Starting phenix.real_space_refine on Fri Oct 30 19:10:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wto_66223/10_2026/9wto_66223.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wto_66223/10_2026/9wto_66223.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/9wto_66223/10_2026/9wto_66223.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wto_66223/10_2026/9wto_66223.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wto_66223/10_2026/9wto_66223.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wto_66223/10_2026/9wto_66223.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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 193 5.16 5 C 23517 2.51 5 N 6568 2.21 5 O 7119 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 37397 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3021 Classifications: {'peptide': 419} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 398} Chain breaks: 2 Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 4, 'GLU:plan': 12, 'ARG:plan': 12, 'GLN:plan1': 4, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 155 Chain: "B" Number of atoms: 3123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3123 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 402} Chain breaks: 2 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1, 'GLU:plan': 8, 'ARG:plan': 7, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 92 Chain: "C" Number of atoms: 3099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3099 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 401} Chain breaks: 2 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 9, 'GLU:plan': 8, 'GLN:plan1': 3, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 109 Chain: "D" Number of atoms: 3128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3128 Classifications: {'peptide': 423} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 402} Chain breaks: 2 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 100 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 2, 'ARG:plan': 8, 'GLN:plan1': 3, 'TYR:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 87 Chain: "E" Number of atoms: 3128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3128 Classifications: {'peptide': 423} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 402} Chain breaks: 2 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 100 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 2, 'ARG:plan': 8, 'GLN:plan1': 3, 'TYR:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 87 Chain: "F" Number of atoms: 3100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3100 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 399} Chain breaks: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 2, 'ASP:plan': 1, 'ARG:plan': 5, 'HIS:plan': 2, 'GLU:plan': 8, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 101 Chain: "G" Number of atoms: 3128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3128 Classifications: {'peptide': 423} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 402} Chain breaks: 2 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 100 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 2, 'ARG:plan': 8, 'GLN:plan1': 3, 'TYR:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 87 Chain: "H" Number of atoms: 3213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3213 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 401} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "I" Number of atoms: 3128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3128 Classifications: {'peptide': 423} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 402} Chain breaks: 2 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 100 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 2, 'ARG:plan': 8, 'GLN:plan1': 3, 'TYR:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 87 Chain: "J" Number of atoms: 3128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3128 Classifications: {'peptide': 423} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 402} Chain breaks: 2 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 100 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 2, 'ARG:plan': 8, 'GLN:plan1': 3, 'TYR:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 87 Chain: "K" Number of atoms: 3128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3128 Classifications: {'peptide': 423} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 402} Chain breaks: 2 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 100 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 2, 'ARG:plan': 8, 'GLN:plan1': 3, 'TYR:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 87 Chain: "L" Number of atoms: 3073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3073 Classifications: {'peptide': 421} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 400} Chain breaks: 2 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 10, 'GLU:plan': 8, 'GLN:plan1': 3, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 109 Time building chain proxies: 8.81, per 1000 atoms: 0.24 Number of scatterers: 37397 At special positions: 0 Unit cell: (130.398, 129.132, 236.742, 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 193 16.00 O 7119 8.00 N 6568 7.00 C 23517 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 38 " - pdb=" SG CYS G 38 " distance=1.96 Simple disulfide: pdb=" SG CYS B 38 " - pdb=" SG CYS H 38 " distance=2.15 Simple disulfide: pdb=" SG CYS C 38 " - pdb=" SG CYS I 38 " distance=1.96 Simple disulfide: pdb=" SG CYS D 38 " - pdb=" SG CYS J 38 " distance=1.72 Simple disulfide: pdb=" SG CYS E 38 " - pdb=" SG CYS K 38 " distance=2.05 Simple disulfide: pdb=" SG CYS F 38 " - pdb=" SG CYS L 38 " distance=1.96 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: 3.72 Conformation dependent library (CDL) restraints added in 2.2 seconds 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9274 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 72 sheets defined 41.7% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 85 through 89 removed outlier: 3.607A pdb=" N ALA A 89 " --> pdb=" O GLU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 148 Processing helix chain 'A' and resid 165 through 177 Processing helix chain 'A' and resid 190 through 203 removed outlier: 3.635A pdb=" N THR A 203 " --> pdb=" O HIS A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 241 removed outlier: 3.945A pdb=" N ALA A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 229 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN A 241 " --> pdb=" O TYR A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 267 removed outlier: 3.732A pdb=" N TYR A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 288 removed outlier: 3.856A pdb=" N PHE A 280 " --> pdb=" O PRO A 276 " (cutoff:3.500A) Proline residue: A 284 - end of helix Processing helix chain 'A' and resid 314 through 323 Processing helix chain 'A' and resid 330 through 336 removed outlier: 3.793A pdb=" N ALA A 334 " --> pdb=" O SER A 330 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 removed outlier: 3.921A pdb=" N VAL A 355 " --> pdb=" O PHE A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 381 Processing helix chain 'A' and resid 391 through 400 Processing helix chain 'A' and resid 400 through 409 Processing helix chain 'A' and resid 417 through 430 removed outlier: 3.807A pdb=" N ASN A 430 " --> pdb=" O ARG A 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 89 removed outlier: 3.608A pdb=" N ALA B 89 " --> pdb=" O GLU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 148 Processing helix chain 'B' and resid 165 through 177 Processing helix chain 'B' and resid 190 through 203 removed outlier: 3.636A pdb=" N THR B 203 " --> pdb=" O HIS B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'B' and resid 220 through 241 removed outlier: 3.946A pdb=" N ALA B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 229 " --> pdb=" O CYS B 225 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN B 241 " --> pdb=" O TYR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 267 removed outlier: 3.731A pdb=" N TYR B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 288 removed outlier: 3.857A pdb=" N PHE B 280 " --> pdb=" O PRO B 276 " (cutoff:3.500A) Proline residue: B 284 - end of helix Processing helix chain 'B' and resid 314 through 323 Processing helix chain 'B' and resid 330 through 336 removed outlier: 3.794A pdb=" N ALA B 334 " --> pdb=" O SER B 330 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG B 336 " --> pdb=" O GLN B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 355 removed outlier: 3.921A pdb=" N VAL B 355 " --> pdb=" O PHE B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 381 