Starting phenix.real_space_refine on Wed Aug 27 01:38:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xot_38540/08_2025/8xot_38540.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xot_38540/08_2025/8xot_38540.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xot_38540/08_2025/8xot_38540.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xot_38540/08_2025/8xot_38540.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xot_38540/08_2025/8xot_38540.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xot_38540/08_2025/8xot_38540.map" } resolution = 3.51 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= 0.003 sd= 0.081 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 276 5.16 5 C 27828 2.51 5 N 8064 2.21 5 O 8364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 44532 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 3711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3711 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 457} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "b" Number of atoms: 3711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3711 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 457} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "B1" Number of atoms: 3711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3711 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 457} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "b1" Number of atoms: 3711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3711 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 457} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "B2" Number of atoms: 3711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3711 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 457} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "b2" Number of atoms: 3711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3711 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 457} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "B3" Number of atoms: 3711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3711 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 457} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "b3" Number of atoms: 3711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3711 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 457} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "B4" Number of atoms: 3711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3711 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 457} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "b4" Number of atoms: 3711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3711 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 457} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "B5" Number of atoms: 3711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3711 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 457} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "b5" Number of atoms: 3711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3711 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 457} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Time building chain proxies: 10.84, per 1000 atoms: 0.24 Number of scatterers: 44532 At special positions: 0 Unit cell: (160.704, 160.704, 134.574, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 276 16.00 O 8364 8.00 N 8064 7.00 C 27828 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS B 123 " - pdb=" SG CYS B 125 " distance=2.03 Simple disulfide: pdb=" SG CYS b 123 " - pdb=" SG CYS b 125 " distance=2.03 Simple disulfide: pdb=" SG CYSB1 123 " - pdb=" SG CYSB1 125 " distance=2.03 Simple disulfide: pdb=" SG CYSb1 123 " - pdb=" SG CYSb1 125 " distance=2.03 Simple disulfide: pdb=" SG CYSB2 123 " - pdb=" SG CYSB2 125 " distance=2.03 Simple disulfide: pdb=" SG CYSb2 123 " - pdb=" SG CYSb2 125 " distance=2.03 Simple disulfide: pdb=" SG CYSB3 123 " - pdb=" SG CYSB3 125 " distance=2.03 Simple disulfide: pdb=" SG CYSb3 123 " - pdb=" SG CYSb3 125 " distance=2.03 Simple disulfide: pdb=" SG CYSB4 123 " - pdb=" SG CYSB4 125 " distance=2.03 Simple disulfide: pdb=" SG CYSb4 123 " - pdb=" SG CYSb4 125 " distance=2.03 Simple disulfide: pdb=" SG CYSB5 123 " - pdb=" SG CYSB5 125 " distance=2.03 Simple disulfide: pdb=" SG CYSb5 123 " - pdb=" SG CYSb5 125 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.16 Conformation dependent library (CDL) restraints added in 2.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10560 Finding SS restraints... Secondary structure from input PDB file: 249 helices and 48 sheets defined 57.6% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'B' and resid 34 through 38 Processing helix chain 'B' and resid 44 through 50 Processing helix chain 'B' and resid 52 through 67 Processing helix chain 'B' and resid 67 through 82 Processing helix chain 'B' and resid 93 through 98 Processing helix chain 'B' and resid 100 through 120 removed outlier: 3.823A pdb=" N GLU B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 149 Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 179 through 183 Processing helix chain 'B' and resid 249 through 253 Processing helix chain 'B' and resid 254 through 276 removed outlier: 3.561A pdb=" N ALA B 276 " --> pdb=" O ALA B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 302 Processing helix chain 'B' and resid 304 through 321 Processing helix chain 'B' and resid 350 through 367 Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.609A pdb=" N LEU B 373 " --> pdb=" O SER B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 403 Processing helix chain 'B' and resid 403 through 422 Processing helix chain 'B' and resid 438 through 444 Processing helix chain 'B' and resid 457 through 470 Processing helix chain 'B' and resid 474 through 482 removed outlier: 3.919A pdb=" N GLU B 478 " --> pdb=" O THR B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 503 Processing helix chain 'b' and resid 34 through 38 Processing helix chain 'b' and resid 49 through 67 removed outlier: 4.574A pdb=" N THR b 54 " --> pdb=" O LEU b 50 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ARG b 55 " --> pdb=" O PRO b 51 " (cutoff:3.500A) Processing helix chain 'b' and resid 67 through 82 removed outlier: 3.625A pdb=" N VAL b 82 " --> pdb=" O GLN b 78 " (cutoff:3.500A) Processing helix chain 'b' and resid 93 through 98 Processing helix chain 'b' and resid 100 through 120 removed outlier: 3.584A pdb=" N GLU b 117 " --> pdb=" O ALA b 113 " (cutoff:3.500A) Processing helix chain 'b' and resid 133 through 149 Processing helix chain 'b' and resid 173 through 177 Processing helix chain 'b' and resid 179 through 183 Processing helix chain 'b' and resid 249 through 253 removed outlier: 3.504A pdb=" N TYR b 252 " --> pdb=" O ASN b 249 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER b 253 " --> pdb=" O VAL b 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 249 through 253' Processing helix chain 'b' and resid 254 through 276 removed outlier: 3.734A pdb=" N ALA b 276 " --> pdb=" O ALA b 272 " (cutoff:3.500A) Processing helix chain 'b' and resid 289 through 302 Processing helix chain 'b' and resid 304 through 321 removed outlier: 3.665A pdb=" N THR b 308 " --> pdb=" O ARG b 304 " (cutoff:3.500A) Processing helix chain 'b' and resid 350 through 367 removed outlier: 3.505A pdb=" N PHE b 354 " --> pdb=" O GLY b 350 " (cutoff:3.500A) Processing helix chain 'b' and resid 369 through 374 Processing helix chain 'b' and resid 381 through 403 Processing helix chain 'b' and resid 403 through 422 Processing helix chain 'b' and resid 438 through 443 Processing helix chain 'b' and resid 457 through 470 Processing helix chain 'b' and resid 474 through 482 removed outlier: 3.745A pdb=" N GLU b 478 " --> pdb=" O THR b 474 " (cutoff:3.500A) Processing helix chain 'b' and resid 485 through 503 Processing helix chain 'B1' and resid 34 through 38 Processing helix chain 'B1' and resid 44 through 50 Processing helix chain 'B1' and resid 52 through 67 Processing helix chain 'B1' and resid 67 through 82 removed outlier: 3.526A pdb=" N ALAB1 71 " --> pdb=" O ASNB1 67 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VALB1 82 " --> pdb=" O GLNB1 78 " (cutoff:3.500A) Processing helix chain 'B1' and resid 93 through 98 Processing helix chain 'B1' and resid 100 through 120 removed outlier: 3.631A pdb=" N GLUB1 120 " --> pdb=" O LYSB1 116 " (cutoff:3.500A) Processing helix chain 'B1' and resid 133 through 149 Processing helix chain 'B1' and resid 173 through 177 Processing helix chain 'B1' and resid 179 through 183 Processing helix chain 'B1' and resid 249 through 253 Processing helix chain 'B1' and resid 254 through 276 Processing helix chain 'B1' and resid 289 through 302 Processing helix chain 'B1' and resid 303 through 321 removed outlier: 4.414A pdb=" N LEUB1 307 " --> pdb=" O GLNB1 303 " (cutoff:3.500A) Processing helix chain 'B1' and resid 350 through 367 Processing helix chain 'B1' and resid 369 through 374 Processing helix chain 'B1' and resid 381 through 403 removed outlier: 3.529A pdb=" N ALAB1 385 " --> pdb=" O SERB1 381 " (cutoff:3.500A) Processing helix chain 'B1' and resid 403 through 422 Processing helix chain 'B1' and resid 438 through 444 Processing helix chain 'B1' and resid 457 through 470 Processing helix chain 'B1' and resid 474 through 481 removed outlier: 3.837A pdb=" N GLUB1 478 " --> pdb=" O THRB1 474 " (cutoff:3.500A) Processing helix chain 'B1' and resid 485 through 503 Processing helix chain 'b1' and resid 34 through 38 Processing helix chain 'b1' and resid 49 through 51 No H-bonds generated for 'chain 'b1' and resid 49 through 51' Processing helix chain 'b1' and resid 52 through 67 Processing helix chain 'b1' and resid 67 through 82 Processing helix chain 'b1' and resid 93 through 98 Processing helix chain 'b1' and resid 100 through 120 removed outlier: 3.626A pdb=" N GLUb1 117 " --> pdb=" O ALAb1 113 " (cutoff:3.500A) Processing helix chain 'b1' and resid 133 through 149 Processing helix chain 'b1' and resid 173 through 177 Processing helix chain 'b1' and resid 179 through 183 Processing helix chain 'b1' and resid 249 through 253 Processing helix chain 'b1' and resid 254 through 276 removed outlier: 3.602A pdb=" N ALAb1 276 " --> pdb=" O ALAb1 272 " (cutoff:3.500A) Processing helix chain 'b1' and resid 288 through 302 Processing helix chain 'b1' and resid 303 through 321 removed outlier: 4.489A pdb=" N LEUb1 307 " --> pdb=" O GLNb1 303 " (cutoff:3.500A) Processing helix chain 'b1' and resid 350 through 367 Processing helix chain 'b1' and resid 369 through 374 Processing helix chain 'b1' and resid 381 through 403 Processing helix chain 'b1' and resid 403 through 422 Processing helix chain 'b1' and resid 438 through 444 Processing helix chain 'b1' and resid 457 through 470 Processing helix chain 'b1' and resid 474 through 481 removed outlier: 3.642A pdb=" N GLUb1 478 " --> pdb=" O THRb1 474 " (cutoff:3.500A) Processing helix chain 'b1' and resid 485 through 503 Processing helix chain 'B2' and resid 34 through 38 Processing helix chain 'B2' and resid 52 through 67 Processing helix chain 'B2' and resid 67 through 82 removed outlier: 3.905A pdb=" N VALB2 82 " --> pdb=" O GLNB2 78 " (cutoff:3.500A) Processing helix chain 'B2' and resid 93 through 98 Processing helix chain 'B2' and resid 100 through 120 removed outlier: 3.664A pdb=" N GLUB2 117 " --> pdb=" O ALAB2 113 " (cutoff:3.500A) Processing helix chain 'B2' and resid 133 through 149 Processing helix chain 'B2' and resid 173 through 177 Processing helix chain 'B2' and resid 179 through 183 Processing helix chain 'B2' and resid 249 through 253 Processing helix chain 'B2' and resid 254 through 276 removed outlier: 3.513A pdb=" N ALAB2 276 " --> pdb=" O ALAB2 272 " (cutoff:3.500A) Processing helix chain 'B2' and resid 289 through 302 Processing helix chain 'B2' and resid 304 through 321 removed outlier: 3.640A pdb=" N TRPB2 310 " --> pdb=" O ARGB2 306 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALAB2 319 " --> pdb=" O ALAB2 315 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALAB2 320 " --> pdb=" O ALAB2 316 " (cutoff:3.500A) Processing helix chain 'B2' and resid 350 through 367 removed outlier: 3.613A pdb=" N GLNB2 356 " --> pdb=" O SERB2 352 " (cutoff:3.500A) Processing helix chain 'B2' and resid 369 through 375 Processing helix chain 'B2' and resid 381 through 403 Processing helix chain 'B2' and resid 403 through 422 Processing helix chain 'B2' and resid 438 through 443 Processing helix chain 'B2' and resid 457 through 470 Processing helix chain 'B2' and resid 474 through 482 removed outlier: 3.849A pdb=" N GLUB2 478 " --> pdb=" O THRB2 474 " (cutoff:3.500A) Processing helix chain 'B2' and resid 485 through 503 Processing helix chain 'b2' and resid 34 through 38 Processing helix chain 'b2' and resid 44 through 50 Processing helix chain 'b2' and resid 52 through 67 Processing helix chain 'b2' and resid 67 through 82 removed outlier: 3.690A pdb=" N VALb2 82 " --> pdb=" O GLNb2 78 " (cutoff:3.500A) Processing helix chain 'b2' and resid 93 through 98 Processing helix chain 'b2' and resid 100 through 120 removed outlier: 3.876A pdb=" N GLUb2 117 " --> pdb=" O ALAb2 113 " (cutoff:3.500A) Processing helix chain 'b2' and resid 133 through 149 Processing helix chain 'b2' and resid 173 through 177 Processing helix chain 'b2' and resid 179 through 183 Processing helix chain 'b2' and resid 249 through 253 Processing helix chain 'b2' and resid 254 through 275 Processing helix chain 'b2' and resid 288 through 302 Processing helix chain 'b2' and resid 303 through 321 removed outlier: 4.281A pdb=" N LEUb2 307 " --> pdb=" O GLNb2 303 " (cutoff:3.500A) Processing helix chain 'b2' and resid 350 through 367 Processing helix chain 'b2' and resid 369 through 375 Processing helix chain 'b2' and resid 381 through 403 Processing helix chain 'b2' and resid 403 through 422 Processing helix chain 'b2' and resid 438 through 444 Processing helix chain 'b2' and resid 457 through 470 Processing helix chain 'b2' and resid 474 through 482 removed outlier: 3.596A pdb=" N GLUb2 478 " --> pdb=" O THRb2 474 " (cutoff:3.500A) Processing helix chain 'b2' and resid 485 through 503 Processing helix chain 'B3' and resid 34 through 38 Processing helix chain 'B3' and resid 44 through 50 Processing helix chain 'B3' and resid 52 through 67 Processing helix chain 'B3' and resid 67 through 82 Processing helix chain 'B3' and resid 93 through 98 Processing helix chain 'B3' and resid 100 through 120 removed outlier: 3.601A pdb=" N GLUB3 117 " --> pdb=" O ALAB3 113 " (cutoff:3.500A) Processing helix chain 'B3' and resid 133 through 149 Processing helix chain 'B3' and resid 173 through 177 Processing helix chain 'B3' and resid 179 through 183 Processing helix chain 'B3' and resid 249 through 253 Processing helix chain 'B3' and resid 254 through 275 Processing helix chain 'B3' and resid 289 through 302 Processing helix chain 'B3' and resid 303 through 321 removed outlier: 4.301A pdb=" N LEUB3 307 " --> pdb=" O GLNB3 303 " (cutoff:3.500A) Processing helix chain 'B3' and resid 350 through 367 Processing helix chain 'B3' and resid 369 through 374 Processing helix chain 'B3' and resid 381 through 403 Processing helix chain 'B3' and resid 403 through 422 Processing helix chain 'B3' and resid 438 through 444 Processing helix chain 'B3' and resid 457 through 470 removed outlier: 3.561A pdb=" N VALB3 461 " --> pdb=" O GLYB3 457 " (cutoff:3.500A) Processing helix chain 'B3' and resid 474 through 482 removed outlier: 3.627A pdb=" N GLUB3 478 " --> pdb=" O THRB3 474 " (cutoff:3.500A) Processing helix chain 'B3' and resid 485 through 503 Processing helix chain 'b3' and resid 34 through 38 Processing helix chain 'b3' and resid 44 through 50 Processing helix chain 'b3' and resid 52 through 67 Processing helix chain 'b3' and resid 67 through 82 removed outlier: 3.873A pdb=" N VALb3 82 " --> pdb=" O GLNb3 78 " (cutoff:3.500A) Processing helix chain 'b3' and resid 93 through 98 Processing helix chain 'b3' and resid 100 through 120 removed outlier: 3.634A pdb=" N GLUb3 117 " --> pdb=" O ALAb3 113 " (cutoff:3.500A) Processing helix chain 'b3' and resid 133 through 149 Processing helix chain 'b3' and resid 173 through 177 Processing helix chain 'b3' and resid 179 through 183 Processing helix chain 'b3' and resid 249 through 253 removed outlier: 3.906A pdb=" N SERb3 253 " --> pdb=" O VALb3 250 " (cutoff:3.500A) Processing helix chain 'b3' and resid 254 through 275 Processing helix chain 'b3' and resid 289 through 302 Processing helix chain 'b3' and resid 304 through 321 removed outlier: 3.943A pdb=" N TRPb3 310 " --> pdb=" O ARGb3 306 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALAb3 320 " --> pdb=" O ALAb3 316 " (cutoff:3.500A) Processing helix chain 'b3' and resid 350 through 367 Processing helix chain 'b3' and resid 369 through 374 Processing helix chain 'b3' and resid 381 through 403 Processing helix chain 'b3' and resid 403 through 422 Processing helix chain 'b3' and resid 438 through 443 Processing helix chain 'b3' and resid 457 through 470 Processing helix chain 'b3' and resid 474 through 481 removed outlier: 3.992A pdb=" N GLUb3 478 " --> pdb=" O THRb3 474 " (cutoff:3.500A) Processing helix chain 'b3' and resid 485 through 503 Processing helix chain 'B4' and resid 34 through 38 Processing helix chain 'B4' and resid 44 through 50 Processing helix chain 'B4' and resid 52 through 67 Processing helix chain 'B4' and resid 67 through 82 Processing helix chain 'B4' and resid 93 through 98 Processing helix chain 'B4' and resid 100 through 120 removed outlier: 3.879A pdb=" N GLUB4 117 " --> pdb=" O ALAB4 113 " (cutoff:3.500A) Processing helix chain 'B4' and resid 133 through 149 Processing helix chain 'B4' and resid 173 through 177 Processing helix chain 'B4' and resid 179 through 183 Processing helix chain 'B4' and resid 249 through 253 removed outlier: 3.628A pdb=" N SERB4 253 " --> pdb=" O VALB4 250 " (cutoff:3.500A) Processing helix chain 'B4' and resid 254 through 276 removed outlier: 3.732A pdb=" N THRB4 263 " --> pdb=" O LYSB4 259 " (cutoff:3.500A) Processing helix chain 'B4' and resid 288 through 302 Processing helix chain 'B4' and resid 303 through 321 removed outlier: 4.318A pdb=" N LEUB4 307 " --> pdb=" O GLNB4 303 " (cutoff:3.500A) Processing helix chain 'B4' and resid 350 through 367 Processing helix chain 'B4' and resid 369 through 374 Processing helix chain 'B4' and resid 381 through 403 Processing helix chain 'B4' and resid 403 through 422 Processing helix chain 'B4' and resid 438 through 444 Processing helix chain 'B4' and resid 457 through 471 Processing helix chain 'B4' and resid 474 through 482 removed outlier: 3.563A pdb=" N GLUB4 478 " --> pdb=" O THRB4 474 " (cutoff:3.500A) Processing helix chain 'B4' and resid 485 through 503 Processing helix chain 'b4' and resid 34 through 38 removed outlier: 3.502A pdb=" N TRPb4 38 " --> pdb=" O LEUb4 35 " (cutoff:3.500A) Processing helix chain 'b4' and resid 44 through 50 Processing helix chain 'b4' and resid 52 through 67 Processing helix chain 'b4' and resid 67 through 82 removed outlier: 3.506A pdb=" N ALAb4 71 " --> pdb=" O ASNb4 67 " (cutoff:3.500A) Processing helix chain 'b4' and resid 93 through 98 Processing helix chain 'b4' and resid 100 through 120 removed outlier: 3.816A pdb=" N GLUb4 120 " --> pdb=" O LYSb4 116 " (cutoff:3.500A) Processing helix chain 'b4' and resid 133 through 149 Processing helix chain 'b4' and resid 173 through 177 Processing helix chain 'b4' and resid 179 through 183 Processing helix chain 'b4' and resid 249 through 253 Processing helix chain 'b4' and resid 254 through 275 Processing helix chain 'b4' and resid 289 through 302 Processing helix chain 'b4' and resid 303 through 321 removed outlier: 4.494A pdb=" N LEUb4 307 " --> pdb=" O GLNb4 303 " (cutoff:3.500A) Processing helix chain 'b4' and resid 350 through 367 Processing helix chain 'b4' and resid 369 through 374 Processing helix chain 'b4' and resid 381 through 403 Processing helix chain 'b4' and resid 403 through 422 Processing helix chain 'b4' and resid 438 through 444 Processing helix chain 'b4' and resid 457 through 470 Processing helix chain 'b4' and resid 474 through 481 Processing helix chain 'b4' and resid 485 through 503 Processing helix chain 'B5' and resid 34 through 38 Processing helix chain 'B5' and resid 44 through 67 Proline residue: B5 51 - end of helix removed outlier: 4.553A pdb=" N THRB5 54 " --> pdb=" O LEUB5 50 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ARGB5 55 " --> pdb=" O PROB5 51 " (cutoff:3.500A) Processing helix chain 'B5' and resid 67 through 82 removed outlier: 3.732A pdb=" N VALB5 82 " --> pdb=" O GLNB5 78 " (cutoff:3.500A) Processing helix chain 'B5' and resid 93 through 98 Processing helix chain 'B5' and resid 100 through 120 removed outlier: 3.675A pdb=" N GLUB5 117 " --> pdb=" O ALAB5 113 " (cutoff:3.500A) Processing helix chain 'B5' and resid 133 through 149 Processing helix chain 'B5' and resid 173 through 177 Processing helix chain 'B5' and resid 179 through 183 Processing helix chain 'B5' and resid 249 through 253 Processing helix chain 'B5' and resid 254 through 275 removed outlier: 3.637A pdb=" N METB5 258 " --> pdb=" O VALB5 254 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYSB5 259 " --> pdb=" O METB5 255 " (cutoff:3.500A) Processing helix chain 'B5' and resid 289 through 302 Processing helix chain 'B5' and resid 303 through 321 removed outlier: 4.408A pdb=" N LEUB5 307 " --> pdb=" O GLNB5 303 " (cutoff:3.500A) Processing helix chain 'B5' and resid 350 through 367 Processing helix chain 'B5' and resid 369 through 375 Processing helix chain 'B5' and resid 381 through 403 Processing helix chain 'B5' and resid 403 through 422 Processing helix chain 'B5' and resid 438 through 443 Processing helix chain 'B5' and resid 457 through 470 Processing helix chain 'B5' and resid 474 through 482 removed outlier: 3.971A pdb=" N GLUB5 478 " --> pdb=" O THRB5 474 " (cutoff:3.500A) Processing helix