Starting phenix.real_space_refine on Sun Jun 29 10:27:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ci2_45608/06_2025/9ci2_45608_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ci2_45608/06_2025/9ci2_45608.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/9ci2_45608/06_2025/9ci2_45608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ci2_45608/06_2025/9ci2_45608.map" model { file = "/net/cci-nas-00/data/ceres_data/9ci2_45608/06_2025/9ci2_45608_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ci2_45608/06_2025/9ci2_45608_neut.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 4 5.21 5 S 220 5.16 5 C 21828 2.51 5 N 6028 2.21 5 O 6404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 89 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 34492 Number of models: 1 Model: "" Number of chains: 20 Chain: "1" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 519 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "2" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 519 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "3" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 519 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "4" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 519 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "A" Number of atoms: 3549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3549 Classifications: {'peptide': 452} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 430} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3568 Classifications: {'peptide': 455} Link IDs: {'PTRANS': 21, 'TRANS': 433} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 3549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3549 Classifications: {'peptide': 452} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 430} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 3568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3568 Classifications: {'peptide': 455} Link IDs: {'PTRANS': 21, 'TRANS': 433} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 3549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3549 Classifications: {'peptide': 452} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 430} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 3568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3568 Classifications: {'peptide': 455} Link IDs: {'PTRANS': 21, 'TRANS': 433} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 3549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3549 Classifications: {'peptide': 452} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 430} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 3568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3568 Classifications: {'peptide': 455} Link IDs: {'PTRANS': 21, 'TRANS': 433} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 965 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 11, 'TRANS': 106} Chain: "J" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 965 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 11, 'TRANS': 106} Chain: "K" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 965 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 11, 'TRANS': 106} Chain: "L" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 965 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 11, 'TRANS': 106} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 26.23, per 1000 atoms: 0.76 Number of scatterers: 34492 At special positions: 0 Unit cell: (134.75, 134.75, 132, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 220 16.00 P 8 15.00 Mg 4 11.99 O 6404 8.00 N 6028 7.00 C 21828 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.44 Conformation dependent library (CDL) restraints added in 5.1 seconds 8656 Ramachandran restraints generated. 4328 Oldfield, 0 Emsley, 4328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7880 Finding SS restraints... Secondary structure from input PDB file: 157 helices and 40 sheets defined 39.4% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.32 Creating SS restraints... Processing helix chain 'A' and resid 49 through 61 removed outlier: 3.501A pdb=" N ALA A 53 " --> pdb=" O PRO A 49 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.888A pdb=" N LEU A 107 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE A 108 " --> pdb=" O LEU A 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 104 through 108' Processing helix chain 'A' and resid 112 through 121 removed outlier: 3.714A pdb=" N MET A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 removed outlier: 3.517A pdb=" N LYS A 146 " --> pdb=" O PRO A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 163 Processing helix chain 'A' and resid 181 through 194 removed outlier: 3.633A pdb=" N GLU A 191 " --> pdb=" O ARG A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 233 removed outlier: 3.732A pdb=" N ARG A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 219 " --> pdb=" O ARG A 215 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY A 233 " --> pdb=" O GLN A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 261 removed outlier: 3.704A pdb=" N ALA A 254 " --> pdb=" O MET A 250 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN A 255 " --> pdb=" O MET A 251 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA A 257 " --> pdb=" O ARG A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 288 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 310 through 322 removed outlier: 3.942A pdb=" N LEU A 314 " --> pdb=" O HIS A 310 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS A 316 " --> pdb=" O ARG A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 348 removed outlier: 3.922A pdb=" N ASP A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 348 " --> pdb=" O GLY A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 386 through 394 removed outlier: 3.545A pdb=" N GLU A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 412 through 433 removed outlier: 3.660A pdb=" N LEU A 424 " --> pdb=" O ASN A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 449 Processing helix chain 'A' and resid 452 through 462 removed outlier: 3.990A pdb=" N ALA A 457 " --> pdb=" O PRO A 453 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 458 " --> pdb=" O GLU A 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 60 Processing helix chain 'B' and resid 104 through 108 removed outlier: 3.985A pdb=" N LEU B 107 " --> pdb=" O PRO B 104 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE B 108 " --> pdb=" O LEU B 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 104 through 108' Processing helix chain 'B' and resid 112 through 121 removed outlier: 3.881A pdb=" N MET B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 127 removed outlier: 3.791A pdb=" N GLY B 126 " --> pdb=" O ASN B 123 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE B 127 " --> pdb=" O VAL B 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 123 through 127' Processing helix chain 'B' and resid 144 through 148 removed outlier: 3.563A pdb=" N THR B 147 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 163 Processing helix chain 'B' and resid 181 through 196 removed outlier: 3.800A pdb=" N GLY B 196 " --> pdb=" O CYS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 233 removed outlier: 3.874A pdb=" N ARG B 217 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 227 " --> pdb=" O GLU B 223 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU B 231 " --> pdb=" O LYS B 227 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR B 232 " --> pdb=" O SER B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 260 removed outlier: 3.861A pdb=" N MET B 250 " --> pdb=" O THR B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 288 removed outlier: 3.686A pdb=" N ASN B 277 " --> pdb=" O GLY B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 Processing helix chain 'B' and resid 310 through 322 removed outlier: 3.924A pdb=" N LEU B 314 " --> pdb=" O HIS B 310 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS B 316 " --> pdb=" O ARG B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 351 Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 383 through 385 No H-bonds generated for 'chain 'B' and resid 383 through 385' Processing helix chain 'B' and resid 386 through 395 Processing helix chain 'B' and resid 413 through 432 removed outlier: 3.748A pdb=" N ALA B 417 " --> pdb=" O ASN B 413 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA B 419 " --> pdb=" O PRO B 415 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 449 removed outlier: 3.985A pdb=" N ILE B 445 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG B 446 " --> pdb=" O ASN B 442 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU B 447 " --> pdb=" O ASP B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 452 No H-bonds generated for 'chain 'B' and resid 450 through 452' Processing helix chain 'B' and resid 454 through 462 removed outlier: 3.828A pdb=" N ALA B 458 " --> pdb=" O GLU B 454 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLU B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 63 removed outlier: 4.056A pdb=" N ALA C 55 " --> pdb=" O GLU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 removed outlier: 3.888A pdb=" N LEU C 107 " --> pdb=" O PRO C 104 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE C 108 " --> pdb=" O LEU C 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 104 through 108' Processing helix chain 'C' and resid 112 through 121 removed outlier: 3.714A pdb=" N MET C 116 " --> pdb=" O SER C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 146 removed outlier: 3.517A pdb=" N LYS C 146 " --> pdb=" O PRO C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 163 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.641A pdb=" N GLU C 191 " --> pdb=" O ARG C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 233 removed outlier: 3.634A pdb=" N ARG C 217 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU C 219 " --> pdb=" O ARG C 215 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU C 231 " --> pdb=" O LYS C 227 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR C 232 " --> pdb=" O SER C 228 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY C 233 " --> pdb=" O GLN C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 261 removed outlier: 3.705A pdb=" N ALA C 254 " --> pdb=" O MET C 250 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN C 255 " --> pdb=" O MET C 251 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE C 256 " --> pdb=" O LYS C 252 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA C 257 " --> pdb=" O ARG C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 288 Processing helix chain 'C' and resid 297 through 301 Processing helix chain 'C' and resid 310 through 322 removed outlier: 3.940A pdb=" N LEU C 314 " --> pdb=" O HIS C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 351 removed outlier: 3.884A pdb=" N ASP C 347 " --> pdb=" O LEU C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 385 No H-bonds generated for 'chain 'C' and resid 383 through 385' Processing helix chain 'C' and resid 386 through 394 Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 412 through 433 Processing helix chain 'C' and resid 441 through 449 Processing helix chain 'C' and resid 452 through 462 removed outlier: 4.064A pdb=" N ALA C 457 " --> pdb=" O PRO C 453 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA C 458 " --> pdb=" O GLU C 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 60 Processing helix chain 'D' and resid 112 through 121 removed outlier: 3.882A pdb=" N MET D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 127 removed outlier: 3.786A pdb=" N GLY D 126 " --> pdb=" O ASN D 123 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE D 127 " --> pdb=" O VAL D 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 123 through 127' Processing helix chain 'D' and resid 144 through 148 removed outlier: 3.554A pdb=" N THR D 147 " --> pdb=" O TYR D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 163 Processing helix chain 'D' and resid 181 through 196 removed outlier: 3.800A pdb=" N GLY D 196 " --> pdb=" O CYS D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 233 removed outlier: 3.874A pdb=" N ARG D 217 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE D 226 " --> pdb=" O ALA D 222 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU D 231 " --> pdb=" O LYS D 227 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR D 232 " --> pdb=" O SER D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 260 removed outlier: 3.865A pdb=" N MET D 250 " --> pdb=" O THR D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 288 removed outlier: 3.680A pdb=" N ASN D 277 " --> pdb=" O GLY D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 301 Processing helix chain 'D' and resid 310 through 322 removed outlier: 3.925A pdb=" N LEU D 314 " --> pdb=" O HIS D 310 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS D 316 " --> pdb=" O ARG D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 351 Processing helix chain 'D' and resid 383 through 385 No H-bonds generated for 'chain 'D' and resid 383 through 385' Processing helix chain 'D' and resid 386 through 395 Processing helix chain 'D' and resid 403 through 408 removed outlier: 3.868A pdb=" N LEU D 407 " --> pdb=" O GLY D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 432 removed outlier: 3.749A pdb=" N ALA D 417 " --> pdb=" O ASN D 413 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL D 418 " --> pdb=" O ALA D 414 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA D 419 " --> pdb=" O PRO D 415 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN D 420 " --> pdb=" O GLY D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 449 removed outlier: 3.985A pdb=" N ILE D 445 " --> pdb=" O GLY D 441 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG D 446 " --> pdb=" O ASN D 442 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU D 447 " --> pdb=" O ASP D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 454 through 462 removed outlier: 3.928A pdb=" N ALA D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLU D 460 " --> pdb=" O ALA D 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 61 removed outlier: 4.081A pdb=" N ALA E 55 " --> pdb=" O GLU E 51 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA E 58 " --> pdb=" O GLY E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 108 removed outlier: 3.889A pdb=" N LEU E 107 " --> pdb=" O PRO E 104 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE E 108 " --> pdb=" O LEU E 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 104 through 108' Processing helix chain 'E' and resid 112 through 121 removed outlier: 3.714A pdb=" N MET E 116 " --> pdb=" O SER E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 146 removed outlier: 3.517A pdb=" N LYS E 146 " --> pdb=" O PRO E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 163 Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.622A pdb=" N GLU E 191 " --> pdb=" O ARG E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 233 removed outlier: 3.634A pdb=" N ARG E 217 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU E 219 " --> pdb=" O ARG E 215 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU E 231 " --> pdb=" O LYS E 227 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR E 232 " --> pdb=" O SER E 228 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY E 233 " --> pdb=" O GLN E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 261 removed outlier: 3.704A pdb=" N ALA E 254 " --> pdb=" O MET E 250 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN E 255 " --> pdb=" O MET E 251 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE E 256 " --> pdb=" O LYS E 252 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA E 257 " --> pdb=" O ARG E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 288 Processing helix chain 'E' and resid 297 through 301 Processing helix chain 'E' and resid 310 through 322 removed outlier: 3.884A pdb=" N LEU E 314 " --> pdb=" O HIS E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 351 Processing helix chain 'E' and resid 383 through 385 No H-bonds generated for 'chain 'E' and resid 383 through 385' Processing helix chain 'E' and resid 386 through 394 Processing helix chain 'E' and resid 403 through 408 removed outlier: 3.516A pdb=" N LEU E 407 " --> pdb=" O GLY E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 433 Processing helix chain 'E' and resid 441 through 450 Processing helix chain 'E' and resid 452 through 462 removed outlier: 4.007A pdb=" N ALA E 457 " --> pdb=" O PRO E 453 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA E 458 " --> pdb=" O GLU E 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 60 removed outlier: 3.564A