" O LEU E 512 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR E 518 " --> pdb=" O LYS E 514 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG E 530 " --> pdb=" O ILE E 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 171 removed outlier: 3.573A pdb=" N LEU F 168 " --> pdb=" O HIS F 164 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN F 169 " --> pdb=" O SER F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 208 through 227 removed outlier: 3.511A pdb=" N LEU F 213 " --> pdb=" O GLU F 209 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL F 214 " --> pdb=" O LYS F 210 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU F 215 " --> pdb=" O ILE F 211 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU F 216 " --> pdb=" O ARG F 212 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR F 217 " --> pdb=" O LEU F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 248 Processing helix chain 'F' and resid 252 through 270 removed outlier: 3.752A pdb=" N GLU F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 285 Processing helix chain 'F' and resid 289 through 297 removed outlier: 4.304A pdb=" N ILE F 293 " --> pdb=" O LYS F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 350 removed outlier: 3.957A pdb=" N LEU F 348 " --> pdb=" O LEU F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 356 through 377 removed outlier: 3.907A pdb=" N TRP F 361 " --> pdb=" O GLU F 357 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA F 372 " --> pdb=" O ALA F 368 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU F 373 " --> pdb=" O LEU F 369 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS F 374 " --> pdb=" O ARG F 370 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TRP F 375 " --> pdb=" O VAL F 371 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE F 376 " --> pdb=" O ALA F 372 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP F 377 " --> pdb=" O GLU F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 395 Processing helix chain 'F' and resid 398 through 419 removed outlier: 3.849A pdb=" N THR F 402 " --> pdb=" O ASN F 398 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA F 403 " --> pdb=" O PRO F 399 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR F 404 " --> pdb=" O PRO F 400 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR F 415 " --> pdb=" O ILE F 411 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU F 416 " --> pdb=" O TYR F 412 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER F 417 " --> pdb=" O LEU F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 434 Processing helix chain 'F' and resid 459 through 461 No H-bonds generated for 'chain 'F' and resid 459 through 461' Processing helix chain 'F' and resid 462 through 483 Processing helix chain 'F' and resid 487 through 501 removed outlier: 3.512A pdb=" N TRP F 498 " --> pdb=" O ARG F 494 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N HIS F 499 " --> pdb=" O TRP F 495 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA F 500 " --> pdb=" O ALA F 496 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU F 501 " --> pdb=" O LEU F 497 " (cutoff:3.500A) Processing helix chain 'F' and resid 502 through 507 removed outlier: 3.832A pdb=" N TRP F 506 " --> pdb=" O ASP F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 508 through 511 removed outlier: 3.711A pdb=" N TRP F 511 " --> pdb=" O ALA F 508 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 508 through 511' Processing helix chain 'F' and resid 512 through 532 removed outlier: 3.588A pdb=" N ILE F 516 " --> pdb=" O LEU F 512 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE F 526 " --> pdb=" O VAL F 522 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG F 530 " --> pdb=" O ILE F 526 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 147 removed outlier: 3.727A pdb=" N ILE G 146 " --> pdb=" O PRO G 142 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR G 147 " --> pdb=" O TRP G 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 142 through 147' Processing helix chain 'G' and resid 159 through 171 removed outlier: 3.600A pdb=" N LEU G 168 " --> pdb=" O HIS G 164 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN G 169 " --> pdb=" O SER G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 194 Processing helix chain 'G' and resid 208 through 227 removed outlier: 4.060A pdb=" N THR G 217 " --> pdb=" O LEU G 213 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU G 218 " --> pdb=" O VAL G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 248 Processing helix chain 'G' and resid 251 through 271 removed outlier: 3.601A pdb=" N VAL G 255 " --> pdb=" O ALA G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 285 Processing helix chain 'G' and resid 289 through 297 removed outlier: 4.176A pdb=" N ILE G 293 " --> pdb=" O LYS G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 341 through 350 removed outlier: 3.523A pdb=" N LEU G 348 " --> pdb=" O LEU G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 356 through 377 removed outlier: 3.608A pdb=" N ALA G 360 " --> pdb=" O SER G 356 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TRP G 361 " --> pdb=" O GLU G 357 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS G 374 " --> pdb=" O ARG G 370 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TRP G 375 " --> pdb=" O VAL G 371 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE G 376 " --> pdb=" O ALA G 372 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP G 377 " --> pdb=" O GLU G 373 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 395 Processing helix chain 'G' and resid 398 through 419 removed outlier: 3.679A pdb=" N THR G 402 " --> pdb=" O ASN G 398 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA G 403 " --> pdb=" O PRO G 399 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR G 404 " --> pdb=" O PRO G 400 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR G 415 " --> pdb=" O ILE G 411 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN G 419 " --> pdb=" O THR G 415 " (cutoff:3.500A) Processing helix chain 'G' and resid 426 through 434 Processing helix chain 'G' and resid 461 through 483 removed outlier: 3.575A pdb=" N TYR G 465 " --> pdb=" O GLN G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 487 through 501 removed outlier: 3.689A pdb=" N HIS G 499 " --> pdb=" O TRP G 495 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU G 501 " --> pdb=" O LEU G 497 " (cutoff:3.500A) Processing helix chain 'G' and resid 502 through 507 removed outlier: 3.760A pdb=" N TRP G 506 " --> pdb=" O ASP G 502 " (cutoff:3.500A) Processing helix chain 'G' and resid 512 through 532 removed outlier: 3.583A pdb=" N ILE G 516 " --> pdb=" O LEU G 512 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL G 522 " --> pdb=" O THR G 518 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU G 527 " --> pdb=" O ALA G 523 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG G 530 " --> pdb=" O ILE G 526 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 116 removed outlier: 4.075A pdb=" N ARG H 116 " --> pdb=" O PRO H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 150 Processing helix chain 'H' and resid 159 through 171 removed outlier: 3.509A pdb=" N LEU H 168 " --> pdb=" O HIS H 164 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN H 169 " --> pdb=" O SER H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 194 removed outlier: 3.623A pdb=" N ALA H 191 " --> pdb=" O GLN H 187 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU H 193 " --> pdb=" O GLN H 189 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS H 194 " --> pdb=" O ILE H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 227 removed outlier: 3.626A pdb=" N GLU H 216 " --> pdb=" O ARG H 212 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR H 217 " --> pdb=" O LEU H 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 248 Processing helix chain 'H' and resid 252 through 270 removed outlier: 3.621A pdb=" N GLU H 258 " --> pdb=" O ILE H 254 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG H 260 " --> pdb=" O GLU H 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 285 Processing helix chain 'H' and resid 289 through 297 removed outlier: 4.283A pdb=" N ILE H 293 " --> pdb=" O LYS H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 341 through 351 removed outlier: 4.098A pdb=" N LEU H 348 " --> pdb=" O LEU H 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 356 through 377 removed outlier: 3.572A pdb=" N ALA H 360 " --> pdb=" O SER H 356 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TRP H 361 " --> pdb=" O GLU H 357 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS H 374 " --> pdb=" O ARG H 370 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TRP H 375 " --> pdb=" O VAL H 371 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE H 376 " --> pdb=" O ALA H 372 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP H 377 " --> pdb=" O GLU H 373 " (cutoff:3.500A) Processing helix chain 'H' and resid 398 through 419 removed outlier: 3.784A pdb=" N THR H 402 " --> pdb=" O ASN H 398 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA H 403 " --> pdb=" O PRO H 399 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR H 404 " --> pdb=" O PRO H 400 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN H 419 " --> pdb=" O THR H 415 " (cutoff:3.500A) Processing helix chain 'H' and resid 426 through 434 Processing helix chain 'H' and resid 459 through 461 No H-bonds generated for 'chain 'H' and resid 459 through 461' Processing helix chain 'H' and resid 462 through 483 Processing helix chain 'H' and resid 487 through 501 removed outlier: 3.569A pdb=" N ALA H 496 " --> pdb=" O GLU H 492 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS H 499 " --> pdb=" O TRP H 495 " (cutoff:3.500A) Processing helix chain 'H' and resid 502 through 507 removed outlier: 3.752A pdb=" N TRP H 506 " --> pdb=" O ASP H 502 " (cutoff:3.500A) Processing helix chain 'H' and resid 512 through 532 removed outlier: 3.505A pdb=" N ILE H 516 " --> pdb=" O LEU H 512 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL H 522 " --> pdb=" O THR H 518 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA H 523 " --> pdb=" O TRP H 519 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG H 530 " --> pdb=" O ILE H 526 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 230 through 232 Processing sheet with id=AA2, first strand: chain 'A' and resid 230 through 232 Processing sheet with id=AA3, first strand: chain 'A' and resid 301 through 305 removed outlier: 5.500A pdb=" N ASN A 442 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE A 439 " --> pdb=" O ASN A 316 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLU A 314 " --> pdb=" O THR A 441 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP C 538 " --> pdb=" O THR C 556 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ARG C 558 " --> pdb=" O ILE C 536 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ILE C 536 " --> pdb=" O ARG C 558 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 301 through 305 removed outlier: 5.500A pdb=" N ASN A 442 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE A 439 " --> pdb=" O ASN A 316 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLU A 314 " --> pdb=" O THR A 441 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 534 through 541 removed outlier: 5.777A pdb=" N ILE A 536 " --> pdb=" O ARG A 558 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG A 558 " --> pdb=" O ILE A 536 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP A 538 " --> pdb=" O THR A 556 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 584 through 585 removed outlier: 3.665A pdb=" N GLU A 584 " --> pdb=" O PHE A 569 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N SER A 616 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ILE A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 230 through 232 removed outlier: 7.799A pdb=" N THR B 177 " --> pdb=" O PHE B 121 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ILE B 123 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ASN B 179 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TRP B 125 " --> pdb=" O ASN B 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 230 through 232 removed outlier: 7.799A pdb=" N THR B 177 " --> pdb=" O PHE B 121 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ILE B 123 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ASN B 179 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TRP B 125 " --> pdb=" O ASN B 179 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N MET B 119 " --> pdb=" O LYS B 423 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 301 through 305 removed outlier: 6.493A pdb=" N THR B 302 " --> pdb=" O PHE B 338 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ARG B 340 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU B 304 " --> pdb=" O ARG B 340 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ASN B 442 " --> pdb=" O ILE B 327 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE B 439 " --> pdb=" O ASN B 316 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLU B 314 " --> pdb=" O THR B 441 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER E 592 " --> pdb=" O ASN E 559 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASP E 538 " --> pdb=" O THR E 556 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ARG E 558 " --> pdb=" O ILE E 536 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ILE E 536 " --> pdb=" O ARG E 558 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 301 through 305 removed outlier: 6.493A pdb=" N THR B 302 " --> pdb=" O PHE B 338 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ARG B 340 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU B 304 " --> pdb=" O ARG B 340 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ASN B 442 " --> pdb=" O ILE B 327 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE B 439 " --> pdb=" O ASN B 316 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLU B 314 " --> pdb=" O THR B 441 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 534 through 541 removed outlier: 5.762A pdb=" N ILE B 536 " --> pdb=" O ARG B 558 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ARG B 558 " --> pdb=" O ILE B 536 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP B 538 " --> pdb=" O THR B 556 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 545 through 546 removed outlier: 6.655A pdb=" N PHE B 545 " --> pdb=" O LYS B 631 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA B 614 " --> pdb=" O ILE B 621 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER B 623 " --> pdb=" O VAL B 612 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL B 612 " --> pdb=" O SER B 623 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE B 625 " --> pdb=" O MET B 610 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N MET B 610 " --> pdb=" O ILE B 625 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ASP B 627 " --> pdb=" O HIS B 608 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N HIS B 608 " --> pdb=" O ASP B 627 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ASN