Processing helix chain 'B' and resid 391 through 400 Processing helix chain 'B' and resid 400 through 409 Processing helix chain 'B' and resid 417 through 430 removed outlier: 3.807A pdb=" N ASN B 430 " --> pdb=" O ARG B 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 89 removed outlier: 3.606A pdb=" N ALA C 89 " --> pdb=" O GLU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 148 Processing helix chain 'C' and resid 165 through 177 Processing helix chain 'C' and resid 190 through 203 removed outlier: 3.635A pdb=" N THR C 203 " --> pdb=" O HIS C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 208 No H-bonds generated for 'chain 'C' and resid 206 through 208' Processing helix chain 'C' and resid 220 through 241 removed outlier: 3.945A pdb=" N ALA C 228 " --> pdb=" O ARG C 224 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU C 229 " --> pdb=" O CYS C 225 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN C 241 " --> pdb=" O TYR C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 267 removed outlier: 3.732A pdb=" N TYR C 255 " --> pdb=" O SER C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 288 removed outlier: 3.857A pdb=" N PHE C 280 " --> pdb=" O PRO C 276 " (cutoff:3.500A) Proline residue: C 284 - end of helix Processing helix chain 'C' and resid 314 through 323 Processing helix chain 'C' and resid 330 through 336 removed outlier: 3.793A pdb=" N ALA C 334 " --> pdb=" O SER C 330 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG C 336 " --> pdb=" O GLN C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 355 removed outlier: 3.921A pdb=" N VAL C 355 " --> pdb=" O PHE C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 381 Processing helix chain 'C' and resid 391 through 400 Processing helix chain 'C' and resid 400 through 409 Processing helix chain 'C' and resid 417 through 430 removed outlier: 3.807A pdb=" N ASN C 430 " --> pdb=" O ARG C 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.606A pdb=" N ALA D 89 " --> pdb=" O GLU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 148 Processing helix chain 'D' and resid 165 through 177 Processing helix chain 'D' and resid 190 through 203 removed outlier: 3.636A pdb=" N THR D 203 " --> pdb=" O HIS D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 241 removed outlier: 3.946A pdb=" N ALA D 228 " --> pdb=" O ARG D 224 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU D 229 " --> pdb=" O CYS D 225 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN D 241 " --> pdb=" O TYR D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 267 removed outlier: 3.732A pdb=" N TYR D 255 " --> pdb=" O SER D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 288 removed outlier: 3.857A pdb=" N PHE D 280 " --> pdb=" O PRO D 276 " (cutoff:3.500A) Proline residue: D 284 - end of helix Processing helix chain 'D' and resid 314 through 323 Processing helix chain 'D' and resid 330 through 336 removed outlier: 3.794A pdb=" N ALA D 334 " --> pdb=" O SER D 330 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG D 336 " --> pdb=" O GLN D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 355 removed outlier: 3.921A pdb=" N VAL D 355 " --> pdb=" O PHE D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 381 Processing helix chain 'D' and resid 391 through 400 Processing helix chain 'D' and resid 400 through 409 Processing helix chain 'D' and resid 417 through 430 removed outlier: 3.807A pdb=" N ASN D 430 " --> pdb=" O ARG D 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 89 removed outlier: 3.606A pdb=" N ALA E 89 " --> pdb=" O GLU E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 148 Processing helix chain 'E' and resid 165 through 177 Processing helix chain 'E' and resid 190 through 203 removed outlier: 3.635A pdb=" N THR E 203 " --> pdb=" O HIS E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 220 through 241 removed outlier: 3.945A pdb=" N ALA E 228 " --> pdb=" O ARG E 224 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU E 229 " --> pdb=" O CYS E 225 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN E 241 " --> pdb=" O TYR E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 267 removed outlier: 3.732A pdb=" N TYR E 255 " --> pdb=" O SER E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 288 removed outlier: 3.857A pdb=" N PHE E 280 " --> pdb=" O PRO E 276 " (cutoff:3.500A) Proline residue: E 284 - end of helix Processing helix chain 'E' and resid 314 through 323 Processing helix chain 'E' and resid 330 through 336 removed outlier: 3.793A pdb=" N ALA E 334 " --> pdb=" O SER E 330 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG E 336 " --> pdb=" O GLN E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 355 removed outlier: 3.921A pdb=" N VAL E 355 " --> pdb=" O PHE E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 381 Processing helix chain 'E' and resid 391 through 400 Processing helix chain 'E' and resid 400 through 409 Processing helix chain 'E' and resid 417 through 430 removed outlier: 3.807A pdb=" N ASN E 430 " --> pdb=" O ARG E 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.607A pdb=" N ALA F 89 " --> pdb=" O GLU F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 148 Processing helix chain 'F' and resid 165 through 177 Processing helix chain 'F' and resid 190 through 203 removed outlier: 3.635A pdb=" N THR F 203 " --> pdb=" O HIS F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 220 through 241 removed outlier: 3.944A pdb=" N ALA F 228 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU F 229 " --> pdb=" O CYS F 225 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN F 241 " --> pdb=" O TYR F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 267 removed outlier: 3.733A pdb=" N TYR F 255 " --> pdb=" O SER F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 288 removed outlier: 3.856A pdb=" N PHE F 280 " --> pdb=" O PRO F 276 " (cutoff:3.500A) Proline residue: F 284 - end of helix Processing helix chain 'F' and resid 314 through 323 Processing helix chain 'F' and resid 330 through 336 removed outlier: 3.793A pdb=" N ALA F 334 " --> pdb=" O SER F 330 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG F 336 " --> pdb=" O GLN F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 355 removed outlier: 3.920A pdb=" N VAL F 355 " --> pdb=" O PHE F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 381 Processing helix chain 'F' and resid 391 through 400 Processing helix chain 'F' and resid 400 through 409 Processing helix chain 'F' and resid 417 through 430 removed outlier: 3.807A pdb=" N ASN F 430 " --> pdb=" O ARG F 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 89 removed outlier: 3.607A pdb=" N ALA G 89 " --> pdb=" O GLU G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 148 Processing helix chain 'G' and resid 165 through 177 Processing helix chain 'G' and resid 190 through 203 removed outlier: 3.636A pdb=" N THR G 203 " --> pdb=" O HIS G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 208 No H-bonds generated for 'chain 'G' and resid 206 through 208' Processing helix chain 'G' and resid 220 through 241 removed outlier: 3.945A pdb=" N ALA G 228 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU G 229 " --> pdb=" O CYS G 225 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN G 241 " --> pdb=" O TYR G 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 267 removed outlier: 3.731A pdb=" N TYR G 255 " --> pdb=" O SER G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 276 through 288 removed outlier: 3.857A pdb=" N PHE G 280 " --> pdb=" O PRO G 276 " (cutoff:3.500A) Proline residue: G 284 - end of helix Processing helix chain 'G' and resid 314 through 323 Processing helix chain 'G' and resid 330 through 336 removed outlier: 3.793A pdb=" N ALA G 334 " --> pdb=" O SER G 330 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG G 336 " --> pdb=" O GLN G 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 355 removed outlier: 3.921A pdb=" N VAL G 355 " --> pdb=" O PHE G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 357 through 381 Processing helix chain 'G' and resid 391 through 400 Processing helix chain 'G' and resid 400 through 409 Processing helix chain 'G' and resid 417 through 430 removed outlier: 3.806A pdb=" N ASN G 430 " --> pdb=" O ARG G 426 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 89 removed outlier: 3.607A pdb=" N ALA H 89 " --> pdb=" O GLU H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 148 Processing helix chain 'H' and resid 165 through 177 Processing helix chain 'H' and resid 190 through 203 removed outlier: 3.635A pdb=" N THR H 203 " --> pdb=" O HIS H 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 208 No H-bonds generated for 'chain 