pdb=" N ALA F 53 " --> pdb=" O PRO F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 108 removed outlier: 3.667A pdb=" N LEU F 107 " --> pdb=" O PRO F 104 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE F 108 " --> pdb=" O LEU F 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 104 through 108' Processing helix chain 'F' and resid 112 through 121 removed outlier: 3.848A pdb=" N MET F 116 " --> pdb=" O SER F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 148 removed outlier: 3.586A pdb=" N THR F 147 " --> pdb=" O TYR F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 163 Processing helix chain 'F' and resid 181 through 196 removed outlier: 3.801A pdb=" N GLY F 196 " --> pdb=" O CYS F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 233 removed outlier: 3.874A pdb=" N ARG F 217 " --> pdb=" O ARG F 213 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE F 226 " --> pdb=" O ALA F 222 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS F 227 " --> pdb=" O GLU F 223 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU F 231 " --> pdb=" O LYS F 227 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR F 232 " --> pdb=" O SER F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 260 removed outlier: 3.855A pdb=" N MET F 250 " --> pdb=" O THR F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 288 removed outlier: 3.681A pdb=" N ASN F 277 " --> pdb=" O GLY F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 301 Processing helix chain 'F' and resid 310 through 322 removed outlier: 3.924A pdb=" N LEU F 314 " --> pdb=" O HIS F 310 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS F 316 " --> pdb=" O ARG F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 351 Processing helix chain 'F' and resid 383 through 385 No H-bonds generated for 'chain 'F' and resid 383 through 385' Processing helix chain 'F' and resid 386 through 395 Processing helix chain 'F' and resid 403 through 408 removed outlier: 3.868A pdb=" N LEU F 407 " --> pdb=" O GLY F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 432 removed outlier: 3.749A pdb=" N ALA F 417 " --> pdb=" O ASN F 413 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL F 418 " --> pdb=" O ALA F 414 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA F 419 " --> pdb=" O PRO F 415 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN F 420 " --> pdb=" O GLY F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 449 removed outlier: 3.985A pdb=" N ILE F 445 " --> pdb=" O GLY F 441 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG F 446 " --> pdb=" O ASN F 442 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU F 447 " --> pdb=" O ASP F 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 450 through 452 No H-bonds generated for 'chain 'F' and resid 450 through 452' Processing helix chain 'G' and resid 49 through 61 removed outlier: 3.526A pdb=" N ALA G 55 " --> pdb=" O GLU G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 108 removed outlier: 3.888A pdb=" N LEU G 107 " --> pdb=" O PRO G 104 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE G 108 " --> pdb=" O LEU G 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 104 through 108' Processing helix chain 'G' and resid 112 through 121 removed outlier: 3.714A pdb=" N MET G 116 " --> pdb=" O SER G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 146 removed outlier: 3.517A pdb=" N LYS G 146 " --> pdb=" O PRO G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 163 Processing helix chain 'G' and resid 181 through 194 removed outlier: 3.624A pdb=" N GLU G 191 " --> pdb=" O ARG G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 233 removed outlier: 3.633A pdb=" N ARG G 217 " --> pdb=" O ARG G 213 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU G 219 " --> pdb=" O ARG G 215 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU G 231 " --> pdb=" O LYS G 227 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR G 232 " --> pdb=" O SER G 228 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY G 233 " --> pdb=" O GLN G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 261 removed outlier: 3.705A pdb=" N ALA G 254 " --> pdb=" O MET G 250 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN G 255 " --> pdb=" O MET G 251 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE G 256 " --> pdb=" O LYS G 252 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA G 257 " --> pdb=" O ARG G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 288 Processing helix chain 'G' and resid 297 through 301 Processing helix chain 'G' and resid 310 through 322 removed outlier: 3.883A pdb=" N LEU G 314 " --> pdb=" O HIS G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 351 Processing helix chain 'G' and resid 383 through 385 No H-bonds generated for 'chain 'G' and resid 383 through 385' Processing helix chain 'G' and resid 386 through 394 Processing helix chain 'G' and resid 403 through 408 removed outlier: 3.524A pdb=" N LEU G 407 " --> pdb=" O GLY G 403 " (cutoff:3.500A) Processing helix chain 'G' and resid 412 through 434 removed outlier: 3.695A pdb=" N ASN G 432 " --> pdb=" O VAL G 428 " (cutoff:3.500A) Processing helix chain 'G' and resid 441 through 450 Processing helix chain 'G' and resid 452 through 462 removed outlier: 3.743A pdb=" N ALA G 457 " --> pdb=" O PRO G 453 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU G 460 " --> pdb=" O ALA G 456 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 60 Processing helix chain 'H' and resid 106 through 108 No H-bonds generated for 'chain 'H' and resid 106 through 108' Processing helix chain 'H' and resid 112 through 121 removed outlier: 3.882A pdb=" N MET H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 127 removed outlier: 3.812A pdb=" N GLY H 126 " --> pdb=" O ASN H 123 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE H 127 " --> pdb=" O VAL H 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 123 through 127' Processing helix chain 'H' and resid 144 through 148 removed outlier: 3.543A pdb=" N THR H 147 " --> pdb=" O TYR H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 163 Processing helix chain 'H' and resid 181 through 196 removed outlier: 3.800A pdb=" N GLY H 196 " --> pdb=" O CYS H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 233 removed outlier: 3.874A pdb=" N ARG H 217 " --> pdb=" O ARG H 213 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE H 226 " --> pdb=" O ALA H 222 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS H 227 " --> pdb=" O GLU H 223 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU H 231 " --> pdb=" O LYS H 227 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR H 232 " --> pdb=" O SER H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 260 removed outlier: 3.856A pdb=" N MET H 250 " --> pdb=" O THR H 246 " (cutoff:3.500A) Processing helix chain 'H' and resid 273 through 288 removed outlier: 3.687A pdb=" N ASN H 277 " --> pdb=" O GLY H 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 301 Processing helix chain 'H' and resid 310 through 322 removed outlier: 3.925A pdb=" N LEU H 314 " --> pdb=" O HIS H 310 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS H 316 " --> pdb=" O ARG H 312 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 351 Processing helix chain 'H' and resid 383 through 385 No H-bonds generated for 'chain 'H' and resid 383 through 385' Processing helix chain 'H' and resid 386 through 395 Processing helix chain 'H' and resid 403 through 408 removed outlier: 3.868A pdb=" N LEU H 407 " --> pdb=" O GLY H 403 " (cutoff:3.500A) Processing helix chain 'H' and resid 413 through 432 removed outlier: 3.749A pdb=" N ALA H 417 " --> pdb=" O ASN H 413 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL H 418 " --> pdb=" O ALA H 414 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA H 419 " --> pdb=" O PRO H 415 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN H 420 " --> pdb=" O GLY H 416 " (cutoff:3.500A) Processing helix chain 'H' and resid 441 through 449 removed outlier: 3.985A pdb=" N ILE H 445 " --> pdb=" O GLY H 441 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG H 446 " --> pdb=" O ASN H 442 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU H 447 " --> pdb=" O ASP H 443 " (cutoff:3.500A) Processing helix chain 'H' and resid 450 through 452 No H-bonds generated for 'chain 'H' and resid 450 through 452' Processing helix chain 'H' and resid 454 through 462 removed outlier: 3.791A pdb=" N ALA H 458 " --> pdb=" O GLU H 454 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLU H 460 " --> pdb=" O ALA H 456 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 36 removed outlier: 3.504A pdb=" N GLU I 29 " --> pdb=" O GLN I 25 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE I 30 " --> pdb=" O ILE I 26 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ASP I 31 " --> pdb=" O ALA I 27 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN I 36 " --> pdb=" O TYR I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 92 removed outlier: 3.526A pdb=" N LEU I 82 " --> pdb=" O ALA I 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 36 removed outlier: 3.508A pdb=" N GLU J 29 " --> pdb=" O GLN J 25 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE J 30 " --> pdb=" O ILE J 26 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASP J 31 " --> pdb=" O ALA J 27 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN J 36 " --> pdb=" O TYR J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 92 removed outlier: 3.522A pdb=" N LEU J 82 " --> pdb=" O ALA J 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 36 removed outlier: 3.535A pdb=" N GLU K 29 " --> pdb=" O GLN K 25 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE K 30 " --> pdb=" O ILE K 26 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASP K 31 " --> pdb=" O ALA K 27 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN K 36 " --> pdb=" O TYR K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 92 Processing helix chain 'L' and resid 22 through 36 removed outlier: 3.593A pdb=" N ILE L 30 " --> pdb=" O ILE L 26 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ASP L 31 " --> pdb=" O ALA L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 92 removed outlier: 4.438A pdb=" N VAL L 81 " --> pdb=" O ASN L 77 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 65 through 66 Processing sheet with id=AA2, first strand: chain '1' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain '2' and resid 65 through 66 removed outlier: 5.453A pdb=" N VAL 2 71 " --> pdb=" O LYS 2 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 80 through 81 Processing sheet with id=AA5, first strand: chain '3' and resid 65 through 66 Processing sheet with id=AA6, first strand: chain '3' and resid 80 through 81 Processing sheet with id=AA7, first strand: chain '4' and resid 65 through 66 removed outlier: 5.401A pdb=" N VAL 4 71 " --> pdb=" O LYS 4 66 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '4' and resid 80 through 81 Processing sheet with id=AA9, first strand: chain 'A' and resid 83 through 89 removed outlier: 6.178A pdb=" N CYS A 84 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ALA A 102 " --> pdb=" O CYS A 84 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASP A 86 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 97 " --> pdb=" O MET A 42 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU A 37 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU A 138 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ALA A 39 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR A 43 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA A 132 " --> pdb=" O THR A 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 199 through 201 removed outlier: 7.131A pdb=" N LEU A 170 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N KCX A 201 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N CYS A 172 " --> pdb=" O KCX A 201 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU A 169 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE A 326 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 240 through 241 removed outlier: 6.147A pdb=" N LEU A 240 " --> pdb=" O MET A 266 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N ASP A 268 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AB4, first strand: chain 'B' and resid 83 through 89 removed outlier: 6.137A pdb=" N CYS B 84 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ALA B 102 " --> pdb=" O CYS B 84 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASP B 86 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE B 40 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B 101 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU B 37 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU B 138 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ALA B 39 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR B 43 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA B 132 " --> pdb=" O THR B 43 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 169 through 172 removed outlier: 6.695A pdb=" N LEU B 169 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N PHE B 402 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLY B 171 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLN B 401 " --> pdb=" O PRO B 376 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ALA B 378 " --> pdb=" O GLN B 401 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE B 326 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N HIS B 327 " --> pdb=" O ILE B 293 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 353 through 354 Processing sheet with id=AB7, first strand: chain 'C' and resid 83 through 89 removed outlier: 6.172A pdb=" N CYS C 84 " --> pdb=" O ALA C 102 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ALA C 102 " --> pdb=" O CYS C 84 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP C 86 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR C 97 " --> pdb=" O MET C 42 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU C 37 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU C 138 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ALA C 39 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR C 43 " --> pdb=" O ALA C 132 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA C 132 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 171 removed outlier: 6.669A pdb=" N LEU C 169 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE C 326 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 240 through 241 removed outlier: 6.255A pdb=" N LEU C 240 " --> pdb=" O MET C 266 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N ASP C 268 " --> pdb=" O LEU C 240 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 353 through 354 Processing sheet with id=AC2, first strand: chain 'D' and resid 83 through 89 removed outlier: 6.152A pdb=" N CYS D 84 " --> pdb=" O ALA D 102 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA D 102 " --> pdb=" O CYS D 84 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASP D 86 " --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE D 40 " --> pdb=" O ALA D 99 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL D 101 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU D 37 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU D 138 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA D 39 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR D 43 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA D 132 " --> pdb=" O THR D 43 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 169 through 172 removed outlier: 6.694A pdb=" N LEU D 169 " --> pdb=" O LEU D 400 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N PHE D 402 " --> pdb=" O LEU D 169 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLY D 171 " --> pdb=" O PHE D 402 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE D 326 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N HIS D 327 " --> pdb=" O ILE D 293 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 353 through 354 Processing sheet with id=AC5, first strand: chain 'E' and resid 83 through 89 removed outlier: 6.138A pdb=" N CYS E 84 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA E 102 " --> pdb=" O CYS E 84 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP E 86 " --> pdb=" O TYR E 100 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR E 97 " --> pdb=" O MET E 42 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU E 37 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU E 138 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ALA E 39 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR E 43 " --> pdb=" O ALA E 132 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA E 132 " --> pdb=" O THR E 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 