Starting phenix.real_space_refine on Sat Feb 7 14:46:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ci2_45608/02_2026/9ci2_45608_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ci2_45608/02_2026/9ci2_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ci2_45608/02_2026/9ci2_45608_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ci2_45608/02_2026/9ci2_45608_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ci2_45608/02_2026/9ci2_45608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ci2_45608/02_2026/9ci2_45608.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/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: 7.52, per 1000 atoms: 0.22 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: 2.96 Conformation dependent library (CDL) restraints added in 1.3 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: 1.05 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: 6.26 Time building geometry restraints manager: 3.85 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: 0.00 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: 12.470 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: 0.040 Extract box with map and model: 0.760 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 30.310 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.680 ------------------------------------------------------------------------------- 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 : 7.58 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (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 ARG 0.007 0.000 ARG F 439 TYR 0.013 0.001 TYR G 24 PHE 0.028 0.001 PHE G 345 TRP 0.014 0.001 TRP C 214 HIS 0.004 0.001 HIS F 238 Details of bonding type rmsd covalent geometry : bond 0.00921 (35340) covalent geometry : angle 1.11437 (47892) hydrogen bonds : bond 0.24773 ( 1176) hydrogen bonds : angle 7.28218 ( 3303) 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 : 1.367 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 96 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7826 (mm-40) 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: 0.8108 (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: 0.5657 (pt0) REVERT: B 42 MET cc_start: 0.8953 (ptp) cc_final: 0.8584 (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: 0.7119 (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: 0.6959 (m-30) REVERT: E 96 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7870 (mm-40) 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: 0.7159 (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 78 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.6949 (p0) REVERT: G 96 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7858 (mm-40) 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: 85 residues processed: 887 average time/residue: 0.7559 time to fit residues: 783.6249 Evaluate side-chains 410 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 310 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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 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 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 197 optimal weight: 5.9990 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 2.9990 chunk 424 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 327 HIS B 45 GLN B 413 ASN C 115 ASN C 327 HIS D 383 HIS D 413 ASN E 115 ASN E 327 HIS F 45 GLN G 115 ASN G 327 HIS H 45 GLN H 413 ASN I 5 ASN K 77 ASN L 90 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.118504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.097835 restraints weight = 46783.885| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.78 r_work: 0.3051 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 35343 Z= 0.155 Angle : 0.658 8.190 47892 Z= 0.352 Chirality : 0.046 0.207 5056 Planarity : 0.006 0.075 6272 Dihedral : 8.239 67.672 5065 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.02 % Favored : 92.63 % Rotamer: Outliers : 6.51 % Allowed : 21.10 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.12), residues: 4328 helix: 0.89 (0.14), residues: 1496 sheet: -0.90 (0.19), residues: 716 loop : -2.88 (0.11), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 83 TYR 0.015 0.001 TYR L 80 PHE 0.029 0.002 PHE G 345 TRP 0.013 0.001 TRP A 385 HIS 0.005 0.001 HIS G 292 Details of bonding type rmsd covalent geometry : bond 0.00331 (35340) covalent geometry : angle 0.65803 (47892) hydrogen bonds : bond 0.06744 ( 1176) hydrogen bonds : angle 4.56516 ( 3303) Misc. bond : bond 0.01851 ( 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 534 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 302 time to evaluate : 1.351 Fit side-chains REVERT: 1 132 SER cc_start: 0.7899 (OUTLIER) cc_final: 0.7390 (p) REVERT: 2 80 CYS cc_start: 0.7455 (p) cc_final: 0.7153 (m) REVERT: 2 115 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6404 (mt-10) REVERT: 2 133 THR cc_start: 0.7217 (OUTLIER) cc_final: 0.6929 (m) REVERT: 3 78 GLU cc_start: 0.8268 (mm-30) cc_final: 0.8032 (mm-30) REVERT: 3 115 GLU cc_start: 0.6850 (mm-30) cc_final: 0.6348 (mt-10) REVERT: 3 132 SER cc_start: 0.7621 (t) cc_final: 0.7385 (p) REVERT: 4 78 GLU cc_start: 0.8262 (mm-30) cc_final: 0.8026 (mm-30) REVERT: 4 133 THR cc_start: 0.7559 (OUTLIER) cc_final: 0.7148 (p) REVERT: A 156 GLN cc_start: 0.8475 (mp-120) cc_final: 0.7229 (tt0) REVERT: A 177 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.6764 (ptmt) REVERT: A 396 ASP cc_start: 0.8320 (p0) cc_final: 0.7700 (p0) REVERT: B 79 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8142 (ttt180) REVERT: B 139 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8560 (tmm160) REVERT: B 295 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8594 (ptt180) REVERT: B 357 ASP cc_start: 0.8107 (t0) cc_final: 0.7781 (t0) REVERT: B 396 ASP cc_start: 0.8400 (p0) cc_final: 0.7690 (p0) REVERT: B 463 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.6789 (mmtp) REVERT: C 156 GLN cc_start: 0.8492 (mp-120) cc_final: 0.7243 (tt0) REVERT: C 177 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.6711 (ptmt) REVERT: C 396 ASP cc_start: 0.8295 (p0) cc_final: 0.7750 (p0) REVERT: C 444 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7691 (mm) REVERT: D 295 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8599 (ptt180) REVERT: D 396 ASP cc_start: 0.8389 (p0) cc_final: 0.7639 (p0) REVERT: D 463 LYS cc_start: 0.7679 (ptpp) cc_final: 0.6593 (mmtt) REVERT: E 128 LYS cc_start: 0.8430 (mppt) cc_final: 0.8230 (mtpt) REVERT: E 156 GLN cc_start: 0.8448 (mp-120) cc_final: 0.7220 (tt0) REVERT: E 396 ASP cc_start: 0.8323 (p0) cc_final: 0.7722 (p0) REVERT: E 439 ARG cc_start: 0.6687 (OUTLIER) cc_final: 0.6236 (mtp85) REVERT: F 77 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7686 (mp) REVERT: F 295 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8599 (ptt180) REVERT: F 396 ASP cc_start: 0.8413 (p0) cc_final: 0.7700 (p0) REVERT: F 455 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7456 (tp) REVERT: F 463 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.6573 (mmtt) REVERT: G 156 GLN cc_start: 0.8493 (mp-120) cc_final: 0.7248 (tt0) REVERT: G 396 ASP cc_start: 0.8283 (p0) cc_final: 0.7707 (p0) REVERT: H 79 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.8257 (ttt180) REVERT: H 180 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8035 (mp) REVERT: H 396 ASP cc_start: 0.8413 (p0) cc_final: 0.7696 (p0) REVERT: H 463 LYS cc_start: 0.7655 (ptpp) cc_final: 0.6546 (mmtt) REVERT: I 28 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.6704 (mtt180) REVERT: I 29 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6565 (mt-10) REVERT: J 8 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.8026 (t0) REVERT: J 28 ARG cc_start: 0.7061 (OUTLIER) cc_final: 0.6588 (mtm-85) REVERT: J 29 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6621 (mt-10) REVERT: K 8 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.8133 (t0) REVERT: L 29 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6395 (mt-10) outliers start: 232 outliers final: 62 residues processed: 505 average time/residue: 0.7030 time to fit residues: 419.1375 Evaluate side-chains 364 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 277 time to evaluate : 1.202 ------------------------------------------------------------------------------- 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 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 80 CYS 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 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 106 ASP Chi-restraints excluded: chain B residue 139 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 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 444 ILE 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 71 THR Chi-restraints excluded: chain D residue 106 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 E residue 23 THR Chi-restraints excluded: chain E residue 192 CYS 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 106 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 455 LEU Chi-restraints excluded: chain F residue 463 LYS Chi-restraints excluded: chain G residue 60 GLU 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 79 ARG Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 