B 629 " --> pdb=" O GLY B 606 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLY B 606 " --> pdb=" O ASN B 629 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE B 605 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N ASP C 622 " --> pdb=" O ILE B 605 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N LYS B 607 " --> pdb=" O ASP C 622 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N LYS C 624 " --> pdb=" O LYS B 607 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N LYS B 609 " --> pdb=" O LYS C 624 " (cutoff:3.500A) removed outlier: 10.256A pdb=" N ILE C 626 " --> pdb=" O LYS B 609 " (cutoff:3.500A) removed outlier: 10.350A pdb=" N VAL B 611 " --> pdb=" O ILE C 626 " (cutoff:3.500A) removed outlier: 13.464A pdb=" N ILE C 628 " --> pdb=" O VAL B 611 " (cutoff:3.500A) removed outlier: 12.530A pdb=" N SER B 613 " --> pdb=" O ILE C 628 " (cutoff:3.500A) removed outlier: 14.505A pdb=" N VAL C 630 " --> pdb=" O SER B 613 " (cutoff:3.500A) removed outlier: 13.462A pdb=" N ILE B 615 " --> pdb=" O VAL C 630 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N PHE C 545 " --> pdb=" O LYS C 631 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 545 through 546 removed outlier: 6.655A pdb=" N PHE B 545 " --> pdb=" O LYS B 631 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LYS C 607 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASP B 622 " --> pdb=" O LYS C 607 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N LYS C 609 " --> pdb=" O ASP B 622 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N LYS B 624 " --> pdb=" O LYS C 609 " (cutoff:3.500A) removed outlier: 10.522A pdb=" N VAL C 611 " --> pdb=" O LYS B 624 " (cutoff:3.500A) removed outlier: 12.288A pdb=" N ILE B 626 " --> pdb=" O VAL C 611 " (cutoff:3.500A) removed outlier: 12.056A pdb=" N SER C 613 " --> pdb=" O ILE B 626 " (cutoff:3.500A) removed outlier: 14.172A pdb=" N ILE B 628 " --> pdb=" O SER C 613 " (cutoff:3.500A) removed outlier: 13.507A pdb=" N ILE C 615 " --> pdb=" O ILE B 628 " (cutoff:3.500A) removed outlier: 15.368A pdb=" N VAL B 630 " --> pdb=" O ILE C 615 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU C 584 " --> pdb=" O PHE C 569 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 545 through 546 removed outlier: 6.655A pdb=" N PHE B 545 " --> pdb=" O LYS B 631 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LYS C 607 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASP B 622 " --> pdb=" O LYS C 607 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N LYS C 609 " --> pdb=" O ASP B 622 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N LYS B 624 " --> pdb=" O LYS C 609 " (cutoff:3.500A) removed outlier: 10.522A pdb=" N VAL C 611 " --> pdb=" O LYS B 624 " (cutoff:3.500A) removed outlier: 12.288A pdb=" N ILE B 626 " --> pdb=" O VAL C 611 " (cutoff:3.500A) removed outlier: 12.056A pdb=" N SER C 613 " --> pdb=" O ILE B 626 " (cutoff:3.500A) removed outlier: 14.172A pdb=" N ILE B 628 " --> pdb=" O SER C 613 " (cutoff:3.500A) removed outlier: 13.507A pdb=" N ILE C 615 " --> pdb=" O ILE B 628 " (cutoff:3.500A) removed outlier: 15.368A pdb=" N VAL B 630 " --> pdb=" O ILE C 615 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP C 622 " --> pdb=" O ALA C 614 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N SER C 616 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ILE C 620 " --> pdb=" O SER C 616 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE B 605 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N ASP C 622 " --> pdb=" O ILE B 605 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N LYS B 607 " --> pdb=" O ASP C 622 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N LYS C 624 " --> pdb=" O LYS B 607 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N LYS B 609 " --> pdb=" O LYS C 624 " (cutoff:3.500A) removed outlier: 10.256A pdb=" N ILE C 626 " --> pdb=" O LYS B 609 " (cutoff:3.500A) removed outlier: 10.350A pdb=" N VAL B 611 " --> pdb=" O ILE C 626 " (cutoff:3.500A) removed outlier: 13.464A pdb=" N ILE C 628 " --> pdb=" O VAL B 611 " (cutoff:3.500A) removed outlier: 12.530A pdb=" N SER B 613 " --> pdb=" O ILE C 628 " (cutoff:3.500A) removed outlier: 14.505A pdb=" N VAL C 630 " --> pdb=" O SER B 613 " (cutoff:3.500A) removed outlier: 13.462A pdb=" N ILE B 615 " --> pdb=" O VAL C 630 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU B 584 " --> pdb=" O PHE B 569 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 230 through 232 removed outlier: 7.741A pdb=" N THR C 177 " --> pdb=" O PHE C 121 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ILE C 123 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ASN C 179 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N TRP C 125 " --> pdb=" O ASN C 179 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 230 through 232 removed outlier: 7.741A pdb=" N THR C 177 " --> pdb=" O PHE C 121 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ILE C 123 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ASN C 179 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N TRP C 125 " --> pdb=" O ASN C 179 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N MET C 119 " --> pdb=" O LYS C 423 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 234 through 235 removed outlier: 7.070A pdb=" N THR C 234 " --> pdb=" O TRP C 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 301 through 305 removed outlier: 5.593A pdb=" N ASN C 442 " --> pdb=" O ILE C 327 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLU C 314 " --> pdb=" O THR C 441 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 230 through 232 Processing sheet with id=AC2, first strand: chain 'D' and resid 230 through 232 removed outlier: 6.879A pdb=" N MET D 119 " --> pdb=" O LYS D 423 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 234 through 235 removed outlier: 6.731A pdb=" N THR D 234 " --> pdb=" O TRP D 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'D' and resid 301 through 305 removed outlier: 6.311A pdb=" N THR D 302 " --> pdb=" O PHE D 338 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ARG D 340 " --> pdb=" O THR D 302 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU D 304 " --> pdb=" O ARG D 340 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N MET D 325 " --> pdb=" O LEU D 440 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASN D 442 " --> pdb=" O MET D 325 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ILE D 327 " --> pdb=" O ASN D 442 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE D 439 " --> pdb=" O ASN D 316 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLU D 314 " --> pdb=" O THR D 441 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR H 595 " --> pdb=" O GLY D 315 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP H 538 " --> pdb=" O THR H 556 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ARG H 558 " --> pdb=" O ILE H 536 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE H 536 " --> pdb=" O ARG H 558 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 301 through 305 removed outlier: 6.311A pdb=" N THR D 302 " --> pdb=" O PHE D 338 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ARG D 340 " --> pdb=" O THR D 302 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU D 304 " --> pdb=" O ARG D 340 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N MET D 325 " --> pdb=" O LEU D 440 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASN D 442 " --> pdb=" O MET D 325 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ILE D 327 " --> pdb=" O ASN D 442 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE D 439 " --> pdb=" O ASN D 316 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLU D 314 " --> pdb=" O THR D 441 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR H 595 " --> pdb=" O GLY D 315 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 534 through 541 removed outlier: 5.731A pdb=" N ILE D 536 " --> pdb=" O ARG D 558 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ARG D 558 " --> pdb=" O ILE D 536 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP D 538 " --> pdb=" O THR D 556 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 584 through 585 removed outlier: 3.852A pdb=" N GLU D 584 " --> pdb=" O PHE D 569 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLY D 606 " --> pdb=" O ASN D 629 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ASN D 629 " --> pdb=" O GLY D 606 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N HIS D 608 " --> pdb=" O ASP D 627 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ASP D 627 " --> pdb=" O HIS D 608 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N MET D 610 " --> pdb=" O ILE D 625 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE D 625 " --> pdb=" O MET D 610 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL D 612 " --> pdb=" O SER D 623 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER D 623 " --> pdb=" O VAL D 612 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ALA D 614 " --> pdb=" O ILE D 621 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 230 through 232 removed outlier: 3.612A pdb=" N ASP E 231 " --> pdb=" O ALA E 176 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N THR E 177 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE E 123 " --> pdb=" O THR E 177 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASN E 179 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP E 125 " --> pdb=" O ASN E 179 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 230 through 232 removed outlier: 3.612A pdb=" N ASP E 231 " --> pdb=" O ALA E 176 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N THR E 177 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE E 123 " --> pdb=" O THR E 177 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASN E 179 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP E 125 " --> pdb=" O ASN E 179 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 234 through 235 removed outlier: 6.905A pdb=" N THR E 234 " --> pdb=" O TRP E 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'E' and resid 301 through 304 Processing sheet with id=AD3, first strand: chain 'E' and resid 314 through 315 removed outlier: 6.529A pdb=" N GLU E 314 " --> pdb=" O THR E 441 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 545 through 546 removed outlier: 6.787A pdb=" N PHE E 545 " --> pdb=" O LYS E 631 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA E 614 " --> pdb=" O ILE E 621 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER E 623 " --> pdb=" O VAL E 612 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL E 612 " --> pdb=" O SER E 623 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ILE E 625 " --> pdb=" O MET E 610 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N MET E 610 " --> pdb=" O ILE E 625 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP E 627 " --> pdb=" O HIS E 608 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N HIS E 608 " --> pdb=" O ASP E 627 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASN E 629 " --> pdb=" O GLY E 606 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLY E 606 " --> pdb=" O ASN E 629 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU E 584 " --> pdb=" O PHE E 569 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 230 through 232 removed outlier: 3.719A pdb=" N ASP F 231 " --> pdb=" O ALA F 176 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP F 125 " --> pdb=" O THR F 177 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 230 through 232 removed outlier: 3.719A pdb=" N ASP F 231 " --> pdb=" O ALA F 176 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP F 125 " --> pdb=" O THR F 177 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N MET F 119 " --> pdb=" O LYS F 423 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 234 through 235 removed outlier: 6.797A pdb=" N THR F 234 " --> pdb=" O TRP F 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'F' and resid 301 through 305 removed outlier: 6.385A pdb=" N THR F 302 " --> pdb=" O PHE F 338 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ARG F 340 " --> pdb=" O THR F 302 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU F 304 " --> pdb=" O ARG F 340 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N MET F 325 " --> pdb=" O LEU F 440 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ASN F 442 " --> pdb=" O MET F 325 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N ILE F 327 " --> pdb=" O ASN F 442 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLU F 314 " --> pdb=" O THR F 441 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 534 through 541 removed outlier: 5.798A pdb=" N ILE F 536 " --> pdb=" O ARG F 558 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ARG F 558 " --> pdb=" O ILE F 536 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP F 538 " --> pdb=" O THR F 556 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN G 316 " --> pdb=" O LEU G 440 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LEU G 440 " --> pdb=" O ASN G 316 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ASN G 442 " --> pdb=" O ILE G 327 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR G 302 " --> pdb=" O PHE G 338 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ARG G 340 " --> pdb=" O THR G 302 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU G 304 " --> pdb=" O ARG G 340 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 545 through 546 removed outlier: 6.934A pdb=" N PHE F 545 " --> pdb=" O LYS F 631 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 584 through 585 removed outlier: 3.893A pdb=" N GLU F 584 " --> pdb=" O PHE F 569 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N SER F 616 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ILE F 620 " --> pdb=" O SER F 616 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 577 through 578 Processing sheet with id=AE4, first strand: chain 'G' and resid 230 through 232 removed outlier: 8.014A pdb=" N THR G 177 " --> pdb=" O PHE G 121 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE G 123 " --> pdb=" O THR G 177 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ASN G 179 " --> pdb=" O ILE G 123 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N TRP G 125 " --> pdb=" O ASN G 179 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 230 through 232 removed outlier: 8.014A pdb=" N THR G 177 " --> pdb=" O PHE G 121 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE G 123 " --> pdb=" O THR G 177 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ASN G 179 " --> pdb=" O ILE G 123 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N TRP G 125 " --> pdb=" O ASN G 179 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N MET G 119 " --> pdb=" O LYS G 423 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 234 through 235 removed outlier: 6.893A pdb=" N THR G 234 " --> pdb=" O TRP G 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'G' and resid 534 through 538 removed outlier: 6.772A pdb=" N THR G 556 " --> pdb=" O ILE G 537 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 584 through 585 removed outlier: 3.942A pdb=" N GLU G 