chain 'B5' and resid 485 through 503 Processing helix chain 'b5' and resid 34 through 38 Processing helix chain 'b5' and resid 44 through 50 Processing helix chain 'b5' and resid 52 through 67 Processing helix chain 'b5' and resid 67 through 82 removed outlier: 3.718A pdb=" N VALb5 82 " --> pdb=" O GLNb5 78 " (cutoff:3.500A) Processing helix chain 'b5' and resid 93 through 98 Processing helix chain 'b5' and resid 100 through 120 removed outlier: 3.974A pdb=" N GLUb5 120 " --> pdb=" O LYSb5 116 " (cutoff:3.500A) Processing helix chain 'b5' and resid 133 through 149 Processing helix chain 'b5' and resid 173 through 177 Processing helix chain 'b5' and resid 179 through 183 Processing helix chain 'b5' and resid 249 through 253 removed outlier: 3.856A pdb=" N SERb5 253 " --> pdb=" O VALb5 250 " (cutoff:3.500A) Processing helix chain 'b5' and resid 254 through 276 Processing helix chain 'b5' and resid 288 through 302 Processing helix chain 'b5' and resid 303 through 321 removed outlier: 4.415A pdb=" N LEUb5 307 " --> pdb=" O GLNb5 303 " (cutoff:3.500A) Processing helix chain 'b5' and resid 350 through 367 Processing helix chain 'b5' and resid 369 through 375 Processing helix chain 'b5' and resid 381 through 403 removed outlier: 4.198A pdb=" N GLUb5 391 " --> pdb=" O ALAb5 387 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SERb5 392 " --> pdb=" O SERb5 388 " (cutoff:3.500A) Processing helix chain 'b5' and resid 403 through 422 Processing helix chain 'b5' and resid 438 through 443 Processing helix chain 'b5' and resid 457 through 470 Processing helix chain 'b5' and resid 474 through 481 removed outlier: 3.647A pdb=" N GLUb5 478 " --> pdb=" O THRb5 474 " (cutoff:3.500A) Processing helix chain 'b5' and resid 485 through 503 Processing sheet with id=AA1, first strand: chain 'B' and resid 87 through 90 Processing sheet with id=AA2, first strand: chain 'B' and resid 167 through 172 removed outlier: 4.025A pdb=" N PHE B 152 " --> pdb=" O VAL B 172 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 189 through 190 removed outlier: 3.666A pdb=" N GLY B 203 " --> pdb=" O GLN B 194 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 281 through 283 removed outlier: 3.727A pdb=" N THR B 281 " --> pdb=" O ASN b 340 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN b 340 " --> pdb=" O THR B 281 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU B 283 " --> pdb=" O SER b 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 337 through 340 removed outlier: 3.559A pdb=" N SER B 338 " --> pdb=" O GLUb5 283 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLUb5 283 " --> pdb=" O SER B 338 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN B 340 " --> pdb=" O THRb5 281 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THRb5 281 " --> pdb=" O ASN B 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'b' and resid 87 through 90 Processing sheet with id=AA7, first strand: chain 'b' and resid 167 through 172 removed outlier: 3.872A pdb=" N PHE b 152 " --> pdb=" O VAL b 172 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 189 through 190 removed outlier: 3.609A pdb=" N GLY b 203 " --> pdb=" O GLN b 194 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 278 through 284 Processing sheet with id=AB1, first strand: chain 'B1' and resid 87 through 90 Processing sheet with id=AB2, first strand: chain 'B1' and resid 167 through 172 removed outlier: 4.086A pdb=" N PHEB1 152 " --> pdb=" O VALB1 172 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B1' and resid 189 through 190 removed outlier: 6.758A pdb=" N GLNB1 194 " --> pdb=" O LEUB1 202 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B1' and resid 279 through 284 removed outlier: 3.533A pdb=" N ALAB1 279 " --> pdb=" O GLNb1 342 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'b1' and resid 87 through 90 Processing sheet with id=AB6, first strand: chain 'b1' and resid 167 through 172 removed outlier: 4.062A pdb=" N PHEb1 152 " --> pdb=" O VALb1 172 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'b1' and resid 189 through 190 removed outlier: 3.636A pdb=" N GLYb1 203 " --> pdb=" O GLNb1 194 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'b1' and resid 281 through 284 removed outlier: 3.750A pdb=" N THRb1 281 " --> pdb=" O ASNB2 340 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLUb1 283 " --> pdb=" O SERB2 338 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B2' and resid 87 through 90 Processing sheet with id=AC1, first strand: chain 'B2' and resid 167 through 172 removed outlier: 3.943A pdb=" N PHEB2 152 " --> pdb=" O VALB2 172 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B2' and resid 189 through 190 removed outlier: 3.644A pdb=" N GLYB2 203 " --> pdb=" O GLNB2 194 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B2' and resid 281 through 284 removed outlier: 3.611A pdb=" N GLUB2 283 " --> pdb=" O SERb2 338 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'b2' and resid 87 through 90 Processing sheet with id=AC5, first strand: chain 'b2' and resid 167 through 172 removed outlier: 4.061A pdb=" N PHEb2 152 " --> pdb=" O VALb2 172 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'b2' and resid 189 through 190 removed outlier: 6.710A pdb=" N GLNb2 194 " --> pdb=" O LEUb2 202 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'b2' and resid 332 through 335 removed outlier: 8.382A pdb=" N LEUb2 333 " --> pdb=" O ALAb2 280 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILEb2 282 " --> pdb=" O LEUb2 333 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N SERb2 284 " --> pdb=" O PROb2 335 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLUb2 283 " --> pdb=" O SERB3 338 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B3' and resid 87 through 90 Processing sheet with id=AC9, first strand: chain 'B3' and resid 167 through 172 removed outlier: 4.074A pdb=" N PHEB3 152 " --> pdb=" O VALB3 172 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B3' and resid 189 through 190 removed outlier: 3.632A pdb=" N GLYB3 203 " --> pdb=" O GLNB3 194 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B3' and resid 281 through 284 removed outlier: 3.645A pdb=" N THRB3 281 " --> pdb=" O ASNb3 340 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLUB3 283 " --> pdb=" O SERb3 338 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'b3' and resid 87 through 90 Processing sheet with id=AD4, first strand: chain 'b3' and resid 167 through 172 removed outlier: 3.950A pdb=" N PHEb3 152 " --> pdb=" O VALb3 172 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'b3' and resid 189 through 190 removed outlier: 6.702A pdb=" N GLNb3 194 " --> pdb=" O LEUb3 202 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'b3' and resid 278 through 284 Processing sheet with id=AD7, first strand: chain 'B4' and resid 87 through 90 Processing sheet with id=AD8, first strand: chain 'B4' and resid 167 through 172 removed outlier: 4.043A pdb=" N PHEB4 152 " --> pdb=" O VALB4 172 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B4' and resid 189 through 190 removed outlier: 6.717A pdb=" N GLNB4 194 " --> pdb=" O LEUB4 202 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B4' and resid 281 through 284 removed outlier: 3.555A pdb=" N THRB4 281 " --> pdb=" O ASNb4 340 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLUB4 283 " --> pdb=" O SERb4 338 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'b4' and resid 87 through 90 Processing sheet with id=AE3, first strand: chain 'b4' and resid 167 through 172 removed outlier: 3.915A pdb=" N PHEb4 152 " --> pdb=" O VALb4 172 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'b4' and resid 189 through 190 removed outlier: 3.666A pdb=" N GLYb4 203 " --> pdb=" O GLNb4 194 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'b4' and resid 281 through 284 removed outlier: 3.865A pdb=" N THRb4 281 " --> pdb=" O ASNB5 340 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASNB5 340 " --> pdb=" O THRb4 281 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLUb4 283 " --> pdb=" O SERB5 338 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B5' and resid 87 through 90 Processing sheet with id=AE7, first strand: chain 'B5' and resid 167 through 172 removed outlier: 3.896A pdb=" N PHEB5 152 " --> pdb=" O VALB5 172 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B5' and resid 189 through 190 removed outlier: 6.753A pdb=" N GLNB5 194 " --> pdb=" O LEUB5 202 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B5' and resid 332 through 335 removed outlier: 7.207A pdb=" N ILEB5 282 " --> pdb=" O LEUB5 333 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N SERB5 284 " --> pdb=" O PROB5 335 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THRB5 281 " --> pdb=" O ASNb5 340 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASNb5 340 " --> pdb=" O THRB5 281 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLUB5 283 " --> pdb=" O SERb5 338 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'b5' and resid 87 through 90 Processing sheet with id=AF2, first strand: chain 'b5' and resid 167 through 172 removed outlier: 4.090A pdb=" N PHEb5 152 " --> pdb=" O VALb5 172 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'b5' and resid 189 through 190 removed outlier: 6.704A pdb=" N GLNb5 194 " --> pdb=" O LEUb5 202 " (cutoff:3.500A) 2529 hydrogen bonds defined for protein. 7236 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: 11.11 Time building geometry restraints manager: 5.36 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: 13563 1.33 - 1.46: 9721 1.46 - 1.58: 21764 1.58 - 1.70: 0 1.70 - 1.83: 468 Bond restraints: 45516 Sorted by residual: bond pdb=" CA PRO B 40 " pdb=" C PRO B 40 " ideal model delta sigma weight residual 1.517 1.499 0.018 6.70e-03 2.23e+04 6.94e+00 bond pdb=" SD METb2 260 " pdb=" CE METb2 260 " ideal model delta sigma weight residual 1.791 1.738 0.053 2.50e-02 1.60e+03 4.46e+00 bond pdb=" CA PROB3 40 " pdb=" C PROB3 40 " ideal model delta sigma weight residual 1.517 1.503 0.014 6.70e-03 2.23e+04 4.25e+00 bond pdb=" CB PROb3 216 " pdb=" CG PROb3 216 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.56e+00 bond pdb=" CB LYSB2 459 " pdb=" CG LYSB2 459 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.30e+00 ... (remaining 45511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 60879 3.24 - 6.48: 589 6.48 - 9.73: 83 9.73 - 12.97: 16 12.97 - 16.21: 5 Bond angle restraints: 61572 Sorted by residual: angle pdb=" CA METb2 260 " pdb=" CB METb2 260 " pdb=" CG METb2 260 " ideal model delta sigma weight residual 114.10 123.84 -9.74 2.00e+00 2.50e-01 2.37e+01 angle pdb=" CA LEU b 341 " pdb=" CB LEU b 341 " pdb=" CG LEU b 341 " ideal model delta sigma weight residual 116.30 132.51 -16.21 3.50e+00 8.16e-02 2.15e+01 angle pdb=" C LYSB4 259 " pdb=" N METB4 260 " pdb=" CA METB4 260 " ideal model delta sigma weight residual 121.14 113.35 7.79 1.75e+00 3.27e-01 1.98e+01 angle pdb=" CA METb4 260 " pdb=" CB METb4 260 " pdb=" CG METb4 260 " ideal model delta sigma weight residual 114.10 122.93 -8.83 2.00e+00 2.50e-01 1.95e+01 angle pdb=" CB METb2 260 " pdb=" CG METb2 260 " pdb=" SD METb2 260 " ideal model delta sigma weight residual 112.70 125.56 -12.86 3.00e+00 1.11e-01 1.84e+01 ... (remaining 61567 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 23254 17.99 - 35.98: 3160 35.98 - 53.97: 631 53.97 - 71.97: 122 71.97 - 89.96: 25 Dihedral angle restraints: 27192 sinusoidal: 10752 harmonic: 16440 Sorted by residual: dihedral pdb=" CA ALAB2 321 " pdb=" C ALAB2 321 " pdb=" N PROB2 322 " pdb=" CA PROB2 322 " ideal model delta harmonic sigma weight residual 180.00 -145.19 -34.81 0 5.00e+00 4.00e-02 4.85e+01 dihedral pdb=" CB CYSb3 123 " pdb=" SG CYSb3 123 " pdb=" SG CYSb3 125 " pdb=" CB CYSb3 125 " ideal model delta sinusoidal sigma weight residual -86.00 -141.71 55.71 1 1.00e+01 1.00e-02 4.19e+01 dihedral pdb=" CB CYSb5 123 " pdb=" SG CYSb5 123 " pdb=" SG CYSb5 125 " pdb=" CB CYSb5 125 " ideal model delta sinusoidal sigma weight residual -86.00 -141.64 55.64 1 1.00e+01 1.00e-02 4.18e+01 ... (remaining 27189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 5424 0.061 - 0.122: 912 0.122 - 0.183: 59 0.183 - 0.244: 12 0.244 - 0.306: 1 Chirality restraints: 6408 Sorted by residual: chirality pdb=" CG LEUb2 76 " pdb=" CB LEUb2 76 " pdb=" CD1 LEUb2 76 " pdb=" CD2 LEUb2 76 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CG LEUB1 76 " pdb=" CB LEUB1 76 " pdb=" CD1 LEUB1 76 " pdb=" CD2 LEUB1 76 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA METb1 260 " pdb=" N METb1 260 " pdb=" C METb1 260 " pdb=" CB METb1 260 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 6405 not shown) Planarity restraints: 8172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALAB2 321 " -0.086 5.00e-02 4.00e+02 1.35e-01 2.91e+01 pdb=" N PROB2 322 " 0.233 5.00e-02 4.00e+02 pdb=" CA PROB2 322 " -0.077 5.00e-02 4.00e+02 pdb=" CD PROB2 322 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALAb5 321 " 0.078 5.00e-02 4.00e+02 1.18e-01 2.23e+01 pdb=" N PROb5 322 " -0.204 5.00e-02 4.00e+02 pdb=" CA PROb5 322 " 0.063 5.00e-02 4.00e+02 pdb=" CD PROb5 322 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALAb1 321 " -0.078 5.00e-02 4.00e+02 1.18e-01 2.22e+01 pdb=" N PROb1 322 " 0.204 5.00e-02 4.00e+02 pdb=" CA PROb1 322 " -0.063 5.00e-02 4.00e+02 pdb=" CD PROb1 322 " -0.063 5.00e-02 4.00e+02 ... (remaining 8169 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 1414 2.67 - 3.23: 47794 3.23 - 3.78: 79023 3.78 - 4.34: 97514 4.34 - 4.90: 156129 Nonbonded interactions: 381874 Sorted by model distance: nonbonded pdb=" OG SERb5 369 " pdb=" OE1 GLNb5 372 " model vdw 2.109 3.040 nonbonded pdb=" OG SERB4 369 " pdb=" OE1 GLUB4 371 " model vdw 2.139 3.040 nonbonded pdb=" OD1 ASNb4 390 " pdb=" NH2 ARGb4 452 " model vdw 2.159 3.120 nonbonded pdb=" OG SER B 369 " pdb=" OE1 GLN B 372 " model vdw 2.162 3.040 nonbonded pdb=" OE1 GLNB1 356 " pdb=" OH TYRB1 370 " model vdw 2.162 3.040 ... (remaining 381869 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: 0.02 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'B1' selection = chain 'B2' selection = chain 'B3' selection = chain 'B4' selection = chain 'B5' selection = chain 'b' selection = chain 'b1' selection = chain 'b2' selection = chain 'b3' selection = chain 'b4' selection = chain 'b5' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.620 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 44.150 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.150 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 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 : 0.005 0.080 45528 Z= 0.214 Angle : 0.809 16.212 61596 Z= 0.414 Chirality : 0.044 0.306 6408 Planarity : 0.006 0.135 8172 Dihedral : 16.394 89.957 16596 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.17 % Favored : 94.47 % Rotamer: Outliers : 0.67 % Allowed : 28.04 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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 aren not related in a simple way. whole: 0.82 (0.11), residues: 5664 helix: 1.25 (0.10), residues: 2772 sheet: -0.22 (0.22), residues: 552 loop : 0.01 (0.14), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARGB1 482 TYR 0.028 0.001 TYRB5 395 PHE 0.040 0.002 PHE B 396 TRP 0.030 0.001 TRPB3 393 HIS 0.005 0.001 HISB2 145 Details of bonding type rmsd covalent geometry : bond 0.00462 (45516) covalent geometry : angle 0.80919 (61572) SS BOND : bond 0.00154 ( 12) SS BOND : angle 0.30754 ( 24) hydrogen bonds : bond 0.12783 ( 2529) hydrogen bonds : angle 6.03080 ( 7236) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 837 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 MET cc_start: 0.9612 (ptp) cc_final: 0.9368 (pmm) REVERT: B 270 GLN cc_start: 0.9632 (mm-40) cc_final: 0.9398 (mm-40) REVERT: b 116 LYS cc_start: 0.9610 (ptpp) cc_final: 0.9402 (ptpp) REVERT: b 399 ARG cc_start: 0.9247 (tpp80) cc_final: 0.8745 (tpp80) REVERT: b 466 MET cc_start: 0.9574 (mmm) cc_final: 0.9373 (mtp) REVERT: B1 75 GLN cc_start: 0.8740 (tp40) cc_final: 0.8465 (tp-100) REVERT: B1 137 MET cc_start: 0.9475 (mmp) cc_final: 0.9263 (mmp) REVERT: B1 238 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8182 (tm-30) REVERT: B1 411 MET cc_start: 0.9608 (mtm) cc_final: 0.9188 (mtm) REVERT: b1 77 HIS cc_start: 0.9517 (m-70) cc_final: 0.9248 (m90) REVERT: b1 79 ASP cc_start: 0.8333 (m-30) cc_final: 0.8066 (m-30) REVERT: b2 411 MET cc_start: 0.9453 (mtm) cc_final: 0.9117 (mtm) REVERT: B3 87 ARG cc_start: 0.8142 (ptm160) cc_final: 0.7850 (ptm160) REVERT: b3 144 MET cc_start: 0.9606 (ttp) cc_final: 0.9327 (ttm) REVERT: b3 277 MET cc_start: 0.9225 (mmm) cc_final: 0.8997 (mmm) REVERT: b4 270 GLN cc_start: 0.9655 (mm-40) cc_final: 0.9340 (mm-40) REVERT: B5 136 MET cc_start: 0.9379 (ptp) cc_final: 0.9135 (pmm) REVERT: B5 255 MET cc_start: 0.9265 (mtp) cc_final: 0.8757 (tpp) REVERT: B5 399 ARG cc_start: 0.9408 (tpp80) cc_final: 0.9084 (tpp80) REVERT: b5 277 MET cc_start: 0.9203 (tpt) cc_final: 0.8900 (tpp) REVERT: b5 397 MET cc_start: 0.9003 (mmm) cc_final: 0.8798 (mmp) REVERT: b5 411 MET cc_start: 0.9631 (mtm) cc_final: 0.9192 (mtm) outliers start: 30 outliers final: 15 residues processed: 853 average time/residue: 0.2886 time to fit residues: 402.2890 Evaluate side-chains 818 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 803 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B1 residue 46 ASP Chi-restraints excluded: chain B2 residue 133 THR Chi-restraints excluded: chain B2 residue 489 ILE Chi-restraints excluded: chain b2 residue 46 ASP Chi-restraints excluded: chain b2 residue 325 LEU Chi-restraints excluded: chain B3 residue 133 THR Chi-restraints excluded: chain B3 residue 430 LYS Chi-restraints excluded: chain b3 residue 84 SER Chi-restraints excluded: chain b3 residue 133 THR Chi-restraints excluded: chain b3 residue 455 ILE Chi-restraints excluded: chain b4 residue 45 VAL Chi-restraints excluded: chain b4 residue 137 MET Chi-restraints excluded: chain B5 residue 133 THR Chi-restraints excluded: chain b5 residue 46 ASP Chi-restraints excluded: chain b5 residue 256 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 394 optimal weight: 5.9990 chunk 430 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 265 optimal weight: 6.9990 chunk 523 optimal weight: 0.8980 chunk 497 optimal weight: 9.9990 chunk 414 optimal weight: 5.9990 chunk 310 optimal weight: 7.9990 chunk 488 optimal weight: 6.9990 chunk 366 optimal weight: 9.9990 chunk 223 optimal weight: 8.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 194 GLN ** b 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 372 GLN b 462 GLN b1 372 GLN b2 340 ASN b2 372 GLN B3 268 GLN B3 372 GLN B4 266 ASN B4 372 GLN b4 75 GLN B5 266 ASN B5 268 GLN B5 372 GLN ** b5 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b5 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.070535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.056916 restraints weight = 173482.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.058582 restraints weight = 99581.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.059708 restraints weight = 69690.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.060449 restraints weight = 54652.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.060954 restraints weight = 46428.326| |-----------------------------------------------------------------------------| r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 45528 Z= 0.227 Angle : 0.674 12.999 61596 Z= 0.356 Chirality : 0.042 0.233 6408 Planarity : 0.006 0.118 8172 Dihedral : 4.798 55.960 6376 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.01 % Favored : 94.69 % Rotamer: Outliers : 3.02 % Allowed : 24.06 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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 aren not related in a simple way. whole: 0.95 (0.11), residues: 5664 helix: 1.35 (0.10), residues: 2868 sheet: -0.32 (0.22), residues: 552 loop : 0.06 (0.14), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG b 399 TYR 0.020 0.001 TYRb4 395 PHE 0.040 0.001 PHEb4 396 TRP 0.023 0.001 TRPB3 393 HIS 0.004 0.001 HISB4 80 Details of bonding type rmsd covalent geometry : bond 0.00483 (45516) covalent geometry : angle 0.67392 (61572) SS BOND : bond 0.00267 ( 12) SS BOND : angle 0.76824 ( 24) hydrogen bonds : bond 0.04700 ( 2529) hydrogen bonds : angle 5.22343 ( 7236) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 985 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 850 time to evaluate : 2.