180 LEU 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 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 107 GLN Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 8 ASP 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 343 optimal weight: 2.9990 chunk 139 optimal weight: 9.9990 chunk 373 optimal weight: 10.0000 chunk 331 optimal weight: 9.9990 chunk 306 optimal weight: 0.6980 chunk 41 optimal weight: 9.9990 chunk 367 optimal weight: 6.9990 chunk 179 optimal weight: 8.9990 chunk 308 optimal weight: 0.9990 chunk 239 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS C 153 HIS D 383 HIS E 153 HIS G 153 HIS I 2 GLN I 25 GLN I 104 ASN J 25 GLN J 104 ASN L 90 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.113985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.092898 restraints weight = 46706.276| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.82 r_work: 0.2965 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 35343 Z= 0.184 Angle : 0.678 8.138 47892 Z= 0.361 Chirality : 0.048 0.193 5056 Planarity : 0.006 0.063 6272 Dihedral : 6.885 59.704 4947 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.88 % Favored : 91.89 % Rotamer: Outliers : 5.47 % Allowed : 21.24 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.12), residues: 4328 helix: 1.17 (0.14), residues: 1492 sheet: -0.70 (0.20), residues: 676 loop : -2.74 (0.11), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 83 TYR 0.014 0.002 TYR H 80 PHE 0.032 0.002 PHE G 345 TRP 0.012 0.001 TRP C 214 HIS 0.006 0.002 HIS H 292 Details of bonding type rmsd covalent geometry : bond 0.00423 (35340) covalent geometry : angle 0.67755 (47892) hydrogen bonds : bond 0.07904 ( 1176) hydrogen bonds : angle 4.31056 ( 3303) Misc. bond : bond 0.00806 ( 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 474 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 279 time to evaluate : 0.910 Fit side-chains REVERT: 1 132 SER cc_start: 0.7732 (t) cc_final: 0.7219 (p) REVERT: 2 98 ASN cc_start: 0.7232 (OUTLIER) cc_final: 0.7025 (t0) REVERT: 2 115 GLU cc_start: 0.7106 (mm-30) cc_final: 0.6384 (mt-10) REVERT: 3 132 SER cc_start: 0.7347 (t) cc_final: 0.7037 (p) REVERT: 4 133 THR cc_start: 0.7574 (OUTLIER) cc_final: 0.7134 (p) REVERT: A 156 GLN cc_start: 0.8504 (mp-120) cc_final: 0.7239 (tt0) REVERT: A 396 ASP cc_start: 0.8347 (p0) cc_final: 0.7734 (p0) REVERT: A 466 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7616 (mttm) REVERT: B 41 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8124 (ptp-170) REVERT: B 79 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8280 (ttt180) REVERT: B 139 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.8697 (tmm160) REVERT: B 295 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8570 (ptt180) REVERT: B 357 ASP cc_start: 0.8309 (t0) cc_final: 0.8039 (t70) REVERT: B 396 ASP cc_start: 0.8506 (p0) cc_final: 0.7745 (p0) REVERT: B 463 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.6816 (mmtt) REVERT: C 156 GLN cc_start: 0.8517 (mp-120) cc_final: 0.7249 (tt0) REVERT: C 396 ASP cc_start: 0.8347 (p0) cc_final: 0.7740 (p0) REVERT: D 41 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8128 (ptp-170) REVERT: D 180 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8036 (mp) REVERT: D 295 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8577 (ptt180) REVERT: D 357 ASP cc_start: 0.8472 (t0) cc_final: 0.8256 (t70) REVERT: D 358 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7735 (mmt-90) REVERT: D 396 ASP cc_start: 0.8479 (p0) cc_final: 0.7734 (p0) REVERT: D 463 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.6614 (mmtt) REVERT: E 156 GLN cc_start: 0.8493 (mp-120) cc_final: 0.7239 (tt0) REVERT: E 396 ASP cc_start: 0.8354 (p0) cc_final: 0.7661 (p0) REVERT: E 463 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8410 (ttpp) REVERT: F 41 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8162 (ptp-170) REVERT: F 127 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7234 (t80) REVERT: F 180 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8034 (mp) REVERT: F 295 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8564 (ptt180) REVERT: F 357 ASP cc_start: 0.8476 (t0) cc_final: 0.8224 (t70) REVERT: F 358 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7749 (mmt-90) REVERT: F 396 ASP cc_start: 0.8475 (p0) cc_final: 0.7720 (p0) REVERT: F 463 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.6625 (mmtt) REVERT: G 156 GLN cc_start: 0.8531 (mp-120) cc_final: 0.7272 (tt0) REVERT: G 396 ASP cc_start: 0.8315 (p0) cc_final: 0.7710 (p0) REVERT: G 466 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7734 (mttm) REVERT: H 41 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8056 (ptp-170) REVERT: H 79 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8257 (ttt180) REVERT: H 180 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8106 (mp) REVERT: H 357 ASP cc_start: 0.8478 (t0) cc_final: 0.8261 (t70) REVERT: H 358 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7721 (mmt-90) REVERT: H 396 ASP cc_start: 0.8491 (p0) cc_final: 0.7757 (p0) REVERT: H 463 LYS cc_start: 0.7727 (ptpp) cc_final: 0.6609 (mmtt) REVERT: I 8 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.8007 (t0) REVERT: I 28 ARG cc_start: 0.7129 (OUTLIER) cc_final: 0.6794 (mtt180) REVERT: I 29 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6523 (mt-10) REVERT: I 86 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7057 (mp0) REVERT: J 8 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.8034 (t0) REVERT: J 28 ARG cc_start: 0.7017 (OUTLIER) cc_final: 0.6591 (mtm-85) REVERT: J 29 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6473 (mt-10) REVERT: J 31 ASP cc_start: 0.8531 (m-30) cc_final: 0.8309 (m-30) REVERT: J 86 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7084 (mp0) REVERT: K 7 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7544 (mm) REVERT: K 8 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.8103 (t0) REVERT: K 29 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6636 (mt-10) outliers start: 195 outliers final: 70 residues processed: 446 average time/residue: 0.7447 time to fit residues: 387.5655 Evaluate side-chains 369 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 263 time to evaluate : 1.306 ------------------------------------------------------------------------------- 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 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 98 ASN 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 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 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 41 ARG 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 106 ASP Chi-restraints excluded: chain B residue 139 ARG 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 72 ASP Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 41 ARG 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 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 463 LYS 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 450 LYS 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 41 ARG 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 106 ASP Chi-restraints excluded: chain F residue 127 PHE 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 78 ASP Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 464 GLU Chi-restraints excluded: chain G residue 466 LYS Chi-restraints excluded: chain G residue 474 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 41 ARG 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 106 ASP Chi-restraints excluded: chain H residue 178 LEU 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 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 100 LEU 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 8 ASP Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain K residue 86 GLU Chi-restraints excluded: chain K residue 100 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 275 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 chunk 282 optimal weight: 8.9990 chunk 290 optimal weight: 9.9990 chunk 336 optimal weight: 0.8980 chunk 245 optimal weight: 9.9990 chunk 402 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 216 optimal weight: 4.9990 chunk 194 optimal weight: 10.0000 chunk 148 optimal weight: 8.