584 " --> pdb=" O PHE G 569 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER G 616 " --> pdb=" O ILE G 620 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ILE G 620 " --> pdb=" O SER G 616 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LYS H 607 " --> pdb=" O ILE G 620 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASP G 622 " --> pdb=" O LYS H 607 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N LYS H 609 " --> pdb=" O ASP G 622 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N LYS G 624 " --> pdb=" O LYS H 609 " (cutoff:3.500A) removed outlier: 10.539A pdb=" N VAL H 611 " --> pdb=" O LYS G 624 " (cutoff:3.500A) removed outlier: 12.555A pdb=" N ILE G 626 " --> pdb=" O VAL H 611 " (cutoff:3.500A) removed outlier: 12.296A pdb=" N SER H 613 " --> pdb=" O ILE G 626 " (cutoff:3.500A) removed outlier: 14.409A pdb=" N ILE G 628 " --> pdb=" O SER H 613 " (cutoff:3.500A) removed outlier: 13.652A pdb=" N ILE H 615 " --> pdb=" O ILE G 628 " (cutoff:3.500A) removed outlier: 15.512A pdb=" N VAL G 630 " --> pdb=" O ILE H 615 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N SER H 616 " --> pdb=" O ILE H 620 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ILE H 620 " --> pdb=" O SER H 616 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N PHE H 545 " --> pdb=" O LYS H 631 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 584 through 585 removed outlier: 3.942A pdb=" N GLU G 584 " --> pdb=" O PHE G 569 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER G 616 " --> pdb=" O ILE G 620 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ILE G 620 " --> pdb=" O SER G 616 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LYS H 607 " --> pdb=" O ILE G 620 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASP G 622 " --> pdb=" O LYS H 607 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N LYS H 609 " --> pdb=" O ASP G 622 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N LYS G 624 " --> pdb=" O LYS H 609 " (cutoff:3.500A) removed outlier: 10.539A pdb=" N VAL H 611 " --> pdb=" O LYS G 624 " (cutoff:3.500A) removed outlier: 12.555A pdb=" N ILE G 626 " --> pdb=" O VAL H 611 " (cutoff:3.500A) removed outlier: 12.296A pdb=" N SER H 613 " --> pdb=" O ILE G 626 " (cutoff:3.500A) removed outlier: 14.409A pdb=" N ILE G 628 " --> pdb=" O SER H 613 " (cutoff:3.500A) removed outlier: 13.652A pdb=" N ILE H 615 " --> pdb=" O ILE G 628 " (cutoff:3.500A) removed outlier: 15.512A pdb=" N VAL G 630 " --> pdb=" O ILE H 615 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU H 584 " --> pdb=" O PHE H 569 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 230 through 232 removed outlier: 3.633A pdb=" N ASP H 231 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TRP H 125 " --> pdb=" O THR H 177 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 230 through 232 removed outlier: 3.633A pdb=" N ASP H 231 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TRP H 125 " --> pdb=" O THR H 177 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N MET H 119 " --> pdb=" O LYS H 423 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 234 through 235 removed outlier: 6.771A pdb=" N THR H 234 " --> pdb=" O TRP H 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'H' and resid 301 through 305 removed outlier: 6.140A pdb=" N MET H 325 " --> pdb=" O LEU H 440 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ASN H 442 " --> pdb=" O MET H 325 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ILE H 327 " --> pdb=" O ASN H 442 " (cutoff:3.500A) 1535 hydrogen bonds defined for protein. 4410 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.40 Time building geometry restraints manager: 4.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 10652 1.33 - 1.45: 6270 1.45 - 1.57: 19717 1.57 - 1.69: 0 1.69 - 1.81: 184 Bond restraints: 36823 Sorted by residual: bond pdb=" N VAL C 567 " pdb=" CA VAL C 567 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.11e-02 8.12e+03 1.05e+01 bond pdb=" N ILE C 565 " pdb=" CA ILE C 565 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.20e-02 6.94e+03 1.01e+01 bond pdb=" N SER E 150 " pdb=" CA SER E 150 " ideal model delta sigma weight residual 1.453 1.492 -0.039 1.22e-02 6.72e+03 1.01e+01 bond pdb=" N GLU A 357 " pdb=" CA GLU A 357 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.04e-02 9.25e+03 8.89e+00 bond pdb=" N VAL C 555 " pdb=" CA VAL C 555 " ideal model delta sigma weight residual 1.458 1.492 -0.033 1.17e-02 7.31e+03 8.14e+00 ... (remaining 36818 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 49548 2.82 - 5.64: 484 5.64 - 8.46: 29 8.46 - 11.28: 0 11.28 - 14.10: 1 Bond angle restraints: 50062 Sorted by residual: angle pdb=" N THR H 329 " pdb=" CA THR H 329 " pdb=" C THR H 329 " ideal model delta sigma weight residual 111.07 119.01 -7.94 1.07e+00 8.73e-01 5.51e+01 angle pdb=" N ARG B 566 " pdb=" CA ARG B 566 " pdb=" C ARG B 566 " ideal model delta sigma weight residual 107.69 121.79 -14.10 2.01e+00 2.48e-01 4.92e+01 angle pdb=" C SER H 319 " pdb=" CA SER H 319 " pdb=" CB SER H 319 " ideal model delta sigma weight residual 110.16 101.84 8.32 1.83e+00 2.99e-01 2.07e+01 angle pdb=" N TYR E 147 " pdb=" CA TYR E 147 " pdb=" C TYR E 147 " ideal model delta sigma weight residual 111.28 106.39 4.89 1.09e+00 8.42e-01 2.02e+01 angle pdb=" N GLN H 320 " pdb=" CA GLN H 320 " pdb=" C GLN H 320 " ideal model delta sigma weight residual 113.15 117.87 -4.72 1.19e+00 7.06e-01 1.57e+01 ... (remaining 50057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 19796 17.77 - 35.53: 1520 35.53 - 53.30: 233 53.30 - 71.06: 45 71.06 - 88.83: 22 Dihedral angle restraints: 21616 sinusoidal: 8864 harmonic: 12752 Sorted by residual: dihedral pdb=" CA HIS H 128 " pdb=" C HIS H 128 " pdb=" N GLN H 129 " pdb=" CA GLN H 129 " ideal model delta harmonic sigma weight residual 180.00 158.94 21.06 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA HIS F 128 " pdb=" C HIS F 128 " pdb=" N GLN F 129 " pdb=" CA GLN F 129 " ideal model delta harmonic sigma weight residual 180.00 159.04 20.96 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA SER G 543 " pdb=" C SER G 543 " pdb=" N GLU G 544 " pdb=" CA GLU G 544 " ideal model delta harmonic sigma weight residual 180.00 160.30 19.70 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 21613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 4606 0.074 - 0.148: 666 0.148 - 0.222: 30 0.222 - 0.296: 1 0.296 - 0.370: 1 Chirality restraints: 5304 Sorted by residual: chirality pdb=" CA ARG C 566 " pdb=" N ARG C 566 " pdb=" C ARG C 566 " pdb=" CB ARG C 566 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CA THR H 329 " pdb=" N THR H 329 " pdb=" C THR H 329 " pdb=" CB THR H 329 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA LYS C 475 " pdb=" N LYS C 475 " pdb=" C LYS C 475 " pdb=" CB LYS C 475 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 5301 not shown) Planarity restraints: 6335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 448 " 0.041 2.00e-02 2.50e+03 3.61e-02 3.26e+01 pdb=" CG TRP B 448 " -0.096 2.00e-02 2.50e+03 pdb=" CD1 TRP B 448 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP B 448 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 448 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 448 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 448 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 448 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 448 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP B 448 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 448 " -0.037 2.00e-02 2.50e+03 3.44e-02 2.96e+01 pdb=" CG TRP A 448 " 0.092 2.00e-02 2.50e+03 pdb=" CD1 TRP A 448 " -0.043 2.00e-02 2.50e+03 pdb=" CD2 TRP A 448 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 448 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 448 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 448 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 448 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 448 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP A 448 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 448 " -0.037 2.00e-02 2.50e+03 3.34e-02 2.79e+01 pdb=" CG TRP C 448 " 0.089 2.00e-02 2.50e+03 pdb=" CD1 TRP C 448 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP C 448 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 448 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 448 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 448 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 448 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 448 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP C 448 " -0.001 2.00e-02 2.50e+03 ... (remaining 6332 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2582 2.74 - 3.28: 35782 3.28 - 3.82: 59941 3.82 - 4.36: 76441 4.36 - 4.90: 129674 Nonbonded interactions: 304420 Sorted by model distance: nonbonded pdb=" OG1 THR A 574 " pdb=" OG SER E 613 " model vdw 2.195 3.040 nonbonded pdb=" OG SER D 578 " pdb=" OD1 ASN D 581 " model vdw 2.218 3.040 nonbonded pdb=" NZ LYS C 607 " pdb=" OD1 ASP C 627 " model vdw 2.232 3.120 nonbonded pdb=" OG SER G 613 " pdb=" OG1 THR H 574 " model vdw 2.239 3.040 nonbonded pdb=" NE2 HIS A 359 " pdb=" OD1 ASN A 363 " model vdw 2.249 3.120 ... (remaining 304415 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 103 through 139 or resid 141 through 640)) selection = (chain 'B' and (resid 103 through 139 or resid 141 through 640)) selection = (chain 'C' and (resid 103 through 139 or resid 141 through 640)) selection = (chain 'D' and (resid 103 through 139 or resid 141 through 640)) selection = (chain 'E' and (resid 103 through 139 or resid 141 through 640)) selection = (chain 'F' and (resid 103 through 139 or resid 141 through 640)) selection = (chain 'G' and (resid 103 through 139 or resid 141 through 640)) selection = (chain 'H' and (resid 103 through 139 or resid 141 through 640)) } 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=0.50 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: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 40.500 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.120 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:8.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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 : 0.004 0.074 36823 Z= 0.215 Angle : 0.758 14.103 50062 Z= 0.470 Chirality : 0.050 0.370 5304 Planarity : 0.005 0.093 6335 Dihedral : 13.003 88.831 13424 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.03 % Allowed : 0.28 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.20 (0.12), residues: 4311 helix: -1.20 (0.12), residues: 1624 sheet: -1.14 (0.18), residues: 880 loop : -1.72 (0.13), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 260 TYR 0.024 0.001 TYR E 334 PHE 0.041 0.002 PHE H 405 TRP 0.096 0.003 TRP B 448 HIS 0.018 0.002 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00424 (36823) covalent geometry : angle 0.75777 (50062) hydrogen bonds : bond 0.25201 ( 1450) hydrogen bonds : angle 8.58322 ( 4410) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 874 time to evaluate : 1.147 Fit side-chains revert: symmetry clash REVERT: A 107 CYS cc_start: 0.8387 (p) cc_final: 0.8087 (p) REVERT: A 190 ILE cc_start: 0.8093 (pt) cc_final: 0.7643 (mt) REVERT: A 268 LYS cc_start: 0.8451 (ttpp) cc_final: 0.8145 (ttpp) REVERT: A 351 ARG cc_start: 0.5421 (mmm160) cc_final: 0.3866 (mmp80) REVERT: A 439 ILE cc_start: 0.8317 (mm) cc_final: 0.8021 (mt) REVERT: B 226 PHE cc_start: 0.7733 (m-80) cc_final: 0.7452 (m-80) REVERT: B 351 ARG cc_start: 0.4427 (mmm160) cc_final: 0.3931 (mmm-85) REVERT: B 404 TYR cc_start: 0.7518 (t80) cc_final: 0.7181 (t80) REVERT: C 108 PHE cc_start: 0.7483 (p90) cc_final: 0.7213 (p90) REVERT: C 163 TYR cc_start: 0.7917 (t80) cc_final: 0.7682 (t80) REVERT: C 168 LEU cc_start: 0.8090 (mt) cc_final: 0.7794 (mt) REVERT: C 351 ARG cc_start: 0.5910 (mmt180) cc_final: 0.5588 (mmm160) REVERT: C 373 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7546 (mt-10) REVERT: C 377 ASP cc_start: 0.7315 (t0) cc_final: 0.6955 (t0) REVERT: C 385 ILE cc_start: 0.8728 (mt) cc_final: 0.7827 (tt) REVERT: C 409 MET cc_start: 0.7118 (tpp) cc_final: 0.6771 (ttp) REVERT: C 623 SER cc_start: 0.7955 (p) cc_final: 0.7735 (p) REVERT: D 105 ASN cc_start: 0.6907 (t0) cc_final: 0.6697 (t0) REVERT: D 108 PHE cc_start: 0.7666 (p90) cc_final: 0.7340 (p90) REVERT: D 203 LYS cc_start: 0.7739 (ptmm) cc_final: 0.7515 (pttm) REVERT: D 288 MET cc_start: 0.8621 (mmm) cc_final: 0.8411 (mmm) REVERT: D 437 ASN cc_start: 0.7034 (p0) cc_final: 0.6648 (m110) REVERT: D 622 ASP cc_start: 0.7702 (t0) cc_final: 0.7234 (t0) REVERT: E 167 MET cc_start: 0.7182 (mmm) cc_final: 0.6720 (mmm) REVERT: E 174 PHE cc_start: 0.8113 (t80) cc_final: 0.7911 (t80) REVERT: E 199 VAL cc_start: 0.7187 (t) cc_final: 0.6909 (p) REVERT: E 319 SER cc_start: 0.7945 (p) cc_final: 0.7702 (t) REVERT: E 329 THR cc_start: 0.7388 (m) cc_final: 0.7155 (p) REVERT: E 351 ARG cc_start: 0.4757 (tpm170) cc_final: 0.2816 (ttt180) REVERT: E 363 ASN cc_start: 0.7369 (m-40) cc_final: 0.6974 (m110) REVERT: E 481 GLU cc_start: 0.7532 (tp30) cc_final: 0.7300 (tm-30) REVERT: E 588 MET cc_start: 0.7696 (ptp) cc_final: 0.7448 (ptt) REVERT: F 256 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7371 (tm-30) REVERT: F 257 GLU cc_start: 0.7750 (pt0) cc_final: 0.7522 (pt0) REVERT: F 275 ASN cc_start: 0.8308 (t0) cc_final: 0.8076 (t0) REVERT: F 332 LYS cc_start: 0.7953 (mmpt) cc_final: 0.7690 (mmtm) REVERT: F 351 ARG cc_start: 0.4880 (tpm170) cc_final: 0.3574 (tpt-90) REVERT: F 373 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7213 (tp30) REVERT: F 381 LYS cc_start: 0.7970 (ttpt) cc_final: 0.7754 (ttmm) REVERT: F 510 PHE cc_start: 0.7921 (m-10) cc_final: 0.7684 (m-80) REVERT: F 585 THR cc_start: 0.7997 (t) cc_final: 0.7397 (m) REVERT: G 110 VAL cc_start: 0.7849 (t) cc_final: 0.7617 (t) REVERT: G 197 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7341 (tm-30) REVERT: G 296 ASP cc_start: 0.7869 (m-30) cc_final: 0.7630 (m-30) REVERT: G 341 ASP cc_start: 0.7928 (t70) cc_final: 0.7704 (t0) REVERT: G 391 ASN cc_start: 0.8250 (m-40) cc_final: 0.7971 (m-40) REVERT: G 411 ILE cc_start: 0.8319 (mt) cc_final: 0.8007 (mm) REVERT: G 420 LYS cc_start: 0.7962 (mmpt) cc_final: 0.7725 (mttm) REVERT: G 596 ARG cc_start: 0.7467 (ptm160) cc_final: 0.7255 (ptp-170) REVERT: H 118 GLN cc_start: 0.7395 (pt0) cc_final: 0.7146 (pt0) REVERT: H 120 TYR cc_start: 0.7779 (m-80) cc_final: 0.7545 (m-80) REVERT: H 163 TYR cc_start: 0.7864 (t80) cc_final: 0.7654 (t80) REVERT: H 226 PHE cc_start: 0.7867 (m-80) cc_final: 0.7626 (m-80) REVERT: H 231 ASP cc_start: 0.7269 (t0) cc_final: 0.6956 (t70) REVERT: H 328 ASP cc_start: 0.7231 (t0) cc_final: 0.6998 (t70) REVERT: H 381 LYS cc_start: 0.7663 (tppt) cc_final: 0.7252 (tppt) REVERT: H 420 LYS cc_start: 0.7578 (mmpt) cc_final: 0.7293 (mtpt) REVERT: H 481 GLU cc_start: 0.7529 (tp30) cc_final: 0.7100 (tp30) REVERT: H 566 ARG cc_start: 0.6990 (ptm-80) cc_final: 0.6717 (ptt-90) outliers start: 1 outliers final: 1 residues processed: 874 average time/residue: 0.7911 time to fit residues: 806.2650 Evaluate side-chains 551 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 550 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 170 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 0.0980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 chunk 401 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 10.