Starting phenix.real_space_refine on Mon Jul 6 09:17:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ci2_45608/07_2026/9ci2_45608_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ci2_45608/07_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_45608/07_2026/9ci2_45608_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ci2_45608/07_2026/9ci2_45608_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ci2_45608/07_2026/9ci2_45608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ci2_45608/07_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-dev-6108/lib/python3.11/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: 8.21, per 1000 atoms: 0.24 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: 3.07 Conformation dependent library (CDL) restraints added in 1.5 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: 1.18 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: 6.88 Time building geometry restraints manager: 4.02 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=" O1 CAP E 502 " pdb=" P1 CAP E 502 " ideal model delta sigma weight residual 1.708 1.606 0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" O1 CAP C 502 " pdb=" P1 CAP C 502 " ideal model delta sigma weight residual 1.708 1.608 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" O1 CAP G 502 " pdb=" P1 CAP G 502 " ideal model delta sigma weight residual 1.708 1.608 0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" O1 CAP A 502 " pdb=" P1 CAP A 502 " ideal model delta sigma weight residual 1.708 1.608 0.100 2.00e-02 2.50e+03 2.48e+01 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 ... (remaining 35335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 42092 1.77 - 3.55: 5261 3.55 - 5.32: 484 5.32 - 7.10: 47 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: 17331 17.92 - 35.84: 2277 35.84 - 53.76: 904 53.76 - 71.68: 261 71.68 - 89.60: 55 Dihedral angle restraints: 20828 sinusoidal: 8408 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=" CA SER E 76 " pdb=" C SER E 76 " pdb=" N LEU E 77 " pdb=" CA LEU E 77 " ideal model delta harmonic sigma weight residual 180.00 157.03 22.97 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA LYS E 175 " pdb=" C LYS E 175 " pdb=" N PRO E 176 " pdb=" CA PRO E 176 " ideal model delta harmonic sigma weight residual 0.00 20.44 -20.44 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 20825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3263 0.063 - 0.126: 1328 0.126 - 0.189: 440 0.189 - 0.252: 25 0.252 - 0.315: 4 Chirality restraints: 5060 Sorted by residual: chirality pdb=" C3 CAP G 502 " pdb=" C2 CAP G 502 " pdb=" C4 CAP G 502 " pdb=" O3 CAP G 502 " both_signs ideal model delta sigma weight residual False -2.19 -2.51 0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" C3 CAP C 502 " pdb=" C2 CAP C 502 " pdb=" C4 CAP C 502 " pdb=" O3 CAP C 502 " both_signs ideal model delta sigma weight residual False -2.19 -2.51 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" C3 CAP E 502 " pdb=" C2 CAP E 502 " pdb=" C4 CAP E 502 " pdb=" O3 CAP E 502 " both_signs ideal model delta sigma weight residual False -2.19 -2.50 0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 5057 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: 11.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.870 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 32.400 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.090 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:7.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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= 0.737 Angle : 1.107 8.869 47892 Z= 0.796 Chirality : 0.072 0.315 5060 Planarity : 0.004 0.047 6272 Dihedral : 19.713 89.604 12948 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/Z covalent geometry : bond 0.00937 / 0.68 (35340) covalent geometry : angle 1.10749 / 0.80 (47892) hydrogen bonds : bond 0.24773 / 16.24 ( 1176) hydrogen bonds : angle 7.28218 / 4.89 ( 3303) Misc. bond : bond 0.31923 / 17.98 ( 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 : 1.394 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: 0.7866 time to fit residues: 820.4742 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 : 1.373 ------------------------------------------------------------------------------- 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... 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 2 GLN I 5 ASN K 77 ASN L 90 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.118356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.097705 restraints weight = 46777.537| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.78 r_work: 0.3046 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 35343 Z= 0.155 Angle : 0.655 7.666 47892 Z= 0.352 Chirality : 0.046 0.197 5060 Planarity : 0.006 0.070 6272 Dihedral : 8.147 57.358 5145 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.21 % Favored : 92.40 % Rotamer: Outliers : 6.57 % Allowed : 21.13 % Favored : 72.31 % 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: 0.90 (0.14), residues: 1492 sheet: -0.88 (0.19), residues: 712 loop : -2.90 (0.11), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 83 TYR 0.016 0.001 TYR J 80 PHE 0.027 0.002 PHE G 345 TRP 0.012 0.001 TRP A 385 HIS 0.005 0.001 HIS G 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (35340) covalent geometry : angle 0.65502 / 0.35 (47892) hydrogen bonds : bond 0.06920 / 4.58 ( 1176) hydrogen bonds : angle 4.60727 / 3.12 ( 3303) Misc. bond : bond 0.01631 / 0.90 ( 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 533 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 234 poor density : 299 time to evaluate : 1.367 Fit side-chains REVERT: 1 132 SER cc_start: 0.7877 (OUTLIER) cc_final: 0.7352 (p) REVERT: 2 80 CYS cc_start: 0.7454 (p) cc_final: 0.7126 (m) REVERT: 2 115 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6406 (mt-10) REVERT: 2 133 THR cc_start: 0.7225 (OUTLIER) cc_final: 0.6931 (m) REVERT: 3 78 GLU cc_start: 0.8238 (mm-30) cc_final: 0.8004 (mm-30) REVERT: 3 115 GLU cc_start: 0.6862 (mm-30) cc_final: 0.6351 (mt-10) REVERT: 3 132 SER cc_start: 0.7612 (t) cc_final: 0.7363 (p) REVERT: 4 78 GLU cc_start: 0.8238 (mm-30) cc_final: 0.8002 (mm-30) REVERT: 4 133 THR cc_start: 0.7547 (OUTLIER) cc_final: 0.7121 (p) REVERT: A 156 GLN cc_start: 0.8478 (mp-120) cc_final: 0.7237 (tt0) REVERT: A 177 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.6753 (ptmt) REVERT: A 396 ASP cc_start: 0.8316 (p0) cc_final: 0.7730 (p0) REVERT: B 79 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8135 (ttt180) REVERT: B 139 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8560 (tmm160) REVERT: B 295 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8599 (ptt180) REVERT: B 357 ASP cc_start: 0.8089 (t0) cc_final: 0.7762 (t0) REVERT: B 396 ASP cc_start: 0.8401 (p0) cc_final: 0.7697 (p0) REVERT: B 463 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.6792 (mmtp) REVERT: C 156 GLN cc_start: 0.8495 (mp-120) cc_final: 0.7243 (tt0) REVERT: C 177 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.6705 (ptmt) REVERT: C 396 ASP cc_start: 0.8286 (p0) cc_final: 0.7743 (p0) REVERT: C 444 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7686 (mm) REVERT: D 295 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8603 (ptt180) REVERT: D 396 ASP cc_start: 0.8404 (p0) cc_final: 0.7658 (p0) REVERT: D 463 LYS cc_start: 0.7690 (ptpp) cc_final: 0.6588 (mmtt) REVERT: E 106 ASP cc_start: 0.8356 (m-30) cc_final: 0.8155 (m-30) REVERT: E 156 GLN cc_start: 0.8448 (mp-120) cc_final: 0.7221 (tt0) REVERT: E 396 ASP cc_start: 0.8328 (p0) cc_final: 0.7731 (p0) REVERT: E 439 ARG cc_start: 0.6695 (OUTLIER) cc_final: 0.6236 (mtp85) REVERT: F 77 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7657 (mp) REVERT: F 295 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8580 (ptt180) REVERT: F 396 ASP cc_start: 0.8412 (p0) cc_final: 0.7708 (p0) REVERT: F 455 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7407 (tp) REVERT: F 463 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.6572 (mmtt) REVERT: G 156 GLN cc_start: 0.8498 (mp-120) cc_final: 0.7247 (tt0) REVERT: G 396 ASP cc_start: 0.8286 (p0) cc_final: 0.7730 (p0) REVERT: H 79 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8255 (ttt180) REVERT: H 180 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8054 (mp) REVERT: H 396 ASP cc_start: 0.8411 (p0) cc_final: 0.7708 (p0) REVERT: H 463 LYS cc_start: 0.7670 (ptpp) cc_final: 0.6565 (mmtt) REVERT: I 28 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.6707 (mtt180) REVERT: I 29 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6604 (mt-10) REVERT: J 8 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.8026 (t0) REVERT: J 28 ARG cc_start: 0.7056 (OUTLIER) cc_final: 0.6713 (mtt180) REVERT: J 29 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6628 (mt-10) REVERT: K 7 ILE cc_start: 0.7820 (OUTLIER) cc_final: 0.7503 (mm) REVERT: K 8 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.8126 (t0) REVERT: K 29 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6681 (mt-10) REVERT: L 29 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6408 (mt-10) outliers start: 234 outliers final: 64 residues processed: 504 average time/residue: 0.6937 time to fit residues: 414.4286 Evaluate side-chains 372 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 281 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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 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 203 ASP 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 173 THR 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 1 MET 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 7 ILE Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 100 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 343 optimal weight: 0.2980 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: 10.0000 chunk 367 optimal weight: 6.9990 chunk 179 optimal weight: 10.0000 chunk 308 optimal weight: 0.6980 chunk 239 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 overall best weight: 1.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 327 HIS D 327 HIS D 383 HIS I 25 GLN I 104 ASN J 25 GLN K 25 GLN L 90 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.117784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.096794 restraints weight = 46472.035| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.82 r_work: 0.3027 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.2267 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= 0.127 Angle : 0.584 6.476 47892 Z= 0.311 Chirality : 0.044 0.168 5060 Planarity : 0.005 0.063 6272 Dihedral : 6.492 59.325 5027 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.93 % Favored : 92.84 % Rotamer: Outliers : 5.33 % Allowed : 21.63 % 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: -1.21 (0.12), residues: 4328 helix: 1.36 (0.14), residues: 1500 sheet: -0.57 (0.20), residues: 648 loop : -2.59 (0.11), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 83 TYR 0.012 0.001 TYR J 80 PHE 0.027 0.001 PHE G 345 TRP 0.011 0.001 TRP C 214 HIS 0.005 0.001 HIS 2 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (35340) covalent geometry : angle 0.58421 / 0.31 (47892) hydrogen bonds : bond 0.05666 / 3.73 ( 1176) hydrogen bonds : angle 4.10895 / 2.78 ( 3303) Misc. bond : bond 0.00436 / 0.25 ( 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 494 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 304 time to evaluate : 1.413 Fit side-chains REVERT: 1 132 SER cc_start: 0.7669 (t) cc_final: 0.7270 (p) REVERT: 2 80 CYS cc_start: 0.7579 (p) cc_final: 0.7084 (m) REVERT: 2 91 VAL cc_start: 0.6994 (t) cc_final: 0.6694 (p) REVERT: 2 98 ASN cc_start: 0.7238 (OUTLIER) cc_final: 0.7007 (t0) REVERT: 2 115 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6418 (mt-10) REVERT: 2 133 THR cc_start: 0.7302 (OUTLIER) cc_final: 0.7051 (m) REVERT: 3 78 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7924 (mm-30) REVERT: 3 132 SER cc_start: 0.7248 (t) cc_final: 0.7040 (p) REVERT: 4 133 THR cc_start: 0.7559 (OUTLIER) cc_final: 0.7145 (p) REVERT: A 156 GLN cc_start: 0.8462 (mp-120) cc_final: 0.7186 (tt0) REVERT: A 396 ASP cc_start: 0.8237 (p0) cc_final: 0.7612 (p0) REVERT: B 79 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8240 (ttt180) REVERT: B 139 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.8567 (tmm160) REVERT: B 177 LYS cc_start: 0.6200 (OUTLIER) cc_final: 0.5874 (mmmt) REVERT: B 295 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8558 (ptt180) REVERT: B 357 ASP cc_start: 0.8205 (t0) cc_final: 0.7844 (t70) REVERT: B 396 ASP cc_start: 0.8442 (p0) cc_final: 0.7696 (p0) REVERT: B 463 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.6789 (mmtt) REVERT: C 156 GLN cc_start: 0.8479 (mp-120) cc_final: 0.7217 (tt0) REVERT: C 396 ASP cc_start: 0.8251 (p0) cc_final: 0.7758 (p0) REVERT: D 180 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.7970 (mp) REVERT: D 295 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8578 (ptt180) REVERT: D 357 ASP cc_start: 0.8450 (t0) cc_final: 0.8212 (t70) REVERT: D 358 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7734 (mmt-90) REVERT: D 396 ASP cc_start: 0.8432 (p0) cc_final: 0.7664 (p0) REVERT: D 463 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.6625 (mmtt) REVERT: E 156 GLN cc_start: 0.8445 (mp-120) cc_final: 0.7185 (tt0) REVERT: E 396 ASP cc_start: 0.8274 (p0) cc_final: 0.7656 (p0) REVERT: E 463 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8349 (ttpp) REVERT: E 474 THR cc_start: 0.7152 (OUTLIER) cc_final: 0.6943 (p) REVERT: F 127 PHE cc_start: 0.8074 (OUTLIER) cc_final: 0.7066 (t80) REVERT: F 180 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.7979 (mp) REVERT: F 295 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8550 (ptt180) REVERT: F 358 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7734 (mmt-90) REVERT: F 396 ASP cc_start: 0.8421 (p0) cc_final: 0.7662 (p0) REVERT: F 455 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7309 (tp) REVERT: F 463 LYS cc_start: 0.7653 (ptpp) cc_final: 0.6588 (mmtt) REVERT: G 156 GLN cc_start: 0.8484 (mp-120) cc_final: 0.7222 (tt0) REVERT: G 396 ASP cc_start: 0.8229 (p0) cc_final: 0.7646 (p0) REVERT: G 466 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7742 (mttm) REVERT: H 79 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8233 (ttt180) REVERT: H 180 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8022 (mp) REVERT: H 357 ASP cc_start: 0.8443 (t0) cc_final: 0.8189 (t70) REVERT: H 396 ASP cc_start: 0.8445 (p0) cc_final: 0.7693 (p0) REVERT: H 463 LYS cc_start: 0.7693 (ptpp) cc_final: 0.6595 (mmtt) REVERT: I 28 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.6749 (mtt180) REVERT: I 29 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6458 (mt-10) REVERT: I 86 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7048 (mp0) REVERT: J 8 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7994 (t0) REVERT: J 28 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.6625 (mtt180) REVERT: J 29 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6407 (mt-10) REVERT: J 31 ASP cc_start: 0.8512 (m-30) cc_final: 0.8292 (m-30) REVERT: J 86 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7074 (mp0) REVERT: K 7 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7375 (mm) REVERT: K 29 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6424 (mt-10) outliers start: 190 outliers final: 70 residues processed: 467 average time/residue: 0.7366 time to fit residues: 405.1705 Evaluate side-chains 374 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 273 time to evaluate : 1.346 ------------------------------------------------------------------------------- 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 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 78 ASP Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 177 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 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 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 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 79 ARG Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 463 LYS Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 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 455 LEU 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 203 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 H residue 14 LYS Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 180 LEU 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 1 MET Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain K residue 100 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 275 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 282 optimal weight: 0.0040 chunk 290 optimal weight: 6.9990 chunk 336 optimal weight: 5.9990 chunk 245 optimal weight: 7.9990 chunk 402 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 216 optimal weight: 2.9990 chunk 194 optimal weight: 20.0000 chunk 148 optimal weight: 1.9990 overall best weight: 3.