'H' and resid 206 through 208' Processing helix chain 'H' and resid 220 through 241 removed outlier: 3.945A pdb=" N ALA H 228 " --> pdb=" O ARG H 224 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU H 229 " --> pdb=" O CYS H 225 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN H 241 " --> pdb=" O TYR H 237 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 267 removed outlier: 3.731A pdb=" N TYR H 255 " --> pdb=" O SER H 251 " (cutoff:3.500A) Processing helix chain 'H' and resid 276 through 288 removed outlier: 3.857A pdb=" N PHE H 280 " --> pdb=" O PRO H 276 " (cutoff:3.500A) Proline residue: H 284 - end of helix Processing helix chain 'H' and resid 314 through 323 Processing helix chain 'H' and resid 330 through 336 removed outlier: 3.794A pdb=" N ALA H 334 " --> pdb=" O SER H 330 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG H 336 " --> pdb=" O GLN H 332 " (cutoff:3.500A) Processing helix chain 'H' and resid 351 through 355 removed outlier: 3.921A pdb=" N VAL H 355 " --> pdb=" O PHE H 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 357 through 381 Processing helix chain 'H' and resid 391 through 400 Processing helix chain 'H' and resid 400 through 409 Processing helix chain 'H' and resid 417 through 430 removed outlier: 3.806A pdb=" N ASN H 430 " --> pdb=" O ARG H 426 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 89 removed outlier: 3.607A pdb=" N ALA I 89 " --> pdb=" O GLU I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 148 Processing helix chain 'I' and resid 165 through 177 Processing helix chain 'I' and resid 190 through 203 removed outlier: 3.636A pdb=" N THR I 203 " --> pdb=" O HIS I 199 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 208 No H-bonds generated for 'chain 'I' and resid 206 through 208' Processing helix chain 'I' and resid 220 through 241 removed outlier: 3.945A pdb=" N ALA I 228 " --> pdb=" O ARG I 224 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU I 229 " --> pdb=" O CYS I 225 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN I 241 " --> pdb=" O TYR I 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 267 removed outlier: 3.732A pdb=" N TYR I 255 " --> pdb=" O SER I 251 " (cutoff:3.500A) Processing helix chain 'I' and resid 276 through 288 removed outlier: 3.857A pdb=" N PHE I 280 " --> pdb=" O PRO I 276 " (cutoff:3.500A) Proline residue: I 284 - end of helix Processing helix chain 'I' and resid 314 through 323 Processing helix chain 'I' and resid 330 through 336 removed outlier: 3.793A pdb=" N ALA I 334 " --> pdb=" O SER I 330 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG I 336 " --> pdb=" O GLN I 332 " (cutoff:3.500A) Processing helix chain 'I' and resid 351 through 355 removed outlier: 3.921A pdb=" N VAL I 355 " --> pdb=" O PHE I 352 " (cutoff:3.500A) Processing helix chain 'I' and resid 357 through 381 Processing helix chain 'I' and resid 391 through 400 Processing helix chain 'I' and resid 400 through 409 Processing helix chain 'I' and resid 417 through 430 removed outlier: 3.807A pdb=" N ASN I 430 " --> pdb=" O ARG I 426 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 89 removed outlier: 3.607A pdb=" N ALA J 89 " --> pdb=" O GLU J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 148 Processing helix chain 'J' and resid 165 through 177 Processing helix chain 'J' and resid 190 through 203 removed outlier: 3.635A pdb=" N THR J 203 " --> pdb=" O HIS J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 208 No H-bonds generated for 'chain 'J' and resid 206 through 208' Processing helix chain 'J' and resid 220 through 241 removed outlier: 3.945A pdb=" N ALA J 228 " --> pdb=" O ARG J 224 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU J 229 " --> pdb=" O CYS J 225 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN J 241 " --> pdb=" O TYR J 237 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 267 removed outlier: 3.732A pdb=" N TYR J 255 " --> pdb=" O SER J 251 " (cutoff:3.500A) Processing helix chain 'J' and resid 276 through 288 removed outlier: 3.857A pdb=" N PHE J 280 " --> pdb=" O PRO J 276 " (cutoff:3.500A) Proline residue: J 284 - end of helix Processing helix chain 'J' and resid 314 through 323 Processing helix chain 'J' and resid 330 through 336 removed outlier: 3.794A pdb=" N ALA J 334 " --> pdb=" O SER J 330 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG J 336 " --> pdb=" O GLN J 332 " (cutoff:3.500A) Processing helix chain 'J' and resid 351 through 355 removed outlier: 3.920A pdb=" N VAL J 355 " --> pdb=" O PHE J 352 " (cutoff:3.500A) Processing helix chain 'J' and resid 357 through 381 Processing helix chain 'J' and resid 391 through 400 Processing helix chain 'J' and resid 400 through 409 Processing helix chain 'J' and resid 417 through 430 removed outlier: 3.807A pdb=" N ASN J 430 " --> pdb=" O ARG J 426 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 89 removed outlier: 3.607A pdb=" N ALA K 89 " --> pdb=" O GLU K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 141 through 148 Processing helix chain 'K' and resid 165 through 177 Processing helix chain 'K' and resid 190 through 203 removed outlier: 3.636A pdb=" N THR K 203 " --> pdb=" O HIS K 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 208 No H-bonds generated for 'chain 'K' and resid 206 through 208' Processing helix chain 'K' and resid 220 through 241 removed outlier: 3.945A pdb=" N ALA K 228 " --> pdb=" O ARG K 224 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU K 229 " --> pdb=" O CYS K 225 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN K 241 " --> pdb=" O TYR K 237 " (cutoff:3.500A) Processing helix chain 'K' and resid 251 through 267 removed outlier: 3.732A pdb=" N TYR K 255 " --> pdb=" O SER K 251 " (cutoff:3.500A) Processing helix chain 'K' and resid 276 through 288 removed outlier: 3.856A pdb=" N PHE K 280 " --> pdb=" O PRO K 276 " (cutoff:3.500A) Proline residue: K 284 - end of helix Processing helix chain 'K' and resid 314 through 323 Processing helix chain 'K' and resid 330 through 336 removed outlier: 3.793A pdb=" N ALA K 334 " --> pdb=" O SER K 330 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG K 336 " --> pdb=" O GLN K 332 " (cutoff:3.500A) Processing helix chain 'K' and resid 351 through 355 removed outlier: 3.921A pdb=" N VAL K 355 " --> pdb=" O PHE K 352 " (cutoff:3.500A) Processing helix chain 'K' and resid 357 through 381 Processing helix chain 'K' and resid 391 through 400 Processing helix chain 'K' and resid 400 through 409 Processing helix chain 'K' and resid 417 through 430 removed outlier: 3.807A pdb=" N ASN K 430 " --> pdb=" O ARG K 426 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 89 removed outlier: 3.607A pdb=" N ALA L 89 " --> pdb=" O GLU L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 148 Processing helix chain 'L' and resid 165 through 177 Processing helix chain 'L' and resid 190 through 203 removed outlier: 3.636A pdb=" N THR L 203 " --> pdb=" O HIS L 199 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 208 No H-bonds generated for 'chain 'L' and resid 206 through 208' Processing helix chain 'L' and resid 220 through 241 removed outlier: 3.945A pdb=" N ALA L 228 " --> pdb=" O ARG L 224 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU L 229 " --> pdb=" O CYS L 225 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN L 241 " --> pdb=" O TYR L 237 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 267 removed outlier: 3.732A pdb=" N TYR L 255 " --> pdb=" O SER L 251 " (cutoff:3.500A) Processing helix chain 'L' and resid 276 through 288 removed outlier: 3.857A pdb=" N PHE L 280 " --> pdb=" O PRO L 276 " (cutoff:3.500A) Proline residue: L 284 - end of helix Processing helix chain 'L' and resid 314 through 323 Processing helix chain 'L' and resid 330 through 336 removed outlier: 3.793A pdb=" N ALA L 334 " --> pdb=" O SER L 330 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG L 336 " --> pdb=" O GLN L 332 " (cutoff:3.500A) Processing helix chain 'L' and resid 351 through 355 removed outlier: 3.921A pdb=" N VAL L 355 " --> pdb=" O PHE L 352 " (cutoff:3.500A) Processing helix chain 'L' and resid 357 through 381 Processing helix chain 'L' and resid 391 through 400 Processing helix chain 'L' and resid 400 through 409 Processing helix chain 'L' and resid 417 through 430 removed outlier: 3.806A pdb=" N ASN L 430 " --> pdb=" O ARG L 426 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 removed outlier: 3.627A pdb=" N ARG A 12 " --> pdb=" O GLU A 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 60 removed outlier: 3.708A pdb=" N GLY A 50 " --> pdb=" O ILE A 57 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N SER A 59 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL A 48 " --> pdb=" O SER A 59 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N GLU A 41 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG A 35 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE A 33 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LYS A 45 " --> pdb=" O CYS A 31 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N CYS A 31 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLN A 47 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLU A 29 " --> pdb=" O GLN A 47 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE A 30 " --> pdb=" O THR A 76 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 83 Processing sheet with id=AA4, first strand: chain 'A' and resid 99 through 102 removed outlier: 6.582A pdb=" N ILE A 92 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYS A 91 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N TYR A 214 " --> pdb=" O LYS A 91 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR A 93 " --> pdb=" O TYR A 214 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N THR A 216 " --> pdb=" O TYR A 93 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 185 " --> pdb=" O PHE A 248 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL A 245 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 136 through 137 removed outlier: 4.515A pdb=" N CYS A 150 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 303 through 305 removed outlier: 6.491A pdb=" N ILE A 158 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N HIS A 326 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N LEU A 345 " --> pdb=" O HIS A 326 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TYR A 328 " --> pdb=" O ASP A 343 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 12 through 13 removed outlier: 3.627A pdb=" N ARG B 12 " --> pdb=" O GLU B 19 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 55 through 60 removed outlier: 3.708A pdb=" N GLY B 50 " --> pdb=" O ILE B 57 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N SER B 59 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL B 48 " --> pdb=" O SER B 59 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N GLU B 41 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG B 35 " --> pdb=" O GLU B 41 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE B 33 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LYS B 45 " --> pdb=" O CYS B 31 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N CYS B 31 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLN B 47 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLU B 29 " --> pdb=" O GLN B 47 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE B 30 " --> pdb=" O THR B 76 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 81 through 83 Processing sheet with id=AB1, first strand: chain 'B' and resid 99 through 102 removed outlier: 6.581A pdb=" N ILE B 92 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYS B 91 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N TYR B 214 " --> pdb=" O LYS B 91 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR B 93 " --> pdb=" O TYR B 214 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N THR B 216 " --> pdb=" O TYR B 93 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA B 185 " --> pdb=" O PHE B 248 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N VAL B 245 " --> pdb=" O THR B 299 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 136 through 137 removed outlier: 4.515A pdb=" N CYS B 150 " --> pdb=" O LEU B 137 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 303 through 305 removed outlier: 6.491A pdb=" N ILE B 158 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 10.032A pdb=" N HIS B 326 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N LEU B 345 " --> pdb=" O HIS B 326 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TYR B 328 " --> pdb=" O ASP B 343 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 12 through 13 removed outlier: 3.628A pdb=" N ARG C 12 " --> pdb=" O GLU C 19 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 55 through 60 removed outlier: 3.708A pdb=" N GLY C 50 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N SER C 59 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL C 48 " --> pdb=" O SER C 59 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N GLU C 41 " --> pdb=" O ARG C 35 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG C 35 " --> pdb=" O GLU C 41 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE C 33 " --> pdb=" O ILE C 43 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LYS C 45 " --> pdb=" O CYS C 31 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N CYS C 31 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLN C 47 " --> pdb=" O GLU C 29 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLU C 29 " --> pdb=" O GLN C 47 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE C 30 " --> pdb=" O THR C 76 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 81 through 83 Processing sheet with id=AB7, first strand: chain 'C' and resid 99 through 102 removed outlier: 6.582A pdb=" N ILE C 92 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LYS C 91 " --> pdb=" O LEU C 212 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N TYR C 214 " --> pdb=" O LYS C 91 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR C 93 " --> pdb=" O TYR C 214 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N THR C 216 " --> pdb=" O TYR C 93 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA C 185 " --> pdb=" O PHE C 248 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N VAL C 245 " --> pdb=" O THR C 299 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 136 through 137 removed outlier: 4.514A pdb=" N CYS C 150 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 303 through 305 removed outlier: 6.491A pdb=" N ILE C 158 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N HIS C 326 " --> pdb=" O LEU C 345 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N LEU C 345 " --> pdb=" O HIS C 326 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TYR C 328 " --> pdb=" O ASP C 343 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 12 through 13 removed outlier: 3.627A pdb=" N ARG D 12 " --> pdb=" O GLU D 19 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 55 through 60 removed outlier: 3.708A pdb=" N GLY D 50 " --> pdb=" O ILE D 57 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N SER D 59 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL D 48 " --> pdb=" O SER D 59 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N GLU D 41 " --> pdb=" O ARG D 35 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG D 35 " --> pdb=" O GLU D 41 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE D 33 " --> pdb=" O ILE D 43 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LYS D 45 " --> pdb=" O CYS D 31 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N CYS D 31 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLN D 47 " --> pdb=" O GLU D 29 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLU D 29 " --> pdb=" O GLN D 47 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE D 30 " --> pdb=" O THR D 76 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 81 through 83 Processing sheet with id=AC4, first strand: chain 'D' and resid 99 through 102 removed outlier: 6.582A pdb=" N ILE D 92 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYS D 91 " --> pdb=" O LEU D 212 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N TYR D 214 " --> pdb=" O LYS D 91 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR D 93 " --> pdb=" O TYR D 214 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N THR D 216 " --> pdb=" O TYR D 93 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA D 185 " --> pdb=" O PHE D 248 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N VAL D 245 " --> pdb=" O THR D 299 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 136 through 137 removed outlier: 4.515A pdb=" N CYS D 150 " --> pdb=" O LEU D 137 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 303 through 305 removed outlier: 6.491A pdb=" N ILE D 158 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N HIS D 326 " --> pdb=" O LEU D 345 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N LEU D 345 " --> pdb=" O HIS D 326 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TYR D 328 " --> pdb=" O ASP D 343 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 12 through 13 removed outlier: 3.626A pdb=" N ARG E 12 " --> pdb=" O GLU E 19 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 55 through 60 removed outlier: 3.708A pdb=" N GLY E 50 " --> pdb=" O ILE E 57 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N SER E 59 