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 GLN cc_start: 0.8718 (tp40) cc_final: 0.8052 (tp-100) REVERT: B 147 PHE cc_start: 0.9269 (p90) cc_final: 0.8985 (p90) REVERT: B 260 MET cc_start: 0.9126 (mtm) cc_final: 0.8687 (mtm) REVERT: B 270 GLN cc_start: 0.9565 (mm-40) cc_final: 0.9239 (mm-40) REVERT: B 399 ARG cc_start: 0.9103 (tpp80) cc_final: 0.8784 (tpp80) REVERT: B 458 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9356 (mm) REVERT: B 473 SER cc_start: 0.9197 (OUTLIER) cc_final: 0.8739 (p) REVERT: b 144 MET cc_start: 0.9627 (ttp) cc_final: 0.9355 (ttp) REVERT: b 266 ASN cc_start: 0.9524 (m110) cc_final: 0.9284 (m110) REVERT: b 380 MET cc_start: 0.8329 (tpt) cc_final: 0.8081 (tpt) REVERT: b 399 ARG cc_start: 0.9235 (tpp80) cc_final: 0.8615 (tpp80) REVERT: b 466 MET cc_start: 0.9572 (mmm) cc_final: 0.9361 (mtp) REVERT: b 477 LYS cc_start: 0.9034 (mtmm) cc_final: 0.8719 (mtmt) REVERT: B1 69 TYR cc_start: 0.9512 (m-80) cc_final: 0.9197 (m-80) REVERT: B1 75 GLN cc_start: 0.9115 (tp40) cc_final: 0.8261 (tp-100) REVERT: B1 87 ARG cc_start: 0.8289 (ttp80) cc_final: 0.8054 (mtm110) REVERT: B1 116 LYS cc_start: 0.9641 (ttpp) cc_final: 0.9423 (pttm) REVERT: B1 238 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8068 (tm-30) REVERT: B1 360 ARG cc_start: 0.9539 (OUTLIER) cc_final: 0.8922 (ttm110) REVERT: B1 397 MET cc_start: 0.8886 (mmm) cc_final: 0.8658 (mmm) REVERT: b1 75 GLN cc_start: 0.8811 (tp40) cc_final: 0.7956 (tp-100) REVERT: b1 91 ARG cc_start: 0.9218 (mmp-170) cc_final: 0.8999 (mmm160) REVERT: b1 147 PHE cc_start: 0.9330 (p90) cc_final: 0.9121 (p90) REVERT: b1 266 ASN cc_start: 0.9530 (m-40) cc_final: 0.9237 (m110) REVERT: b1 399 ARG cc_start: 0.9187 (tpp80) cc_final: 0.8836 (tpp80) REVERT: b1 498 MET cc_start: 0.9404 (ppp) cc_final: 0.9204 (ppp) REVERT: B2 137 MET cc_start: 0.9572 (mmt) cc_final: 0.9083 (mpp) REVERT: B2 399 ARG cc_start: 0.9373 (mmm-85) cc_final: 0.8731 (tpp80) REVERT: b2 75 GLN cc_start: 0.8797 (tp40) cc_final: 0.8227 (tp40) REVERT: b2 79 ASP cc_start: 0.8033 (m-30) cc_final: 0.7358 (m-30) REVERT: b2 137 MET cc_start: 0.9580 (tpp) cc_final: 0.9223 (mmp) REVERT: b2 360 ARG cc_start: 0.9597 (OUTLIER) cc_final: 0.8827 (ttm110) REVERT: b2 372 GLN cc_start: 0.9424 (pt0) cc_final: 0.9015 (pt0) REVERT: B3 87 ARG cc_start: 0.8042 (ptm160) cc_final: 0.7634 (ptm-80) REVERT: B3 91 ARG cc_start: 0.9215 (mmp-170) cc_final: 0.9000 (mmm160) REVERT: B3 116 LYS cc_start: 0.9625 (ptpp) cc_final: 0.9372 (ptpp) REVERT: B3 270 GLN cc_start: 0.9209 (mm-40) cc_final: 0.8989 (mm-40) REVERT: B3 334 MET cc_start: 0.9043 (ppp) cc_final: 0.8836 (tmm) REVERT: B3 473 SER cc_start: 0.9076 (OUTLIER) cc_final: 0.8843 (p) REVERT: b3 144 MET cc_start: 0.9617 (ttp) cc_final: 0.9276 (ttm) REVERT: b3 266 ASN cc_start: 0.9338 (m-40) cc_final: 0.9090 (m110) REVERT: b3 275 LYS cc_start: 0.9234 (mtpt) cc_final: 0.8843 (tttt) REVERT: b3 277 MET cc_start: 0.9175 (mmm) cc_final: 0.8876 (mmm) REVERT: B4 75 GLN cc_start: 0.8858 (tp40) cc_final: 0.8441 (tp-100) REVERT: B4 260 MET cc_start: 0.9280 (mtm) cc_final: 0.9070 (mtm) REVERT: B4 277 MET cc_start: 0.9184 (mmm) cc_final: 0.8812 (tpt) REVERT: B4 325 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8665 (pp) REVERT: B4 360 ARG cc_start: 0.9528 (OUTLIER) cc_final: 0.8922 (ttm110) REVERT: B4 453 MET cc_start: 0.7802 (tpp) cc_final: 0.7368 (tmm) REVERT: b4 69 TYR cc_start: 0.9484 (m-80) cc_final: 0.9242 (m-80) REVERT: b4 116 LYS cc_start: 0.9488 (pptt) cc_final: 0.9286 (pptt) REVERT: b4 270 GLN cc_start: 0.9613 (mm-40) cc_final: 0.9192 (mm-40) REVERT: b4 346 ASP cc_start: 0.8741 (t0) cc_final: 0.8236 (t0) REVERT: b4 371 GLU cc_start: 0.8888 (pm20) cc_final: 0.8664 (pm20) REVERT: b4 376 ASN cc_start: 0.9581 (t0) cc_final: 0.9175 (t0) REVERT: b4 459 LYS cc_start: 0.9410 (mmmm) cc_final: 0.9199 (mmmm) REVERT: B5 255 MET cc_start: 0.9157 (mtp) cc_final: 0.8613 (tpp) REVERT: B5 266 ASN cc_start: 0.9425 (m110) cc_final: 0.9110 (m110) REVERT: B5 277 MET cc_start: 0.9230 (tpt) cc_final: 0.8999 (mmm) REVERT: B5 360 ARG cc_start: 0.9521 (OUTLIER) cc_final: 0.8746 (ttm110) REVERT: B5 399 ARG cc_start: 0.9425 (tpp80) cc_final: 0.8814 (tpp80) REVERT: b5 137 MET cc_start: 0.9456 (mmp) cc_final: 0.9114 (mmt) REVERT: b5 252 TYR cc_start: 0.8982 (OUTLIER) cc_final: 0.8734 (t80) REVERT: b5 371 GLU cc_start: 0.8705 (mp0) cc_final: 0.8416 (mp0) outliers start: 135 outliers final: 81 residues processed: 957 average time/residue: 0.2952 time to fit residues: 458.1101 Evaluate side-chains 888 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 798 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain b residue 133 THR Chi-restraints excluded: chain b residue 182 ASN Chi-restraints excluded: chain b residue 240 VAL Chi-restraints excluded: chain b residue 282 ILE Chi-restraints excluded: chain b residue 323 VAL Chi-restraints excluded: chain b residue 353 VAL Chi-restraints excluded: chain b residue 368 VAL Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain b residue 448 ILE Chi-restraints excluded: chain B1 residue 82 VAL Chi-restraints excluded: chain B1 residue 126 ILE Chi-restraints excluded: chain B1 residue 182 ASN Chi-restraints excluded: chain B1 residue 208 GLU Chi-restraints excluded: chain B1 residue 254 VAL Chi-restraints excluded: chain B1 residue 281 THR Chi-restraints excluded: chain B1 residue 323 VAL Chi-restraints excluded: chain B1 residue 360 ARG Chi-restraints excluded: chain B1 residue 366 LEU Chi-restraints excluded: chain B1 residue 368 VAL Chi-restraints excluded: chain B1 residue 369 SER Chi-restraints excluded: chain b1 residue 93 SER Chi-restraints excluded: chain b1 residue 182 ASN Chi-restraints excluded: chain b1 residue 206 VAL Chi-restraints excluded: chain b1 residue 323 VAL Chi-restraints excluded: chain b1 residue 359 LEU Chi-restraints excluded: chain b1 residue 381 SER Chi-restraints excluded: chain b1 residue 384 THR Chi-restraints excluded: chain b1 residue 452 ARG Chi-restraints excluded: chain B2 residue 133 THR Chi-restraints excluded: chain B2 residue 182 ASN Chi-restraints excluded: chain B2 residue 368 VAL Chi-restraints excluded: chain B2 residue 369 SER Chi-restraints excluded: chain b2 residue 82 VAL Chi-restraints excluded: chain b2 residue 182 ASN Chi-restraints excluded: chain b2 residue 256 GLU Chi-restraints excluded: chain b2 residue 360 ARG Chi-restraints excluded: chain b2 residue 368 VAL Chi-restraints excluded: chain b2 residue 381 SER Chi-restraints excluded: chain b2 residue 448 ILE Chi-restraints excluded: chain B3 residue 182 ASN Chi-restraints excluded: chain B3 residue 206 VAL Chi-restraints excluded: chain B3 residue 323 VAL Chi-restraints excluded: chain B3 residue 391 GLU Chi-restraints excluded: chain B3 residue 473 SER Chi-restraints excluded: chain b3 residue 82 VAL Chi-restraints excluded: chain b3 residue 126 ILE Chi-restraints excluded: chain b3 residue 369 SER Chi-restraints excluded: chain b3 residue 381 SER Chi-restraints excluded: chain b3 residue 448 ILE Chi-restraints excluded: chain b3 residue 455 ILE Chi-restraints excluded: chain b3 residue 463 GLU Chi-restraints excluded: chain b3 residue 466 MET Chi-restraints excluded: chain B4 residue 45 VAL Chi-restraints excluded: chain B4 residue 182 ASN Chi-restraints excluded: chain B4 residue 323 VAL Chi-restraints excluded: chain B4 residue 325 LEU Chi-restraints excluded: chain B4 residue 360 ARG Chi-restraints excluded: chain B4 residue 366 LEU Chi-restraints excluded: chain b4 residue 182 ASN Chi-restraints excluded: chain b4 residue 206 VAL Chi-restraints excluded: chain b4 residue 359 LEU Chi-restraints excluded: chain b4 residue 366 LEU Chi-restraints excluded: chain b4 residue 368 VAL Chi-restraints excluded: chain b4 residue 395 TYR Chi-restraints excluded: chain b4 residue 448 ILE Chi-restraints excluded: chain B5 residue 84 SER Chi-restraints excluded: chain B5 residue 182 ASN Chi-restraints excluded: chain B5 residue 281 THR Chi-restraints excluded: chain B5 residue 360 ARG Chi-restraints excluded: chain B5 residue 368 VAL Chi-restraints excluded: chain B5 residue 448 ILE Chi-restraints excluded: chain B5 residue 489 ILE Chi-restraints excluded: chain b5 residue 82 VAL Chi-restraints excluded: chain b5 residue 126 ILE Chi-restraints excluded: chain b5 residue 182 ASN Chi-restraints excluded: chain b5 residue 240 VAL Chi-restraints excluded: chain b5 residue 252 TYR Chi-restraints excluded: chain b5 residue 323 VAL Chi-restraints excluded: chain b5 residue 381 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 496 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 337 optimal weight: 9.9990 chunk 203 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 chunk 398 optimal weight: 1.9990 chunk 503 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 158 optimal weight: 8.9990 chunk 225 optimal weight: 10.0000 chunk 426 optimal weight: 10.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 372 GLN B1 34 GLN B1 372 GLN b1 372 GLN B2 372 GLN b2 266 ASN B3 340 ASN B3 372 GLN b3 372 GLN B4 372 GLN b5 75 GLN b5 268 GLN ** b5 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.070932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.057305 restraints weight = 171916.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.058977 restraints weight = 99199.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.060090 restraints weight = 69099.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.060851 restraints weight = 54249.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.061348 restraints weight = 46093.652| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 45528 Z= 0.184 Angle : 0.642 11.469 61596 Z= 0.336 Chirality : 0.041 0.265 6408 Planarity : 0.006 0.118 8172 Dihedral : 4.476 48.765 6351 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.26 % Favored : 94.46 % Rotamer: Outliers : 3.44 % Allowed : 24.11 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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 aren not related in a simple way. whole: 1.00 (0.11), residues: 5664 helix: 1.43 (0.10), residues: 2868 sheet: -0.35 (0.22), residues: 552 loop : 0.06 (0.14), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGb3 187 TYR 0.019 0.001 TYRb4 395 PHE 0.030 0.001 PHEb4 396 TRP 0.019 0.001 TRPB3 393 HIS 0.004 0.001 HIS B 332 Details of bonding type rmsd covalent geometry : bond 0.00397 (45516) covalent geometry : angle 0.64194 (61572) SS BOND : bond 0.00143 ( 12) SS BOND : angle 0.69874 ( 24) hydrogen bonds : bond 0.04521 ( 2529) hydrogen bonds : angle 5.03927 ( 7236) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1035 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 881 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 GLN cc_start: 0.8911 (tp40) cc_final: 0.8098 (tp-100) REVERT: B 270 GLN cc_start: 0.9579 (mm-40) cc_final: 0.9256 (mm-40) REVERT: B 399 ARG cc_start: 0.9244 (tpp80) cc_final: 0.8785 (tpp80) REVERT: B 458 LEU cc_start: 0.9648 (OUTLIER) cc_final: 0.9368 (mm) REVERT: B 477 LYS cc_start: 0.9164 (mtmm) cc_final: 0.8677 (mtmt) REVERT: b 116 LYS cc_start: 0.9571 (ptpp) cc_final: 0.9351 (pttm) REVERT: b 144 MET cc_start: 0.9658 (ttp) cc_final: 0.9394 (ttp) REVERT: b 266 ASN cc_start: 0.9557 (m110) cc_final: 0.9289 (m110) REVERT: b 277 MET cc_start: 0.9363 (tpt) cc_final: 0.9144 (tpt) REVERT: b 399 ARG cc_start: 0.9317 (tpp80) cc_final: 0.8881 (tpp80) REVERT: b 466 MET cc_start: 0.9588 (mmm) cc_final: 0.9374 (mtp) REVERT: B1 75 GLN cc_start: 0.9068 (tp40) cc_final: 0.8137 (tp-100) REVERT: B1 87 ARG cc_start: 0.8302 (ttp80) cc_final: 0.8026 (mtm110) REVERT: B1 116 LYS cc_start: 0.9636 (ttpp) cc_final: 0.9418 (pttm) REVERT: B1 209 ASP cc_start: 0.9062 (p0) cc_final: 0.8859 (p0) REVERT: B1 218 LYS cc_start: 0.8510 (mmtm) cc_final: 0.8228 (mmtt) REVERT: B1 238 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8203 (tm-30) REVERT: B1 360 ARG cc_start: 0.9542 (OUTLIER) cc_final: 0.8832 (ttm110) REVERT: B1 377 TYR cc_start: 0.9071 (m-80) cc_final: 0.8773 (m-80) REVERT: B1 397 MET cc_start: 0.8937 (mmm) cc_final: 0.8683 (mmm) REVERT: B1 460 GLU cc_start: 0.8588 (mp0) cc_final: 0.8237 (mp0) REVERT: b1 75 GLN cc_start: 0.8857 (tp40) cc_final: 0.7832 (tp-100) REVERT: b1 91 ARG cc_start: 0.9241 (mmp-170) cc_final: 0.9025 (mmm160) REVERT: b1 131 LYS cc_start: 0.9071 (ptpp) cc_final: 0.8805 (ptpp) REVERT: b1 175 LYS cc_start: 0.9695 (mtpt) cc_final: 0.9277 (ptmt) REVERT: b1 265 GLN cc_start: 0.9556 (mm-40) cc_final: 0.9346 (mm-40) REVERT: b1 266 ASN cc_start: 0.9561 (m-40) cc_final: 0.9304 (m110) REVERT: b1 399 ARG cc_start: 0.9280 (tpp80) cc_final: 0.8792 (tpp80) REVERT: B2 131 LYS cc_start: 0.8876 (pttm) cc_final: 0.8414 (pttm) REVERT: B2 137 MET cc_start: 0.9538 (mmt) cc_final: 0.8802 (mpp) REVERT: B2 144 MET cc_start: 0.9588 (ttp) cc_final: 0.9375 (ttt) REVERT: B2 275 LYS cc_start: 0.9077 (mtpt) cc_final: 0.8829 (ttpt) REVERT: B2 399 ARG cc_start: 0.9370 (mmm-85) cc_final: 0.8702 (tpp80) REVERT: B2 458 LEU cc_start: 0.9624 (OUTLIER) cc_final: 0.9383 (mm) REVERT: b2 69 TYR cc_start: 0.9584 (m-80) cc_final: 0.9368 (m-80) REVERT: b2 137 MET cc_start: 0.9501 (tpp) cc_final: 0.9060 (tpp) REVERT: b2 266 ASN cc_start: 0.9337 (m-40) cc_final: 0.8833 (m110) REVERT: b2 271 SER cc_start: 0.9503 (OUTLIER) cc_final: 0.9178 (p) REVERT: b2 360 ARG cc_start: 0.9482 (OUTLIER) cc_final: 0.8824 (ttm110) REVERT: b2 397 MET cc_start: 0.8996 (mmm) cc_final: 0.8750 (mmm) REVERT: B3 87 ARG cc_start: 0.7961 (ptm160) cc_final: 0.7563 (ptm-80) REVERT: B3 91 ARG cc_start: 0.9218 (mmp-170) cc_final: 0.8998 (mmm160) REVERT: B3 116 LYS cc_start: 0.9624 (ptpp) cc_final: 0.9327 (pttm) REVERT: B3 397 MET cc_start: 0.9283 (mmm) cc_final: 0.9069 (mmp) REVERT: b3 144 MET cc_start: 0.9637 (ttp) cc_final: 0.9295 (ttm) REVERT: b3 266 ASN cc_start: 0.9363 (m-40) cc_final: 0.9074 (m110) REVERT: b3 275 LYS cc_start: 0.9272 (mtpt) cc_final: 0.9070 (ttpt) REVERT: B4 43 GLU cc_start: 0.8612 (pm20) cc_final: 0.8329 (pm20) REVERT: B4 69 TYR cc_start: 0.9530 (m-80) cc_final: 0.9240 (m-80) REVERT: B4 75 GLN cc_start: 0.8919 (tp40) cc_final: 0.8384 (tp-100) REVERT: B4 137 MET cc_start: 0.9625 (tpp) cc_final: 0.9014 (tpp) REVERT: B4 260 MET cc_start: 0.9302 (mtm) cc_final: 0.9073 (mtm) REVERT: B4 277 MET cc_start: 0.9145 (mmm) cc_final: 0.8945 (tpp) REVERT: B4 325 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8744 (pp) REVERT: B4 360 ARG cc_start: 0.9413 (OUTLIER) cc_final: 0.8902 (ttm110) REVERT: B4 458 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.8728 (mm) REVERT: b4 69 TYR cc_start: 0.9518 (m-80) cc_final: 0.9305 (m-80) REVERT: b4 116 LYS cc_start: 0.9477 (pptt) cc_final: 0.9264 (pptt) REVERT: b4 175 LYS cc_start: 0.9637 (mtmt) cc_final: 0.9266 (ptmt) REVERT: b4 270 GLN cc_start: 0.9641 (mm-40) cc_final: 0.9206 (mm-40) REVERT: b4 371 GLU cc_start: 0.8908 (pm20) cc_final: 0.8692 (pm20) REVERT: b4 376 ASN cc_start: 0.9619 (t0) cc_final: 0.9182 (t0) REVERT: b4 450 SER cc_start: 0.9512 (OUTLIER) cc_final: 0.9153 (p) REVERT: B5 78 GLN cc_start: 0.9248 (OUTLIER) cc_final: 0.8747 (mm-40) REVERT: B5 91 ARG cc_start: 0.9090 (mmm160) cc_final: 0.8749 (mmm160) REVERT: B5 144 MET cc_start: 0.9655 (ttp) cc_final: 0.9448 (ttp) REVERT: B5 258 MET cc_start: 0.9339 (mmm) cc_final: 0.8931 (mmm) REVERT: B5 266 ASN cc_start: 0.9416 (m110) cc_final: 0.9083 (m110) REVERT: B5 360 ARG cc_start: 0.9529 (OUTLIER) cc_final: 0.8739 (ttm110) REVERT: B5 399 ARG cc_start: 0.9444 (tpp80) cc_final: 0.8823 (tpp80) REVERT: B5 484 ASP cc_start: 0.8917 (m-30) cc_final: 0.8649 (m-30) REVERT: b5 75 GLN cc_start: 0.8886 (tp40) cc_final: 0.8621 (tp-100) REVERT: b5 136 MET cc_start: 0.9271 (pmm) cc_final: 0.8872 (pmm) REVERT: b5 252 TYR cc_start: 0.8983 (OUTLIER) cc_final: 0.8760 (t80) REVERT: b5 271 SER cc_start: 0.9528 (OUTLIER) cc_final: 0.9311 (p) REVERT: b5 334 MET cc_start: 0.9417 (mmm) cc_final: 0.8994 (mmm) REVERT: b5 371 GLU cc_start: 0.8743 (mp0) cc_final: 0.8279 (mp0) REVERT: b5 390 ASN cc_start: 0.9144 (m110) cc_final: 0.8899 (m110) outliers start: 154 outliers final: 90 residues processed: 996 average time/residue: 0.2850 time to fit residues: 458.6401 Evaluate side-chains 910 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 807 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain b residue 77 HIS Chi-restraints excluded: chain b residue 82 VAL Chi-restraints excluded: chain b residue 131 LYS Chi-restraints excluded: chain b residue 133 THR Chi-restraints excluded: chain b residue 137 MET Chi-restraints excluded: chain b residue 240 VAL Chi-restraints excluded: chain b residue 282 ILE Chi-restraints excluded: chain b residue 323 VAL Chi-restraints excluded: chain b residue 353 VAL Chi-restraints excluded: chain b residue 368 VAL Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain b residue 448 ILE Chi-restraints excluded: chain B1 residue 82 VAL Chi-restraints excluded: chain B1 residue 126 ILE Chi-restraints excluded: chain B1 residue 133 THR Chi-restraints excluded: chain B1 residue 254 VAL Chi-restraints excluded: chain B1 residue 281 THR Chi-restraints excluded: chain B1 residue 323 VAL Chi-restraints excluded: chain B1 residue 347 THR Chi-restraints excluded: chain B1 residue 360 ARG Chi-restraints excluded: chain B1 residue 366 LEU Chi-restraints excluded: chain b1 residue 206 VAL Chi-restraints excluded: chain b1 residue 323 VAL Chi-restraints excluded: chain b1 residue 359 LEU Chi-restraints excluded: chain b1 residue 381 SER Chi-restraints excluded: chain b1 residue 384 THR Chi-restraints excluded: chain b1 residue 391 GLU Chi-restraints excluded: chain b1 residue 452 ARG Chi-restraints excluded: chain B2 residue 49 LEU Chi-restraints excluded: chain B2 residue 55 ARG Chi-restraints excluded: chain B2 residue 63 LEU Chi-restraints excluded: chain B2 residue 133 THR Chi-restraints excluded: chain B2 residue 182 ASN Chi-restraints excluded: chain B2 residue 369 SER Chi-restraints excluded: chain B2 residue 458 LEU Chi-restraints excluded: chain b2 residue 82 VAL Chi-restraints excluded: chain b2 residue 126 ILE Chi-restraints excluded: chain b2 residue 128 VAL Chi-restraints excluded: chain b2 residue 256 GLU Chi-restraints excluded: chain b2 residue 271 SER Chi-restraints excluded: chain b2 residue 360 ARG Chi-restraints excluded: chain b2 residue 381 SER Chi-restraints excluded: chain B3 residue 182 ASN Chi-restraints excluded: chain B3 residue 206 VAL Chi-restraints excluded: chain B3 residue 323 VAL Chi-restraints excluded: chain B3 residue 391 GLU Chi-restraints excluded: chain B3 residue 430 LYS Chi-restraints excluded: chain b3 residue 63 LEU Chi-restraints excluded: chain b3 residue 82 VAL Chi-restraints excluded: chain b3 residue 126 ILE Chi-restraints excluded: chain b3 residue 182 ASN Chi-restraints excluded: chain b3 residue 381 SER Chi-restraints excluded: chain b3 residue 448 ILE Chi-restraints excluded: chain b3 residue 463 GLU Chi-restraints excluded: chain b3 residue 466 MET Chi-restraints excluded: chain B4 residue 49 LEU Chi-restraints excluded: chain B4 residue 126 ILE Chi-restraints excluded: chain B4 residue 323 VAL Chi-restraints excluded: chain B4 residue 325 LEU Chi-restraints excluded: chain B4 residue 330 VAL Chi-restraints excluded: chain B4 residue 360 ARG Chi-restraints excluded: chain B4 residue 458 LEU Chi-restraints excluded: chain b4 residue 74 ILE Chi-restraints excluded: chain b4 residue 206 VAL Chi-restraints excluded: chain b4 residue 254 VAL Chi-restraints excluded: chain b4 residue 282 ILE Chi-restraints excluded: chain b4 residue 359 LEU Chi-restraints excluded: chain b4 residue 368 VAL Chi-restraints excluded: chain b4 residue 448 ILE Chi-restraints excluded: chain b4 residue 450 SER Chi-restraints excluded: chain b4 residue 478 GLU Chi-restraints excluded: chain B5 residue 49 LEU Chi-restraints excluded: chain B5 residue 63 LEU Chi-restraints excluded: chain B5 residue 78 GLN Chi-restraints excluded: chain B5 residue 84 SER Chi-restraints excluded: chain B5 residue 182 ASN Chi-restraints excluded: chain B5 residue 281 THR Chi-restraints excluded: chain B5 residue 353 VAL Chi-restraints excluded: chain B5 residue 360 ARG Chi-restraints excluded: chain B5 residue 369 SER Chi-restraints excluded: chain B5 residue 384 THR Chi-restraints excluded: chain B5 residue 489 ILE Chi-restraints excluded: chain b5 residue 82 VAL Chi-restraints excluded: chain b5 residue 126 ILE Chi-restraints excluded: chain b5 residue 133 THR Chi-restraints excluded: chain b5 residue 240 VAL Chi-restraints excluded: chain b5 residue 252 TYR Chi-restraints excluded: chain b5 residue 271 SER Chi-restraints excluded: chain b5 residue 323 VAL Chi-restraints excluded: chain b5 residue 368 VAL Chi-restraints excluded: chain b5 residue 381 SER Chi-restraints excluded: chain b5 residue 384 THR Chi-restraints excluded: chain b5 residue 448 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 385 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 387 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 251 optimal weight: 5.9990 chunk 195 optimal weight: 7.9990 chunk 284 optimal weight: 0.9990 chunk 247 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 304 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN ** b 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 34 GLN B1 356 GLN B1 372 GLN b1 372 GLN B2 194 GLN B2 372 GLN b2 372 GLN B3 372 GLN b3 372 GLN B4 372 GLN b5 268 GLN b5 356 GLN ** b5 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.071719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.057948 restraints weight = 170847.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.059662 restraints weight = 99045.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.060778 restraints weight = 68504.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.061548 restraints weight = 53990.