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 327 HIS I 25 GLN J 25 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.110397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.089327 restraints weight = 46996.804| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.81 r_work: 0.2908 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 35343 Z= 0.261 Angle : 0.788 9.538 47892 Z= 0.420 Chirality : 0.052 0.211 5056 Planarity : 0.007 0.071 6272 Dihedral : 7.131 59.858 4936 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.88 % Favored : 91.89 % Rotamer: Outliers : 5.72 % Allowed : 20.65 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.12), residues: 4328 helix: 0.97 (0.13), residues: 1496 sheet: -0.62 (0.20), residues: 644 loop : -2.84 (0.11), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 139 TYR 0.016 0.002 TYR H 80 PHE 0.035 0.003 PHE D 345 TRP 0.014 0.002 TRP G 214 HIS 0.008 0.002 HIS D 292 Details of bonding type rmsd covalent geometry : bond 0.00627 (35340) covalent geometry : angle 0.78810 (47892) hydrogen bonds : bond 0.09993 ( 1176) hydrogen bonds : angle 4.41020 ( 3303) Misc. bond : bond 0.01053 ( 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 461 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 257 time to evaluate : 1.348 Fit side-chains revert: symmetry clash REVERT: 1 80 CYS cc_start: 0.7539 (p) cc_final: 0.7260 (m) REVERT: 1 113 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7537 (mttp) REVERT: 2 98 ASN cc_start: 0.7367 (OUTLIER) cc_final: 0.7164 (t0) REVERT: 4 102 LYS cc_start: 0.6089 (OUTLIER) cc_final: 0.5811 (mmtm) REVERT: A 156 GLN cc_start: 0.8554 (mp-120) cc_final: 0.7320 (tt0) REVERT: A 177 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7280 (ptmt) REVERT: A 396 ASP cc_start: 0.8426 (p0) cc_final: 0.7903 (p0) REVERT: B 41 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.7928 (ptp-170) REVERT: B 79 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8328 (ttt180) REVERT: B 139 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.8634 (tmm160) REVERT: B 167 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.6868 (ppt170) REVERT: B 295 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8609 (ptt180) REVERT: B 357 ASP cc_start: 0.8389 (t0) cc_final: 0.8141 (t70) REVERT: B 396 ASP cc_start: 0.8586 (p0) cc_final: 0.7915 (p0) REVERT: B 455 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7389 (tp) REVERT: B 463 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.6880 (mmtt) REVERT: C 156 GLN cc_start: 0.8568 (mp-120) cc_final: 0.7334 (tt0) REVERT: C 177 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7124 (ptmt) REVERT: C 396 ASP cc_start: 0.8420 (p0) cc_final: 0.7933 (p0) REVERT: D 41 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.7899 (ptp-170) REVERT: D 139 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.8510 (tmm160) REVERT: D 167 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.6865 (ppt170) REVERT: D 180 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8126 (mp) REVERT: D 295 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.8622 (ptt180) REVERT: D 357 ASP cc_start: 0.8478 (t0) cc_final: 0.8248 (t70) REVERT: D 358 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7733 (mmt-90) REVERT: D 396 ASP cc_start: 0.8564 (p0) cc_final: 0.7883 (p0) REVERT: D 450 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.6945 (mptm) REVERT: D 463 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.6664 (mmtt) REVERT: E 156 GLN cc_start: 0.8536 (mp-120) cc_final: 0.7316 (tt0) REVERT: E 396 ASP cc_start: 0.8428 (p0) cc_final: 0.7947 (p0) REVERT: E 463 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8393 (ttpp) REVERT: F 41 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.7918 (ptp-170) REVERT: F 77 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7805 (tp) REVERT: F 127 PHE cc_start: 0.8320 (OUTLIER) cc_final: 0.7290 (t80) REVERT: F 139 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8617 (tmm160) REVERT: F 167 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.6905 (ppt170) REVERT: F 180 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8142 (mp) REVERT: F 295 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8599 (ptt180) REVERT: F 357 ASP cc_start: 0.8499 (t0) cc_final: 0.8269 (t70) REVERT: F 358 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7721 (mmt-90) REVERT: F 396 ASP cc_start: 0.8554 (p0) cc_final: 0.7893 (p0) REVERT: F 463 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.6706 (mmtt) REVERT: G 156 GLN cc_start: 0.8578 (mp-120) cc_final: 0.7347 (tt0) REVERT: G 396 ASP cc_start: 0.8397 (p0) cc_final: 0.7910 (p0) REVERT: G 466 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7787 (mttm) REVERT: H 41 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.7847 (ptp-170) REVERT: H 79 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8317 (ttt180) REVERT: H 127 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.7783 (t80) REVERT: H 139 ARG cc_start: 0.9135 (OUTLIER) cc_final: 0.8479 (tmm160) REVERT: H 167 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.6883 (ppt170) REVERT: H 180 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8189 (mp) REVERT: H 357 ASP cc_start: 0.8487 (t0) cc_final: 0.8261 (t70) REVERT: H 358 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7729 (mmt-90) REVERT: H 396 ASP cc_start: 0.8568 (p0) cc_final: 0.7906 (p0) REVERT: H 455 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7481 (tp) REVERT: H 463 LYS cc_start: 0.7783 (OUTLIER) cc_final: 0.6679 (mmtt) REVERT: I 28 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6829 (mtt180) REVERT: I 86 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: J 8 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.8024 (t0) REVERT: J 28 ARG cc_start: 0.7008 (OUTLIER) cc_final: 0.6643 (mtt180) REVERT: J 31 ASP cc_start: 0.8588 (m-30) cc_final: 0.8372 (m-30) REVERT: J 86 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: K 7 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7605 (mm) REVERT: K 8 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.8081 (t0) REVERT: K 86 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7107 (mp0) REVERT: L 29 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6498 (mt-10) REVERT: L 37 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7723 (mttt) outliers start: 204 outliers final: 88 residues processed: 435 average time/residue: 0.8635 time to fit residues: 435.0147 Evaluate side-chains 385 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 247 time to evaluate : 1.364 ------------------------------------------------------------------------------- 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 113 LYS 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 81 VAL 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 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 98 ASN 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 98 ASN Chi-restraints excluded: chain 4 residue 102 LYS 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 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 41 ARG Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 178 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 384 VAL Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 48 VAL 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 139 ARG Chi-restraints excluded: chain D residue 167 ARG 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 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 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 450 LYS 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 41 ARG 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 127 PHE Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 167 ARG Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 180 LEU 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 78 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 G residue 475 LEU Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 41 ARG Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 79 ARG 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 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 455 LEU 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 52 THR Chi-restraints excluded: chain I residue 86 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 52 THR Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 86 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 172 optimal weight: 6.9990 chunk 287 optimal weight: 9.9990 chunk 387 optimal weight: 5.9990 chunk 286 optimal weight: 2.9990 chunk 318 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 chunk 285 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 362 optimal weight: 10.0000 chunk 165 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 HIS F 327 HIS H 327 HIS I 25 GLN J 25 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.112676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.091463 restraints weight = 47170.011| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.85 r_work: 0.2934 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 35343 Z= 0.157 Angle : 0.634 7.604 47892 Z= 0.338 Chirality : 0.046 0.187 5056 Planarity : 0.006 0.071 6272 Dihedral : 6.685 59.431 4936 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.68 % Favored : 93.09 % Rotamer: Outliers : 5.50 % Allowed : 21.07 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.12), residues: 4328 helix: 1.26 (0.14), residues: 1504 sheet: -0.32 (0.20), residues: 672 loop : -2.69 (0.11), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 83 TYR 0.012 0.001 TYR H 80 PHE 0.027 0.002 PHE G 345 TRP 0.016 0.001 TRP G 214 HIS 0.005 0.001 HIS H 292 Details of bonding type rmsd covalent geometry : bond 0.00356 (35340) covalent geometry : angle 0.63450 (47892) hydrogen bonds : bond 0.06799 ( 1176) hydrogen bonds : angle 4.07334 ( 3303) Misc. bond : bond 0.00352 ( 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 456 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 260 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 132 SER cc_start: 0.7739 (t) cc_final: 0.7530 (p) REVERT: 3 102 LYS cc_start: 0.6063 (OUTLIER) cc_final: 0.5727 (mmtm) REVERT: A 156 GLN cc_start: 0.8463 (mp-120) cc_final: 0.7185 (tt0) REVERT: A 396 ASP cc_start: 0.8356 (p0) cc_final: 0.7742 (p0) REVERT: B 41 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8121 (ptp-170) REVERT: B 79 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8233 (ttt180) REVERT: B 127 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.7300 (t80) REVERT: B 139 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8665 (tmm160) REVERT: B 177 LYS cc_start: 0.6527 (OUTLIER) cc_final: 0.5612 (mmmt) REVERT: B 295 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8624 (ptt180) REVERT: B 357 ASP cc_start: 0.8384 (t0) cc_final: 0.8083 (t70) REVERT: B 396 ASP cc_start: 0.8482 (p0) cc_final: 0.7763 (p0) REVERT: B 463 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.6820 (mmtt) REVERT: C 156 GLN cc_start: 0.8478 (mp-120) cc_final: 0.7185 (tt0) REVERT: C 177 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7163 (ptmt) REVERT: C 396 ASP cc_start: 0.8353 (p0) cc_final: 0.7760 (p0) REVERT: D 180 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8058 (mp) REVERT: D 295 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8637 (ptt180) REVERT: D 357 ASP cc_start: 0.8446 (t0) cc_final: 0.8205 (t70) REVERT: D 358 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7701 (mmt-90) REVERT: D 396 ASP cc_start: 0.8488 (p0) cc_final: 0.7723 (p0) REVERT: D 450 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.6880 (mptm) REVERT: D 463 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.6683 (mmtt) REVERT: E 156 GLN cc_start: 0.8453 (mp-120) cc_final: 0.7180 (tt0) REVERT: E 396 ASP cc_start: 0.8379 (p0) cc_final: 0.7789 (p0) REVERT: E 463 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8259 (ttpp) REVERT: F 77 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7742 (tp) REVERT: F 127 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7280 (t80) REVERT: F 139 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.8661 (tmm160) REVERT: F 180 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8098 (mp) REVERT: F 295 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8598 (ptt180) REVERT: F 357 ASP cc_start: 0.8450 (t0) cc_final: 0.8158 (t70) REVERT: F 358 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7681 (mmt-90) REVERT: F 396 ASP cc_start: 0.8456 (p0) cc_final: 0.7730 (p0) REVERT: F 463 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.6646 (mmtt) REVERT: G 81 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8745 (pttt) REVERT: G 156 GLN cc_start: 0.8481 (mp-120) cc_final: 0.7202 (tt0) REVERT: G 396 ASP cc_start: 0.8337 (p0) cc_final: 0.7750 (p0) REVERT: H 79 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8248 (ttt180) REVERT: H 127 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.7623 (t80) REVERT: H 180 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8133 (mp) REVERT: H 295 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8667 (ptt180) REVERT: H 357 ASP cc_start: 0.8455 (t0) cc_final: 0.8216 (t70) REVERT: H 358 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7698 (mmt-90) REVERT: H 396 ASP cc_start: 0.8470 (p0) cc_final: 0.7734 (p0) REVERT: H 463 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.6643 (mmtt) REVERT: I 28 ARG cc_start: 0.6929 (OUTLIER) cc_final: 0.6651 (mtt180) REVERT: I 86 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6994 (mp0) REVERT: J 28 ARG cc_start: 0.6806 (OUTLIER) cc_final: 0.6492 (mtt180) REVERT: J 31 ASP cc_start: 0.8550 (m-30) cc_final: 0.8278 (m-30) REVERT: J 86 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7012 (mp0) REVERT: K 29 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6334 (mt-10) REVERT: K 86 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6979 (mp0) REVERT: L 29 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6365 (mt-10) REVERT: L 37 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7441 (mttt) outliers start: 196 outliers final: 85 residues processed: 420 average time/residue: 0.8449 time to fit residues: 412.6673 Evaluate side-chains 377 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 255 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 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 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 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 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 41 ARG 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 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 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 474 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 127 PHE 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 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 77 LEU 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 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 72 ASP Chi-restraints excluded: chain G residue 81 LYS 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 79 ARG 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 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 52 THR 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 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 1 MET Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain K residue 52 THR 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 111 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 348 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 265 optimal weight: 4.9990 chunk 258 optimal weight: 5.9990 chunk 398 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 chunk 120 optimal weight: 0.0980 chunk 24 optimal weight: 5.9990 chunk 182 optimal weight: 5.9990 chunk 334 optimal weight: 8.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- 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 2 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.112189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.090892 restraints weight = 46960.957| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.85 r_work: 0.2924 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 35343 Z= 0.168 Angle : 0.648 8.045 47892 Z= 0.344 Chirality : 0.047 0.192 5056 Planarity : 0.006 0.068 6272 Dihedral : 6.451 57.765 4934 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.21 % Favored : 92.56 % Rotamer: Outliers : 5.30 % Allowed : 21.32 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.12), residues: 4328 helix: 1.35 (0.14), residues: 1508 sheet: -0.27 (0.20), residues: 672 loop : -2.61 (0.11), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 258 TYR 0.013 0.001 TYR H 80 PHE 0.029 0.002 PHE G 345 TRP 0.014 0.001 TRP A 214 HIS 0.005 0.001 HIS H 292 Details of bonding type rmsd covalent geometry : bond 0.00385 (35340) covalent geometry : angle 0.64765 (47892) hydrogen bonds : bond 0.07302 ( 1176) hydrogen bonds : angle 4.01628 ( 3303) Misc. bond : bond 0.00272 ( 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 456 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 267 time to evaluate : 1.387 Fit side-chains revert: symmetry clash REVERT: 3 102 LYS cc_start: 0.6143 (OUTLIER) cc_final: 0.5813 (mmtm) REVERT: 4 102 LYS cc_start: 0.6072 (OUTLIER) cc_final: 0.5777 (mmtm) REVERT: A 156 GLN cc_start: 0.8477 (mp-120) cc_final: 0.7202 (tt0) REVERT: A 177 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7268 (ptmt) REVERT: A 396 ASP cc_start: 0.8381 (p0) cc_final: 0.7862 (p0) REVERT: B 41 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8042 (ptp-170) REVERT: B 127 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.7343 (t80) REVERT: B 139 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.8700 (tmm160) REVERT: B 167 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.6908 (ppt170) REVERT: B 177 LYS cc_start: 0.6565 (OUTLIER) cc_final: 0.5738 (mmmt) REVERT: B 295 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.8636 (ptt180) REVERT: B 357 ASP cc_start: 0.8404 (t0) cc_final: 0.8099 (t70) REVERT: B 358 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7314 (mmt-90) REVERT: B 396 ASP cc_start: 0.8495 (p0) cc_final: 0.7772 (p0) REVERT: B 463 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.6816 (mmtt) REVERT: C 81 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8736 (pttt) REVERT: C 156 GLN cc_start: 0.8492 (mp-120) cc_final: 0.7207 (tt0) REVERT: C 177 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7159 (ptmt) REVERT: C 396 ASP cc_start: 0.8389 (p0) cc_final: 0.7782 (p0) REVERT: D 41 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7684 (ptp-170) REVERT: D 61 SER cc_start: 0.8230 (OUTLIER) cc_final: 0.8030 (m) REVERT: D 167 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.6797 (ppt170) REVERT: D 180 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8093 (mp) REVERT: D 295 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8647 (ptt180) REVERT: D 357 ASP cc_start: 0.8470 (t0) cc_final: 0.8235 (t70) REVERT: D 358 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7708 (mmt-90) REVERT: D 396 ASP cc_start: 0.8508 (p0) cc_final: 0.7759 (p0) REVERT: D 463 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.6647 (mmtt) REVERT: E 156 GLN cc_start: 0.8474 (mp-120) cc_final: 0.7203 (tt0) REVERT: E 396 ASP cc_start: 0.8382 (p0) cc_final: 0.7810 (p0) REVERT: E 463 