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN A 277 GLN A 316 ASN ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 ASN A 532 ASN A 589 ASN ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 ASN B 273 ASN B 359 HIS C 132 ASN C 164 HIS C 179 ASN C 189 GLN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN C 589 ASN D 171 HIS ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN D 353 ASN D 398 ASN D 461 GLN D 589 ASN E 316 ASN E 379 ASN F 129 GLN F 219 ASN F 277 GLN F 353 ASN G 171 HIS G 391 ASN G 419 ASN G 560 GLN H 127 HIS H 129 GLN H 189 GLN H 353 ASN ** H 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.137981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.108763 restraints weight = 172168.846| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 4.91 r_work: 0.2952 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 36823 Z= 0.150 Angle : 0.625 9.793 50062 Z= 0.336 Chirality : 0.049 0.197 5304 Planarity : 0.005 0.071 6335 Dihedral : 4.754 20.002 4746 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.04 % Allowed : 11.47 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.44 (0.12), residues: 4311 helix: -0.34 (0.12), residues: 1656 sheet: -0.89 (0.18), residues: 904 loop : -1.46 (0.13), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 222 TYR 0.015 0.001 TYR B 321 PHE 0.026 0.002 PHE C 405 TRP 0.068 0.002 TRP C 448 HIS 0.013 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00338 (36823) covalent geometry : angle 0.62542 (50062) hydrogen bonds : bond 0.05249 ( 1450) hydrogen bonds : angle 5.34730 ( 4410) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 602 time to evaluate : 1.483 Fit side-chains revert: symmetry clash REVERT: A 107 CYS cc_start: 0.8707 (p) cc_final: 0.8393 (p) REVERT: A 268 LYS cc_start: 0.8816 (ttpp) cc_final: 0.8553 (ttpt) REVERT: A 398 ASN cc_start: 0.7605 (t0) cc_final: 0.7404 (t0) REVERT: B 226 PHE cc_start: 0.7732 (m-80) cc_final: 0.7431 (m-80) REVERT: B 351 ARG cc_start: 0.5354 (mmm160) cc_final: 0.4641 (mmm-85) REVERT: B 549 GLU cc_start: 0.8050 (tt0) cc_final: 0.7553 (tm-30) REVERT: B 587 LYS cc_start: 0.7983 (tmtt) cc_final: 0.7749 (tptm) REVERT: C 108 PHE cc_start: 0.7611 (p90) cc_final: 0.7313 (p90) REVERT: C 168 LEU cc_start: 0.8084 (mt) cc_final: 0.7671 (mt) REVERT: C 256 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7690 (tm-30) REVERT: C 260 ARG cc_start: 0.8360 (ttp-110) cc_final: 0.7984 (ttm-80) REVERT: C 351 ARG cc_start: 0.6529 (mmt180) cc_final: 0.5897 (mmm-85) REVERT: C 373 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7972 (mt-10) REVERT: C 379 ASN cc_start: 0.7606 (OUTLIER) cc_final: 0.6955 (t0) REVERT: C 385 ILE cc_start: 0.8949 (mt) cc_final: 0.8140 (tt) REVERT: D 105 ASN cc_start: 0.7458 (t0) cc_final: 0.7212 (t0) REVERT: D 108 PHE cc_start: 0.7944 (p90) cc_final: 0.7537 (p90) REVERT: D 136 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7339 (p0) REVERT: D 202 GLU cc_start: 0.7842 (pt0) cc_final: 0.7525 (tt0) REVERT: D 332 LYS cc_start: 0.8100 (mttm) cc_final: 0.7871 (mmmm) REVERT: D 347 ILE cc_start: 0.8470 (tp) cc_final: 0.8232 (mt) REVERT: D 437 ASN cc_start: 0.7293 (p0) cc_final: 0.6620 (m110) REVERT: D 535 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.7781 (pm20) REVERT: D 622 ASP cc_start: 0.7942 (t0) cc_final: 0.7563 (t0) REVERT: E 167 MET cc_start: 0.7548 (mmm) cc_final: 0.6934 (mmm) REVERT: E 174 PHE cc_start: 0.8224 (t80) cc_final: 0.7933 (t80) REVERT: E 189 GLN cc_start: 0.7693 (tp40) cc_final: 0.6666 (tm-30) REVERT: E 199 VAL cc_start: 0.7257 (t) cc_final: 0.6945 (p) REVERT: E 206 PRO cc_start: 0.6433 (Cg_endo) cc_final: 0.6140 (Cg_exo) REVERT: E 283 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7957 (mp0) REVERT: E 351 ARG cc_start: 0.5044 (tpm170) cc_final: 0.2883 (ttt180) REVERT: E 363 ASN cc_start: 0.7384 (m-40) cc_final: 0.6893 (m110) REVERT: E 391 ASN cc_start: 0.7590 (m-40) cc_final: 0.6953 (t0) REVERT: E 420 LYS cc_start: 0.8011 (mmmm) cc_final: 0.7267 (ttpt) REVERT: E 428 ARG cc_start: 0.7834 (tpp80) cc_final: 0.7290 (tpt-90) REVERT: E 481 GLU cc_start: 0.8581 (tp30) cc_final: 0.8234 (tm-30) REVERT: E 587 LYS cc_start: 0.8335 (tmtt) cc_final: 0.7990 (tppt) REVERT: E 588 MET cc_start: 0.8055 (ptp) cc_final: 0.7839 (ptt) REVERT: F 231 ASP cc_start: 0.7960 (t70) cc_final: 0.7473 (t70) REVERT: F 257 GLU cc_start: 0.8370 (pt0) cc_final: 0.8132 (pt0) REVERT: F 274 TYR cc_start: 0.8061 (t80) cc_final: 0.7791 (t80) REVERT: F 275 ASN cc_start: 0.8458 (t0) cc_final: 0.8235 (t0) REVERT: F 332 LYS cc_start: 0.8261 (mmpt) cc_final: 0.7975 (mmtm) REVERT: F 351 ARG cc_start: 0.5391 (tpm170) cc_final: 0.3907 (tpt-90) REVERT: F 373 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7231 (tp30) REVERT: F 376 PHE cc_start: 0.7301 (m-10) cc_final: 0.6885 (m-10) REVERT: F 428 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.7268 (tpt-90) REVERT: F 510 PHE cc_start: 0.8112 (m-10) cc_final: 0.7911 (m-80) REVERT: G 118 GLN cc_start: 0.7149 (pt0) cc_final: 0.6921 (pt0) REVERT: G 189 GLN cc_start: 0.8025 (tp40) cc_final: 0.7565 (tt0) REVERT: G 296 ASP cc_start: 0.8392 (m-30) cc_final: 0.8101 (m-30) REVERT: G 362 ARG cc_start: 0.5482 (ttm110) cc_final: 0.3950 (tmt170) REVERT: G 378 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7814 (mptt) REVERT: H 118 GLN cc_start: 0.7306 (pt0) cc_final: 0.7069 (pt0) REVERT: H 120 TYR cc_start: 0.8197 (m-80) cc_final: 0.7895 (m-80) REVERT: H 163 TYR cc_start: 0.8093 (t80) cc_final: 0.7831 (t80) REVERT: H 231 ASP cc_start: 0.7647 (t0) cc_final: 0.7147 (t70) REVERT: H 260 ARG cc_start: 0.8262 (ttp80) cc_final: 0.7965 (ttp80) REVERT: H 274 TYR cc_start: 0.7536 (t80) cc_final: 0.7256 (t80) REVERT: H 295 TYR cc_start: 0.8543 (t80) cc_final: 0.7837 (t80) REVERT: H 373 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7608 (mm-30) REVERT: H 381 LYS cc_start: 0.8168 (tppt) cc_final: 0.7681 (tppt) REVERT: H 391 ASN cc_start: 0.8522 (m110) cc_final: 0.8246 (t0) REVERT: H 420 LYS cc_start: 0.7567 (mmpt) cc_final: 0.7327 (mtpt) REVERT: H 481 GLU cc_start: 0.8635 (tp30) cc_final: 0.8076 (tp30) REVERT: H 566 ARG cc_start: 0.7849 (ptm-80) cc_final: 0.7220 (ptt-90) outliers start: 79 outliers final: 15 residues processed: 640 average time/residue: 0.7472 time to fit residues: 562.6929 Evaluate side-chains 542 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 520 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 448 TRP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 535 GLN Chi-restraints excluded: chain D residue 585 THR Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 373 GLU Chi-restraints excluded: chain E residue 537 ILE Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 428 ARG Chi-restraints excluded: chain F residue 571 ILE Chi-restraints excluded: chain G residue 378 LYS Chi-restraints excluded: chain H residue 254 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 343 optimal weight: 5.9990 chunk 333 optimal weight: 3.9990 chunk 298 optimal weight: 3.9990 chunk 331 optimal weight: 7.9990 chunk 314 optimal weight: 0.9980 chunk 360 optimal weight: 2.9990 chunk 375 optimal weight: 8.9990 chunk 182 optimal weight: 0.7980 chunk 268 optimal weight: 2.9990 chunk 226 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 HIS A 277 GLN ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 ASN A 560 GLN B 273 ASN B 359 HIS B 461 GLN ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN D 398 ASN D 461 GLN D 589 ASN E 208 HIS E 379 ASN F 316 ASN F 353 ASN G 118 GLN G 391 ASN H 129 GLN H 608 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.135256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.105744 restraints weight = 175596.819| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 4.95 r_work: 0.2893 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 36823 Z= 0.209 Angle : 0.648 8.054 50062 Z= 0.346 Chirality : 0.050 0.186 5304 Planarity : 0.005 0.061 6335 Dihedral : 4.829 20.401 4744 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.37 % Allowed : 13.09 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.18 (0.12), residues: 4311 helix: -0.07 (0.12), residues: 1664 sheet: -0.74 (0.18), residues: 904 loop : -1.38 (0.13), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 222 TYR 0.019 0.002 TYR F 334 PHE 0.020 0.002 PHE B 108 TRP 0.075 0.002 TRP C 448 HIS 0.014 0.002 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00493 (36823) covalent geometry : angle 0.64805 (50062) hydrogen bonds : bond 0.05622 ( 1450) hydrogen bonds : angle 5.07379 ( 4410) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 551 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: A 107 CYS cc_start: 0.8685 (p) cc_final: 0.8334 (p) REVERT: A 212 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.6738 (mmp-170) REVERT: A 268 LYS cc_start: 0.8800 (ttpp) cc_final: 0.8505 (tppt) REVERT: A 379 ASN cc_start: 0.7091 (t0) cc_final: 0.6853 (p0) REVERT: B 227 LYS cc_start: 0.7633 (ttpt) cc_final: 0.7374 (ttmm) REVERT: B 549 GLU cc_start: 0.8088 (tt0) cc_final: 0.7615 (tm-30) REVERT: B 587 LYS cc_start: 0.8335 (tmtt) cc_final: 0.8045 (tptm) REVERT: C 108 PHE cc_start: 0.7618 (p90) cc_final: 0.7286 (p90) REVERT: C 163 TYR cc_start: 0.7988 (t80) cc_final: 0.7593 (t80) REVERT: C 168 LEU cc_start: 0.8110 (mt) cc_final: 0.7735 (mt) REVERT: C 180 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7436 (mt) REVERT: C 215 GLU cc_start: 0.8125 (tp30) cc_final: 0.7875 (pt0) REVERT: C 256 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7877 (tm-30) REVERT: C 351 ARG cc_start: 0.6576 (mmt180) cc_final: 0.6289 (mtp85) REVERT: C 373 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8007 (mt-10) REVERT: C 379 ASN cc_start: 0.7485 (OUTLIER) cc_final: 0.7156 (t0) REVERT: C 385 ILE cc_start: 0.8984 (mt) cc_final: 0.8730 (mm) REVERT: D 108 PHE cc_start: 0.8000 (p90) cc_final: 0.7565 (p90) REVERT: D 136 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7371 (p0) REVERT: D 216 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7523 (tt0) REVERT: D 256 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8068 (tm-30) REVERT: D 437 ASN cc_start: 0.7270 (p0) cc_final: 0.6545 (m110) REVERT: E 174 PHE cc_start: 0.8182 (t80) cc_final: 0.7892 (t80) REVERT: E 189 GLN cc_start: 0.7693 (tp40) cc_final: 0.6817 (tm-30) REVERT: E 199 VAL cc_start: 0.7290 (t) cc_final: 0.6970 (p) REVERT: E 206 PRO cc_start: 0.6520 (Cg_endo) cc_final: 0.6272 (Cg_exo) REVERT: E 256 GLU cc_start: 0.8398 (tt0) cc_final: 0.8084 (tt0) REVERT: E 283 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8063 (mp0) REVERT: E 351 ARG cc_start: 0.5236 (tpm170) cc_final: 0.2978 (ttt180) REVERT: E 363 ASN cc_start: 0.7363 (m-40) cc_final: 0.6815 (m110) REVERT: E 391 ASN cc_start: 0.7588 (m-40) cc_final: 0.6964 (t0) REVERT: E 402 THR cc_start: 0.7630 (m) cc_final: 0.7427 (m) REVERT: E 420 LYS cc_start: 0.7955 (mmmm) cc_final: 0.7250 (ttpt) REVERT: E 423 LYS cc_start: 0.7091 (tttt) cc_final: 0.6765 (tmtt) REVERT: E 428 ARG cc_start: 0.8012 (tpp80) cc_final: 0.7468 (tpt-90) REVERT: E 481 GLU cc_start: 0.8599 (tp30) cc_final: 0.8256 (tm-30) REVERT: E 587 LYS cc_start: 0.8423 (tmtt) cc_final: 0.8130 (ttmt) REVERT: F 154 LYS cc_start: 0.6388 (OUTLIER) cc_final: 0.6136 (mtpp) REVERT: F 231 ASP cc_start: 0.8035 (t70) cc_final: 0.7513 (t70) REVERT: F 257 GLU cc_start: 0.8357 (pt0) cc_final: 0.8152 (pt0) REVERT: F 274 TYR cc_start: 0.8092 (t80) cc_final: 0.7779 (t80) REVERT: F 275 ASN cc_start: 0.8433 (t0) cc_final: 0.8183 (t0) REVERT: F 351 ARG cc_start: 0.5509 (tpm170) cc_final: 0.3989 (tpt-90) REVERT: F 373 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7178 (tp30) REVERT: F 376 PHE cc_start: 0.7418 (m-10) cc_final: 0.7059 (m-10) REVERT: F 381 LYS cc_start: 0.8320 (ttmm) cc_final: 0.7643 (ttpt) REVERT: F 428 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7372 (tpt-90) REVERT: F 488 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: F 492 GLU cc_start: 0.8387 (tt0) cc_final: 0.8052 (mp0) REVERT: F 538 ASP cc_start: 0.7330 (p0) cc_final: 0.7082 (p0) REVERT: F 587 LYS cc_start: 0.8519 (tppp) cc_final: 0.8083 (ttpp) REVERT: F 634 LEU cc_start: 0.8316 (tp) cc_final: 0.8073 (mt) REVERT: G 118 GLN cc_start: 0.7208 (pt0) cc_final: 0.6925 (pt0) REVERT: G 189 GLN cc_start: 0.8147 (tp40) cc_final: 0.7652 (tt0) REVERT: G 296 ASP cc_start: 0.8431 (m-30) cc_final: 0.8140 (m-30) REVERT: G 318 ASP cc_start: 0.7660 (t0) cc_final: 0.7434 (t0) REVERT: G 362 ARG cc_start: 0.5572 (ttm110) cc_final: 0.4010 (tmt170) REVERT: G 538 ASP cc_start: 0.7714 (t70) cc_final: 0.7308 (t70) REVERT: H 118 GLN cc_start: 0.7280 (pt0) cc_final: 0.7020 (pt0) REVERT: H 163 TYR cc_start: 0.8088 (t80) cc_final: 0.7743 (t80) REVERT: H 231 ASP cc_start: 0.7796 (t0) cc_final: 0.7373 (t70) REVERT: H 274 TYR cc_start: 0.7565 (t80) cc_final: 0.7304 (t80) REVERT: H 295 TYR cc_start: 0.8542 (t80) cc_final: 0.7938 (t80) REVERT: H 373 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7654 (mm-30) REVERT: H 381 LYS cc_start: 0.8212 (tppt) cc_final: 0.7599 (tppt) REVERT: H 391 ASN cc_start: 0.8531 (m110) cc_final: 0.8134 (t0) REVERT: H 481 GLU cc_start: 0.8681 (tp30) cc_final: 0.8219 (tp30) REVERT: H 566 ARG cc_start: 0.7882 (ptm-80) cc_final: 0.7262 (tmm-80) outliers start: 92 outliers final: 32 residues processed: 600 average time/residue: 0.7669 time to fit residues: 539.9250 Evaluate side-chains 559 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 516 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 448 TRP Chi-restraints excluded: chain C residue 588 MET Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 535 GLN Chi-restraints excluded: chain D residue 585 THR Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 537 ILE Chi-restraints excluded: chain F residue 154 LYS Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 428 ARG Chi-restraints excluded: chain F residue 488 GLU Chi-restraints excluded: chain F residue 571 ILE Chi-restraints excluded: chain F residue 585 THR Chi-restraints excluded: chain F residue 623 SER Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 585 THR Chi-restraints excluded: chain G residue 626 ILE Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 254 ILE Chi-restraints excluded: chain H residue 554 VAL Chi-restraints excluded: chain H residue 588 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 151 optimal weight: 0.7980 chunk 347 optimal weight: 5.9990 chunk 177 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 159 optimal weight: 7.9990 chunk 190 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 240 optimal weight: 9.9990 chunk 158 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 ASN A 560 GLN B 164 HIS B 273 ASN B 359 HIS B 532 ASN ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN D 398 ASN D 461 GLN E 208 HIS E 379 ASN F 316 ASN G 239 HIS G 391 ASN G 535 GLN H 118 GLN H 129 GLN H 189 GLN ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.136015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.106944 