169 through 171 removed outlier: 6.670A pdb=" N LEU E 169 " --> pdb=" O LEU E 400 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N GLN E 401 " --> pdb=" O PRO E 376 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALA E 378 " --> pdb=" O GLN E 401 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE E 326 " --> pdb=" O VAL E 377 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 240 through 241 removed outlier: 6.264A pdb=" N LEU E 240 " --> pdb=" O MET E 266 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N ASP E 268 " --> pdb=" O LEU E 240 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 353 through 354 Processing sheet with id=AC9, first strand: chain 'F' and resid 83 through 89 removed outlier: 6.153A pdb=" N CYS F 84 " --> pdb=" O ALA F 102 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ALA F 102 " --> pdb=" O CYS F 84 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASP F 86 " --> pdb=" O TYR F 100 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE F 40 " --> pdb=" O ALA F 99 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL F 101 " --> pdb=" O ALA F 38 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU F 37 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU F 138 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ALA F 39 " --> pdb=" O GLU F 136 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR F 43 " --> pdb=" O ALA F 132 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA F 132 " --> pdb=" O THR F 43 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 169 through 172 removed outlier: 6.694A pdb=" N LEU F 169 " --> pdb=" O LEU F 400 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N PHE F 402 " --> pdb=" O LEU F 169 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLY F 171 " --> pdb=" O PHE F 402 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLN F 401 " --> pdb=" O PRO F 376 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA F 378 " --> pdb=" O GLN F 401 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE F 326 " --> pdb=" O VAL F 377 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N HIS F 327 " --> pdb=" O ILE F 293 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 353 through 354 Processing sheet with id=AD3, first strand: chain 'G' and resid 83 through 89 removed outlier: 6.168A pdb=" N CYS G 84 " --> pdb=" O ALA G 102 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ALA G 102 " --> pdb=" O CYS G 84 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP G 86 " --> pdb=" O TYR G 100 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR G 97 " --> pdb=" O MET G 42 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU G 37 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU G 138 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ALA G 39 " --> pdb=" O GLU G 136 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR G 43 " --> pdb=" O ALA G 132 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA G 132 " --> pdb=" O THR G 43 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 169 through 171 removed outlier: 6.674A pdb=" N LEU G 169 " --> pdb=" O LEU G 400 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE G 326 " --> pdb=" O VAL G 377 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 240 through 241 removed outlier: 6.282A pdb=" N LEU G 240 " --> pdb=" O MET G 266 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N ASP G 268 " --> pdb=" O LEU G 240 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 353 through 354 Processing sheet with id=AD7, first strand: chain 'H' and resid 83 through 89 removed outlier: 6.143A pdb=" N CYS H 84 " --> pdb=" O ALA H 102 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ALA H 102 " --> pdb=" O CYS H 84 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASP H 86 " --> pdb=" O TYR H 100 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE H 40 " --> pdb=" O ALA H 99 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL H 101 " --> pdb=" O ALA H 38 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU H 37 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU H 138 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ALA H 39 " --> pdb=" O GLU H 136 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR H 43 " --> pdb=" O ALA H 132 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA H 132 " --> pdb=" O THR H 43 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 169 through 172 removed outlier: 6.694A pdb=" N LEU H 169 " --> pdb=" O LEU H 400 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N PHE H 402 " --> pdb=" O LEU H 169 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLY H 171 " --> pdb=" O PHE H 402 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLN H 401 " --> pdb=" O PRO H 376 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA H 378 " --> pdb=" O GLN H 401 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE H 326 " --> pdb=" O VAL H 377 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N HIS H 327 " --> pdb=" O ILE H 293 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 353 through 354 Processing sheet with id=AE1, first strand: chain 'I' and resid 66 through 67 removed outlier: 3.652A pdb=" N CYS I 41 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ILE I 97 " --> pdb=" O ILE I 114 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ILE I 114 " --> pdb=" O ILE I 97 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL I 99 " --> pdb=" O ALA I 112 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA I 112 " --> pdb=" O VAL I 99 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLY I 101 " --> pdb=" O CYS I 110 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N CYS I 110 " --> pdb=" O GLY I 101 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 66 through 67 removed outlier: 3.655A pdb=" N CYS J 41 " --> pdb=" O LEU J 100 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ILE J 97 " --> pdb=" O ILE J 114 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ILE J 114 " --> pdb=" O ILE J 97 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL J 99 " --> pdb=" O ALA J 112 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA J 112 " --> pdb=" O VAL J 99 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLY J 101 " --> pdb=" O CYS J 110 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N CYS J 110 " --> pdb=" O GLY J 101 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 66 through 67 removed outlier: 3.650A pdb=" N CYS K 41 " --> pdb=" O LEU K 100 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ILE K 97 " --> pdb=" O ILE K 114 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ILE K 114 " --> pdb=" O ILE K 97 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL K 99 " --> pdb=" O ALA K 112 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA K 112 " --> pdb=" O VAL K 99 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLY K 101 " --> pdb=" O CYS K 110 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N CYS K 110 " --> pdb=" O GLY K 101 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 66 through 67 removed outlier: 6.445A pdb=" N ILE L 97 " --> pdb=" O VAL L 115 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY L 101 " --> pdb=" O CYS L 111 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N CYS L 111 " --> pdb=" O GLY L 101 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ASP L 103 " --> pdb=" O GLN L 109 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N GLN L 109 " --> pdb=" O ASP L 103 " (cutoff:3.500A) 1176 hydrogen bonds defined for protein. 3303 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: 13.91 Time building geometry restraints manager: 10.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7235 1.33 - 1.45: 8430 1.45 - 1.57: 19342 1.57 - 1.69: 9 1.69 - 1.81: 324 Bond restraints: 35340 Sorted by residual: bond pdb=" N ILE L 39 " pdb=" CA ILE L 39 " ideal model delta sigma weight residual 1.460 1.494 -0.035 7.50e-03 1.78e+04 2.13e+01 bond pdb=" N ILE H 140 " pdb=" CA ILE H 140 " ideal model delta sigma weight residual 1.460 1.492 -0.032 7.50e-03 1.78e+04 1.84e+01 bond pdb=" CA PRO F 141 " pdb=" C PRO F 141 " ideal model delta sigma weight residual 1.514 1.537 -0.023 5.50e-03 3.31e+04 1.78e+01 bond pdb=" NZ KCX F 201 " pdb=" CX KCX F 201 " ideal model delta sigma weight residual 1.411 1.327 0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" CA PRO D 141 " pdb=" C PRO D 141 " ideal model delta sigma weight residual 1.514 1.537 -0.023 5.50e-03 3.31e+04 1.75e+01 ... (remaining 35335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 42077 1.77 - 3.55: 5240 3.55 - 5.32: 515 5.32 - 7.10: 52 7.10 - 8.87: 8 Bond angle restraints: 47892 Sorted by residual: angle pdb=" CA GLY 3 129 " pdb=" C GLY 3 129 " pdb=" O GLY 3 129 " ideal model delta sigma weight residual 122.22 118.05 4.17 6.50e-01 2.37e+00 4.11e+01 angle pdb=" N VAL A 331 " pdb=" CA VAL A 331 " pdb=" C VAL A 331 " ideal model delta sigma weight residual 113.20 107.67 5.53 9.60e-01 1.09e+00 3.32e+01 angle pdb=" N VAL E 331 " pdb=" CA VAL E 331 " pdb=" C VAL E 331 " ideal model delta sigma weight residual 113.20 107.71 5.49 9.60e-01 1.09e+00 3.27e+01 angle pdb=" C GLU I 13 " pdb=" CA GLU I 13 " pdb=" CB GLU I 13 " ideal model delta sigma weight residual 116.63 110.03 6.60 1.16e+00 7.43e-01 3.24e+01 angle pdb=" C GLU K 13 " pdb=" CA GLU K 13 " pdb=" CB GLU K 13 " ideal model delta sigma weight residual 116.63 110.03 6.60 1.16e+00 7.43e-01 3.24e+01 ... (remaining 47887 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 17304 17.92 - 35.84: 2223 35.84 - 53.76: 901 53.76 - 71.68: 261 71.68 - 89.60: 59 Dihedral angle restraints: 20748 sinusoidal: 8328 harmonic: 12420 Sorted by residual: dihedral pdb=" CA LYS G 175 " pdb=" C LYS G 175 " pdb=" N PRO G 176 " pdb=" CA PRO G 176 " ideal model delta harmonic sigma weight residual 0.00 24.38 -24.38 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" C5 CAP E 502 " pdb=" O5 CAP E 502 " pdb=" P2 CAP E 502 " pdb=" O4P CAP E 502 " ideal model delta sinusoidal sigma weight residual 160.56 71.65 88.91 1 2.00e+01 2.50e-03 2.35e+01 dihedral pdb=" C5 CAP A 502 " pdb=" O5 CAP A 502 " pdb=" P2 CAP A 502 " pdb=" O4P CAP A 502 " ideal model delta sinusoidal sigma weight residual 160.56 73.74 86.81 1 2.00e+01 2.50e-03 2.27e+01 ... (remaining 20745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2732 0.046 - 0.092: 1172 0.092 - 0.138: 840 0.138 - 0.185: 277 0.185 - 0.231: 35 Chirality restraints: 5056 Sorted by residual: chirality pdb=" CG LEU 4 117 " pdb=" CB LEU 4 117 " pdb=" CD1 LEU 4 117 " pdb=" CD2 LEU 4 117 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA ILE 2 94 " pdb=" N ILE 2 94 " pdb=" C ILE 2 94 " pdb=" CB ILE 2 94 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ILE 1 94 " pdb=" N ILE 1 94 " pdb=" C ILE 1 94 " pdb=" CB ILE 1 94 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 5053 not shown) Planarity restraints: 6272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 121 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.78e+00 pdb=" C VAL D 121 " 0.042 2.00e-02 2.50e+03 pdb=" O VAL D 121 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY D 122 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 121 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.72e+00 pdb=" C VAL B 121 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL B 121 " 0.016 2.00e-02 2.50e+03 pdb=" N GLY B 122 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 121 " 0.012 2.00e-02 2.50e+03 2.36e-02 5.57e+00 pdb=" C VAL H 121 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL H 121 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY H 122 " 0.014 2.00e-02 2.50e+03 ... (remaining 6269 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 30 2.40 - 3.03: 19622 3.03 - 3.65: 47190 3.65 - 4.28: 72443 4.28 - 4.90: 125860 Nonbonded interactions: 265145 Sorted by model distance: nonbonded pdb=" OQ2 KCX A 201 " pdb="MG MG A 501 " model vdw 1.781 2.170 nonbonded pdb=" OQ2 KCX C 201 " pdb="MG MG C 501 " model vdw 1.830 2.170 nonbonded pdb=" OQ2 KCX G 201 " pdb="MG MG G 501 " model vdw 1.862 2.170 nonbonded pdb=" OQ2 KCX E 201 " pdb="MG MG E 501 " model vdw 1.866 2.170 nonbonded pdb=" ND2 ASN K 77 " pdb=" CD2 TYR K 80 " model vdw 1.903 3.420 ... (remaining 265140 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: 0.04 Found NCS groups: ncs_group { reference = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' } ncs_group { reference = (chain 'A' and resid 22 through 466) selection = (chain 'B' and (resid 22 through 73 or resid 76 through 466)) selection = (chain 'C' and resid 22 through 466) selection = (chain 'D' and (resid 22 through 73 or resid 76 through 466)) selection = (chain 'E' and resid 22 through 466) selection = (chain 'F' and (resid 22 through 73 or resid 76 through 466)) selection = (chain 'G' and resid 22 through 466) selection = (chain 'H' and (resid 22 through 73 or resid 76 through 466)) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 57.680 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: 0.050 Extract box with map and model: 1.470 Check model and map are aligned: 0.260 Set scattering table: 0.340 Process input model: 85.560 Find NCS groups from input model: 2.050 Set up NCS constraints: 0.210 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:19.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 166.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 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 : 0.010 0.322 35343 Z= 0.732 Angle : 1.114 8.869 47892 Z= 0.797 Chirality : 0.072 0.231 5056 Planarity : 0.004 0.047 6272 Dihedral : 19.757 89.604 12868 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 1.76 % Allowed : 10.49 % Favored : 87.75 % Rotamer: Outliers : 14.93 % Allowed : 18.66 % Favored : 66.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.12), residues: 4328 helix: -0.23 (0.14), residues: 1472 sheet: -0.90 (0.20), residues: 688 loop : -3.32 (0.11), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 214 HIS 0.004 0.001 HIS F 238 PHE 0.028 0.001 PHE G 345 TYR 0.013 0.001 TYR G 24 ARG 0.007 0.000 ARG F 439 Details of bonding type rmsd hydrogen bonds : bond 0.24773 ( 1176) hydrogen bonds : angle 7.28218 ( 3303) covalent geometry : bond 0.00921 (35340) covalent geometry : angle 1.11437 (47892) Misc. bond : bond 0.31923 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8656 Ramachandran restraints generated. 4328 Oldfield, 0 Emsley, 4328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8656 Ramachandran restraints generated. 4328 Oldfield, 0 Emsley, 4328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1052 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 532 poor density : 520 time to evaluate : 5.089 Fit side-chains REVERT: 2 115 GLU cc_start: 0.5849 (mm-30) cc_final: 0.5505 (mt-10) REVERT: 3 92 ASN cc_start: 0.4090 (m-40) cc_final: 0.3882 (m-40) REVERT: 3 115 GLU cc_start: 0.5586 (mm-30) cc_final: 0.5311 (mt-10) REVERT: 4 98 ASN cc_start: 0.6440 (OUTLIER) cc_final: 0.6048 (t0) REVERT: A 106 ASP cc_start: 0.8298 (m-30) cc_final: 0.7982 (m-30) REVERT: A 156 GLN cc_start: 0.7766 (mp-120) cc_final: 0.6076 (tt0) REVERT: A 202 ASP cc_start: 0.6965 (m-30) cc_final: 0.6696 (m-30) REVERT: A 266 MET cc_start: 0.9278 (ttt) cc_final: 0.9051 (ttp) REVERT: A 355 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8107 (tp30) REVERT: A 396 ASP cc_start: 0.8060 (p0) cc_final: 0.7340 (p0) REVERT: A 440 GLU cc_start: 0.6020 (OUTLIER) cc_final: 0.5656 (pt0) REVERT: B 42 MET cc_start: 0.8953 (ptp) cc_final: 0.8585 (ptt) REVERT: B 216 ASP cc_start: 0.7246 (OUTLIER) cc_final: 0.7022 (m-30) REVERT: B 302 ASP cc_start: 0.8355 (p0) cc_final: 0.8061 (p0) REVERT: B 357 ASP cc_start: 0.6832 (t0) cc_final: 0.6578 (t0) REVERT: B 396 ASP cc_start: 0.7892 (p0) cc_final: 0.6998 (p0) REVERT: B 463 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.6427 (mmtt) REVERT: C 78 ASP cc_start: 0.7368 (OUTLIER) cc_final: 0.7114 (p0) REVERT: C 106 ASP cc_start: 0.8302 (m-30) cc_final: 0.7993 (m-30) REVERT: C 156 GLN cc_start: 0.7757 (mp-120) cc_final: 0.6080 (tt0) REVERT: C 202 ASP cc_start: 0.6989 (m-30) cc_final: 0.6716 (m-30) REVERT: C 266 MET cc_start: 0.9261 (ttt) cc_final: 0.8954 (ttm) REVERT: C 396 ASP cc_start: 0.8058 (p0) cc_final: 0.7352 (p0) REVERT: D 42 MET cc_start: 0.8972 (ptp) cc_final: 0.8587 (ptt) REVERT: D 216 ASP cc_start: 0.7257 (OUTLIER) cc_final: 0.7028 (m-30) REVERT: D 302 ASP cc_start: 0.8354 (p0) cc_final: 0.8060 (p0) REVERT: D 357 ASP cc_start: 0.7555 (t0) cc_final: 0.7255 (t0) REVERT: D 396 ASP cc_start: 0.7906 (p0) cc_final: 0.6995 (p0) REVERT: D 455 LEU cc_start: 0.5813 (OUTLIER) cc_final: 0.5594 (tp) REVERT: D 463 LYS cc_start: 0.7274 (ptpp) cc_final: 0.6142 (mmtt) REVERT: E 78 ASP cc_start: 0.7330 (OUTLIER) cc_final: 0.6964 (m-30) REVERT: E 106 ASP cc_start: 0.8322 (m-30) cc_final: 0.8001 (m-30) REVERT: E 156 GLN cc_start: 0.7765 (mp-120) cc_final: 0.6079 (tt0) REVERT: E 202 ASP cc_start: 0.7108 (m-30) cc_final: 0.6866 (m-30) REVERT: E 266 MET cc_start: 0.9265 (ttt) cc_final: 0.8961 (ttm) REVERT: E 355 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8101 (tp30) REVERT: E 396 ASP cc_start: 0.8039 (p0) cc_final: 0.7316 (p0) REVERT: F 42 MET cc_start: 0.8963 (ptp) cc_final: 0.8573 (ptt) REVERT: F 77 LEU cc_start: 0.6728 (OUTLIER) cc_final: 0.6272 (mp) REVERT: F 216 ASP cc_start: 0.7229 (OUTLIER) cc_final: 0.7005 (m-30) REVERT: F 302 ASP cc_start: 0.8346 (p0) cc_final: 0.8055 (p0) REVERT: F 357 ASP cc_start: 0.7552 (t0) cc_final: 0.7160 (t0) REVERT: F 396 ASP cc_start: 0.7889 (p0) cc_final: 0.6962 (p0) REVERT: F 463 LYS cc_start: 0.7253 (ptpp) cc_final: 0.6161 (mmtt) REVERT: G 77 LEU cc_start: 0.5367 (OUTLIER) cc_final: 0.5165 (tp) REVERT: G 78 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.6943 (p0) REVERT: G 106 ASP cc_start: 0.8304 (m-30) cc_final: 0.7997 (m-30) REVERT: G 156 GLN cc_start: 0.7766 (mp-120) cc_final: 0.6079 (tt0) REVERT: G 266 MET cc_start: 0.9289 (ttt) cc_final: 0.9046 (ttp) REVERT: G 355 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8097 (tp30) REVERT: G 396 ASP cc_start: 0.8043 (p0) cc_final: 0.7288 (p0) REVERT: H 42 MET cc_start: 0.8972 (ptp) cc_final: 0.8593 (ptt) REVERT: H 216 ASP cc_start: 0.7249 (OUTLIER) cc_final: 0.7040 (m-30) REVERT: H 302 ASP cc_start: 0.8345 (p0) cc_final: 0.8053 (p0) REVERT: H 357 ASP cc_start: 0.7558 (t0) cc_final: 0.7161 (t0) REVERT: H 396 ASP cc_start: 0.7886 (p0) cc_final: 0.6984 (p0) REVERT: H 463 LYS cc_start: 0.7248 (ptpp) cc_final: 0.6166 (mmtt) outliers start: 532 outliers final: 89 residues processed: 887 average time/residue: 2.1166 time to fit residues: 2229.0212 Evaluate side-chains 412 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 310 time to evaluate : 6.