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8168 (ttpp) REVERT: F 41 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7713 (ptp-170) REVERT: F 127 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.7309 (t80) REVERT: F 139 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.8601 (tmm160) REVERT: F 167 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.6949 (ppt170) REVERT: F 180 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8086 (mp) REVERT: F 295 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8643 (ptt180) REVERT: F 357 ASP cc_start: 0.8493 (t0) cc_final: 0.8242 (t70) REVERT: F 358 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7687 (mmt-90) REVERT: F 396 ASP cc_start: 0.8474 (p0) cc_final: 0.7757 (p0) REVERT: F 463 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.6681 (mmtt) REVERT: G 156 GLN cc_start: 0.8500 (mp-120) cc_final: 0.7224 (tt0) REVERT: G 336 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8575 (tt0) REVERT: G 396 ASP cc_start: 0.8353 (p0) cc_final: 0.7739 (p0) REVERT: H 127 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.7451 (t80) REVERT: H 167 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.6922 (ppt170) REVERT: H 175 LYS cc_start: 0.6063 (OUTLIER) cc_final: 0.5407 (mttt) REVERT: H 180 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8131 (mp) REVERT: H 357 ASP cc_start: 0.8461 (t0) cc_final: 0.8223 (t70) REVERT: H 358 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7681 (mmt-90) REVERT: H 396 ASP cc_start: 0.8481 (p0) cc_final: 0.7726 (p0) REVERT: H 463 LYS cc_start: 0.7732 (OUTLIER) cc_final: 0.6622 (mmtt) REVERT: I 28 ARG cc_start: 0.6928 (OUTLIER) cc_final: 0.6692 (mtt180) REVERT: I 86 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6982 (mp0) REVERT: J 28 ARG cc_start: 0.6836 (OUTLIER) cc_final: 0.6573 (mtt180) REVERT: J 31 ASP cc_start: 0.8548 (m-30) cc_final: 0.8257 (m-30) REVERT: J 86 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7025 (mp0) REVERT: K 7 ILE cc_start: 0.7563 (OUTLIER) cc_final: 0.7085 (mm) REVERT: K 86 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.6988 (mp0) REVERT: L 37 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7478 (mttt) outliers start: 189 outliers final: 90 residues processed: 429 average time/residue: 0.8384 time to fit residues: 418.3649 Evaluate side-chains 386 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 253 time to evaluate : 1.341 ------------------------------------------------------------------------------- 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 81 VAL Chi-restraints excluded: chain 3 residue 94 ILE Chi-restraints excluded: chain 3 residue 98 ASN Chi-restraints excluded: chain 3 residue 102 LYS 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 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 106 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 41 ARG 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 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 81 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 474 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 61 SER 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 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 F residue 23 THR Chi-restraints excluded: chain F residue 41 ARG 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 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 106 ASP Chi-restraints excluded: chain G residue 336 GLU 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 77 LEU 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 227 LYS 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 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 18 optimal weight: 3.9990 chunk 314 optimal weight: 6.9990 chunk 319 optimal weight: 5.9990 chunk 425 optimal weight: 5.9990 chunk 371 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 403 optimal weight: 0.2980 chunk 157 optimal weight: 8.9990 chunk 326 optimal weight: 4.9990 chunk 347 optimal weight: 8.9990 chunk 125 optimal weight: 7.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- 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 = 0.3313 r_free = 0.3313 target = 0.111584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.090301 restraints weight = 47149.463| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.85 r_work: 0.2916 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 35343 Z= 0.181 Angle : 0.666 8.269 47892 Z= 0.354 Chirality : 0.047 0.194 5056 Planarity : 0.006 0.070 6272 Dihedral : 6.436 56.955 4932 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.14 % Favored : 92.63 % Rotamer: Outliers : 5.02 % Allowed : 21.83 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.12), residues: 4328 helix: 1.29 (0.14), residues: 1512 sheet: -0.28 (0.20), residues: 672 loop : -2.59 (0.11), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 339 TYR 0.014 0.002 TYR H 80 PHE 0.030 0.002 PHE E 345 TRP 0.015 0.002 TRP A 214 HIS 0.006 0.001 HIS H 292 Details of bonding type rmsd covalent geometry : bond 0.00422 (35340) covalent geometry : angle 0.66604 (47892) hydrogen bonds : bond 0.07581 ( 1176) hydrogen bonds : angle 4.03654 ( 3303) Misc. bond : bond 0.00269 ( 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 433 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 254 time to evaluate : 1.320 Fit side-chains revert: symmetry clash REVERT: 1 132 SER cc_start: 0.7854 (OUTLIER) cc_final: 0.7556 (p) REVERT: 3 102 LYS cc_start: 0.6179 (OUTLIER) cc_final: 0.5848 (mmtm) REVERT: 4 102 LYS cc_start: 0.6123 (OUTLIER) cc_final: 0.5826 (mmtm) REVERT: 4 113 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7380 (mttp) REVERT: A 156 GLN cc_start: 0.8479 (mp-120) cc_final: 0.7205 (tt0) REVERT: A 177 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7272 (ptmt) REVERT: A 396 ASP cc_start: 0.8352 (p0) cc_final: 0.7781 (p0) REVERT: B 41 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8052 (ptp-170) REVERT: B 127 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.7348 (t80) REVERT: B 139 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.8628 (tmm160) REVERT: B 167 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.6903 (ppt170) REVERT: B 177 LYS cc_start: 0.6632 (OUTLIER) cc_final: 0.5711 (mmmt) REVERT: B 183 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7627 (tttm) REVERT: B 295 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8655 (ptt180) REVERT: B 357 ASP cc_start: 0.8409 (t0) cc_final: 0.8100 (t70) REVERT: B 358 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7354 (mmt-90) REVERT: B 396 ASP cc_start: 0.8478 (p0) cc_final: 0.7708 (p0) REVERT: B 463 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.6831 (mmtt) REVERT: C 156 GLN cc_start: 0.8496 (mp-120) cc_final: 0.7215 (tt0) REVERT: C 177 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7200 (ptmt) REVERT: C 396 ASP cc_start: 0.8378 (p0) cc_final: 0.7712 (p0) REVERT: D 61 SER cc_start: 0.8192 (OUTLIER) cc_final: 0.7966 (m) REVERT: D 167 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.6918 (ppt170) REVERT: D 180 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8129 (mp) REVERT: D 183 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7636 (tttm) REVERT: D 295 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8686 (ptt180) REVERT: D 357 ASP cc_start: 0.8483 (t0) cc_final: 0.8237 (t70) REVERT: D 358 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7706 (mmt-90) REVERT: D 396 ASP cc_start: 0.8485 (p0) cc_final: 0.7728 (p0) REVERT: D 463 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.6648 (mmtt) REVERT: E 156 GLN cc_start: 0.8479 (mp-120) cc_final: 0.7211 (tt0) REVERT: E 396 ASP cc_start: 0.8374 (p0) cc_final: 0.7811 (p0) REVERT: E 463 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8200 (ttpp) REVERT: F 127 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.7299 (t80) REVERT: F 139 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8601 (tmm160) REVERT: F 167 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.6817 (ppt170) REVERT: F 180 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8259 (mp) REVERT: F 183 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7628 (tttm) REVERT: F 295 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8661 (ptt180) REVERT: F 357 ASP cc_start: 0.8492 (t0) cc_final: 0.8156 (t70) REVERT: F 358 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7682 (mmt-90) REVERT: F 396 ASP cc_start: 0.8459 (p0) cc_final: 0.7728 (p0) REVERT: F 463 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.6693 (mmtt) REVERT: G 156 GLN cc_start: 0.8504 (mp-120) cc_final: 0.7236 (tt0) REVERT: G 396 ASP cc_start: 0.8311 (p0) cc_final: 0.7726 (p0) REVERT: H 127 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.7356 (t80) REVERT: H 167 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.6930 (ppt170) REVERT: H 175 LYS cc_start: 0.6058 (OUTLIER) cc_final: 0.5379 (mttt) REVERT: H 180 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8134 (mp) REVERT: H 183 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7618 (tttm) REVERT: H 295 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8705 (ptt180) REVERT: H 357 ASP cc_start: 0.8472 (t0) cc_final: 0.8122 (t70) REVERT: H 358 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7665 (mmt-90) REVERT: H 396 ASP cc_start: 0.8467 (p0) cc_final: 0.7689 (p0) REVERT: H 463 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.6646 (mmtt) REVERT: I 86 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.6953 (mp0) REVERT: J 28 ARG cc_start: 0.6855 (OUTLIER) cc_final: 0.6651 (mtt180) REVERT: J 31 ASP cc_start: 0.8580 (m-30) cc_final: 0.8233 (m-30) REVERT: J 86 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7004 (mp0) REVERT: K 86 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.6992 (mp0) REVERT: L 29 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6284 (mt-10) REVERT: L 37 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7496 (mttt) outliers start: 179 outliers final: 103 residues processed: 409 average time/residue: 0.7655 time to fit residues: 365.6810 Evaluate side-chains 400 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 252 time to evaluate : 1.314 ------------------------------------------------------------------------------- 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 132 SER 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 98 ASN 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 98 ASN Chi-restraints excluded: chain 4 residue 102 LYS Chi-restraints excluded: chain 4 residue 113 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 106 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 41 ARG 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 183 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 72 ASP Chi-restraints excluded: chain C residue 78 ASP 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 474 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 61 SER 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 178 LEU 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 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 F residue 23 THR Chi-restraints excluded: chain F residue 41 ARG 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 106 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 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 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 52 THR 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 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 52 THR 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 306 optimal weight: 6.9990 chunk 115 optimal weight: 20.0000 chunk 380 optimal weight: 4.9990 chunk 311 optimal weight: 9.9990 chunk 270 optimal weight: 10.0000 chunk 199 optimal weight: 9.9990 chunk 233 optimal weight: 9.9990 chunk 300 optimal weight: 0.0770 chunk 62 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 420 optimal weight: 5.9990 overall best weight: 3.1944 ------------------------------------------------------------------------------- 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 J 25 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.113264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.092222 restraints weight = 46756.810| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.80 r_work: 0.2948 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 35343 Z= 0.164 Angle : 0.640 7.854 47892 Z= 0.340 Chirality : 0.046 0.190 5056 Planarity : 0.006 0.068 6272 Dihedral : 6.346 56.559 4932 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.07 % Favored : 92.70 % Rotamer: Outliers : 4.99 % Allowed : 21.91 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.12), residues: 4328 helix: 1.38 (0.14), residues: 1512 sheet: -0.26 (0.20), residues: 672 loop : -2.53 (0.11), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 83 TYR 0.012 0.001 TYR H 80 PHE 0.028 0.002 PHE E 345 TRP 0.015 0.001 TRP E 214 HIS 0.006 0.001 HIS F 292 Details of bonding type rmsd covalent geometry : bond 0.00377 (35340) covalent geometry : angle 0.63953 (47892) hydrogen bonds : bond 0.06976 ( 1176) hydrogen bonds : angle 3.96699 ( 3303) Misc. bond : bond 0.00246 ( 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 434 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 256 time to evaluate : 1.426 Fit side-chains revert: symmetry clash REVERT: 1 132 SER cc_start: 0.7897 (OUTLIER) cc_final: 0.7621 (p) REVERT: 2 136 GLU cc_start: 0.5806 (OUTLIER) cc_final: 0.4766 (pm20) REVERT: 3 102 LYS cc_start: 0.6184 (OUTLIER) cc_final: 0.5876 (mmtm) REVERT: 4 102 LYS cc_start: 0.6202 (OUTLIER) cc_final: 0.5915 (mmtm) REVERT: 4 113 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7438 (mttp) REVERT: A 156 GLN cc_start: 0.8499 (mp-120) cc_final: 0.7264 (tt0) REVERT: A 177 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7291 (ptmt) REVERT: A 396 ASP cc_start: 0.8334 (p0) cc_final: 0.7762 (p0) REVERT: B 127 PHE cc_start: 0.8429 (OUTLIER) cc_final: 0.7411 (t80) REVERT: B 139 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8588 (tmm160) REVERT: B 167 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.7011 (ppt170) REVERT: B 177 LYS cc_start: 0.6654 (OUTLIER) cc_final: 0.5767 (mmmt) REVERT: B 183 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7640 (tttm) REVERT: B 295 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8663 (ptt180) REVERT: B 357 ASP cc_start: 0.8399 (t0) cc_final: 0.8105 (t70) REVERT: B 358 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7408 (mmt-90) REVERT: B 360 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.6609 (mtp85) REVERT: B 396 ASP cc_start: 0.8507 (p0) cc_final: 0.7809 (p0) REVERT: B 463 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.6867 (mmtt) REVERT: C 156 GLN cc_start: 0.8521 (mp-120) cc_final: 0.7294 (tt0) REVERT: C 177 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7226 (ptmt) REVERT: C 396 ASP cc_start: 0.8341 (p0) cc_final: 0.7778 (p0) REVERT: D 167 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.7024 (ppt170) REVERT: D 180 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8283 (mp) REVERT: D 183 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7625 (tttm) REVERT: D 295 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8694 (ptt180) REVERT: D 357 ASP cc_start: 0.8495 (t0) cc_final: 0.8266 (t70) REVERT: D 358 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7748 (mmt-90) REVERT: D 396 ASP cc_start: 0.8497 (p0) cc_final: 0.7801 (p0) REVERT: D 463 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.6683 (mmtt) REVERT: E 156 GLN cc_start: 0.8495 (mp-120) cc_final: 0.7280 (tt0) REVERT: E 177 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7194 (mttt) REVERT: E 396 ASP cc_start: 0.8362 (p0) cc_final: 0.7831 (p0) REVERT: E 463 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8184 (ttpp) REVERT: F 127 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.7340 (t80) REVERT: F 139 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.8576 (tmm160) REVERT: F 167 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.7050 (ppt170) REVERT: F 180 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8326 (mp) REVERT: F 183 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7630 (tttm) REVERT: F 295 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8681 (ptt180) REVERT: F 357 ASP cc_start: 0.8506 (t0) cc_final: 0.8195 (t70) REVERT: F 358 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7734 (mmt-90) REVERT: F 396 ASP cc_start: 0.8491 (p0) cc_final: 0.7788 (p0) REVERT: F 463 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.6723 (mmtt) REVERT: G 156 GLN cc_start: 0.8531 (mp-120) cc_final: 0.7316 (tt0) REVERT: G 336 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8575 (tt0) REVERT: G 396 ASP cc_start: 0.8310 (p0) cc_final: 0.7708 (p0) REVERT: H 127 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.7359 (t80) REVERT: H 167 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.7023 (ppt170) REVERT: H 175 LYS cc_start: 0.6053 (OUTLIER) cc_final: 0.5431 (mttt) REVERT: H 180 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8151 (mp) REVERT: H 183 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7631 (tttm) REVERT: H 295 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.8722 (ptt180) REVERT: H 357 ASP cc_start: 0.8491 (t0) cc_final: 0.8279 (t70) REVERT: H 358 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7725 (mmt-90) REVERT: H 396 ASP cc_start: 0.8502 (p0) cc_final: 0.7809 (p0) REVERT: H 463 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.6668 (mmtt) REVERT: I 29 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.6504 (mt-10) REVERT: I 86 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7043 (mp0) REVERT: J 31 ASP cc_start: 0.8616 (m-30) cc_final: 0.8347 (m-30) REVERT: J 86 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7068 (mp0) REVERT: K 86 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7067 (mp0) REVERT: L 29 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6336 (mt-10) REVERT: L 37 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7595 (mttt) outliers start: 178 outliers final: 95 residues processed: 406 average time/residue: 0.7960 time to fit residues: 376.8177 Evaluate side-chains 397 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 255 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 132 SER 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 2 residue 136 GLU 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 98 ASN 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 98 ASN Chi-restraints