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 153 HIS C 153 HIS E 153 HIS F 327 HIS G 153 HIS I 25 GLN J 25 GLN J 104 ASN K 25 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.112703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.091365 restraints weight = 46940.204| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.86 r_work: 0.2932 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 35343 Z= 0.186 Angle : 0.681 9.560 47892 Z= 0.363 Chirality : 0.048 0.253 5060 Planarity : 0.006 0.081 6272 Dihedral : 6.545 58.981 5015 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.56 % Favored : 92.21 % Rotamer: Outliers : 4.88 % Allowed : 21.94 % Favored : 73.18 % Cbeta Deviations : 0.03 % 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: -1.26 (0.12), residues: 4328 helix: 1.26 (0.14), residues: 1516 sheet: -0.52 (0.20), residues: 668 loop : -2.63 (0.11), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 83 TYR 0.015 0.002 TYR H 80 PHE 0.032 0.002 PHE G 345 TRP 0.011 0.001 TRP G 214 HIS 0.007 0.002 HIS F 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 (35340) covalent geometry : angle 0.68101 / 0.36 (47892) hydrogen bonds : bond 0.07902 / 5.19 ( 1176) hydrogen bonds : angle 4.10786 / 2.79 ( 3303) Misc. bond : bond 0.01490 / 0.82 ( 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 445 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 271 time to evaluate : 1.453 Fit side-chains revert: symmetry clash REVERT: 1 132 SER cc_start: 0.7674 (t) cc_final: 0.7172 (p) REVERT: 2 91 VAL cc_start: 0.7062 (t) cc_final: 0.6762 (p) REVERT: 3 91 VAL cc_start: 0.7129 (t) cc_final: 0.6895 (p) REVERT: 3 132 SER cc_start: 0.7165 (t) cc_final: 0.6801 (p) REVERT: A 156 GLN cc_start: 0.8490 (mp-120) cc_final: 0.7195 (tt0) REVERT: A 177 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7165 (ptmt) REVERT: A 396 ASP cc_start: 0.8386 (p0) cc_final: 0.7820 (p0) REVERT: B 79 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8207 (ttt180) REVERT: B 139 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8602 (tmm160) REVERT: B 295 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8582 (ptt180) REVERT: B 357 ASP cc_start: 0.8316 (t0) cc_final: 0.7917 (t70) REVERT: B 396 ASP cc_start: 0.8549 (p0) cc_final: 0.7792 (p0) REVERT: B 455 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7352 (tp) REVERT: B 463 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.6814 (mmtt) REVERT: C 156 GLN cc_start: 0.8494 (mp-120) cc_final: 0.7198 (tt0) REVERT: C 396 ASP cc_start: 0.8372 (p0) cc_final: 0.7805 (p0) REVERT: D 139 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8505 (tmm160) REVERT: D 295 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8595 (ptt180) REVERT: D 357 ASP cc_start: 0.8449 (t0) cc_final: 0.8187 (t70) REVERT: D 358 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7685 (mmt-90) REVERT: D 396 ASP cc_start: 0.8530 (p0) cc_final: 0.7789 (p0) REVERT: D 463 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.6616 (mmtt) REVERT: E 156 GLN cc_start: 0.8476 (mp-120) cc_final: 0.7188 (tt0) REVERT: E 396 ASP cc_start: 0.8370 (p0) cc_final: 0.7813 (p0) REVERT: F 77 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7568 (tp) REVERT: F 127 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.7135 (t80) REVERT: F 139 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.8672 (tmm160) REVERT: F 295 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8567 (ptt180) REVERT: F 357 ASP cc_start: 0.8476 (t0) cc_final: 0.8274 (t70) REVERT: F 358 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7679 (mmt-90) REVERT: F 396 ASP cc_start: 0.8502 (p0) cc_final: 0.7759 (p0) REVERT: F 455 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7345 (tp) REVERT: F 463 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.6587 (mmtt) REVERT: G 156 GLN cc_start: 0.8503 (mp-120) cc_final: 0.7209 (tt0) REVERT: G 396 ASP cc_start: 0.8337 (p0) cc_final: 0.7763 (p0) REVERT: H 79 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8227 (ttt180) REVERT: H 127 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7541 (t80) REVERT: H 139 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8515 (tmm160) REVERT: H 180 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8088 (mp) REVERT: H 357 ASP cc_start: 0.8449 (t0) cc_final: 0.8188 (t70) REVERT: H 358 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7676 (mmt-90) REVERT: H 396 ASP cc_start: 0.8520 (p0) cc_final: 0.7802 (p0) REVERT: H 463 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.6570 (mmtt) REVERT: I 8 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7950 (t0) REVERT: I 28 ARG cc_start: 0.6979 (OUTLIER) cc_final: 0.6658 (mtt180) REVERT: I 86 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.6999 (mp0) REVERT: J 8 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7995 (t0) REVERT: J 28 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.6534 (mtt180) REVERT: J 31 ASP cc_start: 0.8543 (m-30) cc_final: 0.8292 (m-30) REVERT: J 86 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7032 (mp0) REVERT: K 7 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7397 (mm) REVERT: K 8 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.8002 (t0) REVERT: K 29 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6460 (mt-10) REVERT: L 29 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6342 (mt-10) REVERT: L 37 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7522 (mttt) outliers start: 174 outliers final: 72 residues processed: 425 average time/residue: 0.7862 time to fit residues: 393.1898 Evaluate side-chains 361 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 255 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 70 LEU Chi-restraints excluded: chain 1 residue 81 VAL Chi-restraints excluded: chain 1 residue 94 ILE Chi-restraints excluded: chain 1 residue 98 ASN Chi-restraints excluded: chain 1 residue 134 PHE Chi-restraints excluded: chain 2 residue 65 THR Chi-restraints excluded: chain 2 residue 70 LEU Chi-restraints excluded: chain 2 residue 94 ILE Chi-restraints excluded: chain 2 residue 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 134 PHE Chi-restraints excluded: chain 4 residue 70 LEU Chi-restraints excluded: chain 4 residue 81 VAL Chi-restraints excluded: chain 4 residue 94 ILE Chi-restraints excluded: chain 4 residue 133 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 175 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 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 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 71 THR Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 139 ARG 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 60 GLU 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 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 106 ASP Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 139 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 455 LEU 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 384 VAL 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 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 178 LEU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 347 ASP Chi-restraints excluded: chain H residue 358 ARG Chi-restraints excluded: chain H residue 444 ILE Chi-restraints excluded: chain H residue 463 LYS Chi-restraints excluded: chain I residue 8 ASP Chi-restraints excluded: chain I residue 28 ARG Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain 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 29 GLU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain L residue 111 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 172 optimal weight: 5.9990 chunk 287 optimal weight: 10.0000 chunk 387 optimal weight: 3.9990 chunk 286 optimal weight: 1.9990 chunk 318 optimal weight: 1.9990 chunk 225 optimal weight: 0.9980 chunk 285 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 362 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 327 HIS I 25 GLN J 25 GLN K 25 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.115278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.094233 restraints weight = 46717.569| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.82 r_work: 0.2979 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 35343 Z= 0.144 Angle : 0.601 7.258 47892 Z= 0.320 Chirality : 0.045 0.178 5060 Planarity : 0.005 0.062 6272 Dihedral : 6.391 59.680 5013 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.61 % Favored : 93.16 % Rotamer: Outliers : 5.16 % Allowed : 21.69 % 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: -1.07 (0.12), residues: 4328 helix: 1.41 (0.14), residues: 1520 sheet: -0.44 (0.20), residues: 668 loop : -2.53 (0.11), residues: 2140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 83 TYR 0.015 0.001 TYR J 80 PHE 0.027 0.002 PHE G 345 TRP 0.013 0.001 TRP A 214 HIS 0.005 0.001 HIS H 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (35340) covalent geometry : angle 0.60095 / 0.32 (47892) hydrogen bonds : bond 0.06244 / 4.10 ( 1176) hydrogen bonds : angle 3.95050 / 2.67 ( 3303) Misc. bond : bond 0.00773 / 0.44 ( 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 458 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 274 time to evaluate : 1.347 Fit side-chains REVERT: 1 132 SER cc_start: 0.7744 (t) cc_final: 0.7278 (p) REVERT: 2 91 VAL cc_start: 0.7131 (t) cc_final: 0.6826 (p) REVERT: 3 91 VAL cc_start: 0.7167 (t) cc_final: 0.6911 (p) REVERT: 3 132 SER cc_start: 0.7048 (t) cc_final: 0.6641 (p) REVERT: A 156 GLN cc_start: 0.8465 (mp-120) cc_final: 0.7221 (tt0) REVERT: A 396 ASP cc_start: 0.8278 (p0) cc_final: 0.7652 (p0) REVERT: B 127 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.7183 (t80) REVERT: B 139 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.8650 (tmm160) REVERT: B 175 LYS cc_start: 0.5927 (OUTLIER) cc_final: 0.5353 (mtpt) REVERT: B 177 LYS cc_start: 0.6433 (OUTLIER) cc_final: 0.5790 (mmmt) REVERT: B 295 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8583 (ptt180) REVERT: B 357 ASP cc_start: 0.8305 (t0) cc_final: 0.7928 (t70) REVERT: B 396 ASP cc_start: 0.8503 (p0) cc_final: 0.7791 (p0) REVERT: B 463 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.6848 (mmtt) REVERT: C 156 GLN cc_start: 0.8474 (mp-120) cc_final: 0.7224 (tt0) REVERT: C 396 ASP cc_start: 0.8267 (p0) cc_final: 0.7690 (p0) REVERT: C 439 ARG cc_start: 0.6442 (OUTLIER) cc_final: 0.6058 (mtm110) REVERT: D 180 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8009 (mp) REVERT: D 295 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8593 (ptt180) REVERT: D 357 ASP cc_start: 0.8470 (t0) cc_final: 0.8223 (t70) REVERT: D 358 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7719 (mmt-90) REVERT: D 396 ASP cc_start: 0.8492 (p0) cc_final: 0.7787 (p0) REVERT: D 450 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.7009 (mptm) REVERT: D 463 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.6665 (mmtt) REVERT: E 156 GLN cc_start: 0.8457 (mp-120) cc_final: 0.7211 (tt0) REVERT: E 396 ASP cc_start: 0.8297 (p0) cc_final: 0.7660 (p0) REVERT: E 463 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8233 (ttpp) REVERT: F 77 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7721 (tp) REVERT: F 127 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7282 (t80) REVERT: F 180 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8015 (mp) REVERT: F 295 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8583 (ptt180) REVERT: F 357 ASP cc_start: 0.8463 (t0) cc_final: 0.8256 (t70) REVERT: F 358 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7704 (mmt-90) REVERT: F 396 ASP cc_start: 0.8459 (p0) cc_final: 0.7752 (p0) REVERT: F 455 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7232 (tp) REVERT: F 463 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.6632 (mmtt) REVERT: G 156 GLN cc_start: 0.8479 (mp-120) cc_final: 0.7235 (tt0) REVERT: G 396 ASP cc_start: 0.8251 (p0) cc_final: 0.7665 (p0) REVERT: G 466 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7818 (mttm) REVERT: H 79 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8259 (ttt180) REVERT: H 127 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7606 (t80) REVERT: H 180 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8092 (mp) REVERT: H 357 ASP cc_start: 0.8466 (t0) cc_final: 0.8180 (t70) REVERT: H 358 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7734 (mmt-90) REVERT: H 396 ASP cc_start: 0.8490 (p0) cc_final: 0.7772 (p0) REVERT: H 463 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.6646 (mmtt) REVERT: I 28 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6821 (mtt180) REVERT: I 86 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7024 (mp0) REVERT: J 8 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7979 (t0) REVERT: J 28 ARG cc_start: 0.6967 (OUTLIER) cc_final: 0.6649 (mtt180) REVERT: J 31 ASP cc_start: 0.8570 (m-30) cc_final: 0.8283 (m-30) REVERT: J 86 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7032 (mp0) REVERT: L 29 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6388 (mt-10) REVERT: L 37 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7459 (mttt) outliers start: 184 outliers final: 77 residues processed: 425 average time/residue: 0.7804 time to fit residues: 391.7035 Evaluate side-chains 373 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 263 time to evaluate : 1.240 ------------------------------------------------------------------------------- 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 65 THR Chi-restraints excluded: chain 3 residue 70 LEU 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 78 ASP 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 175 LYS Chi-restraints excluded: chain B residue 177 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 463 LYS Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 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 72 ASP Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 463 LYS Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 173 THR 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 455 LEU 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 203 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 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 127 PHE Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 347 ASP Chi-restraints excluded: chain H residue 358 ARG Chi-restraints excluded: chain H residue 444 ILE Chi-restraints excluded: chain H residue 463 LYS Chi-restraints excluded: chain I residue 8 ASP Chi-restraints excluded: chain I residue 28 ARG Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 107 GLN Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 8 ASP Chi-restraints excluded: chain J residue 28 ARG Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 86 GLU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 100 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 348 optimal weight: 9.9990 chunk 95 optimal weight: 9.9990 chunk 115 optimal weight: 0.4980 chunk 265 optimal weight: 10.0000 chunk 258 optimal weight: 4.9990 chunk 398 optimal weight: 0.0370 chunk 169 optimal weight: 5.9990 chunk 120 optimal weight: 0.0010 chunk 24 optimal weight: 8.9990 chunk 182 optimal weight: 10.0000 chunk 334 optimal weight: 8.9990 overall best weight: 2.3068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 45 GLN I 25 GLN J 25 GLN K 25 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.115442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.094385 restraints weight = 46367.548| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.82 r_work: 0.2988 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 35343 Z= 0.135 Angle : 0.586 7.244 47892 Z= 0.311 Chirality : 0.044 0.178 5060 Planarity : 0.005 0.059 6272 Dihedral : 6.175 59.324 5012 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.65 % Favored : 93.11 % Rotamer: Outliers : 4.52 % Allowed : 22.31 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.82 (0.13), residues: 4328 helix: 1.63 (0.14), residues: 1496 sheet: -0.36 (0.19), residues: 748 loop : -2.39 (0.12), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 83 TYR 0.012 0.001 TYR H 80 PHE 0.028 0.002 PHE G 345 TRP 0.012 0.001 TRP G 214 HIS 0.005 0.001 HIS H 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (35340) covalent geometry : angle 0.58594 / 0.31 (47892) hydrogen bonds : bond 0.05942 / 3.90 ( 1176) hydrogen bonds : angle 3.84175 / 2.60 ( 3303) Misc. bond : bond 0.00291 / 0.17 ( 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 434 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 273 time to evaluate : 1.241 Fit side-chains REVERT: 1 132 SER cc_start: 0.7781 (t) cc_final: 0.7320 (p) REVERT: 2 91 VAL cc_start: 0.7142 (t) cc_final: 0.6814 (p) REVERT: A 156 GLN cc_start: 0.8455 (mp-120) cc_final: 0.7194 (tt0) REVERT: A 396 ASP cc_start: 0.8289 (p0) cc_final: 0.7733 (p0) REVERT: B 127 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.7204 (t80) REVERT: B 139 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8653 (tmm160) REVERT: B 175 LYS cc_start: 0.5880 (OUTLIER) cc_final: 0.5354 (mtpt) REVERT: B 177 LYS cc_start: 0.6462 (OUTLIER) cc_final: 0.5807 (mmmt) REVERT: B 295 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8611 (ptt180) REVERT: B 357 ASP cc_start: 0.8339 (t0) cc_final: 0.7958 (t70) REVERT: B 396 ASP cc_start: 0.8504 (p0) cc_final: 0.7789 (p0) REVERT: B 463 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.6826 (mmtt) REVERT: C 156 GLN cc_start: 0.8468 (mp-120) cc_final: 0.7205 (tt0) REVERT: C 396 ASP cc_start: 0.8293 (p0) cc_final: 0.7675 (p0) REVERT: C 439 ARG cc_start: 0.6383 (OUTLIER) cc_final: 0.5998 (mtm110) REVERT: D 79 