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.062056 restraints weight = 45654.088| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 45528 Z= 0.143 Angle : 0.652 14.057 61596 Z= 0.333 Chirality : 0.041 0.259 6408 Planarity : 0.005 0.117 8172 Dihedral : 4.420 45.530 6349 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.05 % Favored : 94.69 % Rotamer: Outliers : 3.46 % Allowed : 24.49 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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 aren not related in a simple way. whole: 1.03 (0.11), residues: 5664 helix: 1.48 (0.10), residues: 2868 sheet: -0.39 (0.22), residues: 552 loop : 0.05 (0.14), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGb5 482 TYR 0.022 0.001 TYRB3 395 PHE 0.029 0.001 PHE B 396 TRP 0.014 0.001 TRPB3 393 HIS 0.003 0.001 HISB4 80 Details of bonding type rmsd covalent geometry : bond 0.00319 (45516) covalent geometry : angle 0.65155 (61572) SS BOND : bond 0.00092 ( 12) SS BOND : angle 0.63243 ( 24) hydrogen bonds : bond 0.04351 ( 2529) hydrogen bonds : angle 4.92250 ( 7236) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1060 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 905 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 GLN cc_start: 0.8883 (tp40) cc_final: 0.7988 (tp-100) REVERT: B 175 LYS cc_start: 0.9639 (mtmt) cc_final: 0.9176 (pttt) REVERT: B 270 GLN cc_start: 0.9549 (mm-40) cc_final: 0.9219 (mm-40) REVERT: B 282 ILE cc_start: 0.9653 (mm) cc_final: 0.9370 (pt) REVERT: B 329 LYS cc_start: 0.9600 (tppt) cc_final: 0.9376 (tppt) REVERT: B 399 ARG cc_start: 0.9212 (tpp80) cc_final: 0.8924 (tpp80) REVERT: B 458 LEU cc_start: 0.9649 (OUTLIER) cc_final: 0.9363 (mm) REVERT: B 459 LYS cc_start: 0.9377 (mmmm) cc_final: 0.9156 (mmmm) REVERT: B 477 LYS cc_start: 0.9084 (mtmm) cc_final: 0.8862 (mtmt) REVERT: b 116 LYS cc_start: 0.9558 (ptpp) cc_final: 0.9354 (pttm) REVERT: b 144 MET cc_start: 0.9646 (ttp) cc_final: 0.9377 (ttp) REVERT: b 175 LYS cc_start: 0.9622 (mtmt) cc_final: 0.9269 (ptmt) REVERT: b 266 ASN cc_start: 0.9570 (m110) cc_final: 0.9279 (m110) REVERT: b 277 MET cc_start: 0.9336 (tpt) cc_final: 0.9131 (tpt) REVERT: b 399 ARG cc_start: 0.9308 (tpp80) cc_final: 0.8902 (tpp80) REVERT: b 466 MET cc_start: 0.9544 (mmm) cc_final: 0.9257 (tpt) REVERT: B1 69 TYR cc_start: 0.9511 (m-80) cc_final: 0.9224 (m-80) REVERT: B1 75 GLN cc_start: 0.9085 (tp40) cc_final: 0.7958 (tp-100) REVERT: B1 76 LEU cc_start: 0.9791 (mm) cc_final: 0.9423 (mm) REVERT: B1 79 ASP cc_start: 0.8544 (m-30) cc_final: 0.8130 (p0) REVERT: B1 87 ARG cc_start: 0.8268 (ttp80) cc_final: 0.7979 (mtm110) REVERT: B1 116 LYS cc_start: 0.9612 (ttpp) cc_final: 0.9393 (pttm) REVERT: B1 209 ASP cc_start: 0.9032 (p0) cc_final: 0.8826 (p0) REVERT: B1 238 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8056 (tm-30) REVERT: B1 360 ARG cc_start: 0.9458 (OUTLIER) cc_final: 0.8886 (ttm110) REVERT: B1 377 TYR cc_start: 0.9051 (m-80) cc_final: 0.8778 (m-80) REVERT: b1 75 GLN cc_start: 0.8868 (tp40) cc_final: 0.7747 (tp-100) REVERT: b1 175 LYS cc_start: 0.9709 (mtpt) cc_final: 0.9277 (ptmt) REVERT: b1 266 ASN cc_start: 0.9554 (m-40) cc_final: 0.9209 (m110) REVERT: b1 399 ARG cc_start: 0.9280 (tpp80) cc_final: 0.8826 (tpp80) REVERT: b1 473 SER cc_start: 0.9263 (OUTLIER) cc_final: 0.8913 (p) REVERT: B2 116 LYS cc_start: 0.9565 (ptpp) cc_final: 0.9295 (pttm) REVERT: B2 137 MET cc_start: 0.9552 (OUTLIER) cc_final: 0.8846 (mpp) REVERT: B2 144 MET cc_start: 0.9572 (ttp) cc_final: 0.9366 (ttt) REVERT: B2 277 MET cc_start: 0.9121 (tpt) cc_final: 0.8838 (tpt) REVERT: B2 372 GLN cc_start: 0.9385 (pt0) cc_final: 0.9171 (pt0) REVERT: B2 376 ASN cc_start: 0.9701 (t0) cc_final: 0.9269 (t0) REVERT: B2 399 ARG cc_start: 0.9338 (mmm-85) cc_final: 0.8710 (tpp80) REVERT: B2 458 LEU cc_start: 0.9669 (OUTLIER) cc_final: 0.9345 (mm) REVERT: b2 69 TYR cc_start: 0.9563 (m-80) cc_final: 0.9362 (m-80) REVERT: b2 75 GLN cc_start: 0.9072 (tp40) cc_final: 0.8592 (tp-100) REVERT: b2 79 ASP cc_start: 0.8505 (m-30) cc_final: 0.7935 (m-30) REVERT: b2 137 MET cc_start: 0.9431 (tpp) cc_final: 0.9230 (tpp) REVERT: b2 266 ASN cc_start: 0.9420 (m-40) cc_final: 0.8898 (m110) REVERT: b2 275 LYS cc_start: 0.9530 (tttt) cc_final: 0.9221 (tttp) REVERT: b2 360 ARG cc_start: 0.9453 (OUTLIER) cc_final: 0.8757 (ttm110) REVERT: B3 266 ASN cc_start: 0.9495 (m110) cc_final: 0.9288 (m110) REVERT: B3 334 MET cc_start: 0.9047 (ppp) cc_final: 0.8791 (tmm) REVERT: B3 473 SER cc_start: 0.9281 (OUTLIER) cc_final: 0.8821 (p) REVERT: b3 75 GLN cc_start: 0.9323 (OUTLIER) cc_final: 0.8992 (tp-100) REVERT: b3 78 GLN cc_start: 0.9265 (OUTLIER) cc_final: 0.8718 (mm-40) REVERT: b3 137 MET cc_start: 0.9641 (tpp) cc_final: 0.9327 (mmm) REVERT: b3 144 MET cc_start: 0.9627 (ttp) cc_final: 0.9253 (ttm) REVERT: b3 266 ASN cc_start: 0.9381 (m-40) cc_final: 0.9077 (m110) REVERT: b3 275 LYS cc_start: 0.9289 (mtpt) cc_final: 0.9059 (ttpt) REVERT: b3 477 LYS cc_start: 0.9142 (mtmm) cc_final: 0.8787 (pttm) REVERT: B4 69 TYR cc_start: 0.9528 (m-80) cc_final: 0.9320 (m-80) REVERT: B4 75 GLN cc_start: 0.8908 (tp40) cc_final: 0.8276 (tp-100) REVERT: B4 137 MET cc_start: 0.9610 (tpp) cc_final: 0.8941 (tpp) REVERT: B4 252 TYR cc_start: 0.9154 (OUTLIER) cc_final: 0.8698 (t80) REVERT: B4 260 MET cc_start: 0.9291 (mtm) cc_final: 0.9039 (mtm) REVERT: B4 271 SER cc_start: 0.9530 (OUTLIER) cc_final: 0.9304 (p) REVERT: B4 325 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8697 (pp) REVERT: B4 360 ARG cc_start: 0.9401 (OUTLIER) cc_final: 0.8980 (ttm110) REVERT: B4 458 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9125 (mm) REVERT: B4 473 SER cc_start: 0.9505 (OUTLIER) cc_final: 0.9249 (t) REVERT: b4 69 TYR cc_start: 0.9481 (m-80) cc_final: 0.9241 (m-80) REVERT: b4 75 GLN cc_start: 0.9062 (tp40) cc_final: 0.8045 (tp-100) REVERT: b4 136 MET cc_start: 0.9368 (ptp) cc_final: 0.9040 (ptp) REVERT: b4 175 LYS cc_start: 0.9642 (mtmt) cc_final: 0.9245 (pttt) REVERT: b4 376 ASN cc_start: 0.9626 (t0) cc_final: 0.9202 (t0) REVERT: b4 450 SER cc_start: 0.9531 (OUTLIER) cc_final: 0.9207 (p) REVERT: b4 481 LYS cc_start: 0.9313 (mtmm) cc_final: 0.9083 (mtmm) REVERT: B5 78 GLN cc_start: 0.9175 (OUTLIER) cc_final: 0.8746 (mm-40) REVERT: B5 91 ARG cc_start: 0.9087 (mmm160) cc_final: 0.8826 (mmm160) REVERT: B5 255 MET cc_start: 0.9127 (mtp) cc_final: 0.8556 (tpp) REVERT: B5 258 MET cc_start: 0.9296 (mmm) cc_final: 0.8914 (mmm) REVERT: B5 266 ASN cc_start: 0.9396 (m110) cc_final: 0.9043 (m110) REVERT: B5 339 LEU cc_start: 0.9740 (tt) cc_final: 0.9440 (mm) REVERT: B5 360 ARG cc_start: 0.9518 (OUTLIER) cc_final: 0.8742 (ttm110) REVERT: B5 399 ARG cc_start: 0.9421 (tpp80) cc_final: 0.8784 (tpp80) REVERT: B5 484 ASP cc_start: 0.8830 (m-30) cc_final: 0.8559 (m-30) REVERT: b5 69 TYR cc_start: 0.9512 (m-80) cc_final: 0.9034 (m-80) REVERT: b5 74 ILE cc_start: 0.9723 (tp) cc_final: 0.9519 (tp) REVERT: b5 75 GLN cc_start: 0.9074 (tp40) cc_final: 0.8732 (tp-100) REVERT: b5 136 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.8790 (pmm) REVERT: b5 137 MET cc_start: 0.9598 (tpp) cc_final: 0.9337 (mmp) REVERT: b5 252 TYR cc_start: 0.8953 (OUTLIER) cc_final: 0.8748 (t80) REVERT: b5 271 SER cc_start: 0.9550 (OUTLIER) cc_final: 0.9300 (p) REVERT: b5 334 MET cc_start: 0.9505 (mmm) cc_final: 0.9024 (mmm) REVERT: b5 346 ASP cc_start: 0.8945 (m-30) cc_final: 0.8721 (m-30) REVERT: b5 390 ASN cc_start: 0.9061 (m110) cc_final: 0.8797 (m110) outliers start: 155 outliers final: 90 residues processed: 1022 average time/residue: 0.2697 time to fit residues: 446.3263 Evaluate side-chains 931 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 820 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain b residue 77 HIS Chi-restraints excluded: chain b residue 82 VAL Chi-restraints excluded: chain b residue 131 LYS Chi-restraints excluded: chain b residue 133 THR Chi-restraints excluded: chain b residue 137 MET Chi-restraints excluded: chain b residue 171 MET Chi-restraints excluded: chain b residue 240 VAL Chi-restraints excluded: chain b residue 323 VAL Chi-restraints excluded: chain b residue 353 VAL Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain b residue 448 ILE Chi-restraints excluded: chain B1 residue 82 VAL Chi-restraints excluded: chain B1 residue 133 THR Chi-restraints excluded: chain B1 residue 254 VAL Chi-restraints excluded: chain B1 residue 323 VAL Chi-restraints excluded: chain B1 residue 347 THR Chi-restraints excluded: chain B1 residue 356 GLN Chi-restraints excluded: chain B1 residue 359 LEU Chi-restraints excluded: chain B1 residue 360 ARG Chi-restraints excluded: chain B1 residue 366 LEU Chi-restraints excluded: chain B1 residue 368 VAL Chi-restraints excluded: chain B1 residue 369 SER Chi-restraints excluded: chain B1 residue 448 ILE Chi-restraints excluded: chain b1 residue 206 VAL Chi-restraints excluded: chain b1 residue 323 VAL Chi-restraints excluded: chain b1 residue 359 LEU Chi-restraints excluded: chain b1 residue 384 THR Chi-restraints excluded: chain b1 residue 448 ILE Chi-restraints excluded: chain b1 residue 452 ARG Chi-restraints excluded: chain b1 residue 473 SER Chi-restraints excluded: chain B2 residue 49 LEU Chi-restraints excluded: chain B2 residue 55 ARG Chi-restraints excluded: chain B2 residue 63 LEU Chi-restraints excluded: chain B2 residue 133 THR Chi-restraints excluded: chain B2 residue 137 MET Chi-restraints excluded: chain B2 residue 347 THR Chi-restraints excluded: chain B2 residue 368 VAL Chi-restraints excluded: chain B2 residue 369 SER Chi-restraints excluded: chain B2 residue 381 SER Chi-restraints excluded: chain B2 residue 458 LEU Chi-restraints excluded: chain b2 residue 82 VAL Chi-restraints excluded: chain b2 residue 126 ILE Chi-restraints excluded: chain b2 residue 128 VAL Chi-restraints excluded: chain b2 residue 256 GLU Chi-restraints excluded: chain b2 residue 360 ARG Chi-restraints excluded: chain b2 residue 381 SER Chi-restraints excluded: chain b2 residue 448 ILE Chi-restraints excluded: chain B3 residue 206 VAL Chi-restraints excluded: chain B3 residue 323 VAL Chi-restraints excluded: chain B3 residue 370 TYR Chi-restraints excluded: chain B3 residue 381 SER Chi-restraints excluded: chain B3 residue 391 GLU Chi-restraints excluded: chain B3 residue 430 LYS Chi-restraints excluded: chain B3 residue 473 SER Chi-restraints excluded: chain b3 residue 75 GLN Chi-restraints excluded: chain b3 residue 77 HIS Chi-restraints excluded: chain b3 residue 78 GLN Chi-restraints excluded: chain b3 residue 82 VAL Chi-restraints excluded: chain b3 residue 126 ILE Chi-restraints excluded: chain b3 residue 218 LYS Chi-restraints excluded: chain b3 residue 353 VAL Chi-restraints excluded: chain b3 residue 369 SER Chi-restraints excluded: chain b3 residue 381 SER Chi-restraints excluded: chain b3 residue 463 GLU Chi-restraints excluded: chain b3 residue 466 MET Chi-restraints excluded: chain B4 residue 252 TYR Chi-restraints excluded: chain B4 residue 271 SER Chi-restraints excluded: chain B4 residue 323 VAL Chi-restraints excluded: chain B4 residue 325 LEU Chi-restraints excluded: chain B4 residue 330 VAL Chi-restraints excluded: chain B4 residue 360 ARG Chi-restraints excluded: chain B4 residue 366 LEU Chi-restraints excluded: chain B4 residue 448 ILE Chi-restraints excluded: chain B4 residue 458 LEU Chi-restraints excluded: chain B4 residue 473 SER Chi-restraints excluded: chain B4 residue 482 ARG Chi-restraints excluded: chain b4 residue 74 ILE Chi-restraints excluded: chain b4 residue 206 VAL Chi-restraints excluded: chain b4 residue 347 THR Chi-restraints excluded: chain b4 residue 356 GLN Chi-restraints excluded: chain b4 residue 359 LEU Chi-restraints excluded: chain b4 residue 366 LEU Chi-restraints excluded: chain b4 residue 448 ILE Chi-restraints excluded: chain b4 residue 450 SER Chi-restraints excluded: chain B5 residue 63 LEU Chi-restraints excluded: chain B5 residue 78 GLN Chi-restraints excluded: chain B5 residue 281 THR Chi-restraints excluded: chain B5 residue 323 VAL Chi-restraints excluded: chain B5 residue 353 VAL Chi-restraints excluded: chain B5 residue 360 ARG Chi-restraints excluded: chain B5 residue 368 VAL Chi-restraints excluded: chain B5 residue 369 SER Chi-restraints excluded: chain B5 residue 381 SER Chi-restraints excluded: chain B5 residue 384 THR Chi-restraints excluded: chain B5 residue 448 ILE Chi-restraints excluded: chain B5 residue 489 ILE Chi-restraints excluded: chain b5 residue 82 VAL Chi-restraints excluded: chain b5 residue 126 ILE Chi-restraints excluded: chain b5 residue 133 THR Chi-restraints excluded: chain b5 residue 136 MET Chi-restraints excluded: chain b5 residue 252 TYR Chi-restraints excluded: chain b5 residue 271 SER Chi-restraints excluded: chain b5 residue 323 VAL Chi-restraints excluded: chain b5 residue 368 VAL Chi-restraints excluded: chain b5 residue 384 THR Chi-restraints excluded: chain b5 residue 448 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 425 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 chunk 330 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 460 optimal weight: 3.9990 chunk 556 optimal weight: 0.0270 chunk 502 optimal weight: 7.9990 chunk 368 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 199 optimal weight: 8.9990 overall best weight: 2.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 34 GLN B1 372 GLN b1 372 GLN b2 372 GLN B3 75 GLN B3 372 GLN b3 372 GLN B4 372 GLN b4 372 GLN ** b5 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.071641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.057903 restraints weight = 168328.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.059553 restraints weight = 97698.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.060636 restraints weight = 68128.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.061395 restraints weight = 54074.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.061902 restraints weight = 46163.693| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 45528 Z= 0.148 Angle : 0.660 14.038 61596 Z= 0.335 Chirality : 0.041 0.274 6408 Planarity : 0.005 0.117 8172 Dihedral : 4.390 44.746 6349 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.14 % Favored : 94.62 % Rotamer: Outliers : 3.87 % Allowed : 24.78 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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 aren not related in a simple way. whole: 1.02 (0.11), residues: 5664 helix: 1.45 (0.10), residues: 2892 sheet: -0.36 (0.22), residues: 552 loop : 0.05 (0.14), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARGb2 91 TYR 0.027 0.001 TYR b 486 PHE 0.033 0.001 PHE b 396 TRP 0.013 0.001 TRPB3 393 HIS 0.005 0.001 HISB2 80 Details of bonding type rmsd covalent geometry : bond 0.00330 (45516) covalent geometry : angle 0.66047 (61572) SS BOND : bond 0.00116 ( 12) SS BOND : angle 0.56293 ( 24) hydrogen bonds : bond 0.04270 ( 2529) hydrogen bonds : angle 4.87773 ( 7236) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1056 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 883 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 GLN cc_start: 0.8835 (tp40) cc_final: 0.7773 (tp-100) REVERT: B 175 LYS cc_start: 0.9653 (mtmt) cc_final: 0.9191 (pttt) REVERT: B 270 GLN cc_start: 0.9582 (mm-40) cc_final: 0.9216 (mm-40) REVERT: B 275 LYS cc_start: 0.9286 (mmmm) cc_final: 0.9063 (mtpp) REVERT: B 282 ILE cc_start: 0.9673 (mm) cc_final: 0.9367 (pt) REVERT: B 399 ARG cc_start: 0.9180 (tpp80) cc_final: 0.8854 (tpp80) REVERT: B 458 LEU cc_start: 0.9669 (OUTLIER) cc_final: 0.9402 (mm) REVERT: B 477 LYS cc_start: 0.9191 (mtmm) cc_final: 0.8930 (mtmm) REVERT: b 78 GLN cc_start: 0.9359 (mt0) cc_final: 0.8874 (mm-40) REVERT: b 116 LYS cc_start: 0.9554 (ptpp) cc_final: 0.9327 (ptpp) REVERT: b 175 LYS cc_start: 0.9632 (mtmt) cc_final: 0.9310 (ptmt) REVERT: b 266 ASN cc_start: 0.9573 (m110) cc_final: 0.9263 (m110) REVERT: b 277 MET cc_start: 0.9315 (tpt) cc_final: 0.9072 (tpp) REVERT: b 399 ARG cc_start: 0.9301 (tpp80) cc_final: 0.8945 (tpp80) REVERT: b 462 GLN cc_start: 0.9550 (OUTLIER) cc_final: 0.9285 (mm110) REVERT: b 466 MET cc_start: 0.9545 (mmm) cc_final: 0.9237 (tpt) REVERT: B1 69 TYR cc_start: 0.9506 (m-80) cc_final: 0.9138 (m-80) REVERT: B1 75 GLN cc_start: 0.9128 (tp40) cc_final: 0.7985 (tp-100) REVERT: B1 76 LEU cc_start: 0.9786 (OUTLIER) cc_final: 0.9384 (mm) REVERT: B1 79 ASP cc_start: 0.8548 (m-30) cc_final: 0.8134 (p0) REVERT: B1 87 ARG cc_start: 0.8348 (ttp80) cc_final: 0.8034 (mtm110) REVERT: B1 136 MET cc_start: 0.9210 (pmm) cc_final: 0.8832 (pmm) REVERT: B1 238 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8068 (tm-30) REVERT: B1 360 ARG cc_start: 0.9384 (OUTLIER) cc_final: 0.8809 (ttm110) REVERT: B1 377 TYR cc_start: 0.9075 (m-80) cc_final: 0.8842 (m-80) REVERT: B1 460 GLU cc_start: 0.8486 (mp0) cc_final: 0.8139 (mp0) REVERT: b1 75 GLN cc_start: 0.8937 (tp40) cc_final: 0.7791 (tp-100) REVERT: b1 266 ASN cc_start: 0.9549 (m-40) cc_final: 0.9185 (m110) REVERT: b1 275 LYS cc_start: 0.9126 (mttm) cc_final: 0.8813 (mttm) REVERT: b1 399 ARG cc_start: 0.9298 (tpp80) cc_final: 0.8939 (tpp80) REVERT: B2 43 GLU cc_start: 0.8877 (pm20) cc_final: 0.8615 (pm20) REVERT: B2 116 LYS cc_start: 0.9553 (ptpp) cc_final: 0.9301 (pttm) REVERT: B2 137 MET cc_start: 0.9555 (mmt) cc_final: 0.8843 (mpp) REVERT: B2 376 ASN cc_start: 0.9684 (t0) cc_final: 0.9233 (t0) REVERT: B2 399 ARG cc_start: 0.9296 (mmm-85) cc_final: 0.8705 (tpp80) REVERT: B2 458 LEU cc_start: 0.9695 (OUTLIER) cc_final: 0.9332 (mm) REVERT: b2 75 GLN cc_start: 0.9027 (tp40) cc_final: 0.8447 (tp-100) REVERT: b2 79 ASP cc_start: 0.8484 (m-30) cc_final: 0.7798 (m-30) REVERT: b2 137 MET cc_start: 0.9394 (tpp) cc_final: 0.8860 (tpp) REVERT: b2 266 ASN cc_start: 0.9453 (m-40) cc_final: 0.8914 (m110) REVERT: b2 275 LYS cc_start: 0.9524 (tttt) cc_final: 0.9191 (tttp) REVERT: b2 360 ARG cc_start: 0.9450 (OUTLIER) cc_final: 0.8768 (ttm110) REVERT: b2 487 GLN cc_start: 0.9249 (OUTLIER) cc_final: 0.8788 (mp10) REVERT: B3 87 ARG cc_start: 0.8133 (ptm160) cc_final: 0.7698 (ptm-80) REVERT: B3 116 LYS cc_start: 0.9596 (ptpp) cc_final: 0.9339 (pttm) REVERT: B3 266 ASN cc_start: 0.9507 (m110) cc_final: 0.9296 (m110) REVERT: B3 333 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.8973 (tp) REVERT: B3 399 ARG cc_start: 0.9125 (tpp80) cc_final: 0.8564 (tpp80) REVERT: b3 78 GLN cc_start: 0.9267 (OUTLIER) cc_final: 0.8690 (mm-40) REVERT: b3 137 MET cc_start: 0.9593 (tpp) cc_final: 0.9272 (mmt) REVERT: b3 144 MET cc_start: 0.9634 (ttp) cc_final: 0.9237 (ttm) REVERT: b3 175 LYS cc_start: 0.9587 (mtmt) cc_final: 0.9358 (ptmt) REVERT: b3 266 ASN cc_start: 0.9382 (m-40) cc_final: 0.9051 (m110) REVERT: b3 275 LYS cc_start: 0.9315 (mtpt) cc_final: 0.9066 (ttpt) REVERT: b3 399 ARG cc_start: 0.9284 (mmm-85) cc_final: 0.8718 (tpp80) REVERT: B4 75 GLN cc_start: 0.8943 (tp40) cc_final: 0.8257 (tp-100) REVERT: B4 136 MET cc_start: 0.9372 (ptp) cc_final: 0.8895 (ptp) REVERT: B4 137 MET cc_start: 0.9595 (tpp) cc_final: 0.8863 (tpp) REVERT: B4 260 MET cc_start: 0.9267 (mtm) cc_final: 0.9025 (mtm) REVERT: B4 271 SER cc_start: 0.9535 (OUTLIER) cc_final: 0.9307 (p) REVERT: B4 325 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8566 (pp) REVERT: B4 360 ARG cc_start: 0.9412 (OUTLIER) cc_final: 0.8998 (ttm110) REVERT: b4 69 TYR cc_start: 0.9475 (m-80) cc_final: 0.9251 (m-80) REVERT: b4 75 GLN cc_start: 0.9082 (tp40) cc_final: 0.7794 (tp-100) REVERT: b4 79 ASP cc_start: 0.8442 (m-30) cc_final: 0.7439 (m-30) REVERT: b4 136 MET cc_start: 0.9370 (ptp) cc_final: 0.9052 (ptp) REVERT: b4 175 LYS cc_start: 0.9678 (mtmt) cc_final: 0.9264 (pttt) REVERT: b4 270 GLN cc_start: 0.9599 (mm-40) cc_final: 0.9220 (mm-40) REVERT: b4 450 SER cc_start: 0.9547 (OUTLIER) cc_final: 0.9238 (p) REVERT: b4 481 LYS cc_start: 0.9314 (mtmm) cc_final: 0.9033 (mtmm) REVERT: B5 78 GLN cc_start: 0.9186 (OUTLIER) cc_final: 0.8784 (mm-40) REVERT: B5 87 ARG cc_start: 0.8639 (ttp80) cc_final: 0.8105 (mtm110) REVERT: B5 91 ARG cc_start: 0.9108 (mmm160) cc_final: 0.8863 (mmm160) REVERT: B5 255 MET cc_start: 0.9093 (mtp) cc_final: 0.8538 (tpp) REVERT: B5 258 MET cc_start: 0.9275 (mmm) cc_final: 0.8874 (mmm) REVERT: B5 266 ASN cc_start: 0.9388 (m110) cc_final: 0.9040 (m110) REVERT: B5 339 LEU cc_start: 0.9732 (tt) cc_final: 0.9427 (mm) REVERT: B5 360 ARG cc_start: 0.9514 (OUTLIER) cc_final: 0.8815 (ttm110) REVERT: B5 399 ARG cc_start: 0.9411 (tpp80) cc_final: 0.8764 (tpp80) REVERT: B5 453 MET cc_start: 0.7886 (ppp) cc_final: 0.7573 (ppp) REVERT: b5 69 TYR cc_start: 0.9497 (m-80) cc_final: 0.9144 (m-80) REVERT: b5 74 ILE cc_start: 0.9738 (tp) cc_final: 0.9537 (tp) REVERT: b5 75 GLN cc_start: 0.9124 (tp40) cc_final: 0.8737 (tp-100) REVERT: b5 79 ASP cc_start: 0.8390 (m-30) cc_final: 0.8024 (m-30) REVERT: b5 136 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8795 (pmm) REVERT: b5 137 MET cc_start: 0.9595 (tpp) cc_final: 0.9234 (mmp) REVERT: b5 271 SER cc_start: 0.9502 (OUTLIER) cc_final: 0.9262 (p) REVERT: b5 278 TYR cc_start: 0.7005 (t80) cc_final: 0.6782 (t80) REVERT: b5 334 MET cc_start: 0.9557 (mmm) cc_final: 0.9114 (mmm) REVERT: b5 390 ASN cc_start: 0.9078 (m110) cc_final: 0.8725 (m110) REVERT: b5 458 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.8763 (mm) REVERT: b5 476 GLU cc_start: 0.8961 (pm20) cc_final: 0.8760 (pm20) outliers start: 173 outliers final: 107 residues processed: 1013 average time/residue: 0.2726 time to fit residues: 445.7511 Evaluate side-chains 960 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 835 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain b residue 77 HIS Chi-restraints excluded: chain b residue 133 THR Chi-restraints excluded: chain b residue 137 MET Chi-restraints excluded: chain b residue 171 MET Chi-restraints excluded: chain b residue 240 VAL Chi-restraints excluded: chain b residue 323 VAL Chi-restraints excluded: chain b residue 353 VAL Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain b residue 448 ILE Chi-restraints excluded: chain b residue 462 GLN Chi-restraints excluded: chain B1 residue 43 GLU Chi-restraints excluded: chain B1 residue 76 LEU Chi-restraints excluded: chain B1 residue 82 VAL Chi-restraints excluded: chain B1 residue 126 ILE Chi-restraints excluded: chain B1 residue 133 THR Chi-restraints excluded: chain B1 residue 254 VAL Chi-restraints excluded: chain B1 residue 282 ILE Chi-restraints excluded: chain B1 residue 323 VAL Chi-restraints excluded: chain B1 residue 347 THR Chi-restraints excluded: chain B1 residue 359 LEU Chi-restraints excluded: chain B1 residue 360 ARG Chi-restraints excluded: chain B1 residue 366 LEU Chi-restraints excluded: chain B1 residue 368 VAL Chi-restraints excluded: chain B1 residue 448 ILE Chi-restraints excluded: chain b1 residue 206 VAL Chi-restraints excluded: chain b1 residue 323 VAL Chi-restraints excluded: chain b1 residue 353 VAL Chi-restraints excluded: chain b1 residue 359 LEU Chi-restraints excluded: chain b1 residue 381 SER Chi-restraints excluded: chain b1 residue 384 THR Chi-restraints excluded: chain b1 residue 448 ILE Chi-restraints excluded: chain b1 residue 452 ARG Chi-restraints excluded: chain B2 residue 49 LEU Chi-restraints excluded: chain B2 residue 55 ARG Chi-restraints excluded: chain B2 residue 63 LEU Chi-restraints excluded: chain B2 residue 133 THR Chi-restraints excluded: chain B2 residue 206 VAL Chi-restraints excluded: chain B2 residue 323 VAL Chi-restraints excluded: chain B2 residue 347 THR Chi-restraints excluded: chain B2 residue 368 VAL Chi-restraints excluded: chain B2 residue 369 SER Chi-restraints excluded: chain B2 residue 381 SER Chi-restraints excluded: chain B2 residue 458 LEU Chi-restraints excluded: chain B2 residue 489 ILE Chi-restraints excluded: chain b2 residue 82 VAL Chi-restraints excluded: chain b2 residue 128 VAL Chi-restraints excluded: chain b2 residue 256 GLU