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 70 LEU Chi-restraints excluded: chain 1 residue 81 VAL Chi-restraints excluded: chain 1 residue 132 SER Chi-restraints excluded: chain 1 residue 134 PHE Chi-restraints excluded: chain 2 residue 70 LEU Chi-restraints excluded: chain 2 residue 81 VAL Chi-restraints excluded: chain 2 residue 98 ASN Chi-restraints excluded: chain 2 residue 133 THR Chi-restraints excluded: chain 2 residue 134 PHE Chi-restraints excluded: chain 3 residue 70 LEU Chi-restraints excluded: chain 3 residue 81 VAL Chi-restraints excluded: chain 3 residue 134 PHE Chi-restraints excluded: chain 4 residue 70 LEU Chi-restraints excluded: chain 4 residue 98 ASN Chi-restraints excluded: chain 4 residue 133 THR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 96 GLN Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 192 CYS Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 444 ILE Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 175 LYS Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain E residue 41 ARG Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 172 CYS Chi-restraints excluded: chain E residue 192 CYS Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 303 ARG Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 444 ILE Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 175 LYS Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 444 ILE Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 41 ARG Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain G residue 192 CYS Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 369 VAL Chi-restraints excluded: chain G residue 444 ILE Chi-restraints excluded: chain G residue 474 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 40 PHE Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 444 ILE Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain L residue 100 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 8.9990 chunk 327 optimal weight: 7.9990 chunk 181 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 chunk 220 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 338 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 chunk 205 optimal weight: 5.9990 chunk 252 optimal weight: 0.9980 chunk 392 optimal weight: 1.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 74 ASN A 115 ASN A 153 HIS B 45 GLN B 413 ASN C 115 ASN C 153 HIS D 383 HIS D 413 ASN E 115 ASN E 153 HIS F 45 GLN G 115 ASN G 153 HIS G 327 HIS H 45 GLN H 413 ASN I 2 GLN I 104 ASN K 77 ASN L 90 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.114995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.095057 restraints weight = 46598.564| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.60 r_work: 0.3013 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 35343 Z= 0.203 Angle : 0.734 9.220 47892 Z= 0.391 Chirality : 0.050 0.246 5056 Planarity : 0.006 0.073 6272 Dihedral : 8.473 65.551 5070 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.86 % Favored : 91.77 % Rotamer: Outliers : 6.54 % Allowed : 20.99 % Favored : 72.47 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.12), residues: 4328 helix: 0.71 (0.14), residues: 1496 sheet: -0.96 (0.20), residues: 636 loop : -2.94 (0.11), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 385 HIS 0.007 0.002 HIS G 292 PHE 0.031 0.002 PHE G 345 TYR 0.020 0.002 TYR L 80 ARG 0.007 0.001 ARG J 83 Details of bonding type rmsd hydrogen bonds : bond 0.08082 ( 1176) hydrogen bonds : angle 4.60702 ( 3303) covalent geometry : bond 0.00466 (35340) covalent geometry : angle 0.73383 (47892) Misc. bond : bond 0.01909 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8656 Ramachandran restraints generated. 4328 Oldfield, 0 Emsley, 4328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8656 Ramachandran restraints generated. 4328 Oldfield, 0 Emsley, 4328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 287 time to evaluate : 3.568 Fit side-chains REVERT: 1 132 SER cc_start: 0.8015 (OUTLIER) cc_final: 0.7497 (p) REVERT: 2 80 CYS cc_start: 0.7615 (p) cc_final: 0.7257 (m) REVERT: 2 115 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6389 (mt-10) REVERT: 2 133 THR cc_start: 0.7253 (OUTLIER) cc_final: 0.6968 (m) REVERT: 3 78 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8170 (mm-30) REVERT: 3 132 SER cc_start: 0.7724 (t) cc_final: 0.7436 (p) REVERT: 4 78 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8170 (mm-30) REVERT: 4 113 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7541 (mttp) REVERT: 4 133 THR cc_start: 0.7655 (OUTLIER) cc_final: 0.7211 (p) REVERT: A 156 GLN cc_start: 0.8525 (mp-120) cc_final: 0.7387 (tt0) REVERT: A 177 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.6814 (ptmt) REVERT: A 396 ASP cc_start: 0.8311 (p0) cc_final: 0.7724 (p0) REVERT: B 79 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8267 (ttt180) REVERT: B 83 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8455 (mtt90) REVERT: B 94 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7416 (tp30) REVERT: B 139 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.8799 (tmm160) REVERT: B 295 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8651 (ptt180) REVERT: B 357 ASP cc_start: 0.8197 (t0) cc_final: 0.7886 (t70) REVERT: B 396 ASP cc_start: 0.8427 (p0) cc_final: 0.7728 (p0) REVERT: B 463 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.6852 (mmtt) REVERT: C 156 GLN cc_start: 0.8538 (mp-120) cc_final: 0.7404 (tt0) REVERT: C 177 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.6878 (ptmt) REVERT: C 396 ASP cc_start: 0.8310 (p0) cc_final: 0.7768 (p0) REVERT: C 444 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7794 (mm) REVERT: C 466 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7946 (mttm) REVERT: D 180 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8184 (mp) REVERT: D 216 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.7554 (m-30) REVERT: D 295 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8658 (ptt180) REVERT: D 396 ASP cc_start: 0.8418 (p0) cc_final: 0.7724 (p0) REVERT: D 463 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.6670 (mmtt) REVERT: E 106 ASP cc_start: 0.8328 (m-30) cc_final: 0.8125 (m-30) REVERT: E 156 GLN cc_start: 0.8506 (mp-120) cc_final: 0.7382 (tt0) REVERT: E 396 ASP cc_start: 0.8340 (p0) cc_final: 0.7788 (p0) REVERT: E 439 ARG cc_start: 0.6767 (OUTLIER) cc_final: 0.6337 (mtp85) REVERT: F 77 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7814 (mp) REVERT: F 94 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7412 (tp30) REVERT: F 180 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8179 (mp) REVERT: F 216 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7548 (m-30) REVERT: F 295 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8639 (ptt180) REVERT: F 396 ASP cc_start: 0.8423 (p0) cc_final: 0.7705 (p0) REVERT: F 463 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.6654 (mmtt) REVERT: G 156 GLN cc_start: 0.8532 (mp-120) cc_final: 0.7399 (tt0) REVERT: G 396 ASP cc_start: 0.8298 (p0) cc_final: 0.7716 (p0) REVERT: H 79 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8322 (ttt180) REVERT: H 94 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7406 (tp30) REVERT: H 180 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8186 (mp) REVERT: H 216 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7570 (m-30) REVERT: H 396 ASP cc_start: 0.8430 (p0) cc_final: 0.7719 (p0) REVERT: H 463 LYS cc_start: 0.7693 (ptpp) cc_final: 0.6623 (mmtt) REVERT: I 8 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.8050 (t0) REVERT: I 28 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6817 (mtm-85) REVERT: I 29 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6621 (mt-10) REVERT: J 8 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.8042 (t0) REVERT: J 28 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.6809 (mtm-85) REVERT: J 29 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6631 (mt-10) REVERT: K 7 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7771 (mm) REVERT: K 8 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.8149 (t0) REVERT: K 29 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6673 (mt-10) REVERT: L 29 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6655 (mt-10) outliers start: 233 outliers final: 72 residues processed: 493 average time/residue: 1.5919 time to fit residues: 928.5896 Evaluate side-chains 378 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 267 time to evaluate : 3.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 70 LEU Chi-restraints excluded: chain 1 residue 132 SER Chi-restraints excluded: chain 1 residue 134 PHE Chi-restraints excluded: chain 2 residue 70 LEU Chi-restraints excluded: chain 2 residue 98 ASN Chi-restraints excluded: chain 2 residue 133 THR Chi-restraints excluded: chain 2 residue 134 PHE Chi-restraints excluded: chain 3 residue 69 SER Chi-restraints excluded: chain 3 residue 70 LEU Chi-restraints excluded: chain 3 residue 127 ILE Chi-restraints excluded: chain 3 residue 134 PHE Chi-restraints excluded: chain 4 residue 70 LEU Chi-restraints excluded: chain 4 residue 81 VAL Chi-restraints excluded: chain 4 residue 113 LYS Chi-restraints excluded: chain 4 residue 127 ILE Chi-restraints excluded: chain 4 residue 133 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 358 ARG Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain C residue 192 CYS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 444 ILE Chi-restraints excluded: chain C residue 466 LYS Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 463 LYS Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 192 CYS Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 439 ARG Chi-restraints excluded: chain E residue 450 LYS Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain F residue 295 ARG Chi-restraints excluded: chain F residue 347 ASP Chi-restraints excluded: chain F residue 444 ILE Chi-restraints excluded: chain F residue 463 LYS Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 192 CYS Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 450 LYS Chi-restraints excluded: chain G residue 474 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 347 ASP Chi-restraints excluded: chain H residue 444 ILE Chi-restraints excluded: chain I residue 8 ASP Chi-restraints excluded: chain I residue 28 ARG Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 107 GLN Chi-restraints excluded: chain J residue 8 ASP Chi-restraints excluded: chain J residue 28 ARG Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain J residue 107 GLN Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 100 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 70 optimal weight: 9.9990 chunk 265 optimal weight: 3.9990 chunk 364 optimal weight: 10.0000 chunk 227 optimal weight: 0.9990 chunk 171 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 179 optimal weight: 9.9990 chunk 384 optimal weight: 5.9990 chunk 310 optimal weight: 0.0020 chunk 430 optimal weight: 10.0000 chunk 202 optimal weight: 1.9990 overall best weight: 2.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 HIS D 327 HIS F 327 HIS I 25 GLN J 25 GLN J 104 ASN K 25 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.115984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.095305 restraints weight = 46725.845| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.78 r_work: 0.3014 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35343 Z= 0.147 Angle : 0.617 7.046 47892 Z= 0.329 Chirality : 0.045 0.178 5056 Planarity : 0.005 0.064 6272 Dihedral : 6.873 58.957 4957 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.05 % Favored : 92.72 % Rotamer: Outliers : 5.53 % Allowed : 21.30 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.12), residues: 4328 helix: 1.21 (0.14), residues: 1500 sheet: -0.83 (0.20), residues: 672 loop : -2.67 (0.11), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 214 HIS 0.005 0.001 HIS 2 96 PHE 0.028 0.002 PHE G 345 TYR 0.019 0.001 TYR J 80 ARG 0.005 0.000 ARG K 83 Details of bonding type rmsd hydrogen bonds : bond 0.06486 ( 1176) hydrogen bonds : angle 4.18163 ( 3303) covalent geometry : bond 0.00326 (35340) covalent geometry : angle 0.61654 (47892) Misc. bond : bond 0.00135 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8656 Ramachandran restraints generated. 4328 Oldfield, 0 Emsley, 4328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8656 Ramachandran restraints generated. 