restraints weight = 183734.842| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 5.17 r_work: 0.2906 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 36823 Z= 0.167 Angle : 0.597 8.078 50062 Z= 0.319 Chirality : 0.048 0.186 5304 Planarity : 0.005 0.057 6335 Dihedral : 4.679 21.177 4744 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.24 % Allowed : 14.43 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.12), residues: 4311 helix: 0.24 (0.12), residues: 1672 sheet: -0.66 (0.18), residues: 904 loop : -1.25 (0.14), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 222 TYR 0.018 0.001 TYR D 404 PHE 0.020 0.002 PHE B 108 TRP 0.071 0.002 TRP C 448 HIS 0.013 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00393 (36823) covalent geometry : angle 0.59738 (50062) hydrogen bonds : bond 0.04804 ( 1450) hydrogen bonds : angle 4.82884 ( 4410) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 544 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 CYS cc_start: 0.8690 (p) cc_final: 0.8285 (p) REVERT: A 203 LYS cc_start: 0.8504 (ptmm) cc_final: 0.8169 (ptpp) REVERT: A 205 ASP cc_start: 0.7068 (p0) cc_final: 0.6705 (OUTLIER) REVERT: A 268 LYS cc_start: 0.8748 (ttpp) cc_final: 0.8424 (tppt) REVERT: A 347 ILE cc_start: 0.8330 (mt) cc_final: 0.8016 (mp) REVERT: A 351 ARG cc_start: 0.5957 (mmm160) cc_final: 0.3877 (mmp80) REVERT: A 379 ASN cc_start: 0.7010 (t0) cc_final: 0.6776 (p0) REVERT: B 202 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7763 (pt0) REVERT: B 226 PHE cc_start: 0.7732 (m-80) cc_final: 0.7435 (m-80) REVERT: B 227 LYS cc_start: 0.7614 (ttpt) cc_final: 0.7380 (ttmm) REVERT: B 351 ARG cc_start: 0.5186 (mmm160) cc_final: 0.4938 (mmm160) REVERT: B 549 GLU cc_start: 0.8122 (tt0) cc_final: 0.7683 (tm-30) REVERT: B 587 LYS cc_start: 0.8316 (tmtt) cc_final: 0.8019 (tptm) REVERT: C 108 PHE cc_start: 0.7516 (p90) cc_final: 0.7197 (p90) REVERT: C 163 TYR cc_start: 0.7979 (t80) cc_final: 0.7607 (t80) REVERT: C 168 LEU cc_start: 0.8020 (mt) cc_final: 0.7684 (mt) REVERT: C 215 GLU cc_start: 0.8087 (tp30) cc_final: 0.7805 (pt0) REVERT: C 256 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7843 (tm-30) REVERT: C 351 ARG cc_start: 0.6703 (mmt180) cc_final: 0.6234 (mtp85) REVERT: C 373 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8028 (mt-10) REVERT: C 378 LYS cc_start: 0.8047 (tppt) cc_final: 0.7489 (mptp) REVERT: C 385 ILE cc_start: 0.8909 (mt) cc_final: 0.8664 (mm) REVERT: C 409 MET cc_start: 0.7688 (mmm) cc_final: 0.7466 (ttp) REVERT: D 108 PHE cc_start: 0.8068 (p90) cc_final: 0.7625 (p90) REVERT: D 202 GLU cc_start: 0.7869 (pt0) cc_final: 0.7567 (tt0) REVERT: D 216 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7559 (tt0) REVERT: D 535 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7927 (pm20) REVERT: D 564 GLU cc_start: 0.8401 (tt0) cc_final: 0.8169 (tm-30) REVERT: D 566 ARG cc_start: 0.8315 (ptm-80) cc_final: 0.7760 (ptp90) REVERT: E 174 PHE cc_start: 0.8155 (t80) cc_final: 0.7866 (t80) REVERT: E 189 GLN cc_start: 0.7713 (tp40) cc_final: 0.6871 (tm-30) REVERT: E 199 VAL cc_start: 0.7260 (t) cc_final: 0.6943 (p) REVERT: E 206 PRO cc_start: 0.6612 (Cg_endo) cc_final: 0.6367 (Cg_exo) REVERT: E 256 GLU cc_start: 0.8385 (tt0) cc_final: 0.8112 (tt0) REVERT: E 283 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8004 (mp0) REVERT: E 351 ARG cc_start: 0.5158 (tpm170) cc_final: 0.2869 (ttt180) REVERT: E 363 ASN cc_start: 0.7338 (m-40) cc_final: 0.6805 (m110) REVERT: E 391 ASN cc_start: 0.7598 (m-40) cc_final: 0.6974 (t0) REVERT: E 420 LYS cc_start: 0.7893 (mmmm) cc_final: 0.7233 (ttpt) REVERT: E 423 LYS cc_start: 0.7039 (tttt) cc_final: 0.6717 (tmtt) REVERT: E 428 ARG cc_start: 0.8028 (tpp80) cc_final: 0.7485 (tpt-90) REVERT: E 481 GLU cc_start: 0.8555 (tp30) cc_final: 0.8212 (tm-30) REVERT: E 587 LYS cc_start: 0.8443 (tmtt) cc_final: 0.8098 (tppt) REVERT: F 154 LYS cc_start: 0.6511 (OUTLIER) cc_final: 0.6179 (mtpp) REVERT: F 231 ASP cc_start: 0.8024 (t70) cc_final: 0.7498 (t70) REVERT: F 274 TYR cc_start: 0.8082 (t80) cc_final: 0.7768 (t80) REVERT: F 275 ASN cc_start: 0.8404 (t0) cc_final: 0.8139 (t0) REVERT: F 325 MET cc_start: 0.8100 (tpt) cc_final: 0.7850 (tpt) REVERT: F 351 ARG cc_start: 0.5383 (tpm170) cc_final: 0.3758 (tmt-80) REVERT: F 373 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7184 (tp30) REVERT: F 376 PHE cc_start: 0.7409 (m-10) cc_final: 0.7039 (m-10) REVERT: F 428 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7351 (tpt-90) REVERT: F 538 ASP cc_start: 0.7351 (p0) cc_final: 0.7091 (p0) REVERT: F 587 LYS cc_start: 0.8489 (tppp) cc_final: 0.8006 (ttpp) REVERT: F 603 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8338 (tttm) REVERT: G 118 GLN cc_start: 0.7186 (pt0) cc_final: 0.6884 (pt0) REVERT: G 189 GLN cc_start: 0.8129 (tp40) cc_final: 0.7616 (tt0) REVERT: G 212 ARG cc_start: 0.7440 (ttm110) cc_final: 0.7149 (tpp-160) REVERT: G 296 ASP cc_start: 0.8382 (m-30) cc_final: 0.8112 (m-30) REVERT: G 362 ARG cc_start: 0.5630 (ttm110) cc_final: 0.4119 (tmt170) REVERT: G 378 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7713 (mptt) REVERT: G 420 LYS cc_start: 0.8517 (mppt) cc_final: 0.7871 (mppt) REVERT: G 538 ASP cc_start: 0.7665 (t70) cc_final: 0.7273 (t70) REVERT: H 163 TYR cc_start: 0.8029 (t80) cc_final: 0.7636 (t80) REVERT: H 231 ASP cc_start: 0.7682 (t0) cc_final: 0.7224 (t70) REVERT: H 260 ARG cc_start: 0.8317 (ttp80) cc_final: 0.7968 (ttp80) REVERT: H 264 GLU cc_start: 0.7830 (pt0) cc_final: 0.7599 (mt-10) REVERT: H 274 TYR cc_start: 0.7575 (t80) cc_final: 0.7339 (t80) REVERT: H 295 TYR cc_start: 0.8519 (t80) cc_final: 0.7876 (t80) REVERT: H 298 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7881 (t0) REVERT: H 373 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7570 (mm-30) REVERT: H 381 LYS cc_start: 0.8199 (tppt) cc_final: 0.7570 (tppt) REVERT: H 390 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7222 (pm20) REVERT: H 391 ASN cc_start: 0.8564 (m110) cc_final: 0.8106 (t0) REVERT: H 409 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.7420 (mmm) REVERT: H 481 GLU cc_start: 0.8686 (tp30) cc_final: 0.8158 (tp30) REVERT: H 566 ARG cc_start: 0.7878 (ptm-80) cc_final: 0.7329 (ptt-90) outliers start: 87 outliers final: 38 residues processed: 592 average time/residue: 0.7569 time to fit residues: 525.6103 Evaluate side-chains 558 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 509 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 448 TRP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 535 GLN Chi-restraints excluded: chain D residue 585 THR Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 537 ILE Chi-restraints excluded: chain E residue 548 ASP Chi-restraints excluded: chain F residue 154 LYS Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 428 ARG Chi-restraints excluded: chain F residue 571 ILE Chi-restraints excluded: chain F residue 585 THR Chi-restraints excluded: chain F residue 603 LYS Chi-restraints excluded: chain F residue 623 SER Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 378 LYS Chi-restraints excluded: chain G residue 543 SER Chi-restraints excluded: chain G residue 585 THR Chi-restraints excluded: chain G residue 626 ILE Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 298 ASP Chi-restraints excluded: chain H residue 390 GLU Chi-restraints excluded: chain H residue 409 MET Chi-restraints excluded: chain H residue 411 ILE Chi-restraints excluded: chain H residue 554 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 262 optimal weight: 6.9990 chunk 408 optimal weight: 0.7980 chunk 361 optimal weight: 2.9990 chunk 246 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 144 optimal weight: 0.0000 chunk 247 optimal weight: 0.9980 chunk 231 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 325 optimal weight: 5.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN A 359 HIS A 560 GLN B 220 ASN B 273 ASN ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN D 398 ASN E 162 HIS E 171 HIS E 208 HIS E 379 ASN F 219 ASN G 535 GLN H 129 GLN H 164 HIS H 219 ASN ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.138883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.109618 restraints weight = 159009.043| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 4.52 r_work: 0.2980 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 36823 Z= 0.112 Angle : 0.534 8.356 50062 Z= 0.284 Chirality : 0.046 0.182 5304 Planarity : 0.005 0.052 6335 Dihedral : 4.381 20.879 4744 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.93 % Allowed : 15.23 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.13), residues: 4311 helix: 0.58 (0.13), residues: 1680 sheet: -0.52 (0.18), residues: 904 loop : -1.08 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 222 TYR 0.014 0.001 TYR A 334 PHE 0.019 0.001 PHE E 121 TRP 0.058 0.001 TRP C 448 HIS 0.010 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00253 (36823) covalent geometry : angle 0.53382 (50062) hydrogen bonds : bond 0.03873 ( 1450) hydrogen bonds : angle 4.60773 ( 4410) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 569 time to evaluate : 1.296 Fit side-chains revert: symmetry clash REVERT: A 107 CYS cc_start: 0.8617 (p) cc_final: 0.8210 (p) REVERT: A 197 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7282 (tp30) REVERT: A 205 ASP cc_start: 0.7020 (p0) cc_final: 0.6717 (t70) REVERT: A 347 ILE cc_start: 0.8307 (mt) cc_final: 0.8009 (mp) REVERT: A 350 PHE cc_start: 0.7429 (m-10) cc_final: 0.7195 (m-10) REVERT: A 351 ARG cc_start: 0.5829 (mmm160) cc_final: 0.3854 (mmp80) REVERT: A 420 LYS cc_start: 0.8135 (tppt) cc_final: 0.7854 (tppp) REVERT: B 226 PHE cc_start: 0.7673 (m-80) cc_final: 0.7322 (m-80) REVERT: B 227 LYS cc_start: 0.7563 (ttpt) cc_final: 0.7355 (ttmm) REVERT: B 351 ARG cc_start: 0.5167 (mmm160) cc_final: 0.4951 (mmm160) REVERT: B 377 ASP cc_start: 0.7868 (t0) cc_final: 0.6962 (m-30) REVERT: B 549 GLU cc_start: 0.8038 (tt0) cc_final: 0.7598 (tm-30) REVERT: B 587 LYS cc_start: 0.8220 (tmtt) cc_final: 0.7940 (tptm) REVERT: C 108 PHE cc_start: 0.7512 (p90) cc_final: 0.7210 (p90) REVERT: C 163 TYR cc_start: 0.7918 (t80) cc_final: 0.7575 (t80) REVERT: C 193 GLU cc_start: 0.6873 (tm-30) cc_final: 0.6368 (tm-30) REVERT: C 256 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7802 (tm-30) REVERT: C 351 ARG cc_start: 0.6606 (mmt180) cc_final: 0.5956 (mmm160) REVERT: C 373 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7927 (mt-10) REVERT: C 378 LYS cc_start: 0.7969 (tppt) cc_final: 0.7340 (mptp) REVERT: C 385 ILE cc_start: 0.8906 (mt) cc_final: 0.8673 (mm) REVERT: C 514 LYS cc_start: 0.8681 (mptt) cc_final: 0.8305 (mppt) REVERT: D 108 PHE cc_start: 0.8034 (p90) cc_final: 0.7642 (p90) REVERT: D 136 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7431 (p0) REVERT: D 202 GLU cc_start: 0.7807 (pt0) cc_final: 0.7498 (tt0) REVERT: D 216 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7448 (tt0) REVERT: D 366 GLU cc_start: 0.8183 (tp30) cc_final: 0.7907 (tp30) REVERT: D 538 ASP cc_start: 0.8260 (t0) cc_final: 0.7544 (p0) REVERT: D 566 ARG cc_start: 0.8229 (ptm-80) cc_final: 0.7670 (ptp90) REVERT: E 174 PHE cc_start: 0.8129 (t80) cc_final: 0.7718 (t80) REVERT: E 199 VAL cc_start: 0.7215 (t) cc_final: 0.6882 (p) REVERT: E 206 PRO cc_start: 0.6737 (Cg_endo) cc_final: 0.6524 (Cg_exo) REVERT: E 245 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7634 (mm) REVERT: E 283 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7944 (mp0) REVERT: E 288 MET cc_start: 0.9120 (mmm) cc_final: 0.8901 (tpt) REVERT: E 351 ARG cc_start: 0.5217 (tpm170) cc_final: 0.2906 (ttt180) REVERT: E 359 HIS cc_start: 0.7519 (t70) cc_final: 0.7284 (t-90) REVERT: E 363 ASN cc_start: 0.7349 (m-40) cc_final: 0.7106 (m-40) REVERT: E 391 ASN cc_start: 0.7583 (m-40) cc_final: 0.7008 (t0) REVERT: E 420 LYS cc_start: 0.7781 (mmmm) cc_final: 0.7205 (ttpt) REVERT: E 423 LYS cc_start: 0.7100 (tttt) cc_final: 0.6714 (tmtt) REVERT: E 428 ARG cc_start: 0.7863 (tpp80) cc_final: 0.7314 (tpt-90) REVERT: E 481 GLU cc_start: 0.8462 (tp30) cc_final: 0.8213 (tp30) REVERT: E 587 LYS cc_start: 0.8332 (tmtt) cc_final: 0.8027 (tppt) REVERT: F 154 LYS cc_start: 0.6510 (OUTLIER) cc_final: 0.6081 (ttpp) REVERT: F 231 ASP cc_start: 0.8003 (t70) cc_final: 0.7540 (t70) REVERT: F 274 TYR cc_start: 0.8068 (t80) cc_final: 0.7742 (t80) REVERT: F 325 MET cc_start: 0.8025 (tpt) cc_final: 0.7779 (tpt) REVERT: F 351 ARG cc_start: 0.5296 (tpm170) cc_final: 0.3830 (tmt-80) REVERT: F 373 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7058 (tp30) REVERT: F 376 PHE cc_start: 0.7359 (m-10) cc_final: 0.6965 (m-10) REVERT: F 381 LYS cc_start: 0.8196 (ttmm) cc_final: 0.7584 (ttpt) REVERT: F 538 ASP cc_start: 0.7253 (p0) cc_final: 0.7015 (p0) REVERT: G 189 GLN cc_start: 0.8157 (tp40) cc_final: 0.7658 (tt0) REVERT: G 212 ARG cc_start: 0.7650 (ttm110) cc_final: 0.7021 (tpp-160) REVERT: G 296 ASP cc_start: 0.8282 (m-30) cc_final: 0.8047 (m-30) REVERT: G 362 ARG cc_start: 0.5562 (ttm110) cc_final: 0.4136 (tmt170) REVERT: G 378 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7701 (mptt) REVERT: G 420 LYS cc_start: 0.8488 (mppt) cc_final: 0.7869 (mppt) REVERT: G 538 ASP cc_start: 0.7563 (t70) cc_final: 0.7212 (t70) REVERT: H 121 PHE cc_start: 0.8394 (t80) cc_final: 0.8161 (t80) REVERT: H 163 TYR cc_start: 0.8016 (t80) cc_final: 0.7685 (t80) REVERT: H 167 MET cc_start: 0.6820 (mmt) cc_final: 0.6548 (mtp) REVERT: H 231 ASP cc_start: 0.7644 (t70) cc_final: 0.7150 (t70) REVERT: H 260 ARG cc_start: 0.8234 (ttp80) cc_final: 0.7810 (tmm-80) REVERT: H 274 TYR cc_start: 0.7566 (t80) cc_final: 0.7355 (t80) REVERT: H 295 TYR cc_start: 0.8443 (t80) cc_final: 0.7773 (t80) REVERT: H 373 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7605 (mm-30) REVERT: H 381 LYS cc_start: 0.8152 (tppt) cc_final: 0.7549 (tppt) REVERT: H 390 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7171 (pm20) REVERT: H 391 ASN cc_start: 0.8607 (m110) cc_final: 0.8154 (t0) REVERT: H 409 MET cc_start: 0.7630 (OUTLIER) cc_final: 0.7349 (mmm) REVERT: H 462 HIS cc_start: 0.8768 (OUTLIER) cc_final: 0.8188 (m170) REVERT: H 481 GLU cc_start: 0.8614 (tp30) cc_final: 0.8117 (tp30) REVERT: H 549 GLU cc_start: 0.7759 (tt0) cc_final: 0.7335 (pp20) REVERT: H 566 ARG cc_start: 0.7773 (ptm-80) cc_final: 0.7099 (tmm-80) outliers start: 75 outliers final: 27 residues processed: 611 average time/residue: 0.7468 time to fit residues: 536.8676 Evaluate side-chains 561 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 523 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 448 TRP Chi-restraints excluded: chain C residue 462 HIS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 462 HIS Chi-restraints excluded: chain D residue 585 THR Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 537 ILE Chi-restraints excluded: chain E residue 548 ASP Chi-restraints excluded: chain F residue 154 LYS Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 585 THR Chi-restraints excluded: chain F residue 623 SER Chi-restraints excluded: chain G residue 378 LYS Chi-restraints excluded: chain G residue 543 SER Chi-restraints excluded: chain G residue 585 THR Chi-restraints excluded: chain G residue 626 ILE Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 390 GLU Chi-restraints excluded: chain H residue 409 MET Chi-restraints excluded: chain H residue 411 ILE Chi-restraints excluded: chain H residue 462 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 390 optimal weight: 4.9990 chunk 412 optimal weight: 2.9990 chunk 311 optimal weight: 0.9990 chunk 349 optimal weight: 10.0000 chunk 196 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 403 optimal weight: 4.9990 chunk 123 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 159 optimal weight: 7.