excluded: chain 4 residue 102 LYS Chi-restraints excluded: chain 4 residue 113 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 106 ASP Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 384 VAL 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 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 183 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 360 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 106 ASP Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 41 ARG 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 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 463 LYS Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 177 LYS 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 41 ARG 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 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 106 ASP Chi-restraints excluded: chain G residue 336 GLU 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 14 LYS 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 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 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 29 GLU Chi-restraints excluded: chain I residue 52 THR 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 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 52 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 194 optimal weight: 10.0000 chunk 411 optimal weight: 0.4980 chunk 414 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 324 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 323 optimal weight: 6.9990 chunk 202 optimal weight: 3.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- 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 = 0.3330 r_free = 0.3330 target = 0.112236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.091207 restraints weight = 46770.009| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.80 r_work: 0.2941 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 35343 Z= 0.184 Angle : 0.668 8.415 47892 Z= 0.355 Chirality : 0.047 0.196 5056 Planarity : 0.006 0.068 6272 Dihedral : 6.419 56.061 4932 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.37 % Favored : 92.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.12), residues: 4328 helix: 1.32 (0.14), residues: 1512 sheet: -0.30 (0.20), residues: 672 loop : -2.55 (0.11), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 339 TYR 0.014 0.002 TYR H 80 PHE 0.030 0.002 PHE G 345 TRP 0.014 0.002 TRP C 214 HIS 0.006 0.001 HIS F 292 Details of bonding type rmsd covalent geometry : bond 0.00428 (35340) covalent geometry : angle 0.66793 (47892) hydrogen bonds : bond 0.07674 ( 1176) hydrogen bonds : angle 4.00445 ( 3303) Misc. bond : bond 0.00267 ( 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 418 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 251 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 132 SER cc_start: 0.7919 (OUTLIER) cc_final: 0.7636 (p) REVERT: 3 102 LYS cc_start: 0.6188 (OUTLIER) cc_final: 0.5883 (mmtm) REVERT: 4 102 LYS cc_start: 0.6203 (OUTLIER) cc_final: 0.5921 (mmtm) REVERT: 4 113 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7445 (mttp) REVERT: A 156 GLN cc_start: 0.8512 (mp-120) cc_final: 0.7277 (tt0) REVERT: A 177 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7341 (ptmt) REVERT: A 396 ASP cc_start: 0.8327 (p0) cc_final: 0.7780 (p0) REVERT: B 127 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.7452 (t80) REVERT: B 139 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.8764 (tmm160) REVERT: B 167 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.7021 (ppt170) REVERT: B 177 LYS cc_start: 0.6661 (OUTLIER) cc_final: 0.5732 (mmmt) REVERT: B 183 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7689 (tttm) REVERT: B 258 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7889 (ttt90) REVERT: B 295 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8683 (ptt180) REVERT: B 357 ASP cc_start: 0.8403 (t0) cc_final: 0.8116 (t70) REVERT: B 358 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7408 (mmt-90) REVERT: B 360 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.6615 (mtp85) REVERT: B 396 ASP cc_start: 0.8493 (p0) cc_final: 0.7775 (p0) REVERT: B 463 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.6852 (mmtt) REVERT: C 156 GLN cc_start: 0.8524 (mp-120) cc_final: 0.7287 (tt0) REVERT: C 177 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7268 (ptmt) REVERT: C 396 ASP cc_start: 0.8355 (p0) cc_final: 0.7809 (p0) REVERT: D 41 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7732 (ptp-170) REVERT: D 167 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.6905 (ppt170) REVERT: D 180 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8291 (mp) REVERT: D 183 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7673 (tttm) REVERT: D 295 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8694 (ptt180) REVERT: D 357 ASP cc_start: 0.8506 (t0) cc_final: 0.8295 (t70) REVERT: D 358 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7748 (mmt-90) REVERT: D 396 ASP cc_start: 0.8504 (p0) cc_final: 0.7770 (p0) REVERT: D 463 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.6682 (mmtt) REVERT: E 156 GLN cc_start: 0.8507 (mp-120) cc_final: 0.7285 (tt0) REVERT: E 177 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7242 (mttt) REVERT: E 396 ASP cc_start: 0.8365 (p0) cc_final: 0.7827 (p0) REVERT: E 463 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8203 (ttpp) REVERT: F 127 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.7434 (t80) REVERT: F 139 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.8595 (tmm160) REVERT: F 167 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.6933 (ppt170) REVERT: F 180 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8295 (mp) REVERT: F 183 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7677 (tttm) REVERT: F 258 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7880 (ttt90) REVERT: F 295 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8685 (ptt180) REVERT: F 357 ASP cc_start: 0.8507 (t0) cc_final: 0.8279 (t70) REVERT: F 358 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7741 (mmt-90) REVERT: F 396 ASP cc_start: 0.8484 (p0) cc_final: 0.7765 (p0) REVERT: F 463 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.6718 (mmtt) REVERT: G 156 GLN cc_start: 0.8546 (mp-120) cc_final: 0.7330 (tt0) REVERT: G 336 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8573 (tt0) REVERT: G 396 ASP cc_start: 0.8308 (p0) cc_final: 0.7754 (p0) REVERT: H 127 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.7331 (t80) REVERT: H 167 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.7026 (ppt170) REVERT: H 180 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8174 (mp) REVERT: H 183 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7679 (tttm) REVERT: H 295 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8726 (ptt180) REVERT: H 357 ASP cc_start: 0.8492 (t0) cc_final: 0.8275 (t70) REVERT: H 358 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7717 (mmt-90) REVERT: H 396 ASP cc_start: 0.8495 (p0) cc_final: 0.7784 (p0) REVERT: H 463 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.6657 (mmtt) REVERT: I 86 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7033 (mp0) REVERT: J 86 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: K 7 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7209 (mm) REVERT: K 86 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: L 29 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6310 (mt-10) REVERT: L 37 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7607 (mttt) outliers start: 167 outliers final: 96 residues processed: 391 average time/residue: 0.8007 time to fit residues: 365.7904 Evaluate side-chains 392 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 248 time to evaluate : 1.328 ------------------------------------------------------------------------------- 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 132 SER 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 98 ASN 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 98 ASN Chi-restraints excluded: chain 4 residue 102 LYS Chi-restraints excluded: chain 4 residue 113 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 106 ASP Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 384 VAL 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 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 183 LYS 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 360 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 106 ASP Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 41 ARG 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 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 177 LYS 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 41 ARG 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 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 106 ASP Chi-restraints excluded: chain G residue 336 GLU 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 14 LYS 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 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 52 THR 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 7 ILE Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 52 