Chi-restraints excluded: chain b2 residue 323 VAL Chi-restraints excluded: chain b2 residue 347 THR Chi-restraints excluded: chain b2 residue 360 ARG Chi-restraints excluded: chain b2 residue 381 SER Chi-restraints excluded: chain b2 residue 448 ILE Chi-restraints excluded: chain b2 residue 487 GLN Chi-restraints excluded: chain B3 residue 206 VAL Chi-restraints excluded: chain B3 residue 323 VAL Chi-restraints excluded: chain B3 residue 333 LEU Chi-restraints excluded: chain B3 residue 370 TYR Chi-restraints excluded: chain B3 residue 381 SER Chi-restraints excluded: chain B3 residue 391 GLU Chi-restraints excluded: chain B3 residue 430 LYS Chi-restraints excluded: chain b3 residue 77 HIS Chi-restraints excluded: chain b3 residue 78 GLN Chi-restraints excluded: chain b3 residue 82 VAL Chi-restraints excluded: chain b3 residue 126 ILE Chi-restraints excluded: chain b3 residue 218 LYS Chi-restraints excluded: chain b3 residue 353 VAL Chi-restraints excluded: chain b3 residue 369 SER Chi-restraints excluded: chain b3 residue 381 SER Chi-restraints excluded: chain b3 residue 448 ILE Chi-restraints excluded: chain b3 residue 463 GLU Chi-restraints excluded: chain b3 residue 466 MET Chi-restraints excluded: chain B4 residue 271 SER Chi-restraints excluded: chain B4 residue 323 VAL Chi-restraints excluded: chain B4 residue 325 LEU Chi-restraints excluded: chain B4 residue 330 VAL Chi-restraints excluded: chain B4 residue 360 ARG Chi-restraints excluded: chain B4 residue 366 LEU Chi-restraints excluded: chain B4 residue 448 ILE Chi-restraints excluded: chain B4 residue 482 ARG Chi-restraints excluded: chain b4 residue 74 ILE Chi-restraints excluded: chain b4 residue 126 ILE Chi-restraints excluded: chain b4 residue 206 VAL Chi-restraints excluded: chain b4 residue 347 THR Chi-restraints excluded: chain b4 residue 356 GLN Chi-restraints excluded: chain b4 residue 359 LEU Chi-restraints excluded: chain b4 residue 366 LEU Chi-restraints excluded: chain b4 residue 448 ILE Chi-restraints excluded: chain b4 residue 450 SER Chi-restraints excluded: chain b4 residue 476 GLU Chi-restraints excluded: chain B5 residue 49 LEU Chi-restraints excluded: chain B5 residue 63 LEU Chi-restraints excluded: chain B5 residue 78 GLN Chi-restraints excluded: chain B5 residue 84 SER Chi-restraints excluded: chain B5 residue 137 MET Chi-restraints excluded: chain B5 residue 206 VAL Chi-restraints excluded: chain B5 residue 278 TYR Chi-restraints excluded: chain B5 residue 281 THR Chi-restraints excluded: chain B5 residue 323 VAL Chi-restraints excluded: chain B5 residue 353 VAL Chi-restraints excluded: chain B5 residue 360 ARG Chi-restraints excluded: chain B5 residue 368 VAL Chi-restraints excluded: chain B5 residue 369 SER Chi-restraints excluded: chain B5 residue 381 SER Chi-restraints excluded: chain B5 residue 384 THR Chi-restraints excluded: chain B5 residue 448 ILE Chi-restraints excluded: chain B5 residue 489 ILE Chi-restraints excluded: chain b5 residue 82 VAL Chi-restraints excluded: chain b5 residue 86 PHE Chi-restraints excluded: chain b5 residue 133 THR Chi-restraints excluded: chain b5 residue 136 MET Chi-restraints excluded: chain b5 residue 271 SER Chi-restraints excluded: chain b5 residue 323 VAL Chi-restraints excluded: chain b5 residue 368 VAL Chi-restraints excluded: chain b5 residue 381 SER Chi-restraints excluded: chain b5 residue 384 THR Chi-restraints excluded: chain b5 residue 448 ILE Chi-restraints excluded: chain b5 residue 458 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 262 optimal weight: 8.9990 chunk 375 optimal weight: 10.0000 chunk 530 optimal weight: 6.9990 chunk 558 optimal weight: 10.0000 chunk 201 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 383 optimal weight: 8.9990 chunk 354 optimal weight: 20.0000 chunk 134 optimal weight: 8.9990 chunk 466 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 HIS ** b 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 492 GLN B1 34 GLN B1 372 GLN B1 493 GLN b1 80 HIS b1 235 HIS b1 303 GLN b1 372 GLN B2 372 GLN b2 372 GLN B3 372 GLN B4 372 GLN b4 235 HIS b4 372 GLN B5 72 ASN ** b5 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b5 493 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.068422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.055081 restraints weight = 179264.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.056669 restraints weight = 103951.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.057719 restraints weight = 71965.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.058445 restraints weight = 56954.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.058944 restraints weight = 48010.443| |-----------------------------------------------------------------------------| r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 45528 Z= 0.342 Angle : 0.758 12.114 61596 Z= 0.401 Chirality : 0.044 0.302 6408 Planarity : 0.006 0.118 8172 Dihedral : 4.690 44.307 6349 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.40 % Favored : 94.35 % Rotamer: Outliers : 4.80 % Allowed : 24.84 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 2.60 % 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 aren not related in a simple way. whole: 0.85 (0.11), residues: 5664 helix: 1.35 (0.10), residues: 2904 sheet: -0.49 (0.23), residues: 552 loop : -0.10 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG b 130 TYR 0.027 0.002 TYR b 486 PHE 0.034 0.002 PHE B 396 TRP 0.014 0.002 TRPB3 393 HIS 0.007 0.001 HISb3 80 Details of bonding type rmsd covalent geometry : bond 0.00708 (45516) covalent geometry : angle 0.75826 (61572) SS BOND : bond 0.00320 ( 12) SS BOND : angle 0.43866 ( 24) hydrogen bonds : bond 0.04846 ( 2529) hydrogen bonds : angle 5.25124 ( 7236) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1037 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 822 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 GLN cc_start: 0.9004 (tp40) cc_final: 0.8017 (tp-100) REVERT: B 260 MET cc_start: 0.9242 (mtm) cc_final: 0.8876 (mtm) REVERT: B 270 GLN cc_start: 0.9646 (mm-40) cc_final: 0.9270 (mm-40) REVERT: B 399 ARG cc_start: 0.9260 (tpp80) cc_final: 0.8763 (tpp80) REVERT: B 458 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9063 (mm) REVERT: B 477 LYS cc_start: 0.9273 (mtmm) cc_final: 0.9011 (mtmm) REVERT: b 75 GLN cc_start: 0.9275 (OUTLIER) cc_final: 0.8913 (tp-100) REVERT: b 78 GLN cc_start: 0.9339 (mt0) cc_final: 0.8898 (mm-40) REVERT: b 116 LYS cc_start: 0.9565 (ptpp) cc_final: 0.9361 (pttm) REVERT: b 144 MET cc_start: 0.9603 (ttp) cc_final: 0.9317 (ttm) REVERT: b 266 ASN cc_start: 0.9583 (m110) cc_final: 0.9274 (m110) REVERT: b 371 GLU cc_start: 0.8856 (pm20) cc_final: 0.8543 (pm20) REVERT: b 377 TYR cc_start: 0.9254 (m-80) cc_final: 0.9047 (m-80) REVERT: b 399 ARG cc_start: 0.9356 (tpp80) cc_final: 0.8906 (tpp80) REVERT: b 462 GLN cc_start: 0.9526 (OUTLIER) cc_final: 0.9288 (mm110) REVERT: B1 75 GLN cc_start: 0.9332 (tp40) cc_final: 0.8508 (tp-100) REVERT: B1 87 ARG cc_start: 0.8420 (ttp80) cc_final: 0.7695 (ttm170) REVERT: B1 116 LYS cc_start: 0.9639 (ttpp) cc_final: 0.9426 (pttm) REVERT: B1 136 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.8848 (pmm) REVERT: B1 238 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8111 (tm-30) REVERT: B1 277 MET cc_start: 0.9071 (tpp) cc_final: 0.8809 (tpp) REVERT: B1 360 ARG cc_start: 0.9469 (OUTLIER) cc_final: 0.8922 (ttm110) REVERT: b1 75 GLN cc_start: 0.9077 (tp40) cc_final: 0.8483 (tp40) REVERT: b1 253 SER cc_start: 0.9764 (m) cc_final: 0.9472 (t) REVERT: b1 266 ASN cc_start: 0.9602 (m-40) cc_final: 0.9233 (m110) REVERT: b1 277 MET cc_start: 0.8994 (tpp) cc_final: 0.8663 (tpp) REVERT: b1 399 ARG cc_start: 0.9354 (tpp80) cc_final: 0.8846 (tpp80) REVERT: B2 116 LYS cc_start: 0.9569 (ptpp) cc_final: 0.9332 (pttm) REVERT: B2 137 MET cc_start: 0.9529 (OUTLIER) cc_final: 0.9184 (tpp) REVERT: B2 232 SER cc_start: 0.9735 (OUTLIER) cc_final: 0.9298 (p) REVERT: B2 399 ARG cc_start: 0.9342 (mmm-85) cc_final: 0.8730 (tpp80) REVERT: B2 479 CYS cc_start: 0.9054 (m) cc_final: 0.8813 (m) REVERT: B2 481 LYS cc_start: 0.9397 (ptpp) cc_final: 0.9181 (pttm) REVERT: b2 67 ASN cc_start: 0.8948 (t0) cc_final: 0.8698 (t0) REVERT: b2 75 GLN cc_start: 0.9218 (tp40) cc_final: 0.8807 (tm-30) REVERT: b2 137 MET cc_start: 0.9362 (tpp) cc_final: 0.8707 (tpp) REVERT: b2 266 ASN cc_start: 0.9503 (m-40) cc_final: 0.8971 (m110) REVERT: b2 360 ARG cc_start: 0.9469 (OUTLIER) cc_final: 0.8937 (ttm110) REVERT: b2 466 MET cc_start: 0.9576 (mmm) cc_final: 0.9082 (mmm) REVERT: B3 87 ARG cc_start: 0.8175 (ptm160) cc_final: 0.7739 (ptm-80) REVERT: B3 116 LYS cc_start: 0.9623 (ptpp) cc_final: 0.9384 (pttm) REVERT: B3 266 ASN cc_start: 0.9559 (m110) cc_final: 0.9304 (m110) REVERT: B3 270 GLN cc_start: 0.9282 (mm-40) cc_final: 0.9011 (mm-40) REVERT: B3 333 LEU cc_start: 0.9544 (OUTLIER) cc_final: 0.8986 (tp) REVERT: B3 399 ARG cc_start: 0.9149 (tpp80) cc_final: 0.8936 (tpp80) REVERT: B3 473 SER cc_start: 0.9291 (OUTLIER) cc_final: 0.9016 (p) REVERT: B3 482 ARG cc_start: 0.8166 (mtp180) cc_final: 0.7936 (mtp180) REVERT: b3 144 MET cc_start: 0.9599 (ttp) cc_final: 0.9198 (ttm) REVERT: b3 175 LYS cc_start: 0.9572 (mtmt) cc_final: 0.9313 (ptmt) REVERT: b3 266 ASN cc_start: 0.9414 (m-40) cc_final: 0.9066 (m110) REVERT: b3 399 ARG cc_start: 0.9336 (mmm-85) cc_final: 0.8726 (tpp80) REVERT: b3 477 LYS cc_start: 0.9166 (mtmm) cc_final: 0.8948 (ptpp) REVERT: b3 479 CYS cc_start: 0.9266 (m) cc_final: 0.8983 (m) REVERT: B4 75 GLN cc_start: 0.9072 (tp40) cc_final: 0.8359 (tp-100) REVERT: B4 144 MET cc_start: 0.9653 (ttp) cc_final: 0.8893 (tmm) REVERT: B4 232 SER cc_start: 0.9780 (OUTLIER) cc_final: 0.9521 (p) REVERT: B4 260 MET cc_start: 0.9279 (mtm) cc_final: 0.8982 (mtm) REVERT: B4 346 ASP cc_start: 0.9017 (m-30) cc_final: 0.8815 (m-30) REVERT: B4 360 ARG cc_start: 0.9369 (OUTLIER) cc_final: 0.8955 (ttm110) REVERT: B4 458 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8744 (mm) REVERT: B4 487 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.8590 (mp10) REVERT: b4 75 GLN cc_start: 0.9177 (tp40) cc_final: 0.8685 (tp40) REVERT: b4 270 GLN cc_start: 0.9605 (mm-40) cc_final: 0.9110 (mm-40) REVERT: b4 450 SER cc_start: 0.9605 (OUTLIER) cc_final: 0.9273 (p) REVERT: b4 458 LEU cc_start: 0.9680 (OUTLIER) cc_final: 0.9366 (mm) REVERT: b4 481 LYS cc_start: 0.9442 (mtmm) cc_final: 0.9079 (pttm) REVERT: B5 43 GLU cc_start: 0.9041 (pm20) cc_final: 0.8695 (pm20) REVERT: B5 78 GLN cc_start: 0.9198 (mm-40) cc_final: 0.8708 (mm-40) REVERT: B5 91 ARG cc_start: 0.9120 (mmm160) cc_final: 0.8916 (mmm160) REVERT: B5 232 SER cc_start: 0.9728 (OUTLIER) cc_final: 0.9278 (p) REVERT: B5 258 MET cc_start: 0.9346 (mmm) cc_final: 0.8917 (mmm) REVERT: B5 266 ASN cc_start: 0.9469 (m110) cc_final: 0.9100 (m110) REVERT: B5 360 ARG cc_start: 0.9529 (OUTLIER) cc_final: 0.8866 (ttm110) REVERT: B5 399 ARG cc_start: 0.9497 (tpp80) cc_final: 0.8915 (tpp80) REVERT: b5 75 GLN cc_start: 0.9245 (tp40) cc_final: 0.8655 (tp-100) REVERT: b5 136 MET cc_start: 0.9252 (OUTLIER) cc_final: 0.8855 (pmm) REVERT: b5 137 MET cc_start: 0.9559 (tpp) cc_final: 0.9152 (tpp) REVERT: b5 144 MET cc_start: 0.9647 (ttp) cc_final: 0.8883 (tmm) REVERT: b5 260 MET cc_start: 0.9221 (mtm) cc_final: 0.9002 (mtm) REVERT: b5 325 LEU cc_start: 0.8805 (pp) cc_final: 0.8576 (pp) REVERT: b5 476 GLU cc_start: 0.8914 (pm20) cc_final: 0.8695 (pm20) outliers start: 215 outliers final: 144 residues processed: 992 average time/residue: 0.2503 time to fit residues: 402.2281 Evaluate side-chains 945 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 782 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 163 ARG Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 75 GLN Chi-restraints excluded: chain b residue 133 THR Chi-restraints excluded: chain b residue 137 MET Chi-restraints excluded: chain b residue 171 MET Chi-restraints excluded: chain b residue 182 ASN Chi-restraints excluded: chain b residue 240 VAL Chi-restraints excluded: chain b residue 282 ILE Chi-restraints excluded: chain b residue 323 VAL Chi-restraints excluded: chain b residue 353 VAL Chi-restraints excluded: chain b residue 368 VAL Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain b residue 448 ILE Chi-restraints excluded: chain b residue 462 GLN Chi-restraints excluded: chain B1 residue 45 VAL Chi-restraints excluded: chain B1 residue 82 VAL Chi-restraints excluded: chain B1 residue 126 ILE Chi-restraints excluded: chain B1 residue 133 THR Chi-restraints excluded: chain B1 residue 136 MET Chi-restraints excluded: chain B1 residue 182 ASN Chi-restraints excluded: chain B1 residue 208 GLU Chi-restraints excluded: chain B1 residue 281 THR Chi-restraints excluded: chain B1 residue 282 ILE Chi-restraints excluded: chain B1 residue 323 VAL Chi-restraints excluded: chain B1 residue 347 THR Chi-restraints excluded: chain B1 residue 359 LEU Chi-restraints excluded: chain B1 residue 360 ARG Chi-restraints excluded: chain B1 residue 368 VAL Chi-restraints excluded: chain B1 residue 369 SER Chi-restraints excluded: chain B1 residue 448 ILE Chi-restraints excluded: chain b1 residue 74 ILE Chi-restraints excluded: chain b1 residue 182 ASN Chi-restraints excluded: chain b1 residue 206 VAL Chi-restraints excluded: chain b1 residue 323 VAL Chi-restraints excluded: chain b1 residue 353 VAL Chi-restraints excluded: chain b1 residue 359 LEU Chi-restraints excluded: chain b1 residue 375 ARG Chi-restraints excluded: chain b1 residue 381 SER Chi-restraints excluded: chain b1 residue 384 THR Chi-restraints excluded: chain b1 residue 391 GLU Chi-restraints excluded: chain b1 residue 448 ILE Chi-restraints excluded: chain b1 residue 452 ARG Chi-restraints excluded: chain b1 residue 476 GLU Chi-restraints excluded: chain b1 residue 484 ASP Chi-restraints excluded: chain B2 residue 49 LEU Chi-restraints excluded: chain B2 residue 55 ARG Chi-restraints excluded: chain B2 residue 63 LEU Chi-restraints excluded: chain B2 residue 133 THR Chi-restraints excluded: chain B2 residue 137 MET Chi-restraints excluded: chain B2 residue 182 ASN Chi-restraints excluded: chain B2 residue 232 SER Chi-restraints excluded: chain B2 residue 278 TYR Chi-restraints excluded: chain B2 residue 323 VAL Chi-restraints excluded: chain B2 residue 347 THR Chi-restraints excluded: chain B2 residue 353 VAL Chi-restraints excluded: chain B2 residue 368 VAL Chi-restraints excluded: chain B2 residue 381 SER Chi-restraints excluded: chain B2 residue 484 ASP Chi-restraints excluded: chain B2 residue 489 ILE Chi-restraints excluded: chain b2 residue 45 VAL Chi-restraints excluded: chain b2 residue 49 LEU Chi-restraints excluded: chain b2 residue 82 VAL Chi-restraints excluded: chain b2 residue 126 ILE Chi-restraints excluded: chain b2 residue 128 VAL Chi-restraints excluded: chain b2 residue 182 ASN Chi-restraints excluded: chain b2 residue 256 GLU Chi-restraints excluded: chain b2 residue 323 VAL Chi-restraints excluded: chain b2 residue 325 LEU Chi-restraints excluded: chain b2 residue 347 THR Chi-restraints excluded: chain b2 residue 360 ARG Chi-restraints excluded: chain b2 residue 368 VAL Chi-restraints excluded: chain b2 residue 381 SER Chi-restraints excluded: chain b2 residue 448 ILE Chi-restraints excluded: chain B3 residue 182 ASN Chi-restraints excluded: chain B3 residue 206 VAL Chi-restraints excluded: chain B3 residue 254 VAL Chi-restraints excluded: chain B3 residue 333 LEU Chi-restraints excluded: chain B3 residue 368 VAL Chi-restraints excluded: chain B3 residue 370 TYR Chi-restraints excluded: chain B3 residue 381 SER Chi-restraints excluded: chain B3 residue 391 GLU Chi-restraints excluded: chain B3 residue 430 LYS Chi-restraints excluded: chain B3 residue 473 SER Chi-restraints excluded: chain b3 residue 82 VAL Chi-restraints excluded: chain b3 residue 126 ILE Chi-restraints excluded: chain b3 residue 182 ASN Chi-restraints excluded: chain b3 residue 218 LYS Chi-restraints excluded: chain b3 residue 254 VAL Chi-restraints excluded: chain b3 residue 340 ASN Chi-restraints excluded: chain b3 residue 353 VAL Chi-restraints excluded: chain b3 residue 369 SER Chi-restraints excluded: chain b3 residue 381 SER Chi-restraints excluded: chain b3 residue 448 ILE Chi-restraints excluded: chain b3 residue 458 LEU Chi-restraints excluded: chain b3 residue 463 GLU Chi-restraints excluded: chain b3 residue 466 MET Chi-restraints excluded: chain B4 residue 49 LEU Chi-restraints excluded: chain B4 residue 126 ILE Chi-restraints excluded: chain B4 residue 182 ASN Chi-restraints excluded: chain B4 residue 232 SER Chi-restraints excluded: chain B4 residue 323 VAL Chi-restraints excluded: chain B4 residue 330 VAL Chi-restraints excluded: chain B4 residue 360 ARG Chi-restraints excluded: chain B4 residue 366 LEU Chi-restraints excluded: chain B4 residue 448 ILE Chi-restraints excluded: chain B4 residue 458 LEU Chi-restraints excluded: chain B4 residue 487 GLN Chi-restraints excluded: chain b4 residue 74 ILE Chi-restraints excluded: chain b4 residue 126 ILE Chi-restraints excluded: chain b4 residue 182 ASN Chi-restraints excluded: chain b4 residue 206 VAL Chi-restraints excluded: chain b4 residue 254 VAL Chi-restraints excluded: chain b4 residue 323 VAL Chi-restraints excluded: chain b4 residue 347 THR Chi-restraints excluded: chain b4 residue 359 LEU Chi-restraints excluded: chain b4 residue 366 LEU Chi-restraints excluded: chain b4 residue 368 VAL Chi-restraints excluded: chain b4 residue 448 ILE Chi-restraints excluded: chain b4 residue 450 SER Chi-restraints excluded: chain b4 residue 458 LEU Chi-restraints excluded: chain B5 residue 49 LEU Chi-restraints excluded: chain B5 residue 63 LEU Chi-restraints excluded: chain B5 residue 84 SER Chi-restraints excluded: chain B5 residue 182 ASN Chi-restraints excluded: chain B5 residue 232 SER Chi-restraints excluded: chain B5 residue 278 TYR Chi-restraints excluded: chain B5 residue 281 THR Chi-restraints excluded: chain B5 residue 323 VAL Chi-restraints excluded: chain B5 residue 353 VAL Chi-restraints excluded: chain B5 residue 360 ARG Chi-restraints excluded: chain B5 residue 368 VAL Chi-restraints excluded: chain B5 residue 369 SER Chi-restraints excluded: chain B5 residue 381 SER Chi-restraints excluded: chain B5 residue 384 THR Chi-restraints excluded: chain B5 residue 448 ILE Chi-restraints excluded: chain B5 residue 489 ILE Chi-restraints excluded: chain b5 residue 45 VAL Chi-restraints excluded: chain b5 residue 82 VAL Chi-restraints excluded: chain b5 residue 126 ILE Chi-restraints excluded: chain b5 residue 133 THR Chi-restraints excluded: chain b5 residue 136 MET Chi-restraints excluded: chain b5 residue 182 ASN Chi-restraints excluded: chain b5 residue 240 VAL Chi-restraints excluded: chain b5 residue 323 VAL Chi-restraints excluded: chain b5 residue 360 ARG Chi-restraints excluded: chain b5 residue 368 VAL Chi-restraints excluded: chain b5 residue 369 SER Chi-restraints excluded: chain b5 residue 381 SER Chi-restraints excluded: chain b5 residue 384 THR Chi-restraints excluded: chain b5 residue 448 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 494 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 chunk 360 optimal weight: 6.9990 chunk 229 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 428 optimal weight: 1.9990 chunk 550 optimal weight: 1.9990 chunk 353 optimal weight: 8.9990 chunk 238 optimal weight: 9.9990 chunk 348 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 407 GLN B1 34 GLN B1 372 GLN b1 80 HIS b1 372 GLN B2 372 GLN B4 372 GLN ** b5 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.069896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.056444 restraints weight = 173434.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.058103 restraints weight = 99014.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.059199 restraints weight = 68456.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.059931 restraints weight = 53872.