4328 Oldfield, 0 Emsley, 4328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 286 time to evaluate : 5.138 Fit side-chains REVERT: 1 80 CYS cc_start: 0.7551 (p) cc_final: 0.7332 (m) REVERT: 1 91 VAL cc_start: 0.7115 (t) cc_final: 0.6894 (p) REVERT: 1 132 SER cc_start: 0.7792 (t) cc_final: 0.7341 (p) REVERT: 2 98 ASN cc_start: 0.7282 (OUTLIER) cc_final: 0.7052 (t0) REVERT: 2 115 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6409 (mt-10) REVERT: 2 133 THR cc_start: 0.7333 (OUTLIER) cc_final: 0.7066 (m) REVERT: 3 132 SER cc_start: 0.7347 (t) cc_final: 0.7079 (p) REVERT: 4 91 VAL cc_start: 0.7122 (t) cc_final: 0.6914 (p) REVERT: 4 133 THR cc_start: 0.7623 (OUTLIER) cc_final: 0.7181 (p) REVERT: A 156 GLN cc_start: 0.8479 (mp-120) cc_final: 0.7246 (tt0) REVERT: A 396 ASP cc_start: 0.8309 (p0) cc_final: 0.7687 (p0) REVERT: B 79 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8277 (ttt180) REVERT: B 94 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7376 (tp30) REVERT: B 139 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8709 (tmm160) REVERT: B 175 LYS cc_start: 0.6046 (OUTLIER) cc_final: 0.5528 (mtpp) REVERT: B 177 LYS cc_start: 0.6295 (OUTLIER) cc_final: 0.5662 (mmmt) REVERT: B 180 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8218 (mp) REVERT: B 295 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8594 (ptt180) REVERT: B 357 ASP cc_start: 0.8267 (t0) cc_final: 0.7913 (t70) REVERT: B 396 ASP cc_start: 0.8473 (p0) cc_final: 0.7702 (p0) REVERT: B 463 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.6809 (mmtt) REVERT: C 156 GLN cc_start: 0.8496 (mp-120) cc_final: 0.7261 (tt0) REVERT: C 396 ASP cc_start: 0.8302 (p0) cc_final: 0.7730 (p0) REVERT: C 466 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7780 (mttm) REVERT: D 180 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.7993 (mp) REVERT: D 295 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8610 (ptt180) REVERT: D 357 ASP cc_start: 0.8514 (t0) cc_final: 0.8290 (t70) REVERT: D 358 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7769 (mmt-90) REVERT: D 396 ASP cc_start: 0.8432 (p0) cc_final: 0.7655 (p0) REVERT: D 463 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.6629 (mmtt) REVERT: E 156 GLN cc_start: 0.8467 (mp-120) cc_final: 0.7236 (tt0) REVERT: E 396 ASP cc_start: 0.8339 (p0) cc_final: 0.7685 (p0) REVERT: E 463 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8375 (ttpp) REVERT: F 94 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7394 (tp30) REVERT: F 127 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7324 (t80) REVERT: F 139 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.8640 (tmm160) REVERT: F 180 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.7981 (mp) REVERT: F 295 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8602 (ptt180) REVERT: F 357 ASP cc_start: 0.8508 (t0) cc_final: 0.8285 (t70) REVERT: F 358 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7769 (mmt-90) REVERT: F 396 ASP cc_start: 0.8420 (p0) cc_final: 0.7645 (p0) REVERT: F 463 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.6615 (mmtt) REVERT: G 156 GLN cc_start: 0.8482 (mp-120) cc_final: 0.7245 (tt0) REVERT: G 396 ASP cc_start: 0.8286 (p0) cc_final: 0.7676 (p0) REVERT: G 466 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7787 (mttm) REVERT: H 79 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8235 (ttt180) REVERT: H 94 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7372 (tp30) REVERT: H 127 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7515 (t80) REVERT: H 139 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.8491 (tmm160) REVERT: H 180 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8071 (mp) REVERT: H 357 ASP cc_start: 0.8518 (t0) cc_final: 0.8310 (t70) REVERT: H 358 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7749 (mmt-90) REVERT: H 396 ASP cc_start: 0.8452 (p0) cc_final: 0.7698 (p0) REVERT: H 463 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.6588 (mmtt) REVERT: I 8 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7954 (t0) REVERT: I 28 ARG cc_start: 0.7061 (OUTLIER) cc_final: 0.6714 (mtt180) REVERT: I 29 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6448 (mt-10) REVERT: I 86 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7031 (mp0) REVERT: J 8 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7990 (t0) REVERT: J 28 ARG cc_start: 0.7061 (OUTLIER) cc_final: 0.6717 (mtt180) REVERT: J 29 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6461 (mt-10) REVERT: J 31 ASP cc_start: 0.8525 (m-30) cc_final: 0.8316 (m-30) REVERT: J 86 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7032 (mp0) REVERT: K 7 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7467 (mm) REVERT: K 29 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6493 (mt-10) REVERT: L 37 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7491 (mttt) outliers start: 197 outliers final: 65 residues processed: 457 average time/residue: 2.5691 time to fit residues: 1383.9881 Evaluate side-chains 373 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 265 time to evaluate : 3.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 70 LEU Chi-restraints excluded: chain 1 residue 81 VAL Chi-restraints excluded: chain 1 residue 94 ILE Chi-restraints excluded: chain 1 residue 98 ASN Chi-restraints excluded: chain 1 residue 134 PHE Chi-restraints excluded: chain 2 residue 65 THR Chi-restraints excluded: chain 2 residue 70 LEU Chi-restraints excluded: chain 2 residue 94 ILE Chi-restraints excluded: chain 2 residue 98 ASN Chi-restraints excluded: chain 2 residue 133 THR Chi-restraints excluded: chain 2 residue 134 PHE Chi-restraints excluded: chain 3 residue 70 LEU Chi-restraints excluded: chain 3 residue 81 VAL Chi-restraints excluded: chain 3 residue 94 ILE Chi-restraints excluded: chain 3 residue 134 PHE Chi-restraints excluded: chain 4 residue 70 LEU Chi-restraints excluded: chain 4 residue 81 VAL Chi-restraints excluded: chain 4 residue 94 ILE Chi-restraints excluded: chain 4 residue 133 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 466 LYS Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 358 ARG Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 452 SER Chi-restraints excluded: chain D residue 463 LYS Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 463 LYS Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 295 ARG Chi-restraints excluded: chain F residue 358 ARG Chi-restraints excluded: chain F residue 444 ILE Chi-restraints excluded: chain F residue 463 LYS Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 466 LYS Chi-restraints excluded: chain G residue 474 THR Chi-restraints excluded: chain H residue 14 LYS Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 139 ARG Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 358 ARG Chi-restraints excluded: chain H residue 444 ILE Chi-restraints excluded: chain H residue 463 LYS Chi-restraints excluded: chain I residue 8 ASP Chi-restraints excluded: chain I residue 28 ARG Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 107 GLN Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 8 ASP Chi-restraints excluded: chain J residue 28 ARG Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 37 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 297 optimal weight: 5.9990 chunk 313 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 215 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 165 optimal weight: 2.9990 chunk 217 optimal weight: 10.0000 chunk 184 optimal weight: 7.9990 chunk 240 optimal weight: 8.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 327 HIS I 25 GLN J 25 GLN K 2 GLN K 25 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.112260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.091177 restraints weight = 46877.338| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.81 r_work: 0.2937 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 35343 Z= 0.204 Angle : 0.710 9.365 47892 Z= 0.378 Chirality : 0.049 0.225 5056 Planarity : 0.006 0.074 6272 Dihedral : 6.885 59.499 4938 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.72 % Favored : 92.05 % Rotamer: Outliers : 5.39 % Allowed : 21.16 % Favored : 73.46 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.12), residues: 4328 helix: 1.12 (0.13), residues: 1516 sheet: -0.58 (0.21), residues: 592 loop : -2.70 (0.11), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 214 HIS 0.007 0.002 HIS H 292 PHE 0.032 0.002 PHE G 345 TYR 0.015 0.002 TYR L 80 ARG 0.005 0.001 ARG K 83 Details of bonding type rmsd hydrogen bonds : bond 0.08507 ( 1176) hydrogen bonds : angle 4.21015 ( 3303) covalent geometry : bond 0.00477 (35340) covalent geometry : angle 0.70971 (47892) Misc. bond : bond 0.00710 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8656 Ramachandran restraints generated. 4328 Oldfield, 0 Emsley, 4328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8656 Ramachandran restraints generated. 4328 Oldfield, 0 Emsley, 4328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 268 time to evaluate : 3.739 Fit side-chains revert: symmetry clash REVERT: 1 91 VAL cc_start: 0.7173 (t) cc_final: 0.6944 (p) REVERT: 1 132 SER cc_start: 0.7774 (t) cc_final: 0.7557 (p) REVERT: 3 132 SER cc_start: 0.7228 (t) cc_final: 0.6819 (p) REVERT: 4 91 VAL cc_start: 0.7198 (t) cc_final: 0.6984 (p) REVERT: 4 102 LYS cc_start: 0.6007 (OUTLIER) cc_final: 0.5739 (mmtm) REVERT: A 156 GLN cc_start: 0.8514 (mp-120) cc_final: 0.7270 (tt0) REVERT: A 177 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7230 (ptmt) REVERT: A 396 ASP cc_start: 0.8373 (p0) cc_final: 0.7837 (p0) REVERT: A 466 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7703 (mttm) REVERT: B 79 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8280 (ttt180) REVERT: B 94 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7389 (tp30) REVERT: B 127 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7235 (t80) REVERT: B 139 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.8836 (tmm160) REVERT: B 167 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.6849 (ppt170) REVERT: B 175 LYS cc_start: 0.6019 (OUTLIER) cc_final: 0.5475 (mtpp) REVERT: B 177 LYS cc_start: 0.6505 (OUTLIER) cc_final: 0.5684 (mmmt) REVERT: B 180 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8182 (mp) REVERT: B 295 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.8583 (ptt180) REVERT: B 357 ASP cc_start: 0.8333 (t0) cc_final: 0.8059 (t70) REVERT: B 396 ASP cc_start: 0.8526 (p0) cc_final: 0.7832 (p0) REVERT: B 455 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7398 (tp) REVERT: B 463 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.6853 (mmtt) REVERT: C 156 GLN cc_start: 0.8514 (mp-120) cc_final: 0.7273 (tt0) REVERT: C 177 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7144 (ptmt) REVERT: C 396 ASP cc_start: 0.8375 (p0) cc_final: 0.7837 (p0) REVERT: C 439 ARG cc_start: 0.6493 (OUTLIER) cc_final: 0.6114 (mtm110) REVERT: D 167 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.6855 (ppt170) REVERT: D 295 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8592 (ptt180) REVERT: D 357 ASP cc_start: 0.8513 (t0) cc_final: 0.8308 (t70) REVERT: D 358 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7753 (mmt-90) REVERT: D 396 ASP cc_start: 0.8534 (p0) cc_final: 0.7839 (p0) REVERT: D 463 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.6664 (mmtt) REVERT: E 156 GLN cc_start: 0.8496 (mp-120) cc_final: 0.7262 (tt0) REVERT: E 396 ASP cc_start: 0.8387 (p0) cc_final: 0.7863 (p0) REVERT: E 463 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8260 (ttpp) REVERT: F 77 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7750 (tp) REVERT: F 94 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7423 (tp30) REVERT: F 127 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.7371 (t80) REVERT: F 139 ARG cc_start: 0.9155 (OUTLIER) cc_final: 0.8605 (tmm160) REVERT: F 167 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.6899 (ppt170) REVERT: F 295 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8573 (ptt180) REVERT: F 357 ASP cc_start: 0.8504 (t0) cc_final: 0.8301 (t70) REVERT: F 358 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7750 (mmt-90) REVERT: F 396 ASP cc_start: 0.8510 (p0) cc_final: 0.7826 (p0) REVERT: F 463 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.6659 (mmtt) REVERT: G 156 GLN cc_start: 0.8535 (mp-120) cc_final: 0.7298 (tt0) REVERT: G 396 ASP cc_start: 0.8333 (p0) cc_final: 0.7797 (p0) REVERT: H 79 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8280 (ttt180) REVERT: H 94 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7401 (tp30) REVERT: H 127 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7594 (t80) REVERT: H 139 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.8599 (tmm160) REVERT: H 167 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.6874 (ppt170) REVERT: H 180 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8139 (mp) REVERT: H 357 ASP cc_start: 0.8518 (t0) cc_final: 0.8311 (t70) REVERT: H 358 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7738 (mmt-90) REVERT: H 396 ASP cc_start: 0.8526 (p0) cc_final: 0.7850 (p0) REVERT: H 463 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.6671 (mmtt) REVERT: I 28 ARG cc_start: 0.7004 (OUTLIER) cc_final: 0.6661 (mtt180) REVERT: I 86 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: J 8 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.8009 (t0) REVERT: J 28 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.6617 (mtt180) REVERT: J 31 ASP cc_start: 0.8600 (m-30) cc_final: 0.8370 (m-30) REVERT: J 86 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: K 7 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7546 (mm) REVERT: L 29 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6438 (mt-10) REVERT: L 37 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7644 (mttt) outliers start: 192 outliers final: 84 residues processed: 430 average time/residue: 1.7210 time to fit residues: 865.0199 Evaluate side-chains 384 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 255 time to evaluate : 3.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 70 LEU Chi-restraints excluded: chain 1 residue 81 VAL Chi-restraints excluded: chain 1 residue 94 ILE Chi-restraints excluded: chain 1 residue 98 ASN Chi-restraints excluded: chain 1 residue 133 THR Chi-restraints excluded: chain 1 residue 134 PHE Chi-restraints excluded: chain 2 residue 65 THR Chi-restraints excluded: chain 2 residue 70 LEU Chi-restraints excluded: chain 2 residue 94 ILE Chi-restraints excluded: chain 2 residue 133 THR Chi-restraints excluded: chain 2 residue 134 PHE Chi-restraints excluded: chain 3 residue 70 LEU Chi-restraints excluded: chain 3 residue 81 VAL Chi-restraints excluded: chain 3 residue 94 ILE Chi-restraints excluded: chain 3 residue 133 THR Chi-restraints excluded: chain 3 residue 134 PHE Chi-restraints excluded: chain 4 residue 70 LEU Chi-restraints excluded: chain 4 residue 81 VAL Chi-restraints excluded: chain 4 residue 94 ILE Chi-restraints excluded: chain 4 residue 102 LYS Chi-restraints excluded: chain 4 residue 133 THR Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 466 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 167 ARG Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 358 ARG Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 452 SER Chi-restraints excluded: chain D residue 463 LYS Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 463 LYS Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 167 ARG Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 295 ARG Chi-restraints excluded: chain F residue 347 ASP Chi-restraints excluded: chain F residue 358 ARG Chi-restraints excluded: chain F residue 444 ILE Chi-restraints excluded: chain F residue 463 LYS Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 474 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 139 ARG Chi-restraints excluded: chain H residue 167 ARG Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 175 LYS Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 347 ASP Chi-restraints excluded: chain H residue 358 ARG Chi-restraints excluded: chain H residue 444 ILE Chi-restraints excluded: chain H residue 463 LYS Chi-restraints excluded: chain I residue 8 ASP Chi-restraints excluded: chain I residue 28 ARG Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 107 GLN Chi-restraints excluded: chain J residue 8 ASP Chi-restraints excluded: chain J residue 28 ARG Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 86 GLU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain L residue 111 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 259 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 246 optimal weight: 0.0000 chunk 175 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 306 optimal weight: 4.9990 chunk 132 optimal weight: 0.1980 chunk 325 optimal weight: 10.0000 chunk 263 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 overall best weight: 3.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 25 GLN J 25 GLN K 25 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.112835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.091596 restraints weight = 47025.769| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.85 r_work: 0.2936 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 35343 Z= 0.164 Angle : 0.632 7.736 47892 Z= 0.337 Chirality : 0.046 0.186 5056 Planarity : 0.006 0.063 6272 Dihedral : 6.588 59.185 4936 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.84 % Favored : 92.93 % Rotamer: Outliers : 5.53 % Allowed : 20.99 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.12), residues: 4328 helix: 1.35 (0.14), residues: 1504 sheet: -0.45 (0.20), residues: 668 loop : -2.60 (0.11), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 214 HIS 0.006 0.001 HIS F 292 PHE 0.028 0.002 PHE G 345 TYR 0.013 0.001 TYR H 80 ARG 0.004 0.000 ARG K 83 Details of bonding type rmsd hydrogen bonds : bond 0.06934 ( 1176) hydrogen bonds : angle 4.04419 ( 3303) covalent geometry : bond 0.00375 (35340) covalent geometry : angle 0.63222 (47892) Misc. bond : bond 0.00297 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8656 Ramachandran restraints generated. 4328 Oldfield, 0 Emsley, 4328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8656 Ramachandran restraints generated. 