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8133 (ttt180) REVERT: D 180 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8023 (mp) REVERT: D 295 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8600 (ptt180) REVERT: D 357 ASP cc_start: 0.8465 (t0) cc_final: 0.8174 (t70) REVERT: D 358 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7698 (mmt-90) REVERT: D 396 ASP cc_start: 0.8505 (p0) cc_final: 0.7784 (p0) REVERT: D 450 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.7001 (mptm) REVERT: D 463 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.6674 (mmtt) REVERT: E 156 GLN cc_start: 0.8439 (mp-120) cc_final: 0.7189 (tt0) REVERT: E 396 ASP cc_start: 0.8282 (p0) cc_final: 0.7669 (p0) REVERT: E 463 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8149 (ttpp) REVERT: F 127 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.7286 (t80) REVERT: F 139 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8633 (tmm160) REVERT: F 180 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8025 (mp) REVERT: F 295 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8588 (ptt180) REVERT: F 357 ASP cc_start: 0.8494 (t0) cc_final: 0.8272 (t70) REVERT: F 358 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7703 (mmt-90) REVERT: F 396 ASP cc_start: 0.8486 (p0) cc_final: 0.7773 (p0) REVERT: F 455 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7223 (tp) REVERT: F 463 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.6632 (mmtt) REVERT: G 156 GLN cc_start: 0.8466 (mp-120) cc_final: 0.7216 (tt0) REVERT: G 396 ASP cc_start: 0.8255 (p0) cc_final: 0.7709 (p0) REVERT: H 77 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.6912 (tp) REVERT: H 127 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.7637 (t80) REVERT: H 180 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8074 (mp) REVERT: H 357 ASP cc_start: 0.8479 (t0) cc_final: 0.8167 (t70) REVERT: H 358 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7715 (mmt-90) REVERT: H 396 ASP cc_start: 0.8509 (p0) cc_final: 0.7790 (p0) REVERT: H 463 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.6617 (mmtt) REVERT: I 28 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.6800 (mtt180) REVERT: I 86 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7023 (mp0) REVERT: J 28 ARG cc_start: 0.6934 (OUTLIER) cc_final: 0.6650 (mtt180) REVERT: J 31 ASP cc_start: 0.8522 (m-30) cc_final: 0.8238 (m-30) REVERT: J 86 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: K 7 ILE cc_start: 0.7609 (OUTLIER) cc_final: 0.7139 (mm) REVERT: K 29 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6469 (mt-10) REVERT: L 29 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6365 (mt-10) REVERT: L 37 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7461 (mttt) outliers start: 161 outliers final: 71 residues processed: 405 average time/residue: 0.7718 time to fit residues: 368.9624 Evaluate side-chains 364 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 259 time to evaluate : 1.263 ------------------------------------------------------------------------------- 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 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 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 133 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 139 ARG 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 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 384 VAL Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 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 384 VAL Chi-restraints excluded: chain E residue 463 LYS Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 173 THR 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 455 LEU Chi-restraints excluded: chain F residue 463 LYS Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 464 GLU Chi-restraints excluded: chain 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 178 LEU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 347 ASP Chi-restraints excluded: chain H residue 358 ARG Chi-restraints excluded: chain H residue 444 ILE Chi-restraints excluded: chain H residue 463 LYS Chi-restraints excluded: chain I residue 8 ASP Chi-restraints excluded: chain I residue 28 ARG Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain 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 29 GLU Chi-restraints excluded: chain K residue 86 GLU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain L residue 111 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 18 optimal weight: 20.0000 chunk 314 optimal weight: 6.9990 chunk 319 optimal weight: 7.9990 chunk 425 optimal weight: 3.9990 chunk 371 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 403 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 326 optimal weight: 7.9990 chunk 347 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3321 r_free = 0.3321 target = 0.112190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.090893 restraints weight = 47091.530| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.85 r_work: 0.2924 rms_B_bonded: 2.23 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: 0.8904 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 35343 Z= 0.182 Angle : 0.656 8.240 47892 Z= 0.349 Chirality : 0.047 0.190 5060 Planarity : 0.006 0.061 6272 Dihedral : 6.186 57.128 5009 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.12 % Favored : 92.65 % Rotamer: Outliers : 4.63 % Allowed : 22.28 % 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: -1.02 (0.12), residues: 4328 helix: 1.43 (0.14), residues: 1508 sheet: -0.30 (0.20), residues: 632 loop : -2.46 (0.11), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG K 83 TYR 0.014 0.002 TYR H 80 PHE 0.030 0.002 PHE G 345 TRP 0.013 0.001 TRP A 214 HIS 0.006 0.001 HIS H 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (35340) covalent geometry : angle 0.65621 / 0.35 (47892) hydrogen bonds : bond 0.07554 / 4.96 ( 1176) hydrogen bonds : angle 3.97373 / 2.69 ( 3303) Misc. bond : bond 0.00251 / 0.14 ( 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 420 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 255 time to evaluate : 1.483 Fit side-chains revert: symmetry clash REVERT: 1 132 SER cc_start: 0.7768 (t) cc_final: 0.7236 (p) REVERT: 2 91 VAL cc_start: 0.7136 (t) cc_final: 0.6800 (p) REVERT: A 156 GLN cc_start: 0.8484 (mp-120) cc_final: 0.7205 (tt0) REVERT: A 396 ASP cc_start: 0.8346 (p0) cc_final: 0.7772 (p0) REVERT: B 127 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7249 (t80) REVERT: B 139 ARG cc_start: 0.9135 (OUTLIER) cc_final: 0.8625 (tmm160) REVERT: B 167 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.6838 (ppt170) REVERT: B 177 LYS cc_start: 0.6533 (OUTLIER) cc_final: 0.5813 (mmmt) REVERT: B 295 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8637 (ptt180) REVERT: B 357 ASP cc_start: 0.8410 (t0) cc_final: 0.8100 (t70) REVERT: B 358 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7366 (mmt-90) REVERT: B 396 ASP cc_start: 0.8517 (p0) cc_final: 0.7754 (p0) REVERT: B 463 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.6818 (mmtt) REVERT: C 156 GLN cc_start: 0.8498 (mp-120) cc_final: 0.7212 (tt0) REVERT: C 396 ASP cc_start: 0.8364 (p0) cc_final: 0.7699 (p0) REVERT: C 439 ARG cc_start: 0.6396 (OUTLIER) cc_final: 0.6106 (mtm110) REVERT: D 167 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.6849 (ppt170) REVERT: D 180 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8055 (mp) REVERT: D 295 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8652 (ptt180) REVERT: D 357 ASP cc_start: 0.8496 (t0) cc_final: 0.8232 (t70) REVERT: D 358 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7677 (mmt-90) REVERT: D 396 ASP cc_start: 0.8506 (p0) cc_final: 0.7765 (p0) REVERT: D 450 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.6958 (mptm) REVERT: D 463 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.6671 (mmtt) REVERT: E 156 GLN cc_start: 0.8477 (mp-120) cc_final: 0.7197 (tt0) REVERT: E 396 ASP cc_start: 0.8353 (p0) cc_final: 0.7694 (p0) REVERT: E 463 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8185 (ttpp) REVERT: F 127 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.7322 (t80) REVERT: F 139 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8593 (tmm160) REVERT: F 167 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.6760 (ppt170) REVERT: F 180 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8080 (mp) REVERT: F 295 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8644 (ptt180) REVERT: F 357 ASP cc_start: 0.8492 (t70) cc_final: 0.8275 (t70) REVERT: F 358 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7678 (mmt-90) REVERT: F 396 ASP cc_start: 0.8490 (p0) cc_final: 0.7736 (p0) REVERT: F 455 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7244 (tp) REVERT: F 463 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.6631 (mmtt) REVERT: G 156 GLN cc_start: 0.8504 (mp-120) cc_final: 0.7224 (tt0) REVERT: G 396 ASP cc_start: 0.8318 (p0) cc_final: 0.7737 (p0) REVERT: H 127 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.7629 (t80) REVERT: H 167 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.6971 (ppt170) REVERT: H 175 LYS cc_start: 0.6046 (OUTLIER) cc_final: 0.5519 (mtpp) REVERT: H 180 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8140 (mp) REVERT: H 357 ASP cc_start: 0.8492 (t0) cc_final: 0.8225 (t70) REVERT: H 358 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7683 (mmt-90) REVERT: H 396 ASP cc_start: 0.8463 (p0) cc_final: 0.7692 (p0) REVERT: H 463 LYS cc_start: 0.7741 (OUTLIER) cc_final: 0.6627 (mmtt) REVERT: I 28 ARG cc_start: 0.6967 (OUTLIER) cc_final: 0.6746 (mtt180) REVERT: I 86 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.6968 (mp0) REVERT: J 28 ARG cc_start: 0.6840 (OUTLIER) cc_final: 0.6596 (mtt180) REVERT: J 31 ASP cc_start: 0.8547 (m-30) cc_final: 0.8225 (m-30) REVERT: J 86 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7010 (mp0) REVERT: K 7 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7120 (mm) REVERT: L 29 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6402 (mt-10) REVERT: L 37 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7517 (mttt) outliers start: 165 outliers final: 79 residues processed: 388 average time/residue: 0.7768 time to fit residues: 355.1741 Evaluate side-chains 365 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 250 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 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 133 THR Chi-restraints excluded: chain 3 residue 134 PHE Chi-restraints excluded: chain 4 residue 65 THR Chi-restraints excluded: chain 4 residue 70 LEU Chi-restraints excluded: chain 4 residue 81 VAL Chi-restraints excluded: chain 4 residue 94 ILE Chi-restraints excluded: chain 4 residue 133 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 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 384 VAL Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 167 ARG Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 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 384 VAL Chi-restraints excluded: chain E residue 463 LYS Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 167 ARG Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 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 455 LEU Chi-restraints excluded: chain F residue 463 LYS Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 464 GLU 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 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 100 LEU Chi-restraints excluded: chain J residue 8 ASP Chi-restraints excluded: chain J residue 28 ARG Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 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: 0.5980 chunk 115 optimal weight: 0.6980 chunk 380 optimal weight: 3.9990 chunk 311 optimal weight: 8.9990 chunk 270 optimal weight: 6.9990 chunk 199 optimal weight: 5.9990 chunk 233 optimal weight: 9.9990 chunk 300 optimal weight: 3.9990 chunk 62 optimal weight: 0.0570 chunk 136 optimal weight: 3.9990 chunk 420 optimal weight: 0.4980 overall best weight: 1.1700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.118152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.097173 restraints weight = 46412.377| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.82 r_work: 0.3027 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 35343 Z= 0.104 Angle : 0.536 7.820 47892 Z= 0.284 Chirality : 0.042 0.162 5060 Planarity : 0.005 0.060 6272 Dihedral : 5.779 59.196 5009 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.12 % Favored : 93.65 % Rotamer: Outliers : 3.23 % Allowed : 23.88 % Favored : 72.90 % 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: -0.66 (0.13), residues: 4328 helix: 1.75 (0.14), residues: 1504 sheet: -0.27 (0.19), residues: 704 loop : -2.25 (0.12), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 83 TYR 0.009 0.001 TYR I 80 PHE 0.025 0.001 PHE G 345 TRP 0.015 0.001 TRP G 214 HIS 0.004 0.001 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (35340) covalent geometry : angle 0.53631 / 0.28 (47892) hydrogen bonds : bond 0.04290 / 2.82 ( 1176) hydrogen bonds : angle 3.72008 / 2.51 ( 3303) Misc. bond : bond 0.00174 / 0.10 ( 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 401 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 286 time to evaluate : 1.164 Fit side-chains revert: symmetry clash REVERT: 1 132 SER cc_start: 0.7730 (t) cc_final: 0.7291 (p) REVERT: 2 91 VAL cc_start: 0.7103 (t) cc_final: 0.6748 (p) REVERT: A 156 GLN cc_start: 0.8412 (mp-120) cc_final: 0.7155 (tt0) REVERT: A 396 ASP cc_start: 0.8237 (p0) cc_final: 0.7684 (p0) REVERT: B 127 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.7222 (t80) REVERT: B 139 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8579 (tmm160) REVERT: B 167 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.7500 (ppt170) REVERT: B 175 LYS cc_start: 0.5840 (OUTLIER) cc_final: 0.5305 (mtpt) REVERT: B 177 LYS cc_start: 0.6407 (OUTLIER) cc_final: 0.5765 (mmmt) REVERT: B 295 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8605 (ptt180) REVERT: B 357 ASP cc_start: 0.8300 (t0) cc_final: 0.7924 (t70) REVERT: B 396 ASP cc_start: 0.8455 (p0) cc_final: 0.7694 (p0) REVERT: B 463 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.6833 (mmtt) REVERT: C 156 GLN cc_start: 0.8434 (mp-120) cc_final: 0.7177 (tt0) REVERT: C 396 ASP cc_start: 0.8231 (p0) cc_final: 0.7683 (p0) REVERT: D 167 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.7397 (ppt170) REVERT: D 180 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8247 (mp) REVERT: D 295 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8630 (ptt180) REVERT: D 357 ASP cc_start: 0.8492 (t0) cc_final: 0.8183 (t70) REVERT: D 396 ASP cc_start: 0.8449 (p0) cc_final: 0.7745 (p0) REVERT: D 450 LYS cc_start: 0.7506 (OUTLIER) cc_final: 0.6982 (mptm) REVERT: D 463 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.6670 (mmtt) REVERT: E 156 GLN cc_start: 0.8398 (mp-120) cc_final: 0.7148 (tt0) REVERT: E 396 ASP cc_start: 0.8237 (p0) cc_final: 0.7673 (p0) REVERT: E 463 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8134 (ttpp) REVERT: F 127 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7343 (t80) REVERT: F 139 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8560 (tmm160) REVERT: F 167 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.7419 (ppt170) REVERT: F 180 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8282 (mp) REVERT: F 295 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8620 (ptt180) REVERT: F 357 ASP cc_start: 0.8512 (t70) cc_final: 0.8300 (t70) REVERT: F 396 ASP cc_start: 0.8438 (p0) cc_final: 0.7689 (p0) REVERT: F 463 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.6617 (mmtt) REVERT: G 128 LYS cc_start: 0.8727 (mttp) cc_final: 0.8503 (mtmt) REVERT: G 156 GLN cc_start: 0.8429 (mp-120) cc_final: 0.7183 (tt0) REVERT: G 396 ASP cc_start: 0.8209 (p0) cc_final: 0.7576 (p0) REVERT: H 127 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.7553 (t80) REVERT: H 167 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.7514 (ppt170) REVERT: H 180 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8057 (mp) REVERT: H 295 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8632 (ptt180) REVERT: H 357 ASP cc_start: 0.8500 (t0) cc_final: 0.8163 (t70) REVERT: H 358 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7690 (mmt-90) REVERT: H 396 ASP cc_start: 0.8445 (p0) cc_final: 0.7721 (p0) REVERT: H 463 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.6612 (mmtt) REVERT: L 29 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6324 (mt-10) REVERT: L 37 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7283 (mttt) outliers start: 115 outliers final: 62 residues processed: 378 average time/residue: 0.7373 time to fit residues: 330.3918 Evaluate side-chains 359 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 270 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 70 LEU Chi-restraints excluded: chain 1 residue 81 VAL Chi-restraints excluded: chain 1 residue 94 ILE Chi-restraints excluded: chain 1 residue 133 THR Chi-restraints excluded: chain 1 residue 134 PHE Chi-restraints excluded: chain 2 residue 70 LEU Chi-restraints excluded: chain 2 residue 81 VAL Chi-restraints excluded: chain 2 residue 94 ILE Chi-restraints excluded: chain 2 residue 133 THR Chi-restraints excluded: chain 2 residue 134 PHE Chi-restraints