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL E 48 " --> pdb=" O SER E 59 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N GLU E 41 " --> pdb=" O ARG E 35 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG E 35 " --> pdb=" O GLU E 41 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE E 33 " --> pdb=" O ILE E 43 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LYS E 45 " --> pdb=" O CYS E 31 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N CYS E 31 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLN E 47 " --> pdb=" O GLU E 29 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLU E 29 " --> pdb=" O GLN E 47 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE E 30 " --> pdb=" O THR E 76 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 81 through 83 Processing sheet with id=AD1, first strand: chain 'E' and resid 99 through 102 removed outlier: 6.582A pdb=" N ILE E 92 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYS E 91 " --> pdb=" O LEU E 212 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N TYR E 214 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR E 93 " --> pdb=" O TYR E 214 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N THR E 216 " --> pdb=" O TYR E 93 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA E 185 " --> pdb=" O PHE E 248 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N VAL E 245 " --> pdb=" O THR E 299 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 136 through 137 removed outlier: 4.515A pdb=" N CYS E 150 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 303 through 305 removed outlier: 6.491A pdb=" N ILE E 158 " --> pdb=" O VAL E 304 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N HIS E 326 " --> pdb=" O LEU E 345 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N LEU E 345 " --> pdb=" O HIS E 326 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TYR E 328 " --> pdb=" O ASP E 343 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 12 through 13 removed outlier: 3.627A pdb=" N ARG F 12 " --> pdb=" O GLU F 19 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 55 through 60 removed outlier: 3.708A pdb=" N GLY F 50 " --> pdb=" O ILE F 57 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N SER F 59 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL F 48 " --> pdb=" O SER F 59 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N GLU F 41 " --> pdb=" O ARG F 35 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG F 35 " --> pdb=" O GLU F 41 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE F 33 " --> pdb=" O ILE F 43 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LYS F 45 " --> pdb=" O CYS F 31 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N CYS F 31 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLN F 47 " --> pdb=" O GLU F 29 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLU F 29 " --> pdb=" O GLN F 47 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE F 30 " --> pdb=" O THR F 76 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 81 through 83 Processing sheet with id=AD7, first strand: chain 'F' and resid 99 through 102 removed outlier: 6.582A pdb=" N ILE F 92 " --> pdb=" O VAL F 100 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LYS F 91 " --> pdb=" O LEU F 212 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N TYR F 214 " --> pdb=" O LYS F 91 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR F 93 " --> pdb=" O TYR F 214 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N THR F 216 " --> pdb=" O TYR F 93 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA F 185 " --> pdb=" O PHE F 248 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL F 245 " --> pdb=" O THR F 299 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 136 through 137 removed outlier: 4.515A pdb=" N CYS F 150 " --> pdb=" O LEU F 137 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 303 through 305 removed outlier: 6.491A pdb=" N ILE F 158 " --> pdb=" O VAL F 304 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N HIS F 326 " --> pdb=" O LEU F 345 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N LEU F 345 " --> pdb=" O HIS F 326 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TYR F 328 " --> pdb=" O ASP F 343 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 12 through 13 removed outlier: 3.626A pdb=" N ARG G 12 " --> pdb=" O GLU G 19 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 55 through 60 removed outlier: 3.708A pdb=" N GLY G 50 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N SER G 59 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL G 48 " --> pdb=" O SER G 59 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N GLU G 41 " --> pdb=" O ARG G 35 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG G 35 " --> pdb=" O GLU G 41 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE G 33 " --> pdb=" O ILE G 43 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LYS G 45 " --> pdb=" O CYS G 31 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N CYS G 31 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLN G 47 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLU G 29 " --> pdb=" O GLN G 47 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE G 30 " --> pdb=" O THR G 76 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 81 through 83 Processing sheet with id=AE4, first strand: chain 'G' and resid 99 through 102 removed outlier: 6.583A pdb=" N ILE G 92 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYS G 91 " --> pdb=" O LEU G 212 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N TYR G 214 " --> pdb=" O LYS G 91 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TYR G 93 " --> pdb=" O TYR G 214 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N THR G 216 " --> pdb=" O TYR G 93 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA G 185 " --> pdb=" O PHE G 248 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL G 245 " --> pdb=" O THR G 299 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 136 through 137 removed outlier: 4.515A pdb=" N CYS G 150 " --> pdb=" O LEU G 137 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 303 through 305 removed outlier: 6.492A pdb=" N ILE G 158 " --> pdb=" O VAL G 304 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N HIS G 326 " --> pdb=" O LEU G 345 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N LEU G 345 " --> pdb=" O HIS G 326 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TYR G 328 " --> pdb=" O ASP G 343 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 12 through 13 removed outlier: 3.627A pdb=" N ARG H 12 " --> pdb=" O GLU H 19 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 55 through 60 removed outlier: 3.709A pdb=" N GLY H 50 " --> pdb=" O ILE H 57 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N SER H 59 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL H 48 " --> pdb=" O SER H 59 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N GLU H 41 " --> pdb=" O ARG H 35 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG H 35 " --> pdb=" O GLU H 41 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE H 33 " --> pdb=" O ILE H 43 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LYS H 45 " --> pdb=" O CYS H 31 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N CYS H 31 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLN H 47 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLU H 29 " --> pdb=" O GLN H 47 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE H 30 " --> pdb=" O THR H 76 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 81 through 83 Processing sheet with id=AF1, first strand: chain 'H' and resid 99 through 102 removed outlier: 6.582A pdb=" N ILE H 92 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LYS H 91 " --> pdb=" O LEU H 212 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N TYR H 214 " --> pdb=" O LYS H 91 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR H 93 " --> pdb=" O TYR H 214 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N THR H 216 " --> pdb=" O TYR H 93 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA H 185 " --> pdb=" O PHE H 248 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N VAL H 245 " --> pdb=" O THR H 299 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 136 through 137 removed outlier: 4.515A pdb=" N CYS H 150 " --> pdb=" O LEU H 137 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 303 through 305 removed outlier: 6.492A pdb=" N ILE H 158 " --> pdb=" O VAL H 304 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N HIS H 326 " --> pdb=" O LEU H 345 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N LEU H 345 " --> pdb=" O HIS H 326 