4328 Oldfield, 0 Emsley, 4328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 263 time to evaluate : 3.769 Fit side-chains revert: symmetry clash REVERT: 1 91 VAL cc_start: 0.7129 (t) cc_final: 0.6880 (p) REVERT: 1 132 SER cc_start: 0.7710 (t) cc_final: 0.7205 (p) REVERT: 2 91 VAL cc_start: 0.7129 (t) cc_final: 0.6781 (p) REVERT: 3 102 LYS cc_start: 0.6081 (OUTLIER) cc_final: 0.5767 (mmtm) REVERT: 4 91 VAL cc_start: 0.7150 (t) cc_final: 0.6916 (p) REVERT: A 156 GLN cc_start: 0.8469 (mp-120) cc_final: 0.7191 (tt0) REVERT: A 177 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7202 (ptmt) REVERT: A 396 ASP cc_start: 0.8321 (p0) cc_final: 0.7656 (p0) REVERT: B 79 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8252 (ttt180) REVERT: B 94 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7411 (tp30) REVERT: B 127 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.7211 (t80) REVERT: B 139 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8673 (tmm160) REVERT: B 167 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.6815 (ppt170) REVERT: B 177 LYS cc_start: 0.6455 (OUTLIER) cc_final: 0.5733 (mmmt) REVERT: B 295 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8598 (ptt180) REVERT: B 357 ASP cc_start: 0.8361 (t0) cc_final: 0.8059 (t70) REVERT: B 396 ASP cc_start: 0.8455 (p0) cc_final: 0.7691 (p0) REVERT: B 463 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.6812 (mmtt) REVERT: C 156 GLN cc_start: 0.8477 (mp-120) cc_final: 0.7189 (tt0) REVERT: C 177 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7098 (ptmt) REVERT: C 396 ASP cc_start: 0.8340 (p0) cc_final: 0.7670 (p0) REVERT: C 439 ARG cc_start: 0.6427 (OUTLIER) cc_final: 0.6106 (mtm110) REVERT: D 167 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.6830 (ppt170) REVERT: D 180 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8001 (mp) REVERT: D 295 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8618 (ptt180) REVERT: D 357 ASP cc_start: 0.8472 (t0) cc_final: 0.8209 (t70) REVERT: D 358 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7707 (mmt-90) REVERT: D 396 ASP cc_start: 0.8483 (p0) cc_final: 0.7723 (p0) REVERT: D 450 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.6946 (mptm) REVERT: D 463 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.6638 (mmtt) REVERT: E 156 GLN cc_start: 0.8460 (mp-120) cc_final: 0.7181 (tt0) REVERT: E 396 ASP cc_start: 0.8360 (p0) cc_final: 0.7697 (p0) REVERT: E 463 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8183 (ttpp) REVERT: F 77 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7726 (tp) REVERT: F 94 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7421 (tp30) REVERT: F 127 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7416 (t80) REVERT: F 139 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.8678 (tmm160) REVERT: F 167 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.6846 (ppt170) REVERT: F 180 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8028 (mp) REVERT: F 295 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.8597 (ptt180) REVERT: F 357 ASP cc_start: 0.8472 (t0) cc_final: 0.8214 (t70) REVERT: F 358 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7715 (mmt-90) REVERT: F 396 ASP cc_start: 0.8441 (p0) cc_final: 0.7672 (p0) REVERT: F 463 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.6637 (mmtt) REVERT: G 156 GLN cc_start: 0.8482 (mp-120) cc_final: 0.7208 (tt0) REVERT: G 396 ASP cc_start: 0.8322 (p0) cc_final: 0.7729 (p0) REVERT: H 79 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8231 (ttt180) REVERT: H 94 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7430 (tp30) REVERT: H 127 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.7600 (t80) REVERT: H 167 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.6834 (ppt170) REVERT: H 175 LYS cc_start: 0.6013 (OUTLIER) cc_final: 0.5545 (mmtt) REVERT: H 180 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8100 (mp) REVERT: H 295 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8654 (ptt180) REVERT: H 357 ASP cc_start: 0.8475 (t0) cc_final: 0.8188 (t70) REVERT: H 358 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7688 (mmt-90) REVERT: H 396 ASP cc_start: 0.8449 (p0) cc_final: 0.7679 (p0) REVERT: H 463 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.6636 (mmtt) REVERT: I 28 ARG cc_start: 0.6811 (OUTLIER) cc_final: 0.6480 (mtt180) REVERT: I 86 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: J 28 ARG cc_start: 0.6828 (OUTLIER) cc_final: 0.6510 (mtt180) REVERT: J 31 ASP cc_start: 0.8555 (m-30) cc_final: 0.8278 (m-30) REVERT: J 86 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: L 29 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6371 (mt-10) REVERT: L 37 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7443 (mttt) outliers start: 197 outliers final: 89 residues processed: 434 average time/residue: 1.6962 time to fit residues: 869.2087 Evaluate side-chains 387 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 255 time to evaluate : 3.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 70 LEU Chi-restraints excluded: chain 1 residue 81 VAL Chi-restraints excluded: chain 1 residue 94 ILE Chi-restraints excluded: chain 1 residue 98 ASN Chi-restraints excluded: chain 1 residue 133 THR Chi-restraints excluded: chain 1 residue 134 PHE Chi-restraints excluded: chain 2 residue 70 LEU Chi-restraints excluded: chain 2 residue 81 VAL Chi-restraints excluded: chain 2 residue 94 ILE Chi-restraints excluded: chain 2 residue 133 THR Chi-restraints excluded: chain 2 residue 134 PHE Chi-restraints excluded: chain 3 residue 70 LEU Chi-restraints excluded: chain 3 residue 94 ILE Chi-restraints excluded: chain 3 residue 102 LYS Chi-restraints excluded: chain 3 residue 133 THR Chi-restraints excluded: chain 3 residue 134 PHE Chi-restraints excluded: chain 4 residue 65 THR Chi-restraints excluded: chain 4 residue 70 LEU Chi-restraints excluded: chain 4 residue 81 VAL Chi-restraints excluded: chain 4 residue 94 ILE Chi-restraints excluded: chain 4 residue 133 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 358 ARG Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 167 ARG Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 358 ARG Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 463 LYS Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 463 LYS Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 167 ARG Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 227 LYS Chi-restraints excluded: chain F residue 295 ARG Chi-restraints excluded: chain F residue 347 ASP Chi-restraints excluded: chain F residue 358 ARG Chi-restraints excluded: chain F residue 444 ILE Chi-restraints excluded: chain F residue 463 LYS Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 464 GLU Chi-restraints excluded: chain G residue 474 THR Chi-restraints excluded: chain G residue 475 LEU Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 167 ARG Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 175 LYS Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain H residue 295 ARG Chi-restraints excluded: chain H residue 347 ASP Chi-restraints excluded: chain H residue 358 ARG Chi-restraints excluded: chain H residue 444 ILE Chi-restraints excluded: chain H residue 463 LYS Chi-restraints excluded: chain I residue 8 ASP Chi-restraints excluded: chain I residue 28 ARG Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 107 GLN Chi-restraints excluded: chain J residue 8 ASP Chi-restraints excluded: chain J residue 28 ARG Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 86 GLU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 111 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 109 optimal weight: 6.9990 chunk 344 optimal weight: 7.9990 chunk 409 optimal weight: 7.9990 chunk 276 optimal weight: 0.0870 chunk 216 optimal weight: 3.9990 chunk 210 optimal weight: 4.9990 chunk 179 optimal weight: 0.9980 chunk 342 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 303 optimal weight: 0.0570 chunk 132 optimal weight: 4.9990 overall best weight: 1.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 5 ASN I 25 GLN J 25 GLN K 25 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.115895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.094721 restraints weight = 46845.526| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.85 r_work: 0.2981 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 35343 Z= 0.114 Angle : 0.556 6.632 47892 Z= 0.295 Chirality : 0.043 0.172 5056 Planarity : 0.005 0.059 6272 Dihedral : 6.153 58.581 4936 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.24 % Favored : 93.53 % Rotamer: Outliers : 4.80 % Allowed : 22.05 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.13), residues: 4328 helix: 1.59 (0.14), residues: 1512 sheet: -0.30 (0.19), residues: 704 loop : -2.39 (0.12), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 214 HIS 0.004 0.001 HIS D 238 PHE 0.026 0.001 PHE G 345 TYR 0.010 0.001 TYR H 80 ARG 0.006 0.000 ARG J 83 Details of bonding type rmsd hydrogen bonds : bond 0.05013 ( 1176) hydrogen bonds : angle 3.82654 ( 3303) covalent geometry : bond 0.00245 (35340) covalent geometry : angle 0.55575 (47892) Misc. bond : bond 0.00191 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8656 Ramachandran restraints generated. 4328 Oldfield, 0 Emsley, 4328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8656 Ramachandran restraints generated. 4328 Oldfield, 0 Emsley, 4328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 290 time to evaluate : 3.658 Fit side-chains revert: symmetry clash REVERT: 1 91 VAL cc_start: 0.7165 (t) cc_final: 0.6908 (p) REVERT: 1 132 SER cc_start: 0.7691 (t) cc_final: 0.7234 (p) REVERT: 2 91 VAL cc_start: 0.7119 (t) cc_final: 0.6772 (p) REVERT: 4 91 VAL cc_start: 0.7182 (t) cc_final: 0.6923 (p) REVERT: A 156 GLN cc_start: 0.8412 (mp-120) cc_final: 0.7125 (tt0) REVERT: A 396 ASP cc_start: 0.8309 (p0) cc_final: 0.7669 (p0) REVERT: B 79 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8174 (ttt180) REVERT: B 127 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.7196 (t80) REVERT: B 139 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.8617 (tmm160) REVERT: B 177 LYS cc_start: 0.6373 (OUTLIER) cc_final: 0.5707 (mmmt) REVERT: B 295 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8612 (ptt180) REVERT: B 357 ASP cc_start: 0.8328 (t0) cc_final: 0.7936 (t70) REVERT: B 396 ASP cc_start: 0.8447 (p0) cc_final: 0.7694 (p0) REVERT: B 463 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.6819 (mmtt) REVERT: C 156 GLN cc_start: 0.8433 (mp-120) cc_final: 0.7144 (tt0) REVERT: C 396 ASP cc_start: 0.8289 (p0) cc_final: 0.7690 (p0) REVERT: C 439 ARG cc_start: 0.6367 (OUTLIER) cc_final: 0.5997 (mtm110) REVERT: D 180 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7932 (mp) REVERT: D 295 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.8602 (ptt180) REVERT: D 357 ASP cc_start: 0.8496 (t0) cc_final: 0.8192 (t70) REVERT: D 358 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7684 (mmt-90) REVERT: D 396 ASP cc_start: 0.8430 (p0) cc_final: 0.7685 (p0) REVERT: D 450 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.6938 (mptm) REVERT: D 463 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.6648 (mmtt) REVERT: E 156 GLN cc_start: 0.8410 (mp-120) cc_final: 0.7122 (tt0) REVERT: E 396 ASP cc_start: 0.8304 (p0) cc_final: 0.7687 (p0) REVERT: E 463 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8141 (ttpp) REVERT: F 127 PHE cc_start: 0.8319 (OUTLIER) cc_final: 0.7328 (t80) REVERT: F 180 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.7970 (mp) REVERT: F 295 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8612 (ptt180) REVERT: F 357 ASP cc_start: 0.8481 (t0) cc_final: 0.8187 (t70) REVERT: F 358 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7695 (mmt-90) REVERT: F 396 ASP cc_start: 0.8414 (p0) cc_final: 0.7657 (p0) REVERT: F 463 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.6603 (mmtt) REVERT: G 128 LYS cc_start: 0.8719 (mttp) cc_final: 0.8485 (mtmt) REVERT: G 156 GLN cc_start: 0.8435 (mp-120) cc_final: 0.7153 (tt0) REVERT: G 396 ASP cc_start: 0.8256 (p0) cc_final: 0.7696 (p0) REVERT: H 94 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7385 (tp30) REVERT: H 127 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.7501 (t80) REVERT: H 175 LYS cc_start: 0.5994 (OUTLIER) cc_final: 0.5489 (mtpm) REVERT: H 180 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8062 (mp) REVERT: H 357 ASP cc_start: 0.8504 (t0) cc_final: 0.8194 (t70) REVERT: H 358 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7652 (mmt-90) REVERT: H 396 ASP cc_start: 0.8439 (p0) cc_final: 0.7687 (p0) REVERT: H 463 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.6592 (mmtt) REVERT: I 28 ARG cc_start: 0.6798 (OUTLIER) cc_final: 0.6483 (mtt180) REVERT: I 86 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.6923 (mp0) REVERT: J 28 ARG cc_start: 0.6769 (OUTLIER) cc_final: 0.6496 (mtt180) REVERT: J 31 ASP cc_start: 0.8521 (m-30) cc_final: 0.8206 (m-30) REVERT: J 86 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6956 (mp0) REVERT: K 7 ILE cc_start: 0.7403 (OUTLIER) cc_final: 0.6953 (mm) REVERT: K 29 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6304 (mt-10) REVERT: K 86 GLU cc_start: 0.7686 (tp30) cc_final: 0.7482 (tt0) REVERT: L 29 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6303 (mt-10) REVERT: L 37 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.7271 (mttt) outliers start: 171 outliers final: 81 residues processed: 434 average time/residue: 1.5895 time to fit residues: 814.8067 Evaluate side-chains 389 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 276 time to evaluate : 3.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 70 LEU Chi-restraints excluded: chain 1 residue 81 VAL Chi-restraints excluded: chain 1 residue 94 ILE Chi-restraints excluded: chain 1 residue 134 PHE Chi-restraints excluded: chain 2 residue 70 LEU Chi-restraints excluded: chain 2 residue 81 VAL Chi-restraints excluded: chain 2 residue 94 ILE Chi-restraints excluded: chain 2 residue 133 THR Chi-restraints excluded: chain 2 residue 134 PHE Chi-restraints excluded: chain 3 residue 70 LEU Chi-restraints excluded: chain 3 residue 81 VAL Chi-restraints excluded: chain 3 residue 94 ILE Chi-restraints excluded: chain 3 residue 134 PHE Chi-restraints excluded: chain 4 residue 65 THR Chi-restraints excluded: chain 4 residue 70 LEU Chi-restraints excluded: chain 4 residue 81 VAL Chi-restraints excluded: chain 4 residue 94 ILE Chi-restraints excluded: chain 4 residue 98 ASN Chi-restraints excluded: chain 4 residue 133 THR Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 358 ARG Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 358 ARG Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 452 SER Chi-restraints excluded: chain D residue 463 LYS Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 463 LYS Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 295 ARG Chi-restraints excluded: chain F residue 347 ASP Chi-restraints excluded: chain F residue 358 ARG Chi-restraints excluded: chain F residue 444 ILE Chi-restraints excluded: chain F residue 463 LYS Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 464 GLU Chi-restraints excluded: chain G residue 474 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 175 LYS Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 347 ASP Chi-restraints excluded: chain H residue 358 ARG Chi-restraints excluded: chain H residue 444 ILE Chi-restraints excluded: chain H residue 463 LYS Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 8 ASP Chi-restraints excluded: chain I residue 28 ARG Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 107 GLN Chi-restraints excluded: chain J residue 28 ARG Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 107 GLN Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain L residue 111 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 394 optimal weight: 9.9990 chunk 251 optimal weight: 6.9990 chunk 386 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 398 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 425 optimal weight: 6.9990 chunk 121 optimal weight: 0.7980 chunk 69 optimal weight: 7.9990 chunk 204 optimal weight: 9.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 45 GLN I 25 GLN J 25 GLN K 25 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.112311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.090993 restraints weight = 47195.468| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.85 r_work: 0.2926 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 35343 Z= 0.177 Angle : 0.648 8.215 47892 Z= 0.344 Chirality : 0.047 0.189 5056 Planarity : 0.006 0.064 6272 Dihedral : 6.251 57.554 4933 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.28 % Favored : 92.49 % Rotamer: Outliers : 4.83 % Allowed : 22.00 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.12), residues: 4328 helix: 1.47 (0.14), residues: 1512 sheet: -0.29 (0.21), residues: 632 loop : -2.46 (0.11), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 214 HIS 0.006 0.001 HIS H 292 PHE 0.029 0.002 PHE G 345 TYR 0.014 0.002 TYR H 80 ARG 0.005 0.000 ARG I 83 Details of bonding type rmsd hydrogen bonds : bond 0.07375 ( 1176) hydrogen bonds : angle 3.96466 ( 3303) covalent geometry : bond 0.00412 (35340) covalent geometry : angle 0.64824 (47892) Misc. bond : bond 0.00253 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8656 Ramachandran restraints generated. 4328 Oldfield, 0 Emsley, 4328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8656 Ramachandran restraints generated. 4328 Oldfield, 0 Emsley, 4328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 262 time to evaluate : 4.