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN A 277 GLN A 320 GLN A 560 GLN B 220 ASN ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 ASN C 529 ASN ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN D 398 ASN D 461 GLN E 208 HIS E 379 ASN E 629 ASN F 275 ASN F 391 ASN G 118 GLN H 129 GLN ** H 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.135125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.105540 restraints weight = 164298.443| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 4.64 r_work: 0.2909 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 36823 Z= 0.202 Angle : 0.614 8.740 50062 Z= 0.326 Chirality : 0.049 0.183 5304 Planarity : 0.005 0.061 6335 Dihedral : 4.647 20.382 4744 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.65 % Allowed : 14.95 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.12), residues: 4311 helix: 0.42 (0.13), residues: 1696 sheet: -0.50 (0.18), residues: 904 loop : -1.22 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 212 TYR 0.027 0.002 TYR D 404 PHE 0.025 0.002 PHE B 376 TRP 0.074 0.002 TRP C 448 HIS 0.013 0.002 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00480 (36823) covalent geometry : angle 0.61411 (50062) hydrogen bonds : bond 0.05025 ( 1450) hydrogen bonds : angle 4.73661 ( 4410) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 515 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 CYS cc_start: 0.8647 (p) cc_final: 0.8213 (p) REVERT: A 197 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7285 (tp30) REVERT: A 205 ASP cc_start: 0.7113 (OUTLIER) cc_final: 0.6775 (t70) REVERT: A 347 ILE cc_start: 0.8350 (mt) cc_final: 0.8036 (mp) REVERT: A 351 ARG cc_start: 0.6159 (mmm160) cc_final: 0.4053 (mmp80) REVERT: A 420 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8044 (tppp) REVERT: B 227 LYS cc_start: 0.7589 (ttpt) cc_final: 0.7360 (ttmm) REVERT: B 351 ARG cc_start: 0.5197 (mmm160) cc_final: 0.4960 (mmm160) REVERT: B 398 ASN cc_start: 0.7481 (t0) cc_final: 0.6786 (m-40) REVERT: B 524 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8100 (tp30) REVERT: B 549 GLU cc_start: 0.8113 (tt0) cc_final: 0.7666 (tm-30) REVERT: B 587 LYS cc_start: 0.8307 (tmtt) cc_final: 0.8050 (tttm) REVERT: C 108 PHE cc_start: 0.7558 (p90) cc_final: 0.7292 (p90) REVERT: C 163 TYR cc_start: 0.7958 (t80) cc_final: 0.7585 (t80) REVERT: C 256 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7853 (tm-30) REVERT: C 351 ARG cc_start: 0.6709 (mmt180) cc_final: 0.6230 (mtp85) REVERT: C 373 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8066 (mt-10) REVERT: C 378 LYS cc_start: 0.8080 (tppt) cc_final: 0.7461 (mptp) REVERT: C 385 ILE cc_start: 0.8926 (mt) cc_final: 0.8679 (mm) REVERT: D 108 PHE cc_start: 0.8009 (p90) cc_final: 0.7607 (p90) REVERT: D 136 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7380 (p0) REVERT: D 189 GLN cc_start: 0.7985 (tp-100) cc_final: 0.7378 (tt0) REVERT: D 216 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7548 (tt0) REVERT: D 564 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7868 (tm-30) REVERT: D 566 ARG cc_start: 0.8302 (ptm-80) cc_final: 0.7725 (ptp90) REVERT: E 174 PHE cc_start: 0.8169 (t80) cc_final: 0.7903 (t80) REVERT: E 199 VAL cc_start: 0.7211 (t) cc_final: 0.6876 (p) REVERT: E 206 PRO cc_start: 0.6733 (Cg_endo) cc_final: 0.6531 (Cg_exo) REVERT: E 256 GLU cc_start: 0.8441 (tt0) cc_final: 0.8105 (tt0) REVERT: E 283 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8035 (mp0) REVERT: E 351 ARG cc_start: 0.5128 (tpm170) cc_final: 0.2837 (ttt180) REVERT: E 363 ASN cc_start: 0.7360 (m-40) cc_final: 0.6817 (m110) REVERT: E 373 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7425 (mm-30) REVERT: E 391 ASN cc_start: 0.7597 (m-40) cc_final: 0.7016 (t0) REVERT: E 423 LYS cc_start: 0.7109 (tttt) cc_final: 0.6734 (tmtt) REVERT: E 428 ARG cc_start: 0.8018 (tpp80) cc_final: 0.7457 (tpt-90) REVERT: E 481 GLU cc_start: 0.8559 (tp30) cc_final: 0.8304 (tp30) REVERT: E 587 LYS cc_start: 0.8436 (tmtt) cc_final: 0.8052 (tppt) REVERT: F 154 LYS cc_start: 0.6480 (OUTLIER) cc_final: 0.6125 (ttpp) REVERT: F 231 ASP cc_start: 0.8091 (t70) cc_final: 0.7564 (t70) REVERT: F 274 TYR cc_start: 0.8053 (t80) cc_final: 0.7714 (t80) REVERT: F 351 ARG cc_start: 0.5633 (tpm170) cc_final: 0.4040 (tmt-80) REVERT: F 373 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7088 (tp30) REVERT: F 376 PHE cc_start: 0.7382 (m-10) cc_final: 0.6992 (m-10) REVERT: F 428 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7318 (tpt-90) REVERT: F 535 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8493 (mp10) REVERT: F 550 LYS cc_start: 0.8321 (mmtp) cc_final: 0.8030 (mtpm) REVERT: F 587 LYS cc_start: 0.8535 (tppp) cc_final: 0.8057 (ttpp) REVERT: G 118 GLN cc_start: 0.7243 (pt0) cc_final: 0.7024 (pt0) REVERT: G 189 GLN cc_start: 0.8145 (tp40) cc_final: 0.7675 (tt0) REVERT: G 212 ARG cc_start: 0.7716 (ttm110) cc_final: 0.7010 (tpp-160) REVERT: G 296 ASP cc_start: 0.8307 (m-30) cc_final: 0.7932 (m-30) REVERT: G 362 ARG cc_start: 0.5623 (ttm110) cc_final: 0.4150 (tmt170) REVERT: G 378 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7681 (mptt) REVERT: G 420 LYS cc_start: 0.8524 (mppt) cc_final: 0.8158 (mmpt) REVERT: G 486 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8167 (mpt-90) REVERT: G 538 ASP cc_start: 0.7653 (t70) cc_final: 0.7281 (t70) REVERT: H 163 TYR cc_start: 0.8046 (t80) cc_final: 0.7740 (t80) REVERT: H 167 MET cc_start: 0.6919 (mmt) cc_final: 0.6469 (mtp) REVERT: H 215 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.7029 (tp30) REVERT: H 274 TYR cc_start: 0.7649 (t80) cc_final: 0.7387 (t80) REVERT: H 295 TYR cc_start: 0.8526 (t80) cc_final: 0.7873 (t80) REVERT: H 298 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7865 (t0) REVERT: H 381 LYS cc_start: 0.8195 (tppt) cc_final: 0.7589 (tppt) REVERT: H 390 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7228 (pm20) REVERT: H 391 ASN cc_start: 0.8583 (m110) cc_final: 0.8114 (t0) REVERT: H 409 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7235 (mmm) REVERT: H 462 HIS cc_start: 0.8879 (OUTLIER) cc_final: 0.8478 (m170) REVERT: H 481 GLU cc_start: 0.8690 (tp30) cc_final: 0.8254 (tp30) REVERT: H 549 GLU cc_start: 0.7782 (tt0) cc_final: 0.7297 (pp20) REVERT: H 566 ARG cc_start: 0.7871 (ptm-80) cc_final: 0.7425 (tmm-80) outliers start: 103 outliers final: 47 residues processed: 581 average time/residue: 0.7379 time to fit residues: 503.8481 Evaluate side-chains 564 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 498 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 596 ARG Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 462 HIS Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 448 TRP Chi-restraints excluded: chain C residue 462 HIS Chi-restraints excluded: chain C residue 588 MET Chi-restraints excluded: chain C residue 623 SER Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 461 GLN Chi-restraints excluded: chain D residue 462 HIS Chi-restraints excluded: chain D residue 535 GLN Chi-restraints excluded: chain D residue 564 GLU Chi-restraints excluded: chain D residue 585 THR Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 577 SER Chi-restraints excluded: chain F residue 154 LYS Chi-restraints excluded: chain F residue 186 ARG Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 428 ARG Chi-restraints excluded: chain F residue 535 GLN Chi-restraints excluded: chain F residue 585 THR Chi-restraints excluded: chain F residue 623 SER Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 378 LYS Chi-restraints excluded: chain G residue 486 ARG Chi-restraints excluded: chain G residue 543 SER Chi-restraints excluded: chain G residue 585 THR Chi-restraints excluded: chain G residue 626 ILE Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 298 ASP Chi-restraints excluded: chain H residue 390 GLU Chi-restraints excluded: chain H residue 409 MET Chi-restraints excluded: chain H residue 462 HIS Chi-restraints excluded: chain H residue 554 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 314 optimal weight: 0.7980 chunk 138 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 266 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 381 optimal weight: 0.6980 chunk 404 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 300 optimal weight: 2.9990 chunk 217 optimal weight: 10.0000 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN A 560 GLN ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 ASN D 461 GLN E 208 HIS E 220 ASN E 379 ASN F 275 ASN F 316 ASN F 391 ASN H 129 GLN ** H 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.136969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.107613 restraints weight = 153847.595| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 4.44 r_work: 0.2951 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 69 | |-----------------------------------------------------------------------------| r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 36823 Z= 0.140 Angle : 0.562 9.196 50062 Z= 0.298 Chirality : 0.047 0.178 5304 Planarity : 0.005 0.062 6335 Dihedral : 4.508 21.141 4744 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.27 % Allowed : 15.64 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.12), residues: 4311 helix: 0.56 (0.13), residues: 1696 sheet: -0.50 (0.18), residues: 896 loop : -1.16 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 212 TYR 0.023 0.001 TYR D 404 PHE 0.022 0.001 PHE B 376 TRP 0.066 0.001 TRP C 448 HIS 0.011 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00329 (36823) covalent geometry : angle 0.56176 (50062) hydrogen bonds : bond 0.04310 ( 1450) hydrogen bonds : angle 4.63357 ( 4410) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 516 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 CYS cc_start: 0.8657 (p) cc_final: 0.8137 (p) REVERT: A 197 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7275 (tp30) REVERT: A 205 ASP cc_start: 0.6992 (p0) cc_final: 0.6719 (t70) REVERT: A 231 ASP cc_start: 0.8237 (t0) cc_final: 0.7971 (t0) REVERT: A 270 MET cc_start: 0.8640 (mmp) cc_final: 0.7947 (mmt) REVERT: A 347 ILE cc_start: 0.8300 (mt) cc_final: 0.7998 (mp) REVERT: A 350 PHE cc_start: 0.7509 (m-10) cc_final: 0.7256 (m-10) REVERT: A 351 ARG cc_start: 0.6067 (mmm160) cc_final: 0.4015 (mmp80) REVERT: A 420 LYS cc_start: 0.8285 (tppt) cc_final: 0.8005 (tppp) REVERT: B 202 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7707 (pt0) REVERT: B 226 PHE cc_start: 0.7702 (m-80) cc_final: 0.7366 (m-80) REVERT: B 227 LYS cc_start: 0.7576 (ttpt) cc_final: 0.7367 (ttmm) REVERT: B 325 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.8061 (tmm) REVERT: B 348 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8538 (pt) REVERT: B 351 ARG cc_start: 0.5342 (mmm160) cc_final: 0.5036 (mmm160) REVERT: B 393 MET cc_start: 0.8674 (ttm) cc_final: 0.8428 (mtm) REVERT: B 398 ASN cc_start: 0.7441 (t0) cc_final: 0.6827 (m-40) REVERT: B 524 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8074 (tp30) REVERT: B 549 GLU cc_start: 0.8077 (tt0) cc_final: 0.7603 (tm-30) REVERT: B 587 LYS cc_start: 0.8256 (tmtt) cc_final: 0.7993 (tttm) REVERT: C 108 PHE cc_start: 0.7504 (p90) cc_final: 0.7201 (p90) REVERT: C 163 TYR cc_start: 0.7941 (t80) cc_final: 0.7596 (t80) REVERT: C 256 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7829 (tm-30) REVERT: C 351 ARG cc_start: 0.6724 (mmt180) cc_final: 0.6216 (mtp85) REVERT: C 373 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7984 (mt-10) REVERT: C 378 LYS cc_start: 0.8003 (tppt) cc_final: 0.7375 (mptp) REVERT: C 385 ILE cc_start: 0.8870 (mt) cc_final: 0.8640 (mm) REVERT: D 108 PHE cc_start: 0.7983 (p90) cc_final: 0.7591 (p90) REVERT: D 136 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7382 (p0) REVERT: D 154 LYS cc_start: 0.7288 (tppt) cc_final: 0.6897 (ptpt) REVERT: D 189 GLN cc_start: 0.7955 (tp-100) cc_final: 0.7356 (tt0) REVERT: D 216 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7536 (tt0) REVERT: D 366 GLU cc_start: 0.8131 (tp30) cc_final: 0.7885 (tp30) REVERT: D 538 ASP cc_start: 0.8291 (t0) cc_final: 0.7578 (p0) REVERT: D 566 ARG cc_start: 0.8192 (ptm-80) cc_final: 0.7672 (ptp90) REVERT: D 607 LYS cc_start: 0.8993 (tptp) cc_final: 0.8753 (tptt) REVERT: E 174 PHE cc_start: 0.8182 (t80) cc_final: 0.7897 (t80) REVERT: E 199 VAL cc_start: 0.7206 (t) cc_final: 0.6874 (p) REVERT: E 283 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7967 (mp0) REVERT: E 351 ARG cc_start: 0.5036 (tpm170) cc_final: 0.2820 (ttt180) REVERT: E 363 ASN cc_start: 0.7348 (m-40) cc_final: 0.6838 (m110) REVERT: E 373 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7377 (mm-30) REVERT: E 391 ASN cc_start: 0.7622 (m-40) cc_final: 0.7009 (t0) REVERT: E 420 LYS cc_start: 0.7979 (mmmm) cc_final: 0.7663 (mtpt) REVERT: E 423 LYS cc_start: 0.7072 (tttt) cc_final: 0.6719 (tmtt) REVERT: E 428 ARG cc_start: 0.7921 (tpp80) cc_final: 0.7398 (tpt-90) REVERT: E 481 GLU cc_start: 0.8489 (tp30) cc_final: 0.8220 (tp30) REVERT: E 587 LYS cc_start: 0.8356 (tmtt) cc_final: 0.8017 (tppt) REVERT: F 154 LYS cc_start: 0.6573 (pmtt) cc_final: 0.6129 (ttpp) REVERT: F 231 ASP cc_start: 0.8040 (t70) cc_final: 0.7517 (t70) REVERT: F 274 TYR cc_start: 0.7996 (t80) cc_final: 0.7618 (t80) REVERT: F 351 ARG cc_start: 0.5528 (tpm170) cc_final: 0.3982 (tmt-80) REVERT: F 373 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7016 (tp30) REVERT: F 376 PHE cc_start: 0.7456 (m-10) cc_final: 0.7031 (m-10) REVERT: F 381 LYS cc_start: 0.8209 (ttmm) cc_final: 0.7616 (ttpt) REVERT: F 428 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7279 (tpt-90) REVERT: F 535 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8043 (mp10) REVERT: F 550 LYS cc_start: 0.8268 (mmtp) cc_final: 0.8010 (mtpm) REVERT: F 587 LYS cc_start: 0.8520 (tppp) cc_final: 0.8044 (ttpp) REVERT: G 189 GLN cc_start: 0.8126 (tp40) cc_final: 0.7656 (tt0) REVERT: G 212 ARG cc_start: 0.7666 (ttm110) cc_final: 0.7029 (tpp-160) REVERT: G 296 ASP cc_start: 0.8295 (m-30) cc_final: 0.8058 (m-30) REVERT: G 362 ARG cc_start: 0.5579 (ttm110) cc_final: 0.4134 (tmt170) REVERT: G 378 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7671 (mptt) REVERT: G 420 LYS cc_start: 0.8497 (mppt) cc_final: 0.8196 (mmpt) REVERT: G 538 ASP cc_start: 0.7628 (t70) cc_final: 0.7272 (t70) REVERT: H 138 ARG cc_start: 0.7242 (mtp-110) cc_final: 0.6851 (mtp180) REVERT: H 163 TYR cc_start: 0.8030 (t80) cc_final: 0.7681 (t80) REVERT: H 167 MET cc_start: 0.6919 (mmt) cc_final: 0.6503 (mtp) REVERT: H 215 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6967 (tp30) REVERT: H 274 TYR cc_start: 0.7601 (t80) cc_final: 0.7357 (t80) REVERT: H 295 TYR cc_start: 0.8503 (t80) cc_final: 0.7830 (t80) REVERT: H 298 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7908 (t0) REVERT: H 373 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7594 (mm-30) REVERT: H 381 LYS cc_start: 0.8178 (tppt) cc_final: 0.7870 (tptp) REVERT: H 390 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7210 (pm20) REVERT: H 391 ASN cc_start: 0.8529 (m110) cc_final: 0.8069 (t0) REVERT: H 409 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7401 (mmm) REVERT: H 419 ASN cc_start: 0.7196 (m110) cc_final: 0.6079 (t0) REVERT: H 462 HIS cc_start: 0.8823 (OUTLIER) cc_final: 0.8377 (m170) REVERT: H 481 GLU cc_start: 0.8628 (tp30) cc_final: 0.8246 (tp30) REVERT: H 549 GLU cc_start: 0.7777 (tt0) cc_final: 0.7188 (pp20) REVERT: H 566 ARG cc_start: 0.7834 (ptm-80) cc_final: 0.7108 (tmt-80) outliers start: 88 outliers final: 47 residues processed: 573 average time/residue: 0.7636 time to fit residues: 512.7632 Evaluate side-chains 565 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 501 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 462 HIS Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 448 TRP Chi-restraints excluded: chain C residue 462 HIS Chi-restraints excluded: chain C residue 588 MET Chi-restraints excluded: chain C residue 623 SER Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 585 THR Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 548 ASP Chi-restraints excluded: chain E residue 577 SER Chi-restraints excluded: chain F residue 186 ARG Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 428 ARG Chi-restraints excluded: chain F residue 535 GLN Chi-restraints excluded: chain F residue 585 THR Chi-restraints excluded: chain F residue 623 SER Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 378 LYS Chi-restraints excluded: chain G residue 543 SER Chi-restraints excluded: chain G residue 585 THR Chi-restraints excluded: chain G residue 626 ILE Chi-restraints excluded: chain G residue 627 ASP Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 247 ASP Chi-restraints excluded: chain H residue 298 ASP Chi-restraints excluded: chain H residue 390 GLU Chi-restraints excluded: chain H residue 409 MET Chi-restraints excluded: chain H residue 437 ASN Chi-restraints excluded: chain H residue 462 HIS Chi-restraints excluded: chain H residue 554 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 96 optimal weight: 0.0570 chunk 51 optimal weight: 0.0770 chunk 126 optimal weight: 4.9990 chunk 273 optimal weight: 5.9990 chunk 401 optimal weight: 7.9990 chunk 237 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 352 optimal weight: 2.9990 chunk 307 optimal weight: 0.9980 chunk 288 optimal weight: 2.9990 chunk 324 optimal weight: 9.9990 overall best weight: 1.4260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN ** A 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 ASN E 208 HIS E 379 ASN F 275 ASN F 316 ASN F 391 ASN G 118 GLN H 129 GLN H 162 HIS ** H 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.136846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.107510 restraints weight = 170267.776| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 4.79 r_work: 0.2927 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 69 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 69 | |-----------------------------------------------------------------------------| r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 36823 Z= 0.147 Angle : 0.565 9.092 50062 Z= 0.299 Chirality : 0.047 0.186 5304 Planarity : 0.005 0.057 6335 Dihedral : 4.484 20.548 4744 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.27 % Allowed : 15.82 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.12), residues: 4311 helix: 0.61 (0.13), residues: 1696 sheet: -0.46 (0.18), residues: 888 loop : -1.12 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 222 TYR 0.019 0.001 TYR F 334 PHE 0.023 0.001 PHE E 121 TRP 0.066 0.002 TRP C 448 HIS 0.011 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00345 (36823) covalent geometry : angle 0.56532 (50062) hydrogen bonds : bond 0.04328 ( 1450) hydrogen bonds : angle 4.60578 ( 4410) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 519 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 CYS cc_start: 0.8729 (p) cc_final: 0.8213 (p) REVERT: A 190 ILE cc_start: 0.8126 (pt) cc_final: 0.7415 (mt) REVERT: A 197 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7312 (tp30) REVERT: A 205 ASP cc_start: 0.7002 (OUTLIER) cc_final: 0.6708 (t70) REVERT: A 216 GLU cc_start: 0.7556 (pt0) cc_final: 0.7261 (tt0) REVERT: A 231 ASP cc_start: 0.8243 (t0) cc_final: 0.7961 (t0) REVERT: A 347 ILE cc_start: 0.8227 (mt) cc_final: 0.7931 (mp) REVERT: A 350 PHE cc_start: 0.7540 (m-10) cc_final: 0.7283 (m-10) REVERT: A 351 ARG cc_start: 0.6062 (mmm160) cc_final: 0.3992 (mmp80) REVERT: A 420 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.8015 (tppp) REVERT: B 172 PRO cc_start: 0.8200 (Cg_endo) cc_final: 0.7965 (Cg_exo) REVERT: B 202 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7784 (pt0) REVERT: B 226 PHE cc_start: 0.7697 (m-80) cc_final: 0.7350 (m-80) REVERT: B 227 LYS cc_start: 0.7562 (ttpt) cc_final: 0.7358 (ttmm) REVERT: B 325 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.8066 (tmm) REVERT: B 348 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8538 (pt) REVERT: B 351 ARG cc_start: 0.5486 (mmm160) cc_final: 0.5145 (mmm160) REVERT: B 398 ASN cc_start: 0.7499 (t0) cc_final: 0.6923 (m-40) REVERT: B 587 LYS cc_start: 0.8308 (tmtt) cc_final: 0.8044 (tttm) REVERT: C 108 PHE cc_start: 0.7527 (p90) cc_final: 0.7222 (p90) REVERT: C 163 TYR cc_start: 0.7924 (t80) cc_final: 0.7587 (t80) REVERT: C 256 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7861 (tm-30) REVERT: C 351 ARG cc_start: 0.6681 (mmt180) cc_final: 0.6185 (mtp85) REVERT: C 378 LYS cc_start: 0.7975 (tppt) cc_final: 0.7347 (mptp) REVERT: C 385 ILE cc_start: 0.8858 (mt) cc_final: 0.8627 (mm) REVERT: D 108 PHE cc_start: 0.8015 (p90) cc_final: 0.7604 (p90) REVERT: D 136 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7398 (p0) REVERT: D 154 LYS cc_start: 0.7283 (tppt) cc_final: 0.6894 (ptpt) REVERT: D 189 GLN cc_start: 0.7941 (tp-100) cc_final: 0.7269 (tt0) REVERT: D 216 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7559 (tt0) REVERT: D 538 ASP cc_start: 0.8307 (t0) cc_final: 0.7561 (p0) REVERT: D 607 LYS cc_start: 0.8994 (tptp) cc_final: 0.8782 (tptt) REVERT: E 174 PHE cc_start: 0.8167 (t80) cc_final: 0.7887 (t80) REVERT: E 197 GLU cc_start: 0.8030 (tt0) cc_final: 0.7805 (tt0) REVERT: E 199 VAL cc_start: 0.7210 (t) cc_final: 0.6881 (p) REVERT: E 283 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7984 (mp0) REVERT: E 351 ARG cc_start: 0.5123 (tpm170) cc_final: 0.2830 (ttt180) REVERT: E 363 ASN cc_start: 0.7330 (m-40) cc_final: 0.6793 (m110) REVERT: E 373 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7348 (tp30) REVERT: E 420 LYS cc_start: 0.8006 (mmmm) cc_final: 0.7684 (mtpt) REVERT: E 423 LYS cc_start: 0.7034 (tttt) cc_final: 0.6667 (tmtt) REVERT: E 428 ARG cc_start: 0.7931 (tpp80) cc_final: 0.7405 (tpt-90) REVERT: E 481 GLU cc_start: 0.8529 (tp30) cc_final: 0.8279 (tp30) REVERT: E 587 LYS cc_start: 0.8395 (tmtt) cc_final: 0.8100 (ttmt) REVERT: F 154 LYS cc_start: 0.6549 (pmtt) cc_final: 0.6107 (ttpp) REVERT: F 212 ARG cc_start: 0.6894 (mmp-170) cc_final: 0.6231 (mmm160) REVERT: F 231 ASP cc_start: 0.8069 (t70) cc_final: 0.7612 (t70) REVERT: F 274 TYR cc_start: 0.7966 (t80) cc_final: 0.7607 (t80) REVERT: F 351 ARG cc_start: 0.5742 (tpm170) cc_final: 0.4111 (tmt-80) REVERT: F 373 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7059 (tp30) REVERT: F 376 PHE cc_start: 0.7444 (m-10) cc_final: 0.7075 (m-10) REVERT: F 381 LYS cc_start: 0.8143 (ttmm) cc_final: 0.7528 (ttpt) REVERT: F 428 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7322 (tpt-90) REVERT: F 492 GLU cc_start: 0.8307 (tt0) cc_final: 0.7811 (pt0) REVERT: F 535 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8077 (mp10) REVERT: F 550 LYS cc_start: 0.8260 (mmtp) cc_final: 0.7978 (mtpm) REVERT: F 587 LYS cc_start: 0.8566 (tppp) cc_final: 0.8085 (ttpp) REVERT: G 189 GLN cc_start: 0.8141 (tp40) cc_final: 0.7658 (tt0) REVERT: G 212 ARG cc_start: 0.7674 (ttm110) cc_final: 0.7003 (tpp-160) REVERT: G 296 ASP cc_start: 0.8309 (m-30) cc_final: 0.8062 (m-30) REVERT: G 362 ARG cc_start: 0.5586 (ttm110) cc_final: 0.4128 (tmt170) REVERT: G 378 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7699 (mptt) REVERT: G 420 LYS cc_start: 0.8491 (mppt) cc_final: 0.8188 (mmpt) REVERT: G 538 ASP cc_start: 0.7638 (t70) cc_final: 0.7284 (t70) REVERT: H 138 ARG cc_start: 0.7291 (mtp-110) cc_final: 0.6925 (mtp180) REVERT: H 163 TYR cc_start: 0.8001 (t80) cc_final: 0.7697 (t80) REVERT: H 167 MET cc_start: 0.6921 (mmt) cc_final: 0.6507 (mtp) REVERT: H 215 GLU cc_start: 0.7226 (tp30) cc_final: 0.6900 (tp30) REVERT: H 274 TYR cc_start: 0.7591 (t80) cc_final: 0.7346 (t80) REVERT: H 295 TYR cc_start: 0.8486 (t80) cc_final: 0.7809 (t80) REVERT: H 298 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7923 (t0) REVERT: H 373 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7582 (mm-30) REVERT: H 381 LYS cc_start: 0.8187 (tppt) cc_final: 0.7876 (tptp) REVERT: H 390 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7229 (pm20) REVERT: H 391 ASN cc_start: 0.8555 (m110) cc_final: 0.8086 (t0) REVERT: H 394 SER cc_start: 0.8167 (m) cc_final: 0.7864 (p) REVERT: H 419 ASN cc_start: 0.7185 (m110) cc_final: 0.6119 (t0) REVERT: H 462 HIS cc_start: 0.8842 (OUTLIER) cc_final: 0.8409 (m170) REVERT: H 481 GLU cc_start: 0.8653 (tp30) cc_final: 0.8258 (tp30) REVERT: H 549 GLU cc_start: 0.7864 (tt0) cc_final: 0.7132 (pp20) REVERT: H 566 ARG cc_start: 0.7867 (ptm-80) cc_final: 0.7114 (tmt-80) outliers start: 88 outliers final: 48 residues processed: 571 average time/residue: 0.7536 time to fit residues: 506.5255 Evaluate side-chains 561 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 497 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 462 HIS Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 448 TRP Chi-restraints excluded: chain C residue 462 HIS Chi-restraints excluded: chain C residue 588 MET Chi-restraints excluded: chain C residue 623 SER Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 585 THR Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 548 ASP Chi-restraints excluded: chain E residue 577 SER Chi-restraints excluded: chain F residue 186 ARG Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 428 ARG Chi-restraints excluded: chain F residue 535 GLN Chi-restraints excluded: chain F residue 585 THR Chi-restraints excluded: chain F residue 623 SER Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 378 LYS Chi-restraints excluded: chain G residue 543 SER Chi-restraints excluded: chain G residue 585 THR Chi-restraints excluded: chain G residue 626 ILE Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 298 ASP Chi-restraints excluded: chain H residue 390 GLU Chi-restraints excluded: chain H residue 437 ASN Chi-restraints excluded: chain H residue 462 HIS Chi-restraints excluded: chain H residue 554 VAL Chi-restraints excluded: chain H residue 595 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 215 optimal weight: 0.6980 chunk 180 optimal weight: 0.9990 chunk 218 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 123 optimal weight: 7.9990 chunk 203 optimal weight: 0.9990 chunk 240 optimal weight: 9.9990 chunk 324 optimal weight: 10.0000 chunk 169 optimal weight: 7.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN ** A 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 ASN E 208 HIS E 379 ASN F 275 ASN F 316 ASN F 391 ASN G 118 GLN H 129 GLN H 162 HIS ** H 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.136197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.106755 restraints weight = 152661.339| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 4.40 r_work: 0.2934 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 69 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 69 | |-----------------------------------------------------------------------------| r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 36823 Z= 0.165 Angle : 0.585 9.405 50062 Z= 0.310 Chirality : 0.048 0.199 5304 Planarity : 0.005 0.059 6335 Dihedral : 4.556 20.780 4744 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.11 % Allowed : 16.13 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.12), residues: 4311 helix: 0.59 (0.13), residues: 1712 sheet: -0.47 (0.18), residues: 888 loop : -1.10 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 566 TYR 0.031 0.001 TYR D 404 PHE 0.026 0.002 PHE E 121 TRP 0.070 0.002 TRP C 448 HIS 0.012 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00391 (36823) covalent geometry : angle 0.58489 (50062) hydrogen bonds : bond 0.04554 ( 1450) hydrogen bonds : angle 4.64662 ( 4410) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 507 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 CYS cc_start: 0.8706 (p) cc_final: 0.8358 (p) REVERT: A 190 ILE cc_start: 0.8115 (pt) cc_final: 0.7417 (mt) REVERT: A 197 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7317 (tp30) REVERT: A 205 ASP cc_start: 0.7027 (OUTLIER) cc_final: 0.6823 (t70) REVERT: A 216 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7185 (tt0) REVERT: A 231 ASP cc_start: 0.8239 (t0) cc_final: 0.7955 (t0) REVERT: A 347 ILE cc_start: 0.8313 (mt) cc_final: 0.8009 (mp) REVERT: A 350 PHE cc_start: 0.7595 (m-10) cc_final: 0.7322 (m-10) REVERT: A 351 ARG cc_start: 0.6039 (mmm160) cc_final: 0.3985 (mmp80) REVERT: A 420 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.8038 (tppp) REVERT: B 172 PRO cc_start: 0.8213 (Cg_endo) cc_final: 0.7982 (Cg_exo) REVERT: B 202 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7775 (pt0) REVERT: B 226 PHE cc_start: 0.7700 (m-80) cc_final: 0.7360 (m-80) REVERT: B 227 LYS cc_start: 0.7574 (ttpt) cc_final: 0.7368 (ttmm) REVERT: B 325 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.8063 (tmm) REVERT: B 348 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8583 (pt) REVERT: B 351 ARG cc_start: 0.5445 (mmm160) cc_final: 0.4580 (mmm-85) REVERT: B 393 MET cc_start: 0.8672 (ttm) cc_final: 0.8457 (mtm) REVERT: B 398 ASN cc_start: 0.7516 (t0) cc_final: 0.6936 (m-40) REVERT: B 587 LYS cc_start: 0.8335 (tmtt) cc_final: 0.8085 (tttm) REVERT: C 108 PHE cc_start: 0.7532 (p90) cc_final: 0.7227 (p90) REVERT: C 163 TYR cc_start: 0.7933 (t80) cc_final: 0.7571 (t80) REVERT: C 256 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7840 (tm-30) REVERT: C 351 ARG cc_start: 0.6706 (mmt180) cc_final: 0.6086 (mtp85) REVERT: C 373 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8029 (mt-10) REVERT: C 378 LYS cc_start: 0.8007 (tppt) cc_final: 0.7373 (mptp) REVERT: C 385 ILE cc_start: 0.8866 (mt) cc_final: 0.8633 (mm) REVERT: D 108 PHE cc_start: 0.8043 (p90) cc_final: 0.7640 (p90) REVERT: D 136 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7411 (p0) REVERT: D 154 LYS cc_start: 0.7200 (tppt) cc_final: 0.6877 (ptpt) REVERT: D 189 GLN cc_start: 0.7949 (tp-100) cc_final: 0.7291 (tt0) REVERT: D 216 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7559 (tt0) REVERT: D 245 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7354 (mp) REVERT: D 366 GLU cc_start: 0.8114 (tp30) cc_final: 0.7869 (tp30) REVERT: D 538 ASP cc_start: 0.8310 (t0) cc_final: 0.7595 (p0) REVERT: E 174 PHE cc_start: 0.8159 (t80) cc_final: 0.7858 (t80) REVERT: E 199 VAL cc_start: 0.7204 (t) cc_final: 0.6880 (p) REVERT: E 283 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7988 (mp0) REVERT: E 351 ARG cc_start: 0.5297 (tpm170) cc_final: 0.2994 (ttt180) REVERT: E 363 ASN cc_start: 0.7321 (m-40) cc_final: 0.6775 (m110) REVERT: E 373 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7529 (tp30) REVERT: E 420 LYS cc_start: 0.7998 (mmmm) cc_final: 0.7690 (mtpt) REVERT: E 423 LYS cc_start: 0.7016 (tttt) cc_final: 0.6663 (tmtt) REVERT: E 428 ARG cc_start: 0.7996 (tpp80) cc_final: 0.7479 (tpt-90) REVERT: E 481 GLU cc_start: 0.8524 (tp30) cc_final: 0.8301 (tp30) REVERT: E 587 LYS cc_start: 0.8421 (tmtt) cc_final: 0.8116 (ttmt) REVERT: F 154 LYS cc_start: 0.6533 (pmtt) cc_final: 0.6138 (ttpp) REVERT: F 212 ARG cc_start: 0.6908 (mmp-170) cc_final: 0.6332 (mmm160) REVERT: F 231 ASP cc_start: 0.8076 (t70) cc_final: 0.7605 (t70) REVERT: F 274 TYR cc_start: 0.7962 (t80) cc_final: 0.7614 (t80) REVERT: F 351 ARG cc_start: 0.5969 (tpm170) cc_final: 0.4339 (tmt-80) REVERT: F 373 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7629 (mt-10) REVERT: F 376 PHE cc_start: 0.7321 (m-10) cc_final: 0.7018 (m-10) REVERT: F 428 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7322 (tpt-90) REVERT: F 492 GLU cc_start: 0.8315 (tt0) cc_final: 0.7828 (pt0) REVERT: F 535 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8488 (mp10) REVERT: F 550 LYS cc_start: 0.8275 (mmtp) cc_final: 0.8007 (mtpm) REVERT: F 587 LYS cc_start: 0.8533 (tppp) cc_final: 0.8111 (ttpp) REVERT: G 189 GLN cc_start: 0.8116 (tp40) cc_final: 0.7645 (tt0) REVERT: G 212 ARG cc_start: 0.7604 (ttm110) cc_final: 0.6958 (tpp-160) REVERT: G 296 ASP cc_start: 0.8297 (m-30) cc_final: 0.7933 (m-30) REVERT: G 362 ARG cc_start: 0.5565 (ttm110) cc_final: 0.4122 (tmt170) REVERT: G 378 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7716 (mptt) REVERT: G 538 ASP cc_start: 0.7641 (t70) cc_final: 0.7301 (t70) REVERT: H 138 ARG cc_start: 0.7274 (mtp-110) cc_final: 0.6923 (mtp180) REVERT: H 163 TYR cc_start: 0.7978 (t80) cc_final: 0.7562 (t80) REVERT: H 215 GLU cc_start: 0.7244 (tp30) cc_final: 0.6904 (tp30) REVERT: H 274 TYR cc_start: 0.7612 (t80) cc_final: 0.7366 (t80) REVERT: H 295 TYR cc_start: 0.8516 (t80) cc_final: 0.7847 (t80) REVERT: H 298 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7880 (t0) REVERT: H 373 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7592 (mm-30) REVERT: H 381 LYS cc_start: 0.8197 (tppt) cc_final: 0.7887 (tptp) REVERT: H 390 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7227 (pm20) REVERT: H 391 ASN cc_start: 0.8541 (m110) cc_final: 0.8067 (t0) REVERT: H 394 SER cc_start: 0.8173 (m) cc_final: 0.7887 (p) REVERT: H 419 ASN cc_start: 0.7218 (m110) cc_final: 0.6432 (t0) REVERT: H 462 HIS cc_start: 0.8845 (OUTLIER) cc_final: 0.8411 (m170) REVERT: H 481 GLU cc_start: 0.8644 (tp30) cc_final: 0.8253 (tp30) REVERT: H 566 ARG cc_start: 0.7854 (ptm-80) cc_final: 0.7103 (tmt-80) outliers start: 82 outliers final: 49 residues processed: 559 average time/residue: 0.7422 time to fit residues: 487.4227 Evaluate side-chains 559 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 492 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 462 HIS Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 448 TRP Chi-restraints excluded: chain C residue 462 HIS Chi-restraints excluded: chain C residue 588 MET Chi-restraints excluded: chain C residue 623 SER Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 462 HIS Chi-restraints excluded: chain D residue 585 THR Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 548 ASP Chi-restraints excluded: chain E residue 577 SER Chi-restraints excluded: chain F residue 186 ARG Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 428 ARG Chi-restraints excluded: chain F residue 535 GLN Chi-restraints excluded: chain F residue 585 THR Chi-restraints excluded: chain F residue 623 SER Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 378 LYS Chi-restraints excluded: chain G residue 543 SER Chi-restraints excluded: chain G residue 585 THR Chi-restraints excluded: chain G residue 626 ILE Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 298 ASP Chi-restraints excluded: chain H residue 390 GLU Chi-restraints excluded: chain H residue 437 ASN Chi-restraints excluded: chain H residue 462 HIS Chi-restraints excluded: chain H residue 554 VAL Chi-restraints excluded: chain H residue 595 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 79 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 chunk 421 optimal weight: 1.9990 chunk 250 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 0.0370 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN A 560 GLN C 171 HIS ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 ASN E 208 HIS E 379 ASN F 275 ASN F 316 ASN F 391 ASN G 118 GLN H 129 GLN H 162 HIS ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.137795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.108862 restraints weight = 148762.401| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 4.24 r_work: 0.2972 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 69 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36823 Z= 0.124 Angle : 0.548 9.046 50062 Z= 0.290 Chirality : 0.046 0.187 5304 Planarity : 0.005 0.062 6335 Dihedral : 4.397 20.813 4744 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.70 % Allowed : 16.70 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.13), residues: 4311 helix: 0.73 (0.13), residues: 1712 sheet: -0.45 (0.18), residues: 888 loop : -1.03 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 566 TYR 0.027 0.001 TYR D 404 PHE 0.027 0.001 PHE A 108 TRP 0.061 0.001 TRP C 448 HIS 0.010 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00288 (36823) covalent geometry : angle 0.54813 (50062) hydrogen bonds : bond 0.03962 ( 1450) hydrogen bonds : angle 4.55007 ( 4410) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 521 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 CYS cc_start: 0.8852 (p) cc_final: 0.8465 (p) REVERT: A 190 ILE cc_start: 0.8144 (pt) cc_final: 0.7503 (mt) REVERT: A 197 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7309 (tp30) REVERT: A 216 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7159 (tt0) REVERT: A 231 ASP cc_start: 0.8251 (t0) cc_final: 0.7986 (t0) REVERT: A 270 MET cc_start: 0.8634 (mmp) cc_final: 0.7958 (mmt) REVERT: A 347 ILE cc_start: 0.8210 (mt) cc_final: 0.7920 (mp) REVERT: A 350 PHE cc_start: 0.7490 (m-10) cc_final: 0.7239 (m-10) REVERT: A 351 ARG cc_start: 0.6001 (mmm160) cc_final: 0.4010 (mmt-90) REVERT: A 420 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7908 (tppp) REVERT: B 172 PRO cc_start: 0.8181 (Cg_endo) cc_final: 0.7955 (Cg_exo) REVERT: B 202 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7693 (pt0) REVERT: B 226 PHE cc_start: 0.7635 (m-80) cc_final: 0.7293 (m-80) REVERT: B 227 LYS cc_start: 0.7575 (ttpt) cc_final: 0.7008 (ttpt) REVERT: B 348 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8547 (pt) REVERT: B 351 ARG cc_start: 0.5419 (mmm160) cc_final: 0.4540 (mmm-85) REVERT: B 393 MET cc_start: 0.8683 (ttm) cc_final: 0.8455 (mtm) REVERT: B 398 ASN cc_start: 0.7501 (t0) cc_final: 0.6921 (m-40) REVERT: B 566 ARG cc_start: 0.8041 (ttp-110) cc_final: 0.7711 (ptp-170) REVERT: B 587 LYS cc_start: 0.8260 (tmtt) cc_final: 0.8001 (tttm) REVERT: C 108 PHE cc_start: 0.7527 (p90) cc_final: 0.7208 (p90) REVERT: C 163 TYR cc_start: 0.7893 (t80) cc_final: 0.7520 (t80) REVERT: C 256 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7825 (tm-30) REVERT: C 351 ARG cc_start: 0.6708 (mmt180) cc_final: 0.6109 (mtp85) REVERT: C 373 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7978 (mt-10) REVERT: C 378 LYS cc_start: 0.7931 (tppt) cc_final: 0.7334 (mptp) REVERT: C 385 ILE cc_start: 0.8852 (mt) cc_final: 0.8629 (mm) REVERT: D 108 PHE cc_start: 0.8138 (p90) cc_final: 0.7740 (p90) REVERT: D 136 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7462 (p0) REVERT: D 154 LYS cc_start: 0.7235 (tppt) cc_final: 0.6934 (ptpt) REVERT: D 216 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7545 (tt0) REVERT: D 245 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7360 (mp) REVERT: D 538 ASP cc_start: 0.8296 (t0) cc_final: 0.7585 (p0) REVERT: D 566 ARG cc_start: 0.8168 (ptm-80) cc_final: 0.7595 (ptp90) REVERT: D 607 LYS cc_start: 0.8967 (tptp) cc_final: 0.8758 (tptt) REVERT: E 174 PHE cc_start: 0.8130 (t80) cc_final: 0.7787 (t80) REVERT: E 245 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7660 (mm) REVERT: E 283 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7953 (mp0) REVERT: E 351 ARG cc_start: 0.5310 (tpm170) cc_final: 0.3040 (ttt180) REVERT: E 363 ASN cc_start: 0.7289 (m-40) cc_final: 0.6840 (m110) REVERT: E 373 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7513 (tp30) REVERT: E 420 LYS cc_start: 0.7962 (mmmm) cc_final: 0.7653 (mtpt) REVERT: E 423 LYS cc_start: 0.6996 (tttt) cc_final: 0.6663 (tmtt) REVERT: E 428 ARG cc_start: 0.7911 (tpp80) cc_final: 0.7377 (tpt-90) REVERT: E 481 GLU cc_start: 0.8489 (tp30) cc_final: 0.8249 (tp30) REVERT: E 587 LYS cc_start: 0.8374 (tmtt) cc_final: 0.8079 (ttmt) REVERT: E 610 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8315 (ttm) REVERT: F 154 LYS cc_start: 0.6569 (pmtt) cc_final: 0.6125 (ttpp) REVERT: F 189 GLN cc_start: 0.7928 (tt0) cc_final: 0.7681 (tt0) REVERT: F 212 ARG cc_start: 0.6905 (mmp-170) cc_final: 0.6251 (mmm160) REVERT: F 231 ASP cc_start: 0.8038 (t70) cc_final: 0.7580 (t70) REVERT: F 274 TYR cc_start: 0.7974 (t80) cc_final: 0.7633 (t80) REVERT: F 332 LYS cc_start: 0.8128 (mmpt) cc_final: 0.7849 (mmtm) REVERT: F 351 ARG cc_start: 0.5923 (tpm170) cc_final: 0.4286 (tmt-80) REVERT: F 373 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7589 (mt-10) REVERT: F 376 PHE cc_start: 0.7487 (m-10) cc_final: 0.7125 (m-10) REVERT: F 381 LYS cc_start: 0.8173 (ttmm) cc_final: 0.7559 (ttpt) REVERT: F 428 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.7249 (tpt-90) REVERT: F 492 GLU cc_start: 0.8272 (tt0) cc_final: 0.7842 (pt0) REVERT: F 535 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8038 (mp10) REVERT: F 587 LYS cc_start: 0.8469 (tppp) cc_final: 0.8034 (ttpp) REVERT: G 189 GLN cc_start: 0.8130 (tp40) cc_final: 0.7666 (tt0) REVERT: G 212 ARG cc_start: 0.7645 (ttm110) cc_final: 0.7023 (tpp-160) REVERT: G 296 ASP cc_start: 0.8292 (m-30) cc_final: 0.8061 (m-30) REVERT: G 362 ARG cc_start: 0.5538 (ttm110) cc_final: 0.4110 (tmt170) REVERT: G 378 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7682 (mptt) REVERT: G 420 LYS cc_start: 0.8392 (mppt) cc_final: 0.7740 (mppt) REVERT: G 538 ASP cc_start: 0.7610 (t70) cc_final: 0.7271 (t70) REVERT: H 138 ARG cc_start: 0.7293 (mtp-110) cc_final: 0.6931 (mtp180) REVERT: H 163 TYR cc_start: 0.7967 (t80) cc_final: 0.7639 (t80) REVERT: H 167 MET cc_start: 0.6833 (mmt) cc_final: 0.6534 (mtp) REVERT: H 215 GLU cc_start: 0.7186 (tp30) cc_final: 0.6836 (tp30) REVERT: H 274 TYR cc_start: 0.7606 (t80) cc_final: 0.7381 (t80) REVERT: H 295 TYR cc_start: 0.8471 (t80) cc_final: 0.7794 (t80) REVERT: H 298 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7912 (t0) REVERT: H 373 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7534 (mm-30) REVERT: H 381 LYS cc_start: 0.8156 (tppt) cc_final: 0.7842 (tptp) REVERT: H 390 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7193 (pm20) REVERT: H 391 ASN cc_start: 0.8511 (m110) cc_final: 0.8052 (t0) REVERT: H 394 SER cc_start: 0.8149 (m) cc_final: 0.7853 (p) REVERT: H 419 ASN cc_start: 0.7135 (m110) cc_final: 0.6409 (t0) REVERT: H 462 HIS cc_start: 0.8790 (OUTLIER) cc_final: 0.8344 (m170) REVERT: H 481 GLU cc_start: 0.8600 (tp30) cc_final: 0.8232 (tp30) REVERT: H 566 ARG cc_start: 0.7776 (ptm-80) cc_final: 0.7088 (tmt-80) outliers start: 66 outliers final: 40 residues processed: 560 average time/residue: 0.7431 time to fit residues: 490.3779 Evaluate side-chains 558 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 500 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 462 HIS Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 448 TRP Chi-restraints excluded: chain C residue 462 HIS Chi-restraints excluded: chain C residue 623 SER Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 585 THR Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 548 ASP Chi-restraints excluded: chain E residue 610 MET Chi-restraints excluded: chain F residue 186 ARG Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 428 ARG Chi-restraints excluded: chain F residue 535 GLN Chi-restraints excluded: chain F residue 585 THR Chi-restraints excluded: chain F residue 623 SER Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 378 LYS Chi-restraints excluded: chain G residue 543 SER Chi-restraints excluded: chain G residue 585 THR Chi-restraints excluded: chain G residue 626 ILE Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 298 ASP Chi-restraints excluded: chain H residue 390 GLU Chi-restraints excluded: chain H residue 437 ASN Chi-restraints excluded: chain H residue 462 HIS Chi-restraints excluded: chain H residue 554 VAL Chi-restraints excluded: chain H residue 595 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 370 optimal weight: 2.9990 chunk 133 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 298 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 394 optimal weight: 1.9990 chunk 415 optimal weight: 6.9990 chunk 236 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 352 optimal weight: 0.6980 chunk 360 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN A 560 GLN B 220 ASN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 ASN E 208 HIS E 379 ASN F 275 ASN F 316 ASN F 391 ASN H 129 GLN H 162 HIS ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.136524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.107305 restraints weight = 170334.052| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 4.67 r_work: 0.2938 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2937 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| r_final: 0.2937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 36823 Z= 0.152 Angle : 0.574 9.505 50062 Z= 0.303 Chirality : 0.047 0.191 5304 Planarity : 0.005 0.063 6335 Dihedral : 4.472 20.660 4744 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.75 % Allowed : 16.83 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.12), residues: 4311 helix: 0.70 (0.13), residues: 1712 sheet: -0.45 (0.18), residues: 888 loop : -1.04 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 566 TYR 0.030 0.001 TYR D 404 PHE 0.033 0.002 PHE D 376 TRP 0.065 0.002 TRP C 448 HIS 0.011 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00360 (36823) covalent geometry : angle 0.57352 (50062) hydrogen bonds : bond 0.04322 ( 1450) hydrogen bonds : angle 4.59123 ( 4410) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13691.23 seconds wall clock time: 233 minutes 19.49 seconds (13999.49 seconds total)