excluded: chain 3 residue 70 LEU Chi-restraints excluded: chain 3 residue 81 VAL Chi-restraints excluded: chain 3 residue 94 ILE Chi-restraints excluded: chain 3 residue 134 PHE Chi-restraints excluded: chain 4 residue 65 THR Chi-restraints excluded: chain 4 residue 70 LEU Chi-restraints excluded: chain 4 residue 81 VAL Chi-restraints excluded: chain 4 residue 94 ILE Chi-restraints excluded: chain 4 residue 98 ASN Chi-restraints excluded: chain 4 residue 133 THR Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 167 ARG Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 295 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 384 VAL Chi-restraints excluded: chain E residue 463 LYS Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 167 ARG Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 295 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 203 ASP 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 178 LEU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 295 ARG Chi-restraints excluded: chain H residue 358 ARG Chi-restraints excluded: chain H residue 444 ILE Chi-restraints excluded: chain H residue 463 LYS Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 100 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 194 optimal weight: 20.0000 chunk 411 optimal weight: 5.9990 chunk 414 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 58 optimal weight: 0.1980 chunk 324 optimal weight: 9.9990 chunk 66 optimal weight: 0.5980 chunk 103 optimal weight: 9.9990 chunk 323 optimal weight: 2.9990 chunk 202 optimal weight: 6.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 45 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.113717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.092665 restraints weight = 46572.598| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.80 r_work: 0.2958 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 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 0.030 35343 Z= 0.171 Angle : 0.638 8.207 47892 Z= 0.338 Chirality : 0.047 0.186 5060 Planarity : 0.006 0.058 6272 Dihedral : 5.976 56.417 5009 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.30 % Favored : 92.47 % Rotamer: Outliers : 3.54 % Allowed : 23.63 % Favored : 72.84 % 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: -0.81 (0.12), residues: 4328 helix: 1.58 (0.14), residues: 1512 sheet: -0.15 (0.20), residues: 672 loop : -2.37 (0.12), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 83 TYR 0.014 0.001 TYR H 80 PHE 0.029 0.002 PHE E 345 TRP 0.011 0.001 TRP A 214 HIS 0.006 0.001 HIS D 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (35340) covalent geometry : angle 0.63773 / 0.34 (47892) hydrogen bonds : bond 0.07228 / 4.74 ( 1176) hydrogen bonds : angle 3.88006 / 2.63 ( 3303) Misc. bond : bond 0.00265 / 0.15 ( 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 387 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 261 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 132 SER cc_start: 0.7835 (t) cc_final: 0.7311 (p) REVERT: 2 91 VAL cc_start: 0.7140 (t) cc_final: 0.6778 (p) REVERT: 2 136 GLU cc_start: 0.5798 (OUTLIER) cc_final: 0.4690 (pm20) REVERT: A 156 GLN cc_start: 0.8491 (mp-120) cc_final: 0.7258 (tt0) REVERT: A 396 ASP cc_start: 0.8302 (p0) cc_final: 0.7745 (p0) REVERT: B 127 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.7272 (t80) REVERT: B 139 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8700 (tmm160) REVERT: B 167 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.7192 (ppt170) REVERT: B 177 LYS cc_start: 0.6552 (OUTLIER) cc_final: 0.5841 (mmmt) REVERT: B 295 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8655 (ptt180) REVERT: B 357 ASP cc_start: 0.8399 (t0) cc_final: 0.8113 (t70) REVERT: B 358 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7416 (mmt-90) REVERT: B 396 ASP cc_start: 0.8508 (p0) cc_final: 0.7769 (p0) REVERT: B 463 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.6845 (mmtt) REVERT: C 156 GLN cc_start: 0.8516 (mp-120) cc_final: 0.7279 (tt0) REVERT: C 396 ASP cc_start: 0.8324 (p0) cc_final: 0.7761 (p0) REVERT: C 439 ARG cc_start: 0.6375 (OUTLIER) cc_final: 0.6003 (mtm110) REVERT: D 167 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.7072 (ppt170) REVERT: D 180 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8153 (mp) REVERT: D 295 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8669 (ptt180) REVERT: D 357 ASP cc_start: 0.8512 (t0) cc_final: 0.8262 (t70) REVERT: D 358 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7715 (mmt-90) REVERT: D 396 ASP cc_start: 0.8522 (p0) cc_final: 0.7784 (p0) REVERT: D 450 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7056 (mptm) REVERT: D 463 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.6672 (mmtt) REVERT: E 156 GLN cc_start: 0.8489 (mp-120) cc_final: 0.7269 (tt0) REVERT: E 177 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7153 (mttt) REVERT: E 396 ASP cc_start: 0.8333 (p0) cc_final: 0.7782 (p0) REVERT: E 463 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8199 (ttpp) REVERT: F 127 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.7372 (t80) REVERT: F 139 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.8574 (tmm160) REVERT: F 167 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.7092 (ppt170) REVERT: F 180 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8210 (mp) REVERT: F 295 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8650 (ptt180) REVERT: F 357 ASP cc_start: 0.8532 (t70) cc_final: 0.8328 (t70) REVERT: F 396 ASP cc_start: 0.8508 (p0) cc_final: 0.7781 (p0) REVERT: F 463 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.6649 (mmtt) REVERT: G 156 GLN cc_start: 0.8520 (mp-120) cc_final: 0.7300 (tt0) REVERT: G 396 ASP cc_start: 0.8298 (p0) cc_final: 0.7722 (p0) REVERT: H 127 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.7508 (t80) REVERT: H 167 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.7179 (ppt170) REVERT: H 180 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8164 (mp) REVERT: H 258 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7889 (ttt90) REVERT: H 295 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8703 (ptt180) REVERT: H 357 ASP cc_start: 0.8506 (t0) cc_final: 0.8276 (t70) REVERT: H 358 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7720 (mmt-90) REVERT: H 396 ASP cc_start: 0.8491 (p0) cc_final: 0.7744 (p0) REVERT: H 463 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.6628 (mmtt) REVERT: I 86 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7049 (mp0) REVERT: J 86 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: L 29 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6406 (mt-10) REVERT: L 37 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7631 (mttt) outliers start: 126 outliers final: 69 residues processed: 368 average time/residue: 0.7771 time to fit residues: 336.8310 Evaluate side-chains 358 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 255 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 70 LEU Chi-restraints excluded: chain 1 residue 81 VAL Chi-restraints excluded: chain 1 residue 94 ILE Chi-restraints excluded: chain 1 residue 133 THR Chi-restraints excluded: chain 1 residue 134 PHE Chi-restraints excluded: chain 2 residue 70 LEU Chi-restraints excluded: chain 2 residue 81 VAL Chi-restraints excluded: chain 2 residue 94 ILE Chi-restraints excluded: chain 2 residue 133 THR Chi-restraints excluded: chain 2 residue 134 PHE Chi-restraints excluded: chain 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 134 PHE Chi-restraints excluded: chain 4 residue 65 THR Chi-restraints excluded: chain 4 residue 70 LEU Chi-restraints excluded: chain 4 residue 81 VAL Chi-restraints excluded: chain 4 residue 94 ILE Chi-restraints excluded: chain 4 residue 98 ASN Chi-restraints excluded: chain 4 residue 133 THR Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 358 ARG Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 192 CYS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 439 ARG 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 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 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 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 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 295 ARG Chi-restraints excluded: chain F residue 347 ASP Chi-restraints excluded: chain F residue 444 ILE Chi-restraints excluded: chain F residue 463 LYS Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 384 VAL 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 258 ARG Chi-restraints excluded: chain H residue 295 ARG Chi-restraints excluded: chain H residue 347 ASP Chi-restraints excluded: chain H residue 358 ARG Chi-restraints excluded: chain H residue 444 ILE Chi-restraints excluded: chain H residue 463 LYS Chi-restraints excluded: chain I residue 8 ASP Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 19 optimal weight: 9.9990 chunk 196 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 362 optimal weight: 0.5980 chunk 64 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 234 optimal weight: 8.9990 chunk 349 optimal weight: 3.9990 chunk 396 optimal weight: 3.9990 chunk 424 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.113893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.092852 restraints weight = 46646.181| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.80 r_work: 0.2962 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 35343 Z= 0.160 Angle : 0.625 7.959 47892 Z= 0.332 Chirality : 0.046 0.183 5060 Planarity : 0.006 0.059 6272 Dihedral : 5.967 56.187 5009 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.70 % Favored : 93.07 % Rotamer: Outliers : 3.25 % Allowed : 24.13 % Favored : 72.62 % 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: -0.85 (0.12), residues: 4328 helix: 1.53 (0.14), residues: 1512 sheet: -0.17 (0.20), residues: 672 loop : -2.39 (0.11), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 258 TYR 0.013 0.001 TYR H 80 PHE 0.029 0.002 PHE G 345 TRP 0.012 0.001 TRP C 214 HIS 0.006 0.001 HIS H 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (35340) covalent geometry : angle 0.62530 / 0.33 (47892) hydrogen bonds : bond 0.06753 / 4.44 ( 1176) hydrogen bonds : angle 3.86197 / 2.62 ( 3303) Misc. bond : bond 0.00234 / 0.13 ( 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 374 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 258 time to evaluate : 1.437 Fit side-chains revert: symmetry clash REVERT: 1 132 SER cc_start: 0.7849 (t) cc_final: 0.7331 (p) REVERT: A 156 GLN cc_start: 0.8480 (mp-120) cc_final: 0.7239 (tt0) REVERT: A 396 ASP cc_start: 0.8310 (p0) cc_final: 0.7709 (p0) REVERT: B 127 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.7296 (t80) REVERT: B 139 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.8666 (tmm160) REVERT: B 167 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.7155 (ppt170) REVERT: B 175 LYS cc_start: 0.5975 (OUTLIER) cc_final: 0.5553 (mtpt) REVERT: B 177 LYS cc_start: 0.6551 (OUTLIER) cc_final: 0.5813 (mmmt) REVERT: B 258 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7834 (ttt90) REVERT: B 295 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8671 (ptt180) REVERT: B 357 ASP cc_start: 0.8387 (t0) cc_final: 0.8098 (t70) REVERT: B 358 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7413 (mmt-90) REVERT: B 396 ASP cc_start: 0.8513 (p0) cc_final: 0.7781 (p0) REVERT: B 463 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.6824 (mmtt) REVERT: C 156 GLN cc_start: 0.8496 (mp-120) cc_final: 0.7255 (tt0) REVERT: C 396 ASP cc_start: 0.8315 (p0) cc_final: 0.7748 (p0) REVERT: C 439 ARG cc_start: 0.6372 (OUTLIER) cc_final: 0.6000 (mtm110) REVERT: D 167 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.7044 (ppt170) REVERT: D 180 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8351 (mp) REVERT: D 295 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8680 (ptt180) REVERT: D 357 ASP cc_start: 0.8525 (t0) cc_final: 0.8192 (t70) REVERT: D 358 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7710 (mmt-90) REVERT: D 396 ASP cc_start: 0.8513 (p0) cc_final: 0.7785 (p0) REVERT: D 450 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7038 (mptm) REVERT: D 463 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.6658 (mmtt) REVERT: E 156 GLN cc_start: 0.8476 (mp-120) cc_final: 0.7247 (tt0) REVERT: E 177 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7147 (mttt) REVERT: E 396 ASP cc_start: 0.8335 (p0) cc_final: 0.7768 (p0) REVERT: E 463 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8181 (ttpp) REVERT: F 127 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.7356 (t80) REVERT: F 139 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.8661 (tmm160) REVERT: F 167 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.7059 (ppt170) REVERT: F 180 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8377 (mp) REVERT: F 295 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8684 (ptt180) REVERT: F 358 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7719 (mmt-90) REVERT: F 396 ASP cc_start: 0.8515 (p0) cc_final: 0.7789 (p0) REVERT: F 463 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.6663 (mmtt) REVERT: G 156 GLN cc_start: 0.8510 (mp-120) cc_final: 0.7285 (tt0) REVERT: G 396 ASP cc_start: 0.8307 (p0) cc_final: 0.7717 (p0) REVERT: H 127 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.7500 (t80) REVERT: H 167 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.7155 (ppt170) REVERT: H 180 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8169 (mp) REVERT: H 258 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7847 (ttt90) REVERT: H 295 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8698 (ptt180) REVERT: H 357 ASP cc_start: 0.8516 (t0) cc_final: 0.8181 (t70) REVERT: H 358 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7710 (mmt-90) REVERT: H 396 ASP cc_start: 0.8498 (p0) cc_final: 0.7796 (p0) REVERT: H 463 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.6624 (mmtt) REVERT: I 86 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7028 (mp0) REVERT: J 86 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: L 29 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6396 (mt-10) REVERT: L 37 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7525 (mttt) outliers start: 116 outliers final: 70 residues processed: 350 average time/residue: 0.7848 time to fit residues: 323.1941 Evaluate side-chains 361 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 255 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 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 134 PHE Chi-restraints excluded: chain 4 residue 65 THR Chi-restraints excluded: chain 4 residue 70 LEU Chi-restraints excluded: chain 4 residue 81 VAL Chi-restraints excluded: chain 4 residue 94 ILE Chi-restraints excluded: chain 4 residue 98 ASN Chi-restraints excluded: chain 4 residue 133 THR Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 358 ARG Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 167 ARG Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 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 177 LYS Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 463 LYS Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 167 ARG Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 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 464 GLU 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 258 ARG Chi-restraints excluded: chain H residue 295 ARG Chi-restraints excluded: chain H residue 347 ASP Chi-restraints excluded: chain H residue 358 ARG Chi-restraints excluded: chain H residue 444 ILE Chi-restraints excluded: chain H residue 463 LYS Chi-restraints excluded: chain I residue 8 ASP Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 100 LEU 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 28 optimal weight: 1.9990 chunk 403 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 112 optimal weight: 7.9990 chunk 295 optimal weight: 10.0000 chunk 350 optimal weight: 3.9990 chunk 179 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 263 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.114341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.093304 restraints weight = 46559.874| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.80 r_work: 0.2967 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 35343 Z= 0.150 Angle : 0.613 8.484 47892 Z= 0.325 Chirality : 0.046 0.182 5060 Planarity : 0.005 0.058 6272 Dihedral : 5.896 56.025 5008 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.84 % Favored : 92.93 % Rotamer: Outliers : 3.48 % Allowed : 23.91 % Favored : 72.62 % 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: -0.81 (0.12), residues: 4328 helix: 1.58 (0.14), residues: 1512 sheet: -0.17 (0.20), residues: 672 loop : -2.36 (0.11), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 258 TYR 0.013 0.001 TYR H 80 PHE 0.028 0.002 PHE G 345 TRP 0.012 0.001 TRP C 214 HIS 0.005 0.001 HIS H 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (35340) covalent geometry : angle 0.61310 / 0.32 (47892) hydrogen bonds : bond 0.06473 / 4.25 ( 1176) hydrogen bonds : angle 3.83154 / 2.59 ( 3303) Misc. bond : bond 0.00216 / 0.12 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10872.17 seconds wall clock time: 185 minutes 59.11 seconds (11159.11 seconds total)