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 132 SER cc_start: 0.7767 (t) cc_final: 0.7225 (p) REVERT: 2 91 VAL cc_start: 0.7131 (t) cc_final: 0.6769 (p) REVERT: 4 91 VAL cc_start: 0.7215 (t) cc_final: 0.6933 (p) REVERT: A 156 GLN cc_start: 0.8476 (mp-120) cc_final: 0.7199 (tt0) REVERT: A 396 ASP cc_start: 0.8339 (p0) cc_final: 0.7773 (p0) REVERT: B 127 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7242 (t80) REVERT: B 139 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8706 (tmm160) REVERT: B 167 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.7075 (ppt170) REVERT: B 177 LYS cc_start: 0.6485 (OUTLIER) cc_final: 0.5755 (mmmt) REVERT: B 295 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8651 (ptt180) REVERT: B 357 ASP cc_start: 0.8387 (t0) cc_final: 0.8079 (t70) REVERT: B 396 ASP cc_start: 0.8472 (p0) cc_final: 0.7696 (p0) REVERT: B 463 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.6817 (mmtt) REVERT: C 156 GLN cc_start: 0.8494 (mp-120) cc_final: 0.7211 (tt0) REVERT: C 177 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7110 (ptmt) REVERT: C 396 ASP cc_start: 0.8362 (p0) cc_final: 0.7797 (p0) REVERT: D 79 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.8138 (ttt180) REVERT: D 167 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.6949 (ppt170) REVERT: D 180 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8032 (mp) REVERT: D 183 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7668 (tttm) REVERT: D 295 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8667 (ptt180) REVERT: D 357 ASP cc_start: 0.8502 (t0) cc_final: 0.8266 (t70) REVERT: D 358 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7708 (mmt-90) REVERT: D 396 ASP cc_start: 0.8480 (p0) cc_final: 0.7713 (p0) REVERT: D 450 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.6952 (mptm) REVERT: D 463 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.6648 (mmtt) REVERT: E 156 GLN cc_start: 0.8475 (mp-120) cc_final: 0.7200 (tt0) REVERT: E 396 ASP cc_start: 0.8374 (p0) cc_final: 0.7803 (p0) REVERT: E 463 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8201 (ttpp) REVERT: F 127 PHE cc_start: 0.8370 (OUTLIER) cc_final: 0.7364 (t80) REVERT: F 139 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.8607 (tmm160) REVERT: F 167 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.6857 (ppt170) REVERT: F 180 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8044 (mp) REVERT: F 183 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7649 (tttm) REVERT: F 295 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8659 (ptt180) REVERT: F 357 ASP cc_start: 0.8515 (t0) cc_final: 0.8285 (t70) REVERT: F 358 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7710 (mmt-90) REVERT: F 396 ASP cc_start: 0.8447 (p0) cc_final: 0.7673 (p0) REVERT: F 463 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.6635 (mmtt) REVERT: G 156 GLN cc_start: 0.8502 (mp-120) cc_final: 0.7229 (tt0) REVERT: G 396 ASP cc_start: 0.8314 (p0) cc_final: 0.7724 (p0) REVERT: H 77 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.6858 (tp) REVERT: H 94 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7403 (tp30) REVERT: H 127 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.7481 (t80) REVERT: H 167 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.7097 (ppt170) REVERT: H 180 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8129 (mp) REVERT: H 295 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8687 (ptt180) REVERT: H 357 ASP cc_start: 0.8502 (t0) cc_final: 0.8257 (t70) REVERT: H 358 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7674 (mmt-90) REVERT: H 396 ASP cc_start: 0.8452 (p0) cc_final: 0.7681 (p0) REVERT: H 463 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.6613 (mmtt) REVERT: I 28 ARG cc_start: 0.6857 (OUTLIER) cc_final: 0.6561 (mtt180) REVERT: I 86 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.6942 (mp0) REVERT: J 28 ARG cc_start: 0.6803 (OUTLIER) cc_final: 0.6582 (mtt180) REVERT: J 31 ASP cc_start: 0.8559 (m-30) cc_final: 0.8189 (m-30) REVERT: J 86 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: K 7 ILE cc_start: 0.7547 (OUTLIER) cc_final: 0.7072 (mm) REVERT: L 29 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6391 (mt-10) REVERT: L 37 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7490 (mttt) outliers start: 172 outliers final: 92 residues processed: 402 average time/residue: 1.6924 time to fit residues: 803.0149 Evaluate side-chains 386 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 255 time to evaluate : 6.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 70 LEU Chi-restraints excluded: chain 1 residue 81 VAL Chi-restraints excluded: chain 1 residue 94 ILE Chi-restraints excluded: chain 1 residue 133 THR Chi-restraints excluded: chain 1 residue 134 PHE Chi-restraints excluded: chain 2 residue 70 LEU Chi-restraints excluded: chain 2 residue 81 VAL Chi-restraints excluded: chain 2 residue 94 ILE Chi-restraints excluded: chain 2 residue 133 THR Chi-restraints excluded: chain 2 residue 134 PHE Chi-restraints excluded: chain 3 residue 70 LEU Chi-restraints excluded: chain 3 residue 81 VAL Chi-restraints excluded: chain 3 residue 94 ILE Chi-restraints excluded: chain 3 residue 127 ILE Chi-restraints excluded: chain 3 residue 133 THR Chi-restraints excluded: chain 3 residue 134 PHE Chi-restraints excluded: chain 4 residue 65 THR Chi-restraints excluded: chain 4 residue 70 LEU Chi-restraints excluded: chain 4 residue 81 VAL Chi-restraints excluded: chain 4 residue 94 ILE Chi-restraints excluded: chain 4 residue 98 ASN Chi-restraints excluded: chain 4 residue 133 THR Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 358 ARG Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 167 ARG Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 358 ARG Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 452 SER Chi-restraints excluded: chain D residue 463 LYS Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 463 LYS Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 167 ARG Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 295 ARG Chi-restraints excluded: chain F residue 347 ASP Chi-restraints excluded: chain F residue 358 ARG Chi-restraints excluded: chain F residue 444 ILE Chi-restraints excluded: chain F residue 463 LYS Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 464 GLU Chi-restraints excluded: chain G residue 474 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 167 ARG Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 175 LYS Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 295 ARG Chi-restraints excluded: chain H residue 347 ASP Chi-restraints excluded: chain H residue 358 ARG Chi-restraints excluded: chain H residue 444 ILE Chi-restraints excluded: chain H residue 463 LYS Chi-restraints excluded: chain I residue 8 ASP Chi-restraints excluded: chain I residue 28 ARG Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 8 ASP Chi-restraints excluded: chain J residue 28 ARG Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 86 GLU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain L residue 111 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 16 optimal weight: 20.0000 chunk 352 optimal weight: 2.9990 chunk 403 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 230 optimal weight: 0.0570 chunk 369 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 225 optimal weight: 10.0000 chunk 237 optimal weight: 5.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 25 GLN J 25 GLN K 25 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.114424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.093181 restraints weight = 46900.884| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.84 r_work: 0.2959 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 35343 Z= 0.131 Angle : 0.587 7.868 47892 Z= 0.311 Chirality : 0.044 0.176 5056 Planarity : 0.005 0.060 6272 Dihedral : 6.054 57.201 4933 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.61 % Favored : 93.16 % Rotamer: Outliers : 4.69 % Allowed : 22.28 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.13), residues: 4328 helix: 1.60 (0.14), residues: 1512 sheet: -0.23 (0.19), residues: 708 loop : -2.40 (0.12), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 214 HIS 0.004 0.001 HIS H 292 PHE 0.027 0.001 PHE G 345 TYR 0.010 0.001 TYR H 80 ARG 0.005 0.000 ARG I 83 Details of bonding type rmsd hydrogen bonds : bond 0.05733 ( 1176) hydrogen bonds : angle 3.83286 ( 3303) covalent geometry : bond 0.00288 (35340) covalent geometry : angle 0.58655 (47892) Misc. bond : bond 0.00185 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8656 Ramachandran restraints generated. 4328 Oldfield, 0 Emsley, 4328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8656 Ramachandran restraints generated. 4328 Oldfield, 0 Emsley, 4328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 270 time to evaluate : 3.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 91 VAL cc_start: 0.7199 (t) cc_final: 0.6905 (p) REVERT: 1 132 SER cc_start: 0.7735 (t) cc_final: 0.7241 (p) REVERT: 2 91 VAL cc_start: 0.7114 (t) cc_final: 0.6747 (p) REVERT: 4 91 VAL cc_start: 0.7212 (t) cc_final: 0.6920 (p) REVERT: A 156 GLN cc_start: 0.8436 (mp-120) cc_final: 0.7155 (tt0) REVERT: A 396 ASP cc_start: 0.8297 (p0) cc_final: 0.7671 (p0) REVERT: B 127 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7204 (t80) REVERT: B 139 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8640 (tmm160) REVERT: B 167 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.7173 (ppt170) REVERT: B 177 LYS cc_start: 0.6440 (OUTLIER) cc_final: 0.5712 (mmmt) REVERT: B 258 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7710 (ttt90) REVERT: B 295 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8636 (ptt180) REVERT: B 357 ASP cc_start: 0.8347 (t0) cc_final: 0.7935 (t70) REVERT: B 396 ASP cc_start: 0.8445 (p0) cc_final: 0.7681 (p0) REVERT: B 463 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.6820 (mmtt) REVERT: C 156 GLN cc_start: 0.8451 (mp-120) cc_final: 0.7170 (tt0) REVERT: C 396 ASP cc_start: 0.8305 (p0) cc_final: 0.7712 (p0) REVERT: C 439 ARG cc_start: 0.6354 (OUTLIER) cc_final: 0.6036 (mtm110) REVERT: D 167 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.7181 (ppt170) REVERT: D 180 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8023 (mp) REVERT: D 258 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7708 (ttt90) REVERT: D 295 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8645 (ptt180) REVERT: D 357 ASP cc_start: 0.8517 (t0) cc_final: 0.8272 (t70) REVERT: D 358 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7679 (mmt-90) REVERT: D 396 ASP cc_start: 0.8438 (p0) cc_final: 0.7684 (p0) REVERT: D 450 LYS cc_start: 0.7449 (OUTLIER) cc_final: 0.6931 (mptm) REVERT: D 463 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.6637 (mmtt) REVERT: E 156 GLN cc_start: 0.8431 (mp-120) cc_final: 0.7154 (tt0) REVERT: E 396 ASP cc_start: 0.8340 (p0) cc_final: 0.7751 (p0) REVERT: E 463 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8177 (ttpp) REVERT: F 127 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.7287 (t80) REVERT: F 139 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8655 (tmm160) REVERT: F 167 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.7193 (ppt170) REVERT: F 180 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8109 (mp) REVERT: F 258 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7717 (ttt90) REVERT: F 295 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8678 (ptt180) REVERT: F 357 ASP cc_start: 0.8518 (t0) cc_final: 0.8203 (t70) REVERT: F 358 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7678 (mmt-90) REVERT: F 396 ASP cc_start: 0.8420 (p0) cc_final: 0.7657 (p0) REVERT: F 463 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.6592 (mmtt) REVERT: G 128 LYS cc_start: 0.8715 (mttp) cc_final: 0.8488 (mttt) REVERT: G 156 GLN cc_start: 0.8452 (mp-120) cc_final: 0.7179 (tt0) REVERT: G 396 ASP cc_start: 0.8279 (p0) cc_final: 0.7654 (p0) REVERT: H 94 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7389 (tp30) REVERT: H 127 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.7446 (t80) REVERT: H 167 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.7186 (ppt170) REVERT: H 180 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8085 (mp) REVERT: H 183 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7525 (tttm) REVERT: H 258 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7712 (ttt90) REVERT: H 295 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.8680 (ptt180) REVERT: H 357 ASP cc_start: 0.8517 (t0) cc_final: 0.8161 (t70) REVERT: H 358 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7638 (mmt-90) REVERT: H 396 ASP cc_start: 0.8441 (p0) cc_final: 0.7678 (p0) REVERT: H 463 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.6587 (mmtt) REVERT: I 28 ARG cc_start: 0.6799 (OUTLIER) cc_final: 0.6524 (mtt180) REVERT: I 86 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6912 (mp0) REVERT: J 31 ASP cc_start: 0.8547 (m-30) cc_final: 0.8241 (m-30) REVERT: J 86 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.6949 (mp0) REVERT: L 29 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6329 (mt-10) REVERT: L 37 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7339 (mttt) outliers start: 167 outliers final: 86 residues processed: 408 average time/residue: 1.7454 time to fit residues: 840.3694 Evaluate side-chains 385 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 261 time to evaluate : 3.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 70 LEU Chi-restraints excluded: chain 1 residue 81 VAL Chi-restraints excluded: chain 1 residue 94 ILE Chi-restraints excluded: chain 1 residue 133 THR Chi-restraints excluded: chain 1 residue 134 PHE Chi-restraints excluded: chain 2 residue 70 LEU Chi-restraints excluded: chain 2 residue 81 VAL Chi-restraints excluded: chain 2 residue 94 ILE Chi-restraints excluded: chain 2 residue 133 THR Chi-restraints excluded: chain 2 residue 134 PHE Chi-restraints excluded: chain 3 residue 70 LEU Chi-restraints excluded: chain 3 residue 81 VAL Chi-restraints excluded: chain 3 residue 94 ILE Chi-restraints excluded: chain 3 residue 133 THR Chi-restraints excluded: chain 3 residue 134 PHE Chi-restraints excluded: chain 4 residue 65 THR Chi-restraints excluded: chain 4 residue 70 LEU Chi-restraints excluded: chain 4 residue 81 VAL Chi-restraints excluded: chain 4 residue 94 ILE Chi-restraints excluded: chain 4 residue 98 ASN Chi-restraints excluded: chain 4 residue 133 THR Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 358 ARG Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 167 ARG Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 258 ARG Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 358 ARG Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 452 SER Chi-restraints excluded: chain D residue 463 LYS Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 463 LYS Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 167 ARG Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 258 ARG Chi-restraints excluded: chain F residue 295 ARG Chi-restraints excluded: chain F residue 347 ASP Chi-restraints excluded: chain F residue 358 ARG Chi-restraints excluded: chain F residue 444 ILE Chi-restraints excluded: chain F residue 463 LYS Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 474 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 167 ARG Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 175 LYS Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain H residue 258 ARG Chi-restraints excluded: chain H residue 295 ARG Chi-restraints excluded: chain H residue 347 ASP Chi-restraints excluded: chain H residue 358 ARG Chi-restraints excluded: chain H residue 444 ILE Chi-restraints excluded: chain H residue 463 LYS Chi-restraints excluded: chain I residue 8 ASP Chi-restraints excluded: chain I residue 28 ARG Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 8 ASP Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 107 GLN Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain L residue 107 GLN Chi-restraints excluded: chain L residue 111 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 73 optimal weight: 7.9990 chunk 188 optimal weight: 10.0000 chunk 338 optimal weight: 6.9990 chunk 193 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 221 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 266 optimal weight: 1.9990 chunk 388 optimal weight: 9.