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TYR H 328 " --> pdb=" O ASP H 343 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 12 through 13 removed outlier: 3.627A pdb=" N ARG I 12 " --> pdb=" O GLU I 19 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 55 through 60 removed outlier: 3.707A pdb=" N GLY I 50 " --> pdb=" O ILE I 57 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N SER I 59 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL I 48 " --> pdb=" O SER I 59 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N GLU I 41 " --> pdb=" O ARG I 35 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG I 35 " --> pdb=" O GLU I 41 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE I 33 " --> pdb=" O ILE I 43 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LYS I 45 " --> pdb=" O CYS I 31 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N CYS I 31 " --> pdb=" O LYS I 45 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLN I 47 " --> pdb=" O GLU I 29 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLU I 29 " --> pdb=" O GLN I 47 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE I 30 " --> pdb=" O THR I 76 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 81 through 83 Processing sheet with id=AF7, first strand: chain 'I' and resid 99 through 102 removed outlier: 6.582A pdb=" N ILE I 92 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LYS I 91 " --> pdb=" O LEU I 212 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N TYR I 214 " --> pdb=" O LYS I 91 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TYR I 93 " --> pdb=" O TYR I 214 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N THR I 216 " --> pdb=" O TYR I 93 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA I 185 " --> pdb=" O PHE I 248 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N VAL I 245 " --> pdb=" O THR I 299 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 136 through 137 removed outlier: 4.515A pdb=" N CYS I 150 " --> pdb=" O LEU I 137 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 303 through 305 removed outlier: 6.492A pdb=" N ILE I 158 " --> pdb=" O VAL I 304 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N HIS I 326 " --> pdb=" O LEU I 345 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N LEU I 345 " --> pdb=" O HIS I 326 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TYR I 328 " --> pdb=" O ASP I 343 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 12 through 13 removed outlier: 3.627A pdb=" N ARG J 12 " --> pdb=" O GLU J 19 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 55 through 60 removed outlier: 3.708A pdb=" N GLY J 50 " --> pdb=" O ILE J 57 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N SER J 59 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL J 48 " --> pdb=" O SER J 59 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N GLU J 41 " --> pdb=" O ARG J 35 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG J 35 " --> pdb=" O GLU J 41 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE J 33 " --> pdb=" O ILE J 43 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LYS J 45 " --> pdb=" O CYS J 31 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N CYS J 31 " --> pdb=" O LYS J 45 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLN J 47 " --> pdb=" O GLU J 29 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLU J 29 " --> pdb=" O GLN J 47 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE J 30 " --> pdb=" O THR J 76 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 81 through 83 Processing sheet with id=AG4, first strand: chain 'J' and resid 99 through 102 removed outlier: 6.582A pdb=" N ILE J 92 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYS J 91 " --> pdb=" O LEU J 212 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N TYR J 214 " --> pdb=" O LYS J 91 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TYR J 93 " --> pdb=" O TYR J 214 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N THR J 216 " --> pdb=" O TYR J 93 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA J 185 " --> pdb=" O PHE J 248 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N VAL J 245 " --> pdb=" O THR J 299 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 136 through 137 removed outlier: 4.514A pdb=" N CYS J 150 " --> pdb=" O LEU J 137 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 303 through 305 removed outlier: 6.491A pdb=" N ILE J 158 " --> pdb=" O VAL J 304 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N HIS J 326 " --> pdb=" O LEU J 345 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N LEU J 345 " --> pdb=" O HIS J 326 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TYR J 328 " --> pdb=" O ASP J 343 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 12 through 13 removed outlier: 3.626A pdb=" N ARG K 12 " --> pdb=" O GLU K 19 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 55 through 60 removed outlier: 3.708A pdb=" N GLY K 50 " --> pdb=" O ILE K 57 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N SER K 59 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL K 48 " --> pdb=" O SER K 59 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N GLU K 41 " --> pdb=" O ARG K 35 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG K 35 " --> pdb=" O GLU K 41 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE K 33 " --> pdb=" O ILE K 43 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LYS K 45 " --> pdb=" O CYS K 31 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N CYS K 31 " --> pdb=" O LYS K 45 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLN K 47 " --> pdb=" O GLU K 29 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLU K 29 " --> pdb=" O GLN K 47 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE K 30 " --> pdb=" O THR K 76 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 81 through 83 Processing sheet with id=AH1, first strand: chain 'K' and resid 99 through 102 removed outlier: 6.582A pdb=" N ILE K 92 " --> pdb=" O VAL K 100 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYS K 91 " --> pdb=" O LEU K 212 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N TYR K 214 " --> pdb=" O LYS K 91 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR K 93 " --> pdb=" O TYR K 214 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N THR K 216 " --> pdb=" O TYR K 93 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA K 185 " --> pdb=" O PHE K 248 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N VAL K 245 " --> pdb=" O THR K 299 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 136 through 137 removed outlier: 4.516A pdb=" N CYS K 150 " --> pdb=" O LEU K 137 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 303 through 305 removed outlier: 6.490A pdb=" N ILE K 158 " --> pdb=" O VAL K 304 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N HIS K 326 " --> pdb=" O LEU K 345 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N LEU K 345 " --> pdb=" O HIS K 326 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TYR K 328 " --> pdb=" O ASP K 343 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'L' and resid 12 through 13 removed outlier: 3.626A pdb=" N ARG L 12 " --> pdb=" O GLU L 19 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 55 through 60 removed outlier: 3.708A pdb=" N GLY L 50 " --> pdb=" O ILE L 57 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N SER L 59 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL L 48 " --> pdb=" O SER L 59 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N GLU L 41 " --> pdb=" O ARG L 35 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG L 35 " --> pdb=" O GLU L 41 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE L 33 " --> pdb=" O ILE L 43 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LYS L 45 " --> pdb=" O CYS L 31 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N CYS L 31 " --> pdb=" O LYS L 45 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLN L 47 " --> pdb=" O GLU L 29 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLU L 29 " --> pdb=" O GLN L 47 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE L 30 " --> pdb=" O THR L 76 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'L' and resid 81 through 83 Processing sheet with id=AH7, first strand: chain 'L' and resid 99 through 102 removed outlier: 6.582A pdb=" N ILE L 92 " --> pdb=" O VAL L 100 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYS L 91 " --> pdb=" O LEU L 212 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N TYR L 214 " --> pdb=" O LYS L 91 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TYR L 93 " --> pdb=" O TYR L 214 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N THR L 216 " --> pdb=" O TYR L 93 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA L 185 " --> pdb=" O PHE L 248 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N VAL L 245 " --> pdb=" O THR L 299 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 136 through 137 removed outlier: 4.515A pdb=" N CYS L 150 " --> pdb=" O LEU L 137 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 303 through 305 removed outlier: 6.491A pdb=" N ILE L 158 " --> pdb=" O VAL L 304 " (cutoff:3.500A) removed outlier: 10.032A pdb=" N HIS L 326 " --> pdb=" O LEU L 345 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N LEU L 345 " --> pdb=" O HIS L 326 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TYR L 328 " --> pdb=" O ASP L 343 " (cutoff:3.500A) 1608 hydrogen bonds defined for protein. 