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.060438 restraints weight = 45755.467| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 45528 Z= 0.194 Angle : 0.719 13.696 61596 Z= 0.365 Chirality : 0.042 0.186 6408 Planarity : 0.006 0.116 8172 Dihedral : 4.609 43.119 6349 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.42 % Favored : 94.33 % Rotamer: Outliers : 3.62 % Allowed : 26.36 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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 aren not related in a simple way. whole: 0.86 (0.11), residues: 5664 helix: 1.36 (0.10), residues: 2892 sheet: -0.52 (0.23), residues: 552 loop : -0.07 (0.14), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARGb2 501 TYR 0.023 0.002 TYRB5 486 PHE 0.028 0.001 PHE B 396 TRP 0.014 0.001 TRPB3 393 HIS 0.004 0.001 HISB4 80 Details of bonding type rmsd covalent geometry : bond 0.00422 (45516) covalent geometry : angle 0.71876 (61572) SS BOND : bond 0.00181 ( 12) SS BOND : angle 0.44599 ( 24) hydrogen bonds : bond 0.04554 ( 2529) hydrogen bonds : angle 5.04858 ( 7236) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1026 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 864 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 GLN cc_start: 0.8962 (tp40) cc_final: 0.7876 (tp-100) REVERT: B 147 PHE cc_start: 0.9363 (p90) cc_final: 0.8940 (p90) REVERT: B 260 MET cc_start: 0.9105 (mtm) cc_final: 0.8684 (mtm) REVERT: B 270 GLN cc_start: 0.9637 (mm-40) cc_final: 0.9231 (mm-40) REVERT: B 399 ARG cc_start: 0.9290 (tpp80) cc_final: 0.8840 (tpp80) REVERT: B 458 LEU cc_start: 0.9655 (OUTLIER) cc_final: 0.9342 (mm) REVERT: B 466 MET cc_start: 0.9605 (OUTLIER) cc_final: 0.9296 (tpt) REVERT: b 78 GLN cc_start: 0.9337 (mt0) cc_final: 0.8860 (mm-40) REVERT: b 116 LYS cc_start: 0.9568 (ptpp) cc_final: 0.9356 (pttm) REVERT: b 144 MET cc_start: 0.9600 (ttp) cc_final: 0.9280 (ttm) REVERT: b 266 ASN cc_start: 0.9577 (m110) cc_final: 0.9257 (m110) REVERT: b 277 MET cc_start: 0.9158 (tpp) cc_final: 0.8947 (tpt) REVERT: b 371 GLU cc_start: 0.8803 (pm20) cc_final: 0.8529 (pm20) REVERT: b 380 MET cc_start: 0.8445 (tpt) cc_final: 0.7974 (mmm) REVERT: b 399 ARG cc_start: 0.9397 (tpp80) cc_final: 0.9100 (tpp80) REVERT: b 453 MET cc_start: 0.8523 (tpp) cc_final: 0.8196 (tpp) REVERT: b 462 GLN cc_start: 0.9520 (OUTLIER) cc_final: 0.9286 (mm110) REVERT: b 466 MET cc_start: 0.9595 (mmm) cc_final: 0.9309 (tpp) REVERT: b 477 LYS cc_start: 0.9085 (mtmm) cc_final: 0.8839 (mtmt) REVERT: B1 75 GLN cc_start: 0.9211 (tp40) cc_final: 0.8248 (tp-100) REVERT: B1 76 LEU cc_start: 0.9798 (mm) cc_final: 0.9462 (mm) REVERT: B1 136 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.8934 (ptp) REVERT: B1 137 MET cc_start: 0.9680 (tpp) cc_final: 0.9399 (mmp) REVERT: B1 232 SER cc_start: 0.9792 (OUTLIER) cc_final: 0.9553 (p) REVERT: B1 238 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8230 (tm-30) REVERT: B1 346 ASP cc_start: 0.9206 (m-30) cc_final: 0.8942 (m-30) REVERT: B1 360 ARG cc_start: 0.9424 (OUTLIER) cc_final: 0.8894 (ttm110) REVERT: B1 453 MET cc_start: 0.7811 (tmm) cc_final: 0.7602 (tmm) REVERT: B1 460 GLU cc_start: 0.8665 (mp0) cc_final: 0.8446 (mp0) REVERT: B1 482 ARG cc_start: 0.9015 (mtm110) cc_final: 0.8724 (mtm110) REVERT: b1 75 GLN cc_start: 0.9002 (tp40) cc_final: 0.8341 (tp40) REVERT: b1 266 ASN cc_start: 0.9588 (m-40) cc_final: 0.9220 (m110) REVERT: b1 277 MET cc_start: 0.8968 (tpp) cc_final: 0.8632 (tpp) REVERT: b1 399 ARG cc_start: 0.9356 (tpp80) cc_final: 0.8747 (tpp80) REVERT: B2 137 MET cc_start: 0.9536 (OUTLIER) cc_final: 0.9165 (tpp) REVERT: B2 334 MET cc_start: 0.8927 (mmm) cc_final: 0.8653 (mmm) REVERT: B2 372 GLN cc_start: 0.9496 (OUTLIER) cc_final: 0.9213 (pp30) REVERT: B2 399 ARG cc_start: 0.9301 (mmm-85) cc_final: 0.8730 (tpp80) REVERT: b2 75 GLN cc_start: 0.9123 (tp40) cc_final: 0.8675 (tm-30) REVERT: b2 79 ASP cc_start: 0.8525 (m-30) cc_final: 0.8143 (m-30) REVERT: b2 116 LYS cc_start: 0.9633 (ptpp) cc_final: 0.9416 (ptpp) REVERT: b2 137 MET cc_start: 0.9308 (tpp) cc_final: 0.8635 (tpp) REVERT: b2 266 ASN cc_start: 0.9474 (m-40) cc_final: 0.8948 (m110) REVERT: b2 277 MET cc_start: 0.9324 (mmm) cc_final: 0.9047 (tpp) REVERT: b2 360 ARG cc_start: 0.9528 (OUTLIER) cc_final: 0.8938 (ttm110) REVERT: B3 116 LYS cc_start: 0.9592 (ptpp) cc_final: 0.9343 (pttm) REVERT: B3 266 ASN cc_start: 0.9536 (m110) cc_final: 0.9318 (m110) REVERT: B3 277 MET cc_start: 0.9217 (tpt) cc_final: 0.8483 (mmm) REVERT: B3 333 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9134 (mm) REVERT: B3 399 ARG cc_start: 0.9191 (tpp80) cc_final: 0.8974 (tpp80) REVERT: B3 477 LYS cc_start: 0.9232 (mtmm) cc_final: 0.8791 (mtmt) REVERT: b3 78 GLN cc_start: 0.9231 (mm-40) cc_final: 0.8798 (mm-40) REVERT: b3 136 MET cc_start: 0.9439 (ptp) cc_final: 0.9158 (pmm) REVERT: b3 137 MET cc_start: 0.9444 (tpp) cc_final: 0.9046 (tpp) REVERT: b3 144 MET cc_start: 0.9585 (ttp) cc_final: 0.9228 (ttm) REVERT: b3 215 MET cc_start: 0.5129 (ptt) cc_final: 0.4882 (pmm) REVERT: b3 266 ASN cc_start: 0.9412 (m-40) cc_final: 0.9056 (m110) REVERT: b3 275 LYS cc_start: 0.9245 (mtpt) cc_final: 0.9037 (ttpt) REVERT: b3 399 ARG cc_start: 0.9287 (mmm-85) cc_final: 0.8709 (tpp80) REVERT: B4 75 GLN cc_start: 0.9022 (tp40) cc_final: 0.8152 (tp-100) REVERT: B4 137 MET cc_start: 0.9579 (tpp) cc_final: 0.8932 (tpp) REVERT: B4 260 MET cc_start: 0.9310 (mtm) cc_final: 0.8944 (mtm) REVERT: B4 271 SER cc_start: 0.9550 (OUTLIER) cc_final: 0.9329 (p) REVERT: B4 346 ASP cc_start: 0.9042 (m-30) cc_final: 0.8830 (m-30) REVERT: B4 360 ARG cc_start: 0.9359 (OUTLIER) cc_final: 0.8923 (ttm110) REVERT: B4 458 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9024 (mm) REVERT: B4 487 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8598 (mp10) REVERT: b4 75 GLN cc_start: 0.9083 (tp40) cc_final: 0.8471 (tp40) REVERT: b4 260 MET cc_start: 0.9258 (mtm) cc_final: 0.8832 (mtm) REVERT: b4 270 GLN cc_start: 0.9623 (mm-40) cc_final: 0.9225 (mm-40) REVERT: b4 277 MET cc_start: 0.9202 (tpp) cc_final: 0.8931 (tpp) REVERT: b4 333 LEU cc_start: 0.9705 (OUTLIER) cc_final: 0.9427 (mm) REVERT: b4 380 MET cc_start: 0.8381 (tpp) cc_final: 0.7867 (tpp) REVERT: b4 399 ARG cc_start: 0.9309 (tpp80) cc_final: 0.8948 (tpp80) REVERT: b4 450 SER cc_start: 0.9608 (OUTLIER) cc_final: 0.9293 (p) REVERT: b4 458 LEU cc_start: 0.9688 (OUTLIER) cc_final: 0.9255 (mm) REVERT: b4 481 LYS cc_start: 0.9420 (mtmm) cc_final: 0.9011 (pttm) REVERT: B5 78 GLN cc_start: 0.9220 (OUTLIER) cc_final: 0.8761 (mm-40) REVERT: B5 91 ARG cc_start: 0.9116 (mmm160) cc_final: 0.8877 (mmm160) REVERT: B5 136 MET cc_start: 0.9367 (ptp) cc_final: 0.9142 (pmm) REVERT: B5 255 MET cc_start: 0.9235 (mtp) cc_final: 0.8670 (tpp) REVERT: B5 258 MET cc_start: 0.9321 (mmm) cc_final: 0.8873 (mmm) REVERT: B5 266 ASN cc_start: 0.9454 (m110) cc_final: 0.9056 (m110) REVERT: B5 285 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8235 (pp20) REVERT: B5 360 ARG cc_start: 0.9530 (OUTLIER) cc_final: 0.8850 (ttm110) REVERT: B5 399 ARG cc_start: 0.9456 (tpp80) cc_final: 0.9069 (tpp80) REVERT: b5 75 GLN cc_start: 0.9199 (tp40) cc_final: 0.8622 (tp-100) REVERT: b5 136 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8801 (pmm) REVERT: b5 137 MET cc_start: 0.9517 (tpp) cc_final: 0.9020 (tpp) REVERT: b5 277 MET cc_start: 0.9219 (tpt) cc_final: 0.8971 (tpp) REVERT: b5 390 ASN cc_start: 0.9179 (m110) cc_final: 0.8863 (m110) REVERT: b5 476 GLU cc_start: 0.8955 (pm20) cc_final: 0.8713 (pm20) outliers start: 162 outliers final: 124 residues processed: 991 average time/residue: 0.2583 time to fit residues: 412.8448 Evaluate side-chains 965 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 821 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 163 ARG Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 133 THR Chi-restraints excluded: chain b residue 137 MET Chi-restraints excluded: chain b residue 182 ASN Chi-restraints excluded: chain b residue 240 VAL Chi-restraints excluded: chain b residue 323 VAL Chi-restraints excluded: chain b residue 353 VAL Chi-restraints excluded: chain b residue 368 VAL Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain b residue 448 ILE Chi-restraints excluded: chain b residue 462 GLN Chi-restraints excluded: chain B1 residue 43 GLU Chi-restraints excluded: chain B1 residue 82 VAL Chi-restraints excluded: chain B1 residue 126 ILE Chi-restraints excluded: chain B1 residue 133 THR Chi-restraints excluded: chain B1 residue 136 MET Chi-restraints excluded: chain B1 residue 182 ASN Chi-restraints excluded: chain B1 residue 232 SER Chi-restraints excluded: chain B1 residue 281 THR Chi-restraints excluded: chain B1 residue 282 ILE Chi-restraints excluded: chain B1 residue 323 VAL Chi-restraints excluded: chain B1 residue 347 THR Chi-restraints excluded: chain B1 residue 359 LEU Chi-restraints excluded: chain B1 residue 360 ARG Chi-restraints excluded: chain B1 residue 368 VAL Chi-restraints excluded: chain B1 residue 369 SER Chi-restraints excluded: chain B1 residue 448 ILE Chi-restraints excluded: chain b1 residue 206 VAL Chi-restraints excluded: chain b1 residue 323 VAL Chi-restraints excluded: chain b1 residue 353 VAL Chi-restraints excluded: chain b1 residue 359 LEU Chi-restraints excluded: chain b1 residue 375 ARG Chi-restraints excluded: chain b1 residue 381 SER Chi-restraints excluded: chain b1 residue 384 THR Chi-restraints excluded: chain b1 residue 448 ILE Chi-restraints excluded: chain b1 residue 452 ARG Chi-restraints excluded: chain B2 residue 49 LEU Chi-restraints excluded: chain B2 residue 55 ARG Chi-restraints excluded: chain B2 residue 63 LEU Chi-restraints excluded: chain B2 residue 133 THR Chi-restraints excluded: chain B2 residue 137 MET Chi-restraints excluded: chain B2 residue 323 VAL Chi-restraints excluded: chain B2 residue 340 ASN Chi-restraints excluded: chain B2 residue 347 THR Chi-restraints excluded: chain B2 residue 353 VAL Chi-restraints excluded: chain B2 residue 368 VAL Chi-restraints excluded: chain B2 residue 372 GLN Chi-restraints excluded: chain B2 residue 381 SER Chi-restraints excluded: chain b2 residue 82 VAL Chi-restraints excluded: chain b2 residue 126 ILE Chi-restraints excluded: chain b2 residue 182 ASN Chi-restraints excluded: chain b2 residue 256 GLU Chi-restraints excluded: chain b2 residue 323 VAL Chi-restraints excluded: chain b2 residue 325 LEU Chi-restraints excluded: chain b2 residue 347 THR Chi-restraints excluded: chain b2 residue 360 ARG Chi-restraints excluded: chain b2 residue 368 VAL Chi-restraints excluded: chain b2 residue 381 SER Chi-restraints excluded: chain b2 residue 448 ILE Chi-restraints excluded: chain B3 residue 74 ILE Chi-restraints excluded: chain B3 residue 206 VAL Chi-restraints excluded: chain B3 residue 254 VAL Chi-restraints excluded: chain B3 residue 333 LEU Chi-restraints excluded: chain B3 residue 370 TYR Chi-restraints excluded: chain B3 residue 381 SER Chi-restraints excluded: chain B3 residue 391 GLU Chi-restraints excluded: chain B3 residue 430 LYS Chi-restraints excluded: chain b3 residue 82 VAL Chi-restraints excluded: chain b3 residue 126 ILE Chi-restraints excluded: chain b3 residue 182 ASN Chi-restraints excluded: chain b3 residue 218 LYS Chi-restraints excluded: chain b3 residue 254 VAL Chi-restraints excluded: chain b3 residue 340 ASN Chi-restraints excluded: chain b3 residue 353 VAL Chi-restraints excluded: chain b3 residue 369 SER Chi-restraints excluded: chain b3 residue 381 SER Chi-restraints excluded: chain b3 residue 448 ILE Chi-restraints excluded: chain b3 residue 458 LEU Chi-restraints excluded: chain b3 residue 463 GLU Chi-restraints excluded: chain b3 residue 466 MET Chi-restraints excluded: chain B4 residue 182 ASN Chi-restraints excluded: chain B4 residue 271 SER Chi-restraints excluded: chain B4 residue 323 VAL Chi-restraints excluded: chain B4 residue 330 VAL Chi-restraints excluded: chain B4 residue 360 ARG Chi-restraints excluded: chain B4 residue 366 LEU Chi-restraints excluded: chain B4 residue 448 ILE Chi-restraints excluded: chain B4 residue 458 LEU Chi-restraints excluded: chain B4 residue 482 ARG Chi-restraints excluded: chain B4 residue 487 GLN Chi-restraints excluded: chain b4 residue 74 ILE Chi-restraints excluded: chain b4 residue 126 ILE Chi-restraints excluded: chain b4 residue 182 ASN Chi-restraints excluded: chain b4 residue 206 VAL Chi-restraints excluded: chain b4 residue 254 VAL Chi-restraints excluded: chain b4 residue 323 VAL Chi-restraints excluded: chain b4 residue 333 LEU Chi-restraints excluded: chain b4 residue 347 THR Chi-restraints excluded: chain b4 residue 353 VAL Chi-restraints excluded: chain b4 residue 359 LEU Chi-restraints excluded: chain b4 residue 366 LEU Chi-restraints excluded: chain b4 residue 368 VAL Chi-restraints excluded: chain b4 residue 448 ILE Chi-restraints excluded: chain b4 residue 450 SER Chi-restraints excluded: chain b4 residue 458 LEU Chi-restraints excluded: chain B5 residue 49 LEU Chi-restraints excluded: chain B5 residue 63 LEU Chi-restraints excluded: chain B5 residue 78 GLN Chi-restraints excluded: chain B5 residue 84 SER Chi-restraints excluded: chain B5 residue 137 MET Chi-restraints excluded: chain B5 residue 281 THR Chi-restraints excluded: chain B5 residue 323 VAL Chi-restraints excluded: chain B5 residue 353 VAL Chi-restraints excluded: chain B5 residue 360 ARG Chi-restraints excluded: chain B5 residue 368 VAL Chi-restraints excluded: chain B5 residue 369 SER Chi-restraints excluded: chain B5 residue 381 SER Chi-restraints excluded: chain B5 residue 384 THR Chi-restraints excluded: chain B5 residue 448 ILE Chi-restraints excluded: chain B5 residue 489 ILE Chi-restraints excluded: chain b5 residue 82 VAL Chi-restraints excluded: chain b5 residue 126 ILE Chi-restraints excluded: chain b5 residue 133 THR Chi-restraints excluded: chain b5 residue 136 MET Chi-restraints excluded: chain b5 residue 182 ASN Chi-restraints excluded: chain b5 residue 323 VAL Chi-restraints excluded: chain b5 residue 360 ARG Chi-restraints excluded: chain b5 residue 368 VAL Chi-restraints excluded: chain b5 residue 369 SER Chi-restraints excluded: chain b5 residue 381 SER Chi-restraints excluded: chain b5 residue 384 THR Chi-restraints excluded: chain b5 residue 448 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 525 optimal weight: 9.9990 chunk 363 optimal weight: 10.0000 chunk 377 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 421 optimal weight: 2.9990 chunk 519 optimal weight: 10.0000 chunk 244 optimal weight: 4.9990 chunk 412 optimal weight: 9.9990 chunk 349 optimal weight: 7.9990 chunk 483 optimal weight: 10.0000 chunk 411 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 34 GLN B1 372 GLN b1 80 HIS b1 372 GLN B2 372 GLN b2 372 GLN B3 372 GLN B4 372 GLN b4 372 GLN ** b5 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.069614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.056136 restraints weight = 176535.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.057797 restraints weight = 100750.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.058862 restraints weight = 69608.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.059618 restraints weight = 55166.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.060116 restraints weight = 46450.714| |-----------------------------------------------------------------------------| r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 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 : 0.005 0.051 45528 Z= 0.223 Angle : 0.746 13.661 61596 Z= 0.380 Chirality : 0.043 0.262 6408 Planarity : 0.006 0.117 8172 Dihedral : 4.647 42.739 6349 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.35 % Favored : 94.40 % Rotamer: Outliers : 4.04 % Allowed : 26.18 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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 aren not related in a simple way. whole: 0.79 (0.11), residues: 5664 helix: 1.31 (0.10), residues: 2892 sheet: -0.59 (0.22), residues: 552 loop : -0.11 (0.14), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGB5 130 TYR 0.023 0.002 TYRb3 317 PHE 0.025 0.001 PHEb2 396 TRP 0.012 0.001 TRPB3 393 HIS 0.004 0.001 HISB4 80 Details of bonding type rmsd covalent geometry : bond 0.00480 (45516) covalent geometry : angle 0.74575 (61572) SS BOND : bond 0.00198 ( 12) SS BOND : angle 0.46495 ( 24) hydrogen bonds : bond 0.04589 ( 2529) hydrogen bonds : angle 5.11666 ( 7236) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1022 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 841 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 GLN cc_start: 0.8961 (tp40) cc_final: 0.8389 (tp40) REVERT: B 260 MET cc_start: 0.9181 (mtm) cc_final: 0.8766 (mtm) REVERT: B 270 GLN cc_start: 0.9645 (mm-40) cc_final: 0.9250 (mm-40) REVERT: B 399 ARG cc_start: 0.9325 (tpp80) cc_final: 0.8807 (tpp80) REVERT: B 458 LEU cc_start: 0.9641 (OUTLIER) cc_final: 0.9348 (mm) REVERT: B 466 MET cc_start: 0.9594 (OUTLIER) cc_final: 0.9300 (tpt) REVERT: b 78 GLN cc_start: 0.9352 (mt0) cc_final: 0.8892 (mm-40) REVERT: b 116 LYS cc_start: 0.9555 (ptpp) cc_final: 0.9335 (pttm) REVERT: b 144 MET cc_start: 0.9605 (ttp) cc_final: 0.9265 (ttm) REVERT: b 232 SER cc_start: 0.9701 (OUTLIER) cc_final: 0.9254 (p) REVERT: b 266 ASN cc_start: 0.9577 (m110) cc_final: 0.9247 (m110) REVERT: b 277 MET cc_start: 0.9206 (tpp) cc_final: 0.8968 (tpt) REVERT: b 371 GLU cc_start: 0.8801 (pm20) cc_final: 0.8590 (pm20) REVERT: b 399 ARG cc_start: 0.9435 (tpp80) cc_final: 0.9117 (tpp80) REVERT: b 477 LYS cc_start: 0.9107 (mtmm) cc_final: 0.8742 (mtmt) REVERT: B1 75 GLN cc_start: 0.9309 (tp40) cc_final: 0.8615 (tm-30) REVERT: B1 136 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8806 (pmm) REVERT: B1 144 MET cc_start: 0.9637 (ttp) cc_final: 0.8902 (tmm) REVERT: B1 232 SER cc_start: 0.9793 (OUTLIER) cc_final: 0.9563 (p) REVERT: B1 238 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8251 (tm-30) REVERT: B1 360 ARG cc_start: 0.9457 (OUTLIER) cc_final: 0.8922 (ttm110) REVERT: B1 460 GLU cc_start: 0.8780 (mp0) cc_final: 0.8528 (mp0) REVERT: B1 482 ARG cc_start: 0.8955 (mtm110) cc_final: 0.8677 (mtm110) REVERT: b1 75 GLN cc_start: 0.9014 (tp40) cc_final: 0.8328 (tp40) REVERT: b1 116 LYS cc_start: 0.9629 (ptpp) cc_final: 0.9400 (pttm) REVERT: b1 136 MET cc_start: 0.9509 (ptp) cc_final: 0.9080 (pmm) REVERT: b1 260 MET cc_start: 0.9154 (mtm) cc_final: 0.8683 (mtm) REVERT: b1 266 ASN cc_start: 0.9589 (m-40) cc_final: 0.9163 (m110) REVERT: b1 277 MET cc_start: 0.8914 (tpp) cc_final: 0.8528 (tpp) REVERT: b1 399 ARG cc_start: 0.9402 (tpp80) cc_final: 0.8766 (tpp80) REVERT: b1 458 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9266 (mm) REVERT: B2 116 LYS cc_start: 0.9561 (ptpp) cc_final: 0.9316 (pttm) REVERT: B2 137 MET cc_start: 0.9521 (OUTLIER) cc_final: 0.9254 (tpp) REVERT: B2 232 SER cc_start: 0.9725 (OUTLIER) cc_final: 0.9290 (p) REVERT: B2 334 MET cc_start: 0.9132 (mmm) cc_final: 0.8899 (mmm) REVERT: B2 380 MET cc_start: 0.8347 (mmm) cc_final: 0.7635 (tpp) REVERT: B2 399 ARG cc_start: 0.9327 (mmm-85) cc_final: 0.8740 (tpp80) REVERT: B2 479 CYS cc_start: 0.9002 (m) cc_final: 0.8726 (m) REVERT: b2 75 GLN cc_start: 0.9150 (tp40) cc_final: 0.8709 (tm-30) REVERT: b2 79 ASP cc_start: 0.8537 (m-30) cc_final: 0.8136 (m-30) REVERT: b2 116 LYS cc_start: 0.9633 (ptpp) cc_final: 0.9411 (ptpp) REVERT: b2 137 MET cc_start: 0.9300 (tpp) cc_final: 0.8623 (tpp) REVERT: b2 232 SER cc_start: 0.9788 (OUTLIER) cc_final: 0.9540 (p) REVERT: b2 266 ASN cc_start: 0.9468 (m-40) cc_final: 0.8949 (m110) REVERT: b2 356 GLN cc_start: 0.9370 (mm-40) cc_final: 0.9147 (mm-40) REVERT: b2 360 ARG cc_start: 0.9492 (OUTLIER) cc_final: 0.8845 (ttm110) REVERT: B3 87 ARG cc_start: 0.8357 (mtm110) cc_final: 0.7848 (mtm-85) REVERT: B3 116 LYS cc_start: 0.9612 (ptpp) cc_final: 0.9358 (pttm) REVERT: B3 255 MET cc_start: 0.8939 (mmm) cc_final: 0.8715 (mmm) REVERT: B3 266 ASN cc_start: 0.9526 (m110) cc_final: 0.9258 (m110) REVERT: B3 270 GLN cc_start: 0.9246 (mm-40) cc_final: 0.9009 (mm-40) REVERT: B3 277 MET cc_start: 0.9147 (tpt) cc_final: 0.8503 (mmm) REVERT: B3 333 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9186 (mm) REVERT: B3 334 MET cc_start: 0.9150 (tmm) cc_final: 0.8834 (ppp) REVERT: B3 399 ARG cc_start: 0.9191 (tpp80) cc_final: 0.8953 (tpp80) REVERT: B3 473 SER cc_start: 0.9303 (OUTLIER) cc_final: 0.9006 (p) REVERT: b3 78 GLN cc_start: 0.9285 (OUTLIER) cc_final: 0.8828 (mm-40) REVERT: b3 144 MET cc_start: 0.9573 (ttp) cc_final: 0.9213 (ttm) REVERT: b3 215 MET cc_start: 0.5209 (ptt) cc_final: 0.4912 (pmm) REVERT: b3 266 ASN cc_start: 0.9415 (m-40) cc_final: 0.9060 (m110) REVERT: b3 275 LYS cc_start: 0.9260 (mtpt) cc_final: 0.9018 (ttpt) REVERT: b3 334 MET cc_start: 0.8442 (mmm) cc_final: 0.8163 (mmm) REVERT: b3 380 MET cc_start: 0.8137 (tpp) cc_final: 0.7822 (tpp) REVERT: b3 399 ARG cc_start: 0.9302 (mmm-85) cc_final: 0.8734 (tpp80) REVERT: b3 479 CYS cc_start: 0.9300 (m) cc_final: 0.9014 (m) REVERT: B4 75 GLN cc_start: 0.9063 (tp40) cc_final: 0.8176 (tp-100) REVERT: B4 137 MET cc_start: 0.9587 (tpp) cc_final: 0.8832 (tpp) REVERT: B4 144 MET cc_start: 0.9652 (ttp) cc_final: 0.8856 (tmm) REVERT: B4 260 MET cc_start: 0.9273 (mtm) cc_final: 0.8880 (mtm) REVERT: B4 271 SER cc_start: 0.9551 (OUTLIER) cc_final: 0.9331 (p) REVERT: B4 346 ASP cc_start: 0.9046 (m-30) cc_final: 0.8715 (m-30) REVERT: B4 360 ARG cc_start: 0.9355 (OUTLIER) cc_final: 0.8948 (ttm110) REVERT: B4 458 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9060 (mm) REVERT: B4 487 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8561 (mp10) REVERT: b4 75 GLN cc_start: 0.9087 (tp40) cc_final: 0.8300 (tp40) REVERT: b4 79 ASP cc_start: 0.8528 (m-30) cc_final: 0.8013 (m-30) REVERT: b4 151 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9149 (pp) REVERT: b4 256 GLU cc_start: 0.9088 (pm20) cc_final: 0.8822 (pm20) REVERT: b4 260 MET cc_start: 0.9280 (mtm) cc_final: 0.8792 (mtm) REVERT: b4 270 GLN cc_start: 0.9624 (mm-40) cc_final: 0.9205 (mm-40) REVERT: b4 277 MET cc_start: 0.9165 (tpp) cc_final: 0.8894 (tpp) REVERT: b4 380 MET cc_start: 0.8512 (tpp) cc_final: 0.8017 (tpp) REVERT: b4 399 ARG cc_start: 0.9305 (tpp80) cc_final: 0.8931 (tpp80) REVERT: b4 450 SER cc_start: 0.9625 (OUTLIER) cc_final: 0.9298 (p) REVERT: b4 458 LEU cc_start: 0.9658 (OUTLIER) cc_final: 0.9353 (mm) REVERT: b4 481 LYS cc_start: 0.9422 (mtmm) cc_final: 0.9182 (mtmm) REVERT: B5 78 GLN cc_start: 0.9196 (OUTLIER) cc_final: 0.8715 (mm-40) REVERT: B5 91 ARG cc_start: 0.9116 (mmm160) cc_final: 0.8888 (mmm160) REVERT: B5 232 SER cc_start: 0.9712 (OUTLIER) cc_final: 0.9267 (p) REVERT: B5 255 MET cc_start: 0.9191 (mtp) cc_final: 0.8652 (tpp) REVERT: B5 258 MET cc_start: 0.9353 (mmm) cc_final: 0.8878 (mmm) REVERT: B5 266 ASN cc_start: 0.9459 (m110) cc_final: 0.9062 (m110) REVERT: B5 277 MET cc_start: 0.9457 (tpt) cc_final: 0.9254 (tpt) REVERT: B5 360 ARG cc_start: 0.9533 (OUTLIER) cc_final: 0.8851 (ttm110) REVERT: B5 399 ARG cc_start: 0.9474 (tpp80) cc_final: 0.9073 (tpp80) REVERT: b5 75 GLN cc_start: 0.9230 (tp40) cc_final: 0.8612 (tp-100) REVERT: b5 136 MET cc_start: 0.9227 (OUTLIER) cc_final: 0.8805 (pmm) REVERT: b5 137 MET cc_start: 0.9528 (tpp) cc_final: 0.8983 (tpp) REVERT: b5 144 MET cc_start: 0.9644 (ttp) cc_final: 0.8751 (tmm) REVERT: b5 278 TYR cc_start: 0.7480 (t80) cc_final: 0.7149 (t80) REVERT: b5 325 LEU cc_start: 0.8788 (pp) cc_final: 0.8566 (pp) REVERT: b5 372 GLN cc_start: 0.9294 (pm20) cc_final: 0.8665 (pm20) REVERT: b5 390 ASN cc_start: 0.9173 (m110) cc_final: 0.8861 (m110) outliers start: 181 outliers final: 135 residues processed: 983 average time/residue: 0.2466 time to fit residues: 393.3595 Evaluate side-chains 973 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 813 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 163 ARG Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 133 THR Chi-restraints excluded: chain b residue 137 MET Chi-restraints excluded: chain b residue 171 MET Chi-restraints excluded: chain b residue 182 ASN Chi-restraints excluded: chain b residue 232 SER Chi-restraints excluded: chain b residue 240 VAL Chi-restraints excluded: chain b residue 323 VAL