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 25 GLN J 2 GLN K 25 GLN L 2 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.110525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.089214 restraints weight = 47448.009| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 1.85 r_work: 0.2899 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 35343 Z= 0.222 Angle : 0.709 8.996 47892 Z= 0.377 Chirality : 0.050 0.202 5056 Planarity : 0.006 0.060 6272 Dihedral : 6.442 56.369 4933 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.81 % Favored : 91.96 % Rotamer: Outliers : 4.26 % Allowed : 22.62 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.12), residues: 4328 helix: 1.32 (0.13), residues: 1508 sheet: -0.38 (0.20), residues: 632 loop : -2.53 (0.11), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 214 HIS 0.007 0.002 HIS H 292 PHE 0.032 0.002 PHE E 345 TYR 0.016 0.002 TYR H 80 ARG 0.004 0.001 ARG A 139 Details of bonding type rmsd hydrogen bonds : bond 0.08633 ( 1176) hydrogen bonds : angle 4.06412 ( 3303) covalent geometry : bond 0.00530 (35340) covalent geometry : angle 0.70906 (47892) Misc. bond : bond 0.00302 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8656 Ramachandran restraints generated. 4328 Oldfield, 0 Emsley, 4328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8656 Ramachandran restraints generated. 4328 Oldfield, 0 Emsley, 4328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 255 time to evaluate : 4.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 GLN cc_start: 0.8512 (mp-120) cc_final: 0.7236 (tt0) REVERT: A 396 ASP cc_start: 0.8380 (p0) cc_final: 0.7806 (p0) REVERT: B 127 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.7331 (t80) REVERT: B 139 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.8666 (tmm160) REVERT: B 167 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.6814 (ppt170) REVERT: B 177 LYS cc_start: 0.6608 (OUTLIER) cc_final: 0.5784 (mmmt) REVERT: B 295 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8679 (ptt180) REVERT: B 357 ASP cc_start: 0.8450 (t0) cc_final: 0.8141 (t70) REVERT: B 396 ASP cc_start: 0.8494 (p0) cc_final: 0.7744 (p0) REVERT: B 463 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.6811 (mmtt) REVERT: C 156 GLN cc_start: 0.8523 (mp-120) cc_final: 0.7244 (tt0) REVERT: C 177 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7102 (ptmt) REVERT: C 396 ASP cc_start: 0.8399 (p0) cc_final: 0.7850 (p0) REVERT: D 167 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.6830 (ppt170) REVERT: D 180 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8130 (mp) REVERT: D 183 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7721 (tttm) REVERT: D 295 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.8696 (ptt180) REVERT: D 357 ASP cc_start: 0.8522 (t0) cc_final: 0.8305 (t70) REVERT: D 358 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7723 (mmt-90) REVERT: D 396 ASP cc_start: 0.8489 (p0) cc_final: 0.7736 (p0) REVERT: D 450 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.6960 (mptm) REVERT: D 463 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.6632 (mmtt) REVERT: E 156 GLN cc_start: 0.8513 (mp-120) cc_final: 0.7237 (tt0) REVERT: E 396 ASP cc_start: 0.8412 (p0) cc_final: 0.7866 (p0) REVERT: E 463 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8218 (ttpp) REVERT: F 127 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.7354 (t80) REVERT: F 139 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8623 (tmm160) REVERT: F 167 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.6858 (ppt170) REVERT: F 180 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8133 (mp) REVERT: F 183 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7705 (tttm) REVERT: F 295 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8689 (ptt180) REVERT: F 357 ASP cc_start: 0.8523 (t0) cc_final: 0.8311 (t70) REVERT: F 358 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7722 (mmt-90) REVERT: F 396 ASP cc_start: 0.8476 (p0) cc_final: 0.7722 (p0) REVERT: F 463 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.6665 (mmtt) REVERT: G 156 GLN cc_start: 0.8535 (mp-120) cc_final: 0.7266 (tt0) REVERT: G 396 ASP cc_start: 0.8373 (p0) cc_final: 0.7803 (p0) REVERT: H 94 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7422 (tp30) REVERT: H 127 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.7401 (t80) REVERT: H 167 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.6833 (ppt170) REVERT: H 180 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8177 (mp) REVERT: H 183 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7678 (tttm) REVERT: H 295 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.8722 (ptt180) REVERT: H 357 ASP cc_start: 0.8520 (t0) cc_final: 0.8297 (t70) REVERT: H 358 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7662 (mmt-90) REVERT: H 396 ASP cc_start: 0.8464 (p0) cc_final: 0.7709 (p0) REVERT: H 463 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.6625 (mmtt) REVERT: I 28 ARG cc_start: 0.6887 (OUTLIER) cc_final: 0.6626 (mtt180) REVERT: I 86 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.6989 (mp0) REVERT: J 86 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7031 (mp0) REVERT: L 37 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7607 (mttt) outliers start: 152 outliers final: 95 residues processed: 384 average time/residue: 1.8735 time to fit residues: 856.2848 Evaluate side-chains 377 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 247 time to evaluate : 3.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 70 LEU Chi-restraints excluded: chain 1 residue 81 VAL Chi-restraints excluded: chain 1 residue 94 ILE Chi-restraints excluded: chain 1 residue 133 THR Chi-restraints excluded: chain 1 residue 134 PHE Chi-restraints excluded: chain 2 residue 70 LEU Chi-restraints excluded: chain 2 residue 81 VAL Chi-restraints excluded: chain 2 residue 94 ILE Chi-restraints excluded: chain 2 residue 133 THR Chi-restraints excluded: chain 2 residue 134 PHE Chi-restraints excluded: chain 3 residue 70 LEU Chi-restraints excluded: chain 3 residue 81 VAL Chi-restraints excluded: chain 3 residue 94 ILE Chi-restraints excluded: chain 3 residue 133 THR Chi-restraints excluded: chain 3 residue 134 PHE Chi-restraints excluded: chain 4 residue 65 THR Chi-restraints excluded: chain 4 residue 70 LEU Chi-restraints excluded: chain 4 residue 81 VAL Chi-restraints excluded: chain 4 residue 94 ILE Chi-restraints excluded: chain 4 residue 98 ASN Chi-restraints excluded: chain 4 residue 133 THR Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 358 ARG Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 167 ARG Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 358 ARG Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 452 SER Chi-restraints excluded: chain D residue 463 LYS Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 463 LYS Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 167 ARG Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 295 ARG Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 347 ASP Chi-restraints excluded: chain F residue 358 ARG Chi-restraints excluded: chain F residue 444 ILE Chi-restraints excluded: chain F residue 463 LYS Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 474 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 167 ARG Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 175 LYS Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 295 ARG Chi-restraints excluded: chain H residue 347 ASP Chi-restraints excluded: chain H residue 358 ARG Chi-restraints excluded: chain H residue 444 ILE Chi-restraints excluded: chain H residue 463 LYS Chi-restraints excluded: chain I residue 8 ASP Chi-restraints excluded: chain I residue 28 ARG Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 8 ASP Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain L residue 111 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 372 optimal weight: 10.0000 chunk 370 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 297 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 247 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 86 optimal weight: 0.0070 chunk 308 optimal weight: 2.9990 chunk 419 optimal weight: 1.9990 chunk 393 optimal weight: 1.9990 overall best weight: 1.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 100 GLN I 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.116749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.095806 restraints weight = 46449.751| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.80 r_work: 0.3008 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 35343 Z= 0.115 Angle : 0.559 7.708 47892 Z= 0.296 Chirality : 0.043 0.171 5056 Planarity : 0.005 0.060 6272 Dihedral : 5.967 56.915 4933 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.38 % Favored : 93.39 % Rotamer: Outliers : 3.17 % Allowed : 23.82 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.13), residues: 4328 helix: 1.60 (0.14), residues: 1512 sheet: -0.29 (0.19), residues: 704 loop : -2.30 (0.12), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 214 HIS 0.004 0.001 HIS 2 96 PHE 0.027 0.001 PHE G 345 TYR 0.010 0.001 TYR H 80 ARG 0.005 0.000 ARG I 83 Details of bonding type rmsd hydrogen bonds : bond 0.04765 ( 1176) hydrogen bonds : angle 3.76527 ( 3303) covalent geometry : bond 0.00251 (35340) covalent geometry : angle 0.55890 (47892) Misc. bond : bond 0.00145 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8656 Ramachandran restraints generated. 4328 Oldfield, 0 Emsley, 4328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8656 Ramachandran restraints generated. 4328 Oldfield, 0 Emsley, 4328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 274 time to evaluate : 5.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 132 SER cc_start: 0.7811 (t) cc_final: 0.7364 (p) REVERT: A 156 GLN cc_start: 0.8442 (mp-120) cc_final: 0.7205 (tt0) REVERT: A 396 ASP cc_start: 0.8259 (p0) cc_final: 0.7643 (p0) REVERT: B 127 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.7271 (t80) REVERT: B 139 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.8579 (tmm160) REVERT: B 167 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.7375 (ppt170) REVERT: B 177 LYS cc_start: 0.6465 (OUTLIER) cc_final: 0.5662 (mmmt) REVERT: B 295 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8664 (ptt180) REVERT: B 357 ASP cc_start: 0.8305 (t0) cc_final: 0.7947 (t70) REVERT: B 396 ASP cc_start: 0.8450 (p0) cc_final: 0.7712 (p0) REVERT: B 463 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.6852 (mmtt) REVERT: C 156 GLN cc_start: 0.8457 (mp-120) cc_final: 0.7215 (tt0) REVERT: C 396 ASP cc_start: 0.8271 (p0) cc_final: 0.7666 (p0) REVERT: D 167 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.7365 (ppt170) REVERT: D 295 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8684 (ptt180) REVERT: D 357 ASP cc_start: 0.8512 (t0) cc_final: 0.8216 (t70) REVERT: D 358 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7707 (mmt-90) REVERT: D 396 ASP cc_start: 0.8442 (p0) cc_final: 0.7701 (p0) REVERT: D 450 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7010 (mptm) REVERT: D 463 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.6659 (mmtt) REVERT: E 156 GLN cc_start: 0.8430 (mp-120) cc_final: 0.7198 (tt0) REVERT: E 396 ASP cc_start: 0.8280 (p0) cc_final: 0.7706 (p0) REVERT: E 463 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8175 (ttpp) REVERT: F 127 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.7322 (t80) REVERT: F 139 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8604 (tmm160) REVERT: F 167 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.7386 (ppt170) REVERT: F 295 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8666 (ptt180) REVERT: F 357 ASP cc_start: 0.8523 (t0) cc_final: 0.8279 (t70) REVERT: F 358 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7713 (mmt-90) REVERT: F 396 ASP cc_start: 0.8434 (p0) cc_final: 0.7707 (p0) REVERT: F 463 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.6626 (mmtt) REVERT: G 128 LYS cc_start: 0.8756 (mttp) cc_final: 0.8547 (mtmt) REVERT: G 156 GLN cc_start: 0.8464 (mp-120) cc_final: 0.7237 (tt0) REVERT: G 396 ASP cc_start: 0.8227 (p0) cc_final: 0.7622 (p0) REVERT: H 94 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7338 (tp30) REVERT: H 127 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.7356 (t80) REVERT: H 167 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.7380 (ppt170) REVERT: H 180 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8086 (mp) REVERT: H 295 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8692 (ptt180) REVERT: H 357 ASP cc_start: 0.8510 (t0) cc_final: 0.8208 (t70) REVERT: H 358 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7679 (mmt-90) REVERT: H 396 ASP cc_start: 0.8445 (p0) cc_final: 0.7694 (p0) REVERT: H 463 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.6609 (mmtt) REVERT: I 86 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7008 (mp0) REVERT: J 86 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7044 (mp0) REVERT: L 29 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6266 (mt-10) REVERT: L 37 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7341 (mttt) outliers start: 113 outliers final: 65 residues processed: 368 average time/residue: 2.2550 time to fit residues: 985.4906 Evaluate side-chains 360 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 266 time to evaluate : 4.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 70 LEU Chi-restraints excluded: chain 1 residue 81 VAL Chi-restraints excluded: chain 1 residue 94 ILE Chi-restraints excluded: chain 1 residue 133 THR Chi-restraints excluded: chain 1 residue 134 PHE Chi-restraints excluded: chain 2 residue 70 LEU Chi-restraints excluded: chain 2 residue 81 VAL Chi-restraints excluded: chain 2 residue 94 ILE Chi-restraints excluded: chain 2 residue 133 THR Chi-restraints excluded: chain 2 residue 134 PHE Chi-restraints excluded: chain 3 residue 65 THR Chi-restraints excluded: chain 3 residue 70 LEU Chi-restraints excluded: chain 3 residue 81 VAL Chi-restraints excluded: chain 3 residue 94 ILE Chi-restraints excluded: chain 3 residue 134 PHE Chi-restraints excluded: chain 4 residue 65 THR Chi-restraints excluded: chain 4 residue 70 LEU Chi-restraints excluded: chain 4 residue 81 VAL Chi-restraints excluded: chain 4 residue 94 ILE Chi-restraints excluded: chain 4 residue 98 ASN Chi-restraints excluded: chain 4 residue 133 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 358 ARG Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 167 ARG Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 358 ARG Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 452 SER Chi-restraints excluded: chain D residue 463 LYS Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 463 LYS Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 167 ARG Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 295 ARG Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 358 ARG Chi-restraints excluded: chain F residue 444 ILE Chi-restraints excluded: chain F residue 463 LYS Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 464 GLU Chi-restraints excluded: chain G residue 474 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 167 ARG Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 175 LYS Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 295 ARG Chi-restraints excluded: chain H residue 358 ARG Chi-restraints excluded: chain H residue 444 ILE Chi-restraints excluded: chain H residue 463 LYS Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 8 ASP Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 227 optimal weight: 0.9990 chunk 190 optimal weight: 9.9990 chunk 139 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 326 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 310 optimal weight: 0.0570 chunk 220 optimal weight: 2.9990 chunk 247 optimal weight: 10.0000 chunk 396 optimal weight: 0.6980 overall best weight: 1.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.116304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.095310 restraints weight = 46595.968| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.80 r_work: 0.3002 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 35343 Z= 0.120 Angle : 0.562 7.462 47892 Z= 0.297 Chirality : 0.044 0.173 5056 Planarity : 0.005 0.058 6272 Dihedral : 5.799 56.640 4932 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.49 % Favored : 93.28 % Rotamer: Outliers : 2.97 % Allowed : 24.02 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.13), residues: 4328 helix: 1.77 (0.14), residues: 1504 sheet: -0.26 (0.19), residues: 748 loop : -2.23 (0.12), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 214 HIS 0.004 0.001 HIS B 292 PHE 0.027 0.001 PHE E 345 TYR 0.011 0.001 TYR H 80 ARG 0.005 0.000 ARG J 83 Details of bonding type rmsd hydrogen bonds : bond 0.05269 ( 1176) hydrogen bonds : angle 3.67066 ( 3303) covalent geometry : bond 0.00261 (35340) covalent geometry : angle 0.56208 (47892) Misc. bond : bond 0.00155 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24776.98 seconds wall clock time: 441 minutes 15.37 seconds (26475.37 seconds total)