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 19 optimal weight: 9.9990 chunk 196 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 362 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 234 optimal weight: 5.9990 chunk 349 optimal weight: 3.9990 chunk 396 optimal weight: 8.9990 chunk 424 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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 = 0.3330 r_free = 0.3330 target = 0.112229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.091184 restraints weight = 46893.710| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.80 r_work: 0.2941 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 35343 Z= 0.184 Angle : 0.668 8.341 47892 Z= 0.355 Chirality : 0.048 0.196 5056 Planarity : 0.006 0.067 6272 Dihedral : 6.441 55.755 4932 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.30 % Favored : 92.47 % Rotamer: Outliers : 4.43 % Allowed : 22.59 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.12), residues: 4328 helix: 1.32 (0.14), residues: 1512 sheet: -0.30 (0.20), residues: 672 loop : -2.54 (0.11), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 339 TYR 0.014 0.002 TYR H 80 PHE 0.030 0.002 PHE E 345 TRP 0.015 0.002 TRP G 214 HIS 0.006 0.001 HIS H 292 Details of bonding type rmsd covalent geometry : bond 0.00429 (35340) covalent geometry : angle 0.66819 (47892) hydrogen bonds : bond 0.07607 ( 1176) hydrogen bonds : angle 3.99822 ( 3303) Misc. bond : bond 0.00270 ( 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 406 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 248 time to evaluate : 1.320 Fit side-chains revert: symmetry clash REVERT: 1 132 SER cc_start: 0.7925 (OUTLIER) cc_final: 0.7652 (p) REVERT: 3 102 LYS cc_start: 0.6201 (OUTLIER) cc_final: 0.5899 (mmtm) REVERT: 4 102 LYS cc_start: 0.6192 (OUTLIER) cc_final: 0.5911 (mmtm) REVERT: 4 113 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7447 (mttp) REVERT: A 156 GLN cc_start: 0.8510 (mp-120) cc_final: 0.7276 (tt0) REVERT: A 177 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7339 (ptmt) REVERT: A 396 ASP cc_start: 0.8348 (p0) cc_final: 0.7762 (p0) REVERT: B 127 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.7451 (t80) REVERT: B 139 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.8770 (tmm160) REVERT: B 167 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.7007 (ppt170) REVERT: B 177 LYS cc_start: 0.6675 (OUTLIER) cc_final: 0.5744 (mmmt) REVERT: B 183 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7657 (tttm) REVERT: B 258 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7871 (ttt90) REVERT: B 295 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.8674 (ptt180) REVERT: B 357 ASP cc_start: 0.8411 (t0) cc_final: 0.8113 (t70) REVERT: B 358 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7414 (mmt-90) REVERT: B 360 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.6607 (mtp85) REVERT: B 396 ASP cc_start: 0.8527 (p0) cc_final: 0.7821 (p0) REVERT: B 463 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.6850 (mmtt) REVERT: C 156 GLN cc_start: 0.8518 (mp-120) cc_final: 0.7279 (tt0) REVERT: C 177 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7283 (ptmt) REVERT: C 396 ASP cc_start: 0.8349 (p0) cc_final: 0.7770 (p0) REVERT: D 167 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.6901 (ppt170) REVERT: D 180 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8288 (mp) REVERT: D 183 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7650 (tttm) REVERT: D 295 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8689 (ptt180) REVERT: D 357 ASP cc_start: 0.8507 (t0) cc_final: 0.8293 (t70) REVERT: D 358 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7750 (mmt-90) REVERT: D 396 ASP cc_start: 0.8509 (p0) cc_final: 0.7819 (p0) REVERT: D 463 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.6684 (mmtt) REVERT: E 156 GLN cc_start: 0.8508 (mp-120) cc_final: 0.7283 (tt0) REVERT: E 177 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7259 (mttt) REVERT: E 396 ASP cc_start: 0.8364 (p0) cc_final: 0.7821 (p0) REVERT: E 463 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8209 (ttpp) REVERT: F 127 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.7426 (t80) REVERT: F 139 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.8597 (tmm160) REVERT: F 167 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.6928 (ppt170) REVERT: F 180 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8285 (mp) REVERT: F 183 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7654 (tttm) REVERT: F 258 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7880 (ttt90) REVERT: F 295 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8684 (ptt180) REVERT: F 357 ASP cc_start: 0.8511 (t0) cc_final: 0.8282 (t70) REVERT: F 358 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7742 (mmt-90) REVERT: F 396 ASP cc_start: 0.8509 (p0) cc_final: 0.7806 (p0) REVERT: F 463 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.6747 (mmtt) REVERT: G 156 GLN cc_start: 0.8546 (mp-120) cc_final: 0.7327 (tt0) REVERT: G 336 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8568 (tt0) REVERT: G 396 ASP cc_start: 0.8337 (p0) cc_final: 0.7754 (p0) REVERT: H 127 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.7309 (t80) REVERT: H 167 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.7016 (ppt170) REVERT: H 175 LYS cc_start: 0.6034 (OUTLIER) cc_final: 0.5521 (mptt) REVERT: H 180 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8181 (mp) REVERT: H 183 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7668 (tttm) REVERT: H 295 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8741 (ptt180) REVERT: H 357 ASP cc_start: 0.8490 (t0) cc_final: 0.8271 (t70) REVERT: H 358 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7721 (mmt-90) REVERT: H 396 ASP cc_start: 0.8518 (p0) cc_final: 0.7813 (p0) REVERT: H 463 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.6657 (mmtt) REVERT: I 86 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7043 (mp0) REVERT: J 86 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7070 (mp0) REVERT: K 86 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7076 (mp0) REVERT: L 29 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6291 (mt-10) REVERT: L 37 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7607 (mttt) outliers start: 158 outliers final: 91 residues processed: 381 average time/residue: 0.8148 time to fit residues: 361.2865 Evaluate side-chains 384 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 246 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 132 SER 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 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 98 ASN Chi-restraints excluded: chain 4 residue 102 LYS Chi-restraints excluded: chain 4 residue 113 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 78 ASP Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 384 VAL 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 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 183 LYS 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 360 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 106 ASP Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 41 ARG 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 463 LYS 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 177 LYS 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 41 ARG 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 258 ARG 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 106 ASP Chi-restraints excluded: chain G residue 336 GLU 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 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 52 THR 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 52 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 28 optimal weight: 9.9990 chunk 403 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 112 optimal weight: 4.9990 chunk 295 optimal weight: 20.0000 chunk 350 optimal weight: 2.9990 chunk 179 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 263 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.112536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.091602 restraints weight = 46659.386| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.79 r_work: 0.2955 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 35343 Z= 0.157 Angle : 0.629 7.699 47892 Z= 0.334 Chirality : 0.046 0.189 5056 Planarity : 0.006 0.067 6272 Dihedral : 6.305 55.699 4932 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.07 % Favored : 92.70 % Rotamer: Outliers : 4.15 % Allowed : 22.87 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.12), residues: 4328 helix: 1.44 (0.14), residues: 1512 sheet: -0.26 (0.20), residues: 672 loop : -2.48 (0.11), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 83 TYR 0.013 0.001 TYR H 80 PHE 0.028 0.002 PHE G 345 TRP 0.015 0.001 TRP G 214 HIS 0.005 0.001 HIS H 292 Details of bonding type rmsd covalent geometry : bond 0.00357 (35340) covalent geometry : angle 0.62884 (47892) hydrogen bonds : bond 0.06717 ( 1176) hydrogen bonds : angle 3.92077 ( 3303) Misc. bond : bond 0.00230 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11017.77 seconds wall clock time: 188 minutes 36.48 seconds (11316.48 seconds total)