Chi-restraints excluded: chain b residue 353 VAL Chi-restraints excluded: chain b residue 368 VAL Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain b residue 448 ILE Chi-restraints excluded: chain B1 residue 43 GLU Chi-restraints excluded: chain B1 residue 82 VAL Chi-restraints excluded: chain B1 residue 126 ILE Chi-restraints excluded: chain B1 residue 133 THR Chi-restraints excluded: chain B1 residue 136 MET Chi-restraints excluded: chain B1 residue 182 ASN Chi-restraints excluded: chain B1 residue 232 SER Chi-restraints excluded: chain B1 residue 281 THR Chi-restraints excluded: chain B1 residue 282 ILE Chi-restraints excluded: chain B1 residue 323 VAL Chi-restraints excluded: chain B1 residue 347 THR Chi-restraints excluded: chain B1 residue 359 LEU Chi-restraints excluded: chain B1 residue 360 ARG Chi-restraints excluded: chain B1 residue 366 LEU Chi-restraints excluded: chain B1 residue 368 VAL Chi-restraints excluded: chain B1 residue 369 SER Chi-restraints excluded: chain B1 residue 448 ILE Chi-restraints excluded: chain B1 residue 455 ILE Chi-restraints excluded: chain b1 residue 206 VAL Chi-restraints excluded: chain b1 residue 323 VAL Chi-restraints excluded: chain b1 residue 353 VAL Chi-restraints excluded: chain b1 residue 359 LEU Chi-restraints excluded: chain b1 residue 375 ARG Chi-restraints excluded: chain b1 residue 381 SER Chi-restraints excluded: chain b1 residue 384 THR Chi-restraints excluded: chain b1 residue 448 ILE Chi-restraints excluded: chain b1 residue 452 ARG Chi-restraints excluded: chain b1 residue 458 LEU Chi-restraints excluded: chain B2 residue 49 LEU Chi-restraints excluded: chain B2 residue 55 ARG Chi-restraints excluded: chain B2 residue 63 LEU Chi-restraints excluded: chain B2 residue 133 THR Chi-restraints excluded: chain B2 residue 137 MET Chi-restraints excluded: chain B2 residue 232 SER Chi-restraints excluded: chain B2 residue 323 VAL Chi-restraints excluded: chain B2 residue 340 ASN Chi-restraints excluded: chain B2 residue 347 THR Chi-restraints excluded: chain B2 residue 353 VAL Chi-restraints excluded: chain B2 residue 368 VAL Chi-restraints excluded: chain B2 residue 372 GLN Chi-restraints excluded: chain B2 residue 381 SER Chi-restraints excluded: chain B2 residue 484 ASP Chi-restraints excluded: chain B2 residue 489 ILE Chi-restraints excluded: chain b2 residue 82 VAL Chi-restraints excluded: chain b2 residue 126 ILE Chi-restraints excluded: chain b2 residue 182 ASN Chi-restraints excluded: chain b2 residue 232 SER Chi-restraints excluded: chain b2 residue 256 GLU Chi-restraints excluded: chain b2 residue 323 VAL Chi-restraints excluded: chain b2 residue 325 LEU Chi-restraints excluded: chain b2 residue 347 THR Chi-restraints excluded: chain b2 residue 360 ARG Chi-restraints excluded: chain b2 residue 368 VAL Chi-restraints excluded: chain b2 residue 381 SER Chi-restraints excluded: chain b2 residue 448 ILE Chi-restraints excluded: chain B3 residue 74 ILE Chi-restraints excluded: chain B3 residue 182 ASN Chi-restraints excluded: chain B3 residue 206 VAL Chi-restraints excluded: chain B3 residue 254 VAL Chi-restraints excluded: chain B3 residue 333 LEU Chi-restraints excluded: chain B3 residue 370 TYR Chi-restraints excluded: chain B3 residue 381 SER Chi-restraints excluded: chain B3 residue 391 GLU Chi-restraints excluded: chain B3 residue 430 LYS Chi-restraints excluded: chain B3 residue 473 SER Chi-restraints excluded: chain b3 residue 78 GLN Chi-restraints excluded: chain b3 residue 82 VAL Chi-restraints excluded: chain b3 residue 126 ILE Chi-restraints excluded: chain b3 residue 182 ASN Chi-restraints excluded: chain b3 residue 218 LYS Chi-restraints excluded: chain b3 residue 254 VAL Chi-restraints excluded: chain b3 residue 340 ASN Chi-restraints excluded: chain b3 residue 353 VAL Chi-restraints excluded: chain b3 residue 369 SER Chi-restraints excluded: chain b3 residue 381 SER Chi-restraints excluded: chain b3 residue 448 ILE Chi-restraints excluded: chain b3 residue 458 LEU Chi-restraints excluded: chain b3 residue 463 GLU Chi-restraints excluded: chain b3 residue 466 MET Chi-restraints excluded: chain B4 residue 49 LEU Chi-restraints excluded: chain B4 residue 126 ILE Chi-restraints excluded: chain B4 residue 182 ASN Chi-restraints excluded: chain B4 residue 271 SER Chi-restraints excluded: chain B4 residue 323 VAL Chi-restraints excluded: chain B4 residue 330 VAL Chi-restraints excluded: chain B4 residue 360 ARG Chi-restraints excluded: chain B4 residue 366 LEU Chi-restraints excluded: chain B4 residue 381 SER Chi-restraints excluded: chain B4 residue 448 ILE Chi-restraints excluded: chain B4 residue 458 LEU Chi-restraints excluded: chain B4 residue 482 ARG Chi-restraints excluded: chain B4 residue 487 GLN Chi-restraints excluded: chain b4 residue 45 VAL Chi-restraints excluded: chain b4 residue 74 ILE Chi-restraints excluded: chain b4 residue 126 ILE Chi-restraints excluded: chain b4 residue 151 LEU Chi-restraints excluded: chain b4 residue 182 ASN Chi-restraints excluded: chain b4 residue 206 VAL Chi-restraints excluded: chain b4 residue 323 VAL Chi-restraints excluded: chain b4 residue 347 THR Chi-restraints excluded: chain b4 residue 359 LEU Chi-restraints excluded: chain b4 residue 366 LEU Chi-restraints excluded: chain b4 residue 368 VAL Chi-restraints excluded: chain b4 residue 448 ILE Chi-restraints excluded: chain b4 residue 450 SER Chi-restraints excluded: chain b4 residue 458 LEU Chi-restraints excluded: chain B5 residue 49 LEU Chi-restraints excluded: chain B5 residue 63 LEU Chi-restraints excluded: chain B5 residue 78 GLN Chi-restraints excluded: chain B5 residue 84 SER Chi-restraints excluded: chain B5 residue 137 MET Chi-restraints excluded: chain B5 residue 232 SER Chi-restraints excluded: chain B5 residue 278 TYR Chi-restraints excluded: chain B5 residue 281 THR Chi-restraints excluded: chain B5 residue 323 VAL Chi-restraints excluded: chain B5 residue 353 VAL Chi-restraints excluded: chain B5 residue 360 ARG Chi-restraints excluded: chain B5 residue 368 VAL Chi-restraints excluded: chain B5 residue 369 SER Chi-restraints excluded: chain B5 residue 381 SER Chi-restraints excluded: chain B5 residue 384 THR Chi-restraints excluded: chain B5 residue 448 ILE Chi-restraints excluded: chain B5 residue 489 ILE Chi-restraints excluded: chain b5 residue 82 VAL Chi-restraints excluded: chain b5 residue 126 ILE Chi-restraints excluded: chain b5 residue 133 THR Chi-restraints excluded: chain b5 residue 136 MET Chi-restraints excluded: chain b5 residue 182 ASN Chi-restraints excluded: chain b5 residue 323 VAL Chi-restraints excluded: chain b5 residue 359 LEU Chi-restraints excluded: chain b5 residue 360 ARG Chi-restraints excluded: chain b5 residue 368 VAL Chi-restraints excluded: chain b5 residue 369 SER Chi-restraints excluded: chain b5 residue 381 SER Chi-restraints excluded: chain b5 residue 384 THR Chi-restraints excluded: chain b5 residue 448 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 110 optimal weight: 0.0870 chunk 262 optimal weight: 20.0000 chunk 405 optimal weight: 7.9990 chunk 418 optimal weight: 6.9990 chunk 251 optimal weight: 7.9990 chunk 189 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 194 optimal weight: 2.9990 chunk 323 optimal weight: 8.9990 chunk 387 optimal weight: 8.9990 chunk 475 optimal weight: 8.9990 overall best weight: 5.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 462 GLN B1 34 GLN B1 372 GLN b1 80 HIS b1 372 GLN B2 372 GLN b2 372 GLN ** B3 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 372 GLN B4 372 GLN ** b5 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.069410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.055885 restraints weight = 177303.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.057547 restraints weight = 103420.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.058625 restraints weight = 72261.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.059359 restraints weight = 56579.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.059849 restraints weight = 48100.624| |-----------------------------------------------------------------------------| r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 45528 Z= 0.229 Angle : 0.775 13.765 61596 Z= 0.392 Chirality : 0.044 0.242 6408 Planarity : 0.006 0.117 8172 Dihedral : 4.695 42.422 6349 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.49 % Favored : 94.28 % Rotamer: Outliers : 3.98 % Allowed : 26.47 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 3.65 % 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 aren not related in a simple way. whole: 0.72 (0.11), residues: 5664 helix: 1.25 (0.10), residues: 2892 sheet: -0.63 (0.22), residues: 552 loop : -0.14 (0.14), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGB5 130 TYR 0.026 0.002 TYRb3 317 PHE 0.027 0.001 PHEB1 396 TRP 0.013 0.001 TRPB3 393 HIS 0.004 0.001 HISB4 80 Details of bonding type rmsd covalent geometry : bond 0.00492 (45516) covalent geometry : angle 0.77481 (61572) SS BOND : bond 0.00210 ( 12) SS BOND : angle 0.45936 ( 24) hydrogen bonds : bond 0.04630 ( 2529) hydrogen bonds : angle 5.14928 ( 7236) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1017 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 839 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 GLN cc_start: 0.8996 (tp40) cc_final: 0.8442 (tp40) REVERT: B 87 ARG cc_start: 0.8338 (ptm160) cc_final: 0.8010 (ptm160) REVERT: B 270 GLN cc_start: 0.9640 (mm-40) cc_final: 0.9245 (mm-40) REVERT: B 399 ARG cc_start: 0.9344 (tpp80) cc_final: 0.8738 (tpp80) REVERT: B 458 LEU cc_start: 0.9673 (OUTLIER) cc_final: 0.9395 (mm) REVERT: B 466 MET cc_start: 0.9594 (OUTLIER) cc_final: 0.9315 (tpt) REVERT: b 78 GLN cc_start: 0.9319 (mt0) cc_final: 0.8886 (mm-40) REVERT: b 116 LYS cc_start: 0.9568 (ptpp) cc_final: 0.9356 (pttm) REVERT: b 144 MET cc_start: 0.9603 (ttp) cc_final: 0.9258 (ttm) REVERT: b 232 SER cc_start: 0.9702 (OUTLIER) cc_final: 0.9256 (p) REVERT: b 266 ASN cc_start: 0.9583 (m110) cc_final: 0.9244 (m110) REVERT: b 277 MET cc_start: 0.9259 (tpp) cc_final: 0.8992 (tpt) REVERT: b 371 GLU cc_start: 0.8767 (pm20) cc_final: 0.8524 (pm20) REVERT: b 377 TYR cc_start: 0.9222 (m-80) cc_final: 0.8718 (m-80) REVERT: b 380 MET cc_start: 0.8370 (tpt) cc_final: 0.7677 (tpt) REVERT: b 399 ARG cc_start: 0.9422 (tpp80) cc_final: 0.9113 (tpp80) REVERT: b 477 LYS cc_start: 0.9122 (mtmm) cc_final: 0.8784 (mtmt) REVERT: B1 75 GLN cc_start: 0.9183 (tp40) cc_final: 0.8321 (tp-100) REVERT: B1 79 ASP cc_start: 0.8554 (m-30) cc_final: 0.7942 (m-30) REVERT: B1 116 LYS cc_start: 0.9553 (pttm) cc_final: 0.9341 (pptt) REVERT: B1 136 MET cc_start: 0.9213 (OUTLIER) cc_final: 0.8786 (pmm) REVERT: B1 137 MET cc_start: 0.9647 (tpp) cc_final: 0.9133 (tpp) REVERT: B1 144 MET cc_start: 0.9625 (ttp) cc_final: 0.8875 (tmm) REVERT: B1 232 SER cc_start: 0.9792 (OUTLIER) cc_final: 0.9564 (p) REVERT: B1 238 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8275 (tm-30) REVERT: B1 334 MET cc_start: 0.9136 (mmm) cc_final: 0.8897 (mmm) REVERT: B1 360 ARG cc_start: 0.9461 (OUTLIER) cc_final: 0.8905 (ttm110) REVERT: b1 75 GLN cc_start: 0.9028 (tp40) cc_final: 0.8310 (tp40) REVERT: b1 266 ASN cc_start: 0.9576 (m-40) cc_final: 0.9208 (m110) REVERT: b1 277 MET cc_start: 0.8925 (tpp) cc_final: 0.8573 (tpp) REVERT: b1 399 ARG cc_start: 0.9390 (tpp80) cc_final: 0.8725 (tpp80) REVERT: b1 458 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9282 (mm) REVERT: b1 459 LYS cc_start: 0.9139 (mmtm) cc_final: 0.8935 (mmtm) REVERT: B2 116 LYS cc_start: 0.9579 (ptpp) cc_final: 0.9313 (pttm) REVERT: B2 137 MET cc_start: 0.9468 (OUTLIER) cc_final: 0.9084 (tpp) REVERT: B2 232 SER cc_start: 0.9725 (OUTLIER) cc_final: 0.9290 (p) REVERT: B2 334 MET cc_start: 0.9135 (mmm) cc_final: 0.8709 (mmm) REVERT: B2 372 GLN cc_start: 0.9464 (OUTLIER) cc_final: 0.9077 (pp30) REVERT: B2 380 MET cc_start: 0.8350 (mmm) cc_final: 0.7660 (tpp) REVERT: B2 399 ARG cc_start: 0.9314 (mmm-85) cc_final: 0.8770 (tpp80) REVERT: B2 479 CYS cc_start: 0.9082 (m) cc_final: 0.8825 (m) REVERT: b2 75 GLN cc_start: 0.9174 (tp40) cc_final: 0.8677 (tm-30) REVERT: b2 79 ASP cc_start: 0.8540 (m-30) cc_final: 0.8127 (m-30) REVERT: b2 129 GLU cc_start: 0.8427 (tp30) cc_final: 0.8067 (tp30) REVERT: b2 137 MET cc_start: 0.9288 (tpp) cc_final: 0.8558 (tpp) REVERT: b2 232 SER cc_start: 0.9787 (OUTLIER) cc_final: 0.9541 (p) REVERT: b2 266 ASN cc_start: 0.9461 (m-40) cc_final: 0.8910 (m110) REVERT: b2 360 ARG cc_start: 0.9479 (OUTLIER) cc_final: 0.8862 (ttm110) REVERT: b2 386 ARG cc_start: 0.9211 (ttt90) cc_final: 0.8520 (ttt90) REVERT: b2 411 MET cc_start: 0.9548 (mtm) cc_final: 0.9101 (mtm) REVERT: b2 459 LYS cc_start: 0.9224 (mmtm) cc_final: 0.8985 (mmtm) REVERT: B3 87 ARG cc_start: 0.8352 (mtm110) cc_final: 0.7795 (mtm110) REVERT: B3 116 LYS cc_start: 0.9611 (ptpp) cc_final: 0.9356 (pttm) REVERT: B3 255 MET cc_start: 0.8979 (mmm) cc_final: 0.8739 (mmm) REVERT: B3 266 ASN cc_start: 0.9529 (m110) cc_final: 0.9256 (m110) REVERT: B3 270 GLN cc_start: 0.9260 (mm-40) cc_final: 0.9004 (mm-40) REVERT: B3 277 MET cc_start: 0.9136 (tpt) cc_final: 0.8506 (mmm) REVERT: B3 333 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9209 (mm) REVERT: B3 334 MET cc_start: 0.9129 (tmm) cc_final: 0.8786 (ppp) REVERT: B3 380 MET cc_start: 0.8178 (tpp) cc_final: 0.7915 (tpp) REVERT: B3 399 ARG cc_start: 0.9177 (tpp80) cc_final: 0.8917 (tpp80) REVERT: B3 453 MET cc_start: 0.8515 (tpt) cc_final: 0.8199 (tpp) REVERT: B3 473 SER cc_start: 0.9345 (OUTLIER) cc_final: 0.8884 (p) REVERT: B3 482 ARG cc_start: 0.9368 (ttm110) cc_final: 0.8954 (mtp180) REVERT: b3 78 GLN cc_start: 0.9322 (OUTLIER) cc_final: 0.8908 (mm-40) REVERT: b3 136 MET cc_start: 0.9423 (ptp) cc_final: 0.9051 (pmm) REVERT: b3 144 MET cc_start: 0.9567 (ttp) cc_final: 0.9215 (ttm) REVERT: b3 215 MET cc_start: 0.5256 (ptt) cc_final: 0.4954 (pmm) REVERT: b3 232 SER cc_start: 0.9718 (OUTLIER) cc_final: 0.9276 (p) REVERT: b3 266 ASN cc_start: 0.9417 (m-40) cc_final: 0.9055 (m110) REVERT: b3 275 LYS cc_start: 0.9273 (mtpt) cc_final: 0.9007 (ttpt) REVERT: b3 334 MET cc_start: 0.8559 (mmm) cc_final: 0.8286 (mmm) REVERT: b3 349 ASN cc_start: 0.9412 (p0) cc_final: 0.9160 (p0) REVERT: b3 399 ARG cc_start: 0.9326 (mmm-85) cc_final: 0.8739 (tpp80) REVERT: b3 479 CYS cc_start: 0.9325 (m) cc_final: 0.9016 (m) REVERT: B4 75 GLN cc_start: 0.9029 (tp40) cc_final: 0.8120 (tp-100) REVERT: B4 144 MET cc_start: 0.9645 (ttp) cc_final: 0.8853 (tmm) REVERT: B4 260 MET cc_start: 0.9297 (mtm) cc_final: 0.8923 (mtm) REVERT: B4 271 SER cc_start: 0.9543 (OUTLIER) cc_final: 0.9334 (p) REVERT: B4 360 ARG cc_start: 0.9381 (OUTLIER) cc_final: 0.8978 (ttm110) REVERT: B4 458 LEU cc_start: 0.9557 (OUTLIER) cc_final: 0.9137 (mm) REVERT: B4 487 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.8540 (mp10) REVERT: b4 75 GLN cc_start: 0.9095 (tp40) cc_final: 0.8316 (tp40) REVERT: b4 79 ASP cc_start: 0.8512 (m-30) cc_final: 0.7990 (m-30) REVERT: b4 151 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9127 (pp) REVERT: b4 256 GLU cc_start: 0.9090 (pm20) cc_final: 0.8812 (pm20) REVERT: b4 260 MET cc_start: 0.9293 (mtm) cc_final: 0.8796 (mtm) REVERT: b4 270 GLN cc_start: 0.9619 (mm-40) cc_final: 0.9192 (mm-40) REVERT: b4 277 MET cc_start: 0.9199 (tpp) cc_final: 0.8944 (tpp) REVERT: b4 380 MET cc_start: 0.8496 (tpp) cc_final: 0.8153 (tpp) REVERT: b4 399 ARG cc_start: 0.9275 (tpp80) cc_final: 0.8887 (tpp80) REVERT: b4 450 SER cc_start: 0.9614 (OUTLIER) cc_final: 0.9313 (p) REVERT: b4 458 LEU cc_start: 0.9678 (OUTLIER) cc_final: 0.9300 (mm) REVERT: b4 481 LYS cc_start: 0.9423 (mtmm) cc_final: 0.9172 (mtmm) REVERT: B5 69 TYR cc_start: 0.9626 (m-80) cc_final: 0.8977 (m-80) REVERT: B5 78 GLN cc_start: 0.9201 (OUTLIER) cc_final: 0.8717 (mm-40) REVERT: B5 91 ARG cc_start: 0.9120 (mmm160) cc_final: 0.8896 (mmm160) REVERT: B5 136 MET cc_start: 0.9342 (ptp) cc_final: 0.9094 (pmm) REVERT: B5 232 SER cc_start: 0.9714 (OUTLIER) cc_final: 0.9270 (p) REVERT: B5 258 MET cc_start: 0.9350 (mmm) cc_final: 0.8911 (mmm) REVERT: B5 266 ASN cc_start: 0.9464 (m110) cc_final: 0.9066 (m110) REVERT: B5 360 ARG cc_start: 0.9532 (OUTLIER) cc_final: 0.8862 (ttm110) REVERT: B5 399 ARG cc_start: 0.9463 (tpp80) cc_final: 0.9060 (tpp80) REVERT: b5 136 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8801 (pmm) REVERT: b5 137 MET cc_start: 0.9516 (tpp) cc_final: 0.8952 (tpp) REVERT: b5 144 MET cc_start: 0.9644 (ttp) cc_final: 0.8790 (tmm) REVERT: b5 232 SER cc_start: 0.9785 (OUTLIER) cc_final: 0.9515 (p) REVERT: b5 372 GLN cc_start: 0.9305 (pm20) cc_final: 0.8821 (pm20) REVERT: b5 390 ASN cc_start: 0.9196 (m110) cc_final: 0.8984 (m110) outliers start: 178 outliers final: 141 residues processed: 974 average time/residue: 0.2211 time to fit residues: 350.5305 Evaluate side-chains 994 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 825 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 163 ARG Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 133 THR Chi-restraints excluded: chain b residue 137 MET Chi-restraints excluded: chain b residue 171 MET Chi-restraints excluded: chain b residue 182 ASN Chi-restraints excluded: chain b residue 232 SER Chi-restraints excluded: chain b residue 240 VAL Chi-restraints excluded: chain b residue 307 LEU Chi-restraints excluded: chain b residue 323 VAL Chi-restraints excluded: chain b residue 353 VAL Chi-restraints excluded: chain b residue 368 VAL Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain b residue 448 ILE Chi-restraints excluded: chain B1 residue 43 GLU Chi-restraints excluded: chain B1 residue 82 VAL Chi-restraints excluded: chain B1 residue 126 ILE Chi-restraints excluded: chain B1 residue 133 THR Chi-restraints excluded: chain B1 residue 136 MET Chi-restraints excluded: chain B1 residue 182 ASN Chi-restraints excluded: chain B1 residue 232 SER Chi-restraints excluded: chain B1 residue 281 THR Chi-restraints excluded: chain B1 residue 282 ILE Chi-restraints excluded: chain B1 residue 323 VAL Chi-restraints excluded: chain B1 residue 347 THR Chi-restraints excluded: chain B1 residue 359 LEU Chi-restraints excluded: chain B1 residue 360 ARG Chi-restraints excluded: chain B1 residue 366 LEU Chi-restraints excluded: chain B1 residue 368 VAL Chi-restraints excluded: chain B1 residue 369 SER Chi-restraints excluded: chain B1 residue 448 ILE Chi-restraints excluded: chain b1 residue 126 ILE Chi-restraints excluded: chain b1 residue 206 VAL Chi-restraints excluded: chain b1 residue 323 VAL Chi-restraints excluded: chain b1 residue 353 VAL Chi-restraints excluded: chain b1 residue 359 LEU Chi-restraints excluded: chain b1 residue 375 ARG Chi-restraints excluded: chain b1 residue 381 SER Chi-restraints excluded: chain b1 residue 384 THR Chi-restraints excluded: chain b1 residue 391 GLU Chi-restraints excluded: chain b1 residue 448 ILE Chi-restraints excluded: chain b1 residue 452 ARG Chi-restraints excluded: chain b1 residue 458 LEU Chi-restraints excluded: chain B2 residue 49 LEU Chi-restraints excluded: chain B2 residue 55 ARG Chi-restraints excluded: chain B2 residue 63 LEU Chi-restraints excluded: chain B2 residue 133 THR Chi-restraints excluded: chain B2 residue 137 MET Chi-restraints excluded: chain B2 residue 182 ASN Chi-restraints excluded: chain B2 residue 232 SER Chi-restraints excluded: chain B2 residue 307 LEU Chi-restraints excluded: chain B2 residue 323 VAL Chi-restraints excluded: chain B2 residue 340 ASN Chi-restraints excluded: chain B2 residue 347 THR Chi-restraints excluded: chain B2 residue 353 VAL Chi-restraints excluded: chain B2 residue 368 VAL Chi-restraints excluded: chain B2 residue 372 GLN Chi-restraints excluded: chain B2 residue 381 SER Chi-restraints excluded: chain B2 residue 484 ASP Chi-restraints excluded: chain B2 residue 489 ILE Chi-restraints excluded: chain b2 residue 82 VAL Chi-restraints excluded: chain b2 residue 126 ILE Chi-restraints excluded: chain b2 residue 182 ASN Chi-restraints excluded: chain b2 residue 232 SER Chi-restraints excluded: chain b2 residue 256 GLU Chi-restraints excluded: chain b2 residue 323 VAL Chi-restraints excluded: chain b2 residue 325 LEU Chi-restraints excluded: chain b2 residue 347 THR Chi-restraints excluded: chain b2 residue 359 LEU Chi-restraints excluded: chain b2 residue 360 ARG Chi-restraints excluded: chain b2 residue 368 VAL Chi-restraints excluded: chain b2 residue 381 SER Chi-restraints excluded: chain b2 residue 448 ILE Chi-restraints excluded: chain B3 residue 74 ILE Chi-restraints excluded: chain B3 residue 182 ASN Chi-restraints excluded: chain B3 residue 206 VAL Chi-restraints excluded: chain B3 residue 254 VAL Chi-restraints excluded: chain B3 residue 333 LEU Chi-restraints excluded: chain B3 residue 370 TYR Chi-restraints excluded: chain B3 residue 381 SER Chi-restraints excluded: chain B3 residue 391 GLU Chi-restraints excluded: chain B3 residue 430 LYS Chi-restraints excluded: chain B3 residue 473 SER Chi-restraints excluded: chain b3 residue 78 GLN Chi-restraints excluded: chain b3 residue 126 ILE Chi-restraints excluded: chain b3 residue 182 ASN Chi-restraints excluded: chain b3 residue 218 LYS Chi-restraints excluded: chain b3 residue 232 SER Chi-restraints excluded: chain b3 residue 254 VAL Chi-restraints excluded: chain b3 residue 340 ASN Chi-restraints excluded: chain b3 residue 353 VAL Chi-restraints excluded: chain b3 residue 369 SER Chi-restraints excluded: chain b3 residue 381 SER Chi-restraints excluded: chain b3 residue 448 ILE Chi-restraints excluded: chain b3 residue 458 LEU Chi-restraints excluded: chain b3 residue 463 GLU Chi-restraints excluded: chain b3 residue 466 MET Chi-restraints excluded: chain B4 residue 49 LEU Chi-restraints excluded: chain B4 residue 126 ILE Chi-restraints excluded: chain B4 residue 182 ASN Chi-restraints excluded: chain B4 residue 271 SER Chi-restraints excluded: chain B4 residue 323 VAL Chi-restraints excluded: chain B4 residue 330 VAL Chi-restraints excluded: chain B4 residue 359 LEU Chi-restraints excluded: chain B4 residue 