4608 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: 10.42 Time building geometry restraints manager: 4.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 12761 1.34 - 1.46: 7477 1.46 - 1.58: 17474 1.58 - 1.71: 0 1.71 - 1.83: 292 Bond restraints: 38004 Sorted by residual: bond pdb=" N CYS E 38 " pdb=" CA CYS E 38 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.12e-02 7.97e+03 9.70e+00 bond pdb=" N GLN E 39 " pdb=" CA GLN E 39 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.41e-02 5.03e+03 6.96e+00 bond pdb=" N LEU E 37 " pdb=" CA LEU E 37 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.18e-02 7.18e+03 5.11e+00 bond pdb=" N PRO E 40 " pdb=" CA PRO E 40 " ideal model delta sigma weight residual 1.469 1.492 -0.023 1.28e-02 6.10e+03 3.28e+00 bond pdb=" N PRO E 40 " pdb=" CD PRO E 40 " ideal model delta sigma weight residual 1.473 1.495 -0.022 1.40e-02 5.10e+03 2.56e+00 ... (remaining 37999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 51453 3.26 - 6.52: 205 6.52 - 9.78: 26 9.78 - 13.04: 25 13.04 - 16.30: 1 Bond angle restraints: 51710 Sorted by residual: angle pdb=" C HIS H 0 " pdb=" N MET H 1 " pdb=" CA MET H 1 " ideal model delta sigma weight residual 121.54 130.84 -9.30 1.91e+00 2.74e-01 2.37e+01 angle pdb=" CA GLU F 53 " pdb=" CB GLU F 53 " pdb=" CG GLU F 53 " ideal model delta sigma weight residual 114.10 123.46 -9.36 2.00e+00 2.50e-01 2.19e+01 angle pdb=" CA GLU L 53 " pdb=" CB GLU L 53 " pdb=" CG GLU L 53 " ideal model delta sigma weight residual 114.10 123.44 -9.34 2.00e+00 2.50e-01 2.18e+01 angle pdb=" CA GLU A 53 " pdb=" CB GLU A 53 " pdb=" CG GLU A 53 " ideal model delta sigma weight residual 114.10 123.44 -9.34 2.00e+00 2.50e-01 2.18e+01 angle pdb=" CA GLU I 53 " pdb=" CB GLU I 53 " pdb=" CG GLU I 53 " ideal model delta sigma weight residual 114.10 123.43 -9.33 2.00e+00 2.50e-01 2.18e+01 ... (remaining 51705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 20033 17.69 - 35.39: 2136 35.39 - 53.08: 527 53.08 - 70.77: 124 70.77 - 88.46: 43 Dihedral angle restraints: 22863 sinusoidal: 8448 harmonic: 14415 Sorted by residual: dihedral pdb=" CA HIS G 0 " pdb=" C HIS G 0 " pdb=" N MET G 1 " pdb=" CA MET G 1 " ideal model delta harmonic sigma weight residual 180.00 149.53 30.47 0 5.00e+00 4.00e-02 3.71e+01 dihedral pdb=" CA HIS J 0 " pdb=" C HIS J 0 " pdb=" N MET J 1 " pdb=" CA MET J 1 " ideal model delta harmonic sigma weight residual 180.00 156.99 23.01 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA HIS E 0 " pdb=" C HIS E 0 " pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta harmonic sigma weight residual 180.00 157.30 22.70 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 22860 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 4776 0.041 - 0.083: 903 0.083 - 0.124: 461 0.124 - 0.166: 3 0.166 - 0.207: 21 Chirality restraints: 6164 Sorted by residual: chirality pdb=" CG LEU C 3 " pdb=" CB LEU C 3 " pdb=" CD1 LEU C 3 " pdb=" CD2 LEU C 3 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA CYS D 38 " pdb=" N CYS D 38 " pdb=" C CYS D 38 " pdb=" CB CYS D 38 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA CYS J 38 " pdb=" N CYS J 38 " pdb=" C CYS J 38 " pdb=" CB CYS J 38 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 6161 not shown) Planarity restraints: 6823 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU K 53 " -0.017 2.00e-02 2.50e+03 3.40e-02 1.15e+01 pdb=" CD GLU K 53 " 0.059 2.00e-02 2.50e+03 pdb=" OE1 GLU K 53 " -0.021 2.00e-02 2.50e+03 pdb=" OE2 GLU K 53 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 53 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.15e+01 pdb=" CD GLU C 53 " -0.059 2.00e-02 2.50e+03 pdb=" OE1 GLU C 53 " 0.021 2.00e-02 2.50e+03 pdb=" OE2 GLU C 53 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU F 53 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" CD GLU F 53 " 0.059 2.00e-02 2.50e+03 pdb=" OE1 GLU F 53 " -0.021 2.00e-02 2.50e+03 pdb=" OE2 GLU F 53 " -0.021 2.00e-02 2.50e+03 ... (remaining 6820 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2343 2.74 - 3.28: 37905 3.28 - 3.82: 61605 3.82 - 4.36: 68790 4.36 - 4.90: 119802 Nonbonded interactions: 290445 Sorted by model distance: nonbonded pdb=" CB CYS D 38 " pdb=" CB CYS J 38 " model vdw 2.201 3.072 nonbonded pdb=" O VAL I 127 " pdb=" OG1 THR J 195 " model vdw 2.266 3.040 nonbonded pdb=" O GLU F 427 " pdb=" OD1 ASN F 430 " model vdw 2.474 3.040 nonbonded pdb=" O GLU H 427 " pdb=" OD1 ASN H 430 " model vdw 2.478 3.040 nonbonded pdb=" O PHE B 4 " pdb=" O PHE G 4 " model vdw 2.488 3.040 ... (remaining 290440 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 1 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 18 or (resid 19 through 20 and (na \ me N or name CA or name C or name O or name CB )) or resid 21 through 22 or (res \ id 23 and (name N or name CA or name C or name O or name CB )) or resid 24 throu \ gh 33 or (resid 34 and (name N or name CA or name C or name O or name CB )) or r \ esid 35 through 36 or (resid 37 and (name N or name CA or name C or name O or na \ me CB )) or resid 38 through 51 or (resid 52 and (name N or name CA or name C or \ name O or name CB )) or resid 53 through 68 or (resid 69 through 70 and (name N \ or name CA or name C or name O or name CB )) or resid 71 through 82 or (resid 8 \ 3 through 84 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 5 through 90 or (resid 91 and (name N or name CA or name C or name O or name CB \ )) or resid 92 through 97 or (resid 98 through 99 and (name N or name CA or name \ C or name O or name CB )) or resid 100 through 105 or resid 115 through 141 or \ (resid 142 through 143 and (name N or name CA or name C or name O or name CB )) \ or resid 144 through 189 or (resid 190 and (name N or name CA or name C or name \ O or name CB )) or resid 191 through 205 or (resid 206 through 209 and (name N o \ r name CA or name C or name O or name CB )) or resid 210 through 217 or (resid 2 \ 18 and (name N or name CA or name C or name O or name CB )) or resid 219 through \ 222 or (resid 223 and (name N or name CA or name C or name O or name CB )) or r \ esid 224 through 287 or (resid 288 and (name N or name CA or name C or name O or \ name CB )) or resid 289 through 307 or (resid 308 and (name N or name CA or nam \ e C or name O or name CB )) or resid 313 through 317 or (resid 318 and (name N o \ r name CA or name C or name O or name CB )) or resid 319 through 331 or (resid 3 \ 32 and (name N or name CA or name C or name O or name CB )) or resid 333 through \ 335 or (resid 336 and (name N or name CA or name C or name O or name CB )) or r \ esid 337 through 349 or (resid 350 and (name N or name CA or name C or name O or \ name CB )) or resid 351 through 353 or (resid 354 and (name N or name CA or nam \ e C or name O or name CB )) or resid 355 through 360 or (resid 361 through 362 a \ nd (name N or name CA or name C or name O or name CB )) or resid 363 through 368 \ or (resid 369 through 370 and (name N or name CA or name C or name O or name CB \ )) or resid 371 through 384 or (resid 385 and (name N or name CA or name C or n \ ame O or name CB )) or resid 386 through 389 or (resid 390 and (name N or name C \ A or name C or name O or name CB )) or resid 391 through 400 or (resid 401 throu \ gh 402 and (name N or name CA or name C or name O or name CB )) or resid 403 thr \ ough 412 or (resid 413 through 414 and (name N or name CA or name C or name O or \ name CB )) or resid 415 through 423 or (resid 424 and (name N or name CA or nam \ e C or name O or name CB )) or resid 425 through 426 or (resid 427 and (name N o \ r name CA or name C or name O or name CB )) or resid 428 through 430)) selection = (chain 'B' and ((resid 1 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 22 or (resid 23 and (name N or nam \ e CA or name C or name O or name CB )) or resid 24 through 28 or (resid 29 and ( \ name N or name CA or name C or name O or name CB )) or resid 30 through 36 