360 ARG Chi-restraints excluded: chain B4 residue 366 LEU Chi-restraints excluded: chain B4 residue 381 SER Chi-restraints excluded: chain B4 residue 448 ILE Chi-restraints excluded: chain B4 residue 458 LEU Chi-restraints excluded: chain B4 residue 487 GLN Chi-restraints excluded: chain b4 residue 45 VAL Chi-restraints excluded: chain b4 residue 74 ILE Chi-restraints excluded: chain b4 residue 126 ILE Chi-restraints excluded: chain b4 residue 151 LEU Chi-restraints excluded: chain b4 residue 182 ASN Chi-restraints excluded: chain b4 residue 206 VAL Chi-restraints excluded: chain b4 residue 254 VAL Chi-restraints excluded: chain b4 residue 323 VAL Chi-restraints excluded: chain b4 residue 347 THR Chi-restraints excluded: chain b4 residue 359 LEU Chi-restraints excluded: chain b4 residue 366 LEU Chi-restraints excluded: chain b4 residue 368 VAL Chi-restraints excluded: chain b4 residue 448 ILE Chi-restraints excluded: chain b4 residue 450 SER Chi-restraints excluded: chain b4 residue 458 LEU Chi-restraints excluded: chain B5 residue 49 LEU Chi-restraints excluded: chain B5 residue 63 LEU Chi-restraints excluded: chain B5 residue 78 GLN Chi-restraints excluded: chain B5 residue 84 SER Chi-restraints excluded: chain B5 residue 137 MET Chi-restraints excluded: chain B5 residue 182 ASN Chi-restraints excluded: chain B5 residue 232 SER Chi-restraints excluded: chain B5 residue 278 TYR Chi-restraints excluded: chain B5 residue 281 THR Chi-restraints excluded: chain B5 residue 323 VAL Chi-restraints excluded: chain B5 residue 353 VAL Chi-restraints excluded: chain B5 residue 360 ARG Chi-restraints excluded: chain B5 residue 368 VAL Chi-restraints excluded: chain B5 residue 369 SER Chi-restraints excluded: chain B5 residue 375 ARG Chi-restraints excluded: chain B5 residue 381 SER Chi-restraints excluded: chain B5 residue 384 THR Chi-restraints excluded: chain B5 residue 448 ILE Chi-restraints excluded: chain B5 residue 489 ILE Chi-restraints excluded: chain b5 residue 82 VAL Chi-restraints excluded: chain b5 residue 126 ILE Chi-restraints excluded: chain b5 residue 133 THR Chi-restraints excluded: chain b5 residue 136 MET Chi-restraints excluded: chain b5 residue 182 ASN Chi-restraints excluded: chain b5 residue 232 SER Chi-restraints excluded: chain b5 residue 240 VAL Chi-restraints excluded: chain b5 residue 323 VAL Chi-restraints excluded: chain b5 residue 359 LEU Chi-restraints excluded: chain b5 residue 360 ARG Chi-restraints excluded: chain b5 residue 368 VAL Chi-restraints excluded: chain b5 residue 369 SER Chi-restraints excluded: chain b5 residue 381 SER Chi-restraints excluded: chain b5 residue 384 THR Chi-restraints excluded: chain b5 residue 448 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 62 optimal weight: 8.9990 chunk 346 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 175 optimal weight: 0.9990 chunk 374 optimal weight: 7.9990 chunk 299 optimal weight: 6.9990 chunk 378 optimal weight: 4.9990 chunk 311 optimal weight: 5.9990 chunk 556 optimal weight: 9.9990 chunk 557 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 34 GLN B1 372 GLN b1 80 HIS b1 372 GLN B2 372 GLN b2 356 GLN b2 372 GLN ** B3 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 372 GLN B4 372 GLN b4 303 GLN ** b5 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.069620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.056272 restraints weight = 178361.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.057789 restraints weight = 101442.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.058835 restraints weight = 71898.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.059575 restraints weight = 56927.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.060067 restraints weight = 48400.202| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 45528 Z= 0.230 Angle : 0.790 14.498 61596 Z= 0.401 Chirality : 0.044 0.257 6408 Planarity : 0.006 0.117 8172 Dihedral : 4.730 42.147 6349 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.49 % Favored : 94.28 % Rotamer: Outliers : 3.93 % Allowed : 26.83 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 3.65 % 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 aren not related in a simple way. whole: 0.66 (0.11), residues: 5664 helix: 1.20 (0.10), residues: 2892 sheet: -0.64 (0.22), residues: 552 loop : -0.16 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGB5 130 TYR 0.028 0.002 TYRb3 317 PHE 0.029 0.001 PHEb1 396 TRP 0.015 0.001 TRPb4 115 HIS 0.004 0.001 HISB4 80 Details of bonding type rmsd covalent geometry : bond 0.00495 (45516) covalent geometry : angle 0.78994 (61572) SS BOND : bond 0.00204 ( 12) SS BOND : angle 0.47024 ( 24) hydrogen bonds : bond 0.04659 ( 2529) hydrogen bonds : angle 5.18904 ( 7236) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1007 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 831 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 GLN cc_start: 0.8950 (tp40) cc_final: 0.8161 (tp40) REVERT: B 79 ASP cc_start: 0.8652 (m-30) cc_final: 0.8033 (m-30) REVERT: B 87 ARG cc_start: 0.8285 (ptm160) cc_final: 0.8054 (ptm160) REVERT: B 270 GLN cc_start: 0.9650 (mm-40) cc_final: 0.9253 (mm-40) REVERT: B 377 TYR cc_start: 0.9158 (m-80) cc_final: 0.8922 (m-10) REVERT: B 399 ARG cc_start: 0.9336 (tpp80) cc_final: 0.8695 (tpp80) REVERT: B 458 LEU cc_start: 0.9682 (OUTLIER) cc_final: 0.9409 (mm) REVERT: B 466 MET cc_start: 0.9590 (OUTLIER) cc_final: 0.9315 (tpt) REVERT: b 75 GLN cc_start: 0.9265 (OUTLIER) cc_final: 0.8985 (tp40) REVERT: b 78 GLN cc_start: 0.9347 (mt0) cc_final: 0.8842 (mm-40) REVERT: b 116 LYS cc_start: 0.9570 (ptpp) cc_final: 0.9358 (pttm) REVERT: b 144 MET cc_start: 0.9602 (ttp) cc_final: 0.9247 (ttm) REVERT: b 232 SER cc_start: 0.9688 (OUTLIER) cc_final: 0.9236 (p) REVERT: b 266 ASN cc_start: 0.9593 (m110) cc_final: 0.9251 (m110) REVERT: b 277 MET cc_start: 0.9255 (tpp) cc_final: 0.8972 (tpt) REVERT: b 371 GLU cc_start: 0.8798 (pm20) cc_final: 0.8556 (pm20) REVERT: b 377 TYR cc_start: 0.9244 (m-80) cc_final: 0.8728 (m-80) REVERT: b 380 MET cc_start: 0.8513 (tpt) cc_final: 0.7775 (tpt) REVERT: b 399 ARG cc_start: 0.9440 (tpp80) cc_final: 0.9110 (tpp80) REVERT: b 477 LYS cc_start: 0.9104 (mtmm) cc_final: 0.8687 (mtmm) REVERT: B1 75 GLN cc_start: 0.9219 (tp40) cc_final: 0.8359 (tp-100) REVERT: B1 87 ARG cc_start: 0.8597 (ttp80) cc_final: 0.8010 (mtp180) REVERT: B1 116 LYS cc_start: 0.9562 (pttm) cc_final: 0.9359 (pptt) REVERT: B1 136 MET cc_start: 0.9212 (OUTLIER) cc_final: 0.8777 (pmm) REVERT: B1 137 MET cc_start: 0.9642 (tpp) cc_final: 0.9125 (tpp) REVERT: B1 144 MET cc_start: 0.9628 (ttp) cc_final: 0.8865 (tmm) REVERT: B1 232 SER cc_start: 0.9788 (OUTLIER) cc_final: 0.9548 (p) REVERT: B1 238 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8243 (tm-30) REVERT: B1 360 ARG cc_start: 0.9454 (OUTLIER) cc_final: 0.8898 (ttm110) REVERT: B1 482 ARG cc_start: 0.9573 (mtp85) cc_final: 0.9156 (mtm110) REVERT: b1 75 GLN cc_start: 0.9019 (tp40) cc_final: 0.8313 (tp40) REVERT: b1 266 ASN cc_start: 0.9579 (m-40) cc_final: 0.9207 (m110) REVERT: b1 277 MET cc_start: 0.9036 (tpp) cc_final: 0.8695 (tpp) REVERT: b1 399 ARG cc_start: 0.9402 (tpp80) cc_final: 0.8707 (tpp80) REVERT: B2 69 TYR cc_start: 0.9617 (m-80) cc_final: 0.8990 (m-80) REVERT: B2 116 LYS cc_start: 0.9577 (ptpp) cc_final: 0.9313 (pttm) REVERT: B2 136 MET cc_start: 0.9566 (ptp) cc_final: 0.9118 (pmm) REVERT: B2 232 SER cc_start: 0.9702 (OUTLIER) cc_final: 0.9258 (p) REVERT: B2 334 MET cc_start: 0.9205 (mmm) cc_final: 0.8801 (mmm) REVERT: B2 380 MET cc_start: 0.8329 (mmm) cc_final: 0.7639 (tpp) REVERT: B2 399 ARG cc_start: 0.9322 (mmm-85) cc_final: 0.8775 (tpp80) REVERT: B2 479 CYS cc_start: 0.9077 (m) cc_final: 0.8823 (m) REVERT: b2 75 GLN cc_start: 0.9194 (tp40) cc_final: 0.8693 (tm-30) REVERT: b2 79 ASP cc_start: 0.8553 (m-30) cc_final: 0.8154 (m-30) REVERT: b2 232 SER cc_start: 0.9782 (OUTLIER) cc_final: 0.9532 (p) REVERT: b2 266 ASN cc_start: 0.9534 (m-40) cc_final: 0.9072 (m110) REVERT: b2 277 MET cc_start: 0.9358 (tpp) cc_final: 0.9123 (tpp) REVERT: b2 356 GLN cc_start: 0.9299 (mm-40) cc_final: 0.9076 (mm-40) REVERT: b2 386 ARG cc_start: 0.9222 (ttt90) cc_final: 0.8529 (ttt90) REVERT: b2 411 MET cc_start: 0.9571 (mtm) cc_final: 0.9159 (mtm) REVERT: B3 87 ARG cc_start: 0.8306 (mtm110) cc_final: 0.7760 (mtm-85) REVERT: B3 116 LYS cc_start: 0.9614 (ptpp) cc_final: 0.9362 (pttm) REVERT: B3 136 MET cc_start: 0.9573 (ptp) cc_final: 0.9111 (pmm) REVERT: B3 255 MET cc_start: 0.8960 (mmm) cc_final: 0.8702 (mmm) REVERT: B3 266 ASN cc_start: 0.9535 (m110) cc_final: 0.9262 (m110) REVERT: B3 270 GLN cc_start: 0.9279 (mm-40) cc_final: 0.9033 (mm-40) REVERT: B3 277 MET cc_start: 0.9162 (tpt) cc_final: 0.8479 (mmm) REVERT: B3 333 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9212 (mm) REVERT: B3 334 MET cc_start: 0.9125 (tmm) cc_final: 0.8771 (ppp) REVERT: B3 399 ARG cc_start: 0.9225 (tpp80) cc_final: 0.8952 (tpp80) REVERT: B3 482 ARG cc_start: 0.9346 (ttm110) cc_final: 0.8906 (mtp180) REVERT: b3 78 GLN cc_start: 0.9271 (OUTLIER) cc_final: 0.8902 (mm-40) REVERT: b3 136 MET cc_start: 0.9431 (ptp) cc_final: 0.9086 (pmm) REVERT: b3 144 MET cc_start: 0.9581 (ttp) cc_final: 0.9236 (ttm) REVERT: b3 215 MET cc_start: 0.5358 (ptt) cc_final: 0.5034 (pmm) REVERT: b3 232 SER cc_start: 0.9698 (OUTLIER) cc_final: 0.9254 (p) REVERT: b3 266 ASN cc_start: 0.9422 (m-40) cc_final: 0.8927 (m110) REVERT: b3 275 LYS cc_start: 0.9269 (mtpt) cc_final: 0.8994 (ttpt) REVERT: b3 277 MET cc_start: 0.9213 (mmm) cc_final: 0.8847 (mmm) REVERT: b3 334 MET cc_start: 0.8677 (mmm) cc_final: 0.8446 (mmm) REVERT: b3 349 ASN cc_start: 0.9387 (p0) cc_final: 0.9102 (p0) REVERT: b3 399 ARG cc_start: 0.9336 (mmm-85) cc_final: 0.8798 (tpp80) REVERT: b3 479 CYS cc_start: 0.9282 (m) cc_final: 0.9015 (m) REVERT: B4 75 GLN cc_start: 0.9028 (tp40) cc_final: 0.8114 (tp-100) REVERT: B4 137 MET cc_start: 0.9580 (tpp) cc_final: 0.8976 (tpp) REVERT: B4 144 MET cc_start: 0.9643 (ttp) cc_final: 0.8846 (tmm) REVERT: B4 260 MET cc_start: 0.9305 (mtm) cc_final: 0.8923 (mtm) REVERT: B4 271 SER cc_start: 0.9534 (OUTLIER) cc_final: 0.9333 (p) REVERT: B4 360 ARG cc_start: 0.9383 (OUTLIER) cc_final: 0.8974 (ttm110) REVERT: B4 397 MET cc_start: 0.9055 (mmm) cc_final: 0.8744 (mmp) REVERT: B4 458 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9063 (mm) REVERT: B4 487 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8544 (mp10) REVERT: b4 75 GLN cc_start: 0.9096 (tp40) cc_final: 0.8303 (tp40) REVERT: b4 79 ASP cc_start: 0.8523 (m-30) cc_final: 0.7994 (m-30) REVERT: b4 151 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9118 (pp) REVERT: b4 270 GLN cc_start: 0.9624 (mm-40) cc_final: 0.9201 (mm-40) REVERT: b4 277 MET cc_start: 0.9231 (tpp) cc_final: 0.9005 (tpp) REVERT: b4 380 MET cc_start: 0.8499 (tpp) cc_final: 0.8145 (tpp) REVERT: b4 399 ARG cc_start: 0.9309 (tpp80) cc_final: 0.8909 (tpp80) REVERT: b4 450 SER cc_start: 0.9618 (OUTLIER) cc_final: 0.9309 (p) REVERT: b4 458 LEU cc_start: 0.9647 (OUTLIER) cc_final: 0.9384 (mm) REVERT: b4 481 LYS cc_start: 0.9433 (mtmm) cc_final: 0.9193 (mtmm) REVERT: B5 69 TYR cc_start: 0.9639 (m-80) cc_final: 0.8998 (m-80) REVERT: B5 78 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.8710 (mm-40) REVERT: B5 91 ARG cc_start: 0.9133 (mmm160) cc_final: 0.8900 (mmm160) REVERT: B5 232 SER cc_start: 0.9683 (OUTLIER) cc_final: 0.9225 (p) REVERT: B5 255 MET cc_start: 0.9257 (mtp) cc_final: 0.8701 (tpp) REVERT: B5 266 ASN cc_start: 0.9475 (m110) cc_final: 0.9078 (m110) REVERT: B5 360 ARG cc_start: 0.9538 (OUTLIER) cc_final: 0.8870 (ttm110) REVERT: B5 399 ARG cc_start: 0.9460 (tpp80) cc_final: 0.9044 (tpp80) REVERT: b5 67 ASN cc_start: 0.8985 (t0) cc_final: 0.8542 (t0) REVERT: b5 136 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8795 (pmm) REVERT: b5 137 MET cc_start: 0.9510 (tpp) cc_final: 0.8930 (tpp) REVERT: b5 144 MET cc_start: 0.9650 (ttp) cc_final: 0.8785 (tmm) REVERT: b5 232 SER cc_start: 0.9776 (OUTLIER) cc_final: 0.9523 (p) REVERT: b5 372 GLN cc_start: 0.9322 (pm20) cc_final: 0.8803 (pm20) REVERT: b5 390 ASN cc_start: 0.9194 (m110) cc_final: 0.8967 (m110) outliers start: 176 outliers final: 138 residues processed: 966 average time/residue: 0.2232 time to fit residues: 352.0387 Evaluate side-chains 983 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 821 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 163 ARG Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 75 GLN Chi-restraints excluded: chain b residue 133 THR Chi-restraints excluded: chain b residue 137 MET Chi-restraints excluded: chain b residue 171 MET Chi-restraints excluded: chain b residue 182 ASN Chi-restraints excluded: chain b residue 232 SER Chi-restraints excluded: chain b residue 240 VAL Chi-restraints excluded: chain b residue 307 LEU Chi-restraints excluded: chain b residue 323 VAL Chi-restraints excluded: chain b residue 353 VAL Chi-restraints excluded: chain b residue 368 VAL Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain b residue 448 ILE Chi-restraints excluded: chain B1 residue 43 GLU Chi-restraints excluded: chain B1 residue 82 VAL Chi-restraints excluded: chain B1 residue 126 ILE Chi-restraints excluded: chain B1 residue 133 THR Chi-restraints excluded: chain B1 residue 136 MET Chi-restraints excluded: chain B1 residue 182 ASN Chi-restraints excluded: chain B1 residue 232 SER Chi-restraints excluded: chain B1 residue 281 THR Chi-restraints excluded: chain B1 residue 282 ILE Chi-restraints excluded: chain B1 residue 323 VAL Chi-restraints excluded: chain B1 residue 347 THR Chi-restraints excluded: chain B1 residue 359 LEU Chi-restraints excluded: chain B1 residue 360 ARG Chi-restraints excluded: chain B1 residue 366 LEU Chi-restraints excluded: chain B1 residue 368 VAL Chi-restraints excluded: chain B1 residue 369 SER Chi-restraints excluded: chain B1 residue 448 ILE Chi-restraints excluded: chain b1 residue 206 VAL Chi-restraints excluded: chain b1 residue 323 VAL Chi-restraints excluded: chain b1 residue 353 VAL Chi-restraints excluded: chain b1 residue 359 LEU Chi-restraints excluded: chain b1 residue 375 ARG Chi-restraints excluded: chain b1 residue 381 SER Chi-restraints excluded: chain b1 residue 384 THR Chi-restraints excluded: chain b1 residue 391 GLU Chi-restraints excluded: chain b1 residue 448 ILE Chi-restraints excluded: chain b1 residue 452 ARG Chi-restraints excluded: chain B2 residue 49 LEU Chi-restraints excluded: chain B2 residue 55 ARG Chi-restraints excluded: chain B2 residue 63 LEU Chi-restraints excluded: chain B2 residue 133 THR Chi-restraints excluded: chain B2 residue 182 ASN Chi-restraints excluded: chain B2 residue 232 SER Chi-restraints excluded: chain B2 residue 307 LEU Chi-restraints excluded: chain B2 residue 323 VAL Chi-restraints excluded: chain B2 residue 340 ASN Chi-restraints excluded: chain B2 residue 347 THR Chi-restraints excluded: chain B2 residue 368 VAL Chi-restraints excluded: chain B2 residue 381 SER Chi-restraints excluded: chain B2 residue 484 ASP Chi-restraints excluded: chain B2 residue 489 ILE Chi-restraints excluded: chain b2 residue 82 VAL Chi-restraints excluded: chain b2 residue 126 ILE Chi-restraints excluded: chain b2 residue 128 VAL Chi-restraints excluded: chain b2 residue 182 ASN Chi-restraints excluded: chain b2 residue 232 SER Chi-restraints excluded: chain b2 residue 256 GLU Chi-restraints excluded: chain b2 residue 323 VAL Chi-restraints excluded: chain b2 residue 325 LEU Chi-restraints excluded: chain b2 residue 347 THR Chi-restraints excluded: chain b2 residue 368 VAL Chi-restraints excluded: chain b2 residue 381 SER Chi-restraints excluded: chain b2 residue 448 ILE Chi-restraints excluded: chain B3 residue 74 ILE Chi-restraints excluded: chain B3 residue 182 ASN Chi-restraints excluded: chain B3 residue 206 VAL Chi-restraints excluded: chain B3 residue 254 VAL Chi-restraints excluded: chain B3 residue 333 LEU Chi-restraints excluded: chain B3 residue 370 TYR Chi-restraints excluded: chain B3 residue 381 SER Chi-restraints excluded: chain B3 residue 391 GLU Chi-restraints excluded: chain B3 residue 430 LYS Chi-restraints excluded: chain b3 residue 78 GLN Chi-restraints excluded: chain b3 residue 126 ILE Chi-restraints excluded: chain b3 residue 182 ASN Chi-restraints excluded: chain b3 residue 218 LYS Chi-restraints excluded: chain b3 residue 232 SER Chi-restraints excluded: chain b3 residue 254 VAL Chi-restraints excluded: chain b3 residue 340 ASN Chi-restraints excluded: chain b3 residue 353 VAL Chi-restraints excluded: chain b3 residue 369 SER Chi-restraints excluded: chain b3 residue 381 SER Chi-restraints excluded: chain b3 residue 448 ILE Chi-restraints excluded: chain b3 residue 458 LEU Chi-restraints excluded: chain b3 residue 463 GLU Chi-restraints excluded: chain b3 residue 466 MET Chi-restraints excluded: chain B4 residue 49 LEU Chi-restraints excluded: chain B4 residue 126 ILE Chi-restraints excluded: chain B4 residue 182 ASN Chi-restraints excluded: chain B4 residue 271 SER Chi-restraints excluded: chain B4 residue 323 VAL Chi-restraints excluded: chain B4 residue 330 VAL Chi-restraints excluded: chain B4 residue 359 LEU Chi-restraints excluded: chain B4 residue 360 ARG Chi-restraints excluded: chain B4 residue 366 LEU Chi-restraints excluded: chain B4 residue 381 SER Chi-restraints excluded: chain B4 residue 448 ILE Chi-restraints excluded: chain B4 residue 458 LEU Chi-restraints excluded: chain B4 residue 487 GLN Chi-restraints excluded: chain b4 residue 45 VAL Chi-restraints excluded: chain b4 residue 74 ILE Chi-restraints excluded: chain b4 residue 126 ILE Chi-restraints excluded: chain b4 residue 151 LEU Chi-restraints excluded: chain b4 residue 182 ASN Chi-restraints excluded: chain b4 residue 206 VAL Chi-restraints excluded: chain b4 residue 323 VAL Chi-restraints excluded: chain b4 residue 347 THR Chi-restraints excluded: chain b4 residue 359 LEU Chi-restraints excluded: chain b4 residue 366 LEU Chi-restraints excluded: chain b4 residue 368 VAL Chi-restraints excluded: chain b4 residue 372 GLN Chi-restraints excluded: chain b4 residue 448 ILE Chi-restraints excluded: chain b4 residue 450 SER Chi-restraints excluded: chain b4 residue 458 LEU Chi-restraints excluded: chain B5 residue 49 LEU Chi-restraints excluded: chain B5 residue 63 LEU Chi-restraints excluded: chain B5 residue 78 GLN Chi-restraints excluded: chain B5 residue 84 SER Chi-restraints excluded: chain B5 residue 137 MET Chi-restraints excluded: chain B5 residue 182 ASN Chi-restraints excluded: chain B5 residue 232 SER Chi-restraints excluded: chain B5 residue 278 TYR Chi-restraints excluded: chain B5 residue 281 THR Chi-restraints excluded: chain B5 residue 323 VAL Chi-restraints excluded: chain B5 residue 353 VAL Chi-restraints excluded: chain B5 residue 360 ARG Chi-restraints excluded: chain B5 residue 368 VAL Chi-restraints excluded: chain B5 residue 369 SER Chi-restraints excluded: chain B5 residue 381 SER Chi-restraints excluded: chain B5 residue 384 THR Chi-restraints excluded: chain B5 residue 448 ILE Chi-restraints excluded: chain B5 residue 489 ILE Chi-restraints excluded: chain b5 residue 82 VAL Chi-restraints excluded: chain b5 residue 126 ILE Chi-restraints excluded: chain b5 residue 133 THR Chi-restraints excluded: chain b5 residue 136 MET Chi-restraints excluded: chain b5 residue 182 ASN Chi-restraints excluded: chain b5 residue 232 SER Chi-restraints excluded: chain b5 residue 240 VAL Chi-restraints excluded: chain b5 residue 323 VAL Chi-restraints excluded: chain b5 residue 359 LEU Chi-restraints excluded: chain b5 residue 360 ARG Chi-restraints excluded: chain b5 residue 368 VAL Chi-restraints excluded: chain b5 residue 369 SER Chi-restraints excluded: chain b5 residue 381 SER Chi-restraints excluded: chain b5 residue 384 THR Chi-restraints excluded: chain b5 residue 448 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 263 optimal weight: 9.9990 chunk 543 optimal weight: 5.9990 chunk 509 optimal weight: 6.9990 chunk 451 optimal weight: 5.9990 chunk 166 optimal weight: 20.0000 chunk 104 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 268 optimal weight: 2.9990 chunk 537 optimal weight: 9.9990 chunk 552 optimal weight: 10.0000 chunk 233 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 34 GLN B1 372 GLN b1 80 HIS b1 372 GLN b2 372 GLN ** B3 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 372 GLN B4 372 GLN B5 356 GLN ** b5 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.069681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.056210 restraints weight = 176749.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.057863 restraints weight = 101393.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.058956 restraints weight = 69664.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.059786 restraints weight = 54017.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.060285 restraints weight = 45515.287| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 45528 Z= 0.211 Angle : 0.795 15.173 61596 Z= 0.400 Chirality : 0.044 0.291 6408 Planarity : 0.006 0.117 8172 Dihedral : 4.723 42.217 6349 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.51 % Favored : 94.26 % Rotamer: Outliers : 3.64 % Allowed : 27.23 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 3.65 % 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 aren not related in a simple way. whole: 0.66 (0.11), residues: 5664 helix: 1.20 (0.10), residues: 2880 sheet: -0.65 (0.22), residues: 552 loop : -0.15 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG b 187 TYR 0.031 0.002 TYRb3 317 PHE 0.025 0.001 PHEB1 396 TRP 0.013 0.001 TRPB3 393 HIS 0.004 0.001 HISB4 80 Details of bonding type rmsd covalent geometry : bond 0.00459 (45516) covalent geometry : angle 0.79535 (61572) SS BOND : bond 0.00170 ( 12) SS BOND : angle 0.47178 ( 24) hydrogen bonds : bond 0.04625 ( 2529) hydrogen bonds : angle 5.16188 ( 7236) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8466.47 seconds wall clock time: 147 minutes 7.14 seconds (8827.14 seconds total)