or (r \ esid 37 and (name N or name CA or name C or name O or name CB )) or resid 38 thr \ ough 68 or (resid 69 through 70 and (name N or name CA or name C or name O or na \ me CB )) or resid 71 through 73 or (resid 74 and (name N or name CA or name C or \ name O or name CB )) or resid 75 through 82 or (resid 83 through 84 and (name N \ or name CA or name C or name O or name CB )) or resid 85 or (resid 86 and (name \ N or name CA or name C or name O or name CB )) or resid 87 through 90 or (resid \ 91 and (name N or name CA or name C or name O or name CB )) or resid 92 through \ 97 or (resid 98 through 99 and (name N or name CA or name C or name O or name C \ B )) or resid 100 through 104 or (resid 105 and (name N or name CA or name C or \ name O or name CB )) or resid 115 through 130 or (resid 131 and (name N or name \ CA or name C or name O or name CB )) or resid 132 through 141 or (resid 142 thro \ ugh 143 and (name N or name CA or name C or name O or name CB )) or resid 144 th \ rough 188 or (resid 189 through 190 and (name N or name CA or name C or name O o \ r name CB )) or resid 191 or (resid 192 through 193 and (name N or name CA or na \ me C or name O or name CB )) or resid 194 through 195 or (resid 196 and (name N \ or name CA or name C or name O or name CB )) or resid 197 through 199 or (resid \ 200 and (name N or name CA or name C or name O or name CB )) or resid 201 throug \ h 205 or (resid 206 through 209 and (name N or name CA or name C or name O or na \ me CB )) or resid 210 through 217 or (resid 218 and (name N or name CA or name C \ or name O or name CB )) or resid 219 through 235 or (resid 236 and (name N or n \ ame CA or name C or name O or name CB )) or resid 237 through 242 or (resid 243 \ through 244 and (name N or name CA or name C or name O or name CB )) or resid 24 \ 5 through 253 or (resid 254 and (name N or name CA or name C or name O or name C \ B )) or resid 255 through 256 or (resid 257 through 258 and (name N or name CA o \ r name C or name O or name CB )) or resid 259 through 260 or (resid 261 and (nam \ e N or name CA or name C or name O or name CB )) or resid 262 through 267 or (re \ sid 268 through 269 and (name N or name CA or name C or name O or name CB )) or \ resid 270 through 271 or (resid 272 through 273 and (name N or name CA or name C \ or name O or name CB )) or resid 274 through 287 or (resid 288 and (name N or n \ ame CA or name C or name O or name CB )) or resid 289 through 293 or (resid 294 \ and (name N or name CA or name C or name O or name CB )) or resid 295 through 30 \ 6 or (resid 307 through 308 and (name N or name CA or name C or name O or name C \ B )) or resid 313 through 331 or (resid 332 and (name N or name CA or name C or \ name O or name CB )) or resid 333 through 353 or (resid 354 and (name N or name \ CA or name C or name O or name CB )) or resid 355 through 358 or (resid 359 and \ (name N or name CA or name C or name O or name CB )) or resid 360 or (resid 361 \ through 362 and (name N or name CA or name C or name O or name CB )) or resid 36 \ 3 through 368 or (resid 369 through 370 and (name N or name CA or name C or name \ O or name CB )) or resid 371 through 379 or (resid 380 and (name N or name CA o \ r name C or name O or name CB )) or resid 381 through 389 or (resid 390 and (nam \ e N or name CA or name C or name O or name CB )) or resid 391 through 398 or (re \ sid 399 and (name N or name CA or name C or name O or name CB )) or resid 400 or \ (resid 401 through 402 and (name N or name CA or name C or name O or name CB )) \ or resid 403 through 411 or (resid 412 through 414 and (name N or name CA or na \ me C or name O or name CB )) or resid 415 through 423 or (resid 424 and (name N \ or name CA or name C or name O or name CB )) or resid 425 or (resid 426 through \ 427 and (name N or name CA or name C or name O or name CB )) or resid 428 throug \ h 430)) selection = (chain 'C' and ((resid 1 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 22 or (resid 23 and (name N or name \ CA or name C or name O or name CB )) or resid 24 through 33 or (resid 34 and (na \ me N or name CA or name C or name O or name CB )) or resid 35 through 36 or (res \ id 37 and (name N or name CA or name C or name O or name CB )) or resid 38 throu \ gh 69 or (resid 70 and (name N or name CA or name C or name O or name CB )) or r \ esid 71 through 73 or (resid 74 and (name N or name CA or name C or name O or na \ me CB )) or resid 75 through 83 or (resid 84 and (name N or name CA or name C or \ name O or name CB )) or resid 85 or (resid 86 and (name N or name CA or name C \ or name O or name CB )) or resid 87 through 90 or (resid 91 and (name N or name \ CA or name C or name O or name CB )) or resid 92 through 97 or (resid 98 through \ 99 and (name N or name CA or name C or name O or name CB )) or resid 100 throug \ h 105 or resid 115 through 130 or (resid 131 and (name N or name CA or name C or \ name O or name CB )) or resid 132 through 199 or (resid 200 and (name N or name \ CA or name C or name O or name CB )) or resid 201 through 235 or (resid 236 and \ (name N or name CA or name C or name O or name CB )) or resid 237 through 242 o \ r (resid 243 through 244 and (name N or name CA or name C or name O or name CB ) \ ) or resid 245 through 253 or (resid 254 and (name N or name CA or name C or nam \ e O or name CB )) or resid 255 through 256 or (resid 257 through 258 and (name N \ or name CA or name C or name O or name CB )) or resid 259 through 260 or (resid \ 261 and (name N or name CA or name C or name O or name CB )) or resid 262 throu \ gh 267 or (resid 268 through 269 and (name N or name CA or name C or name O or n \ ame CB )) or resid 270 through 271 or (resid 272 through 273 and (name N or name \ CA or name C or name O or name CB )) or resid 274 through 280 or (resid 281 and \ (name N or name CA or name C or name O or name CB )) or resid 282 through 287 o \ r (resid 288 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 89 through 293 or (resid 294 and (name N or name CA or name C or name O or name \ CB )) or resid 295 through 317 or (resid 318 and (name N or name CA or name C or \ name O or name CB )) or resid 319 through 349 or (resid 350 and (name N or name \ CA or name C or name O or name CB )) or resid 351 through 353 or (resid 354 and \ (name N or name CA or name C or name O or name CB )) or resid 355 through 358 o \ r (resid 359 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 60 or (resid 361 through 362 and (name N or name CA or name C or name O or name \ CB )) or resid 363 through 367 or (resid 368 through 370 and (name N or name CA \ or name C or name O or name CB )) or resid 371 through 372 or (resid 373 and (na \ me N or name CA or name C or name O or name CB )) or resid 374 through 375 or (r \ esid 376 and (name N or name CA or name C or name O or name CB )) or resid 377 t \ hrough 379 or (resid 380 and (name N or name CA or name C or name O or name CB ) \ ) or resid 381 through 384 or (resid 385 and (name N or name CA or name C or nam \ e O or name CB )) or resid 386 through 387 or (resid 388 and (name N or name CA \ or name C or name O or name CB )) or resid 389 or (resid 390 and (name N or name \ CA or name C or name O or name CB )) or resid 391 through 398 or (resid 399 and \ (name N or name CA or name C or name O or name CB )) or resid 400 through 411 o \ r (resid 412 through 414 and (name N or name CA or name C or name O or name CB ) \ ) or resid 415 through 423 or (resid 424 and (name N or name CA or name C or nam \ e O or name CB )) or resid 425 or (resid 426 through 427 and (name N or name CA \ or name C or name O or name CB )) or resid 428 through 429 or (resid 430 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'D' and ((resid 1 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 18 or (resid 19 through 20 and (na \ me N or name CA or name C or name O or name CB )) or resid 21 through 22 or (res \ id 23 and (name N or name CA or name C or name O or name CB )) or resid 24 throu \ gh 28 or (resid 29 and (name N or name CA or name C or name O or name CB )) or r \ esid 30 through 33 or (resid 34 and (name N or name CA or name C or name O or na \ me CB )) or resid 35 through 36 or (resid 37 and (name N or name CA or name C or \ name O or name CB )) or resid 38 through 51 or (resid 52 and (name N or name CA \ or name C or name O or name CB )) or resid 53 through 64 or (resid 65 and (name \ N or name CA or name C or name O or name CB )) or resid 66 through 68 or (resid \ 69 through 70 and (name N or name CA or name C or name O or name CB )) or resid \ 71 through 73 or (resid 74 and (name N or name CA or name C or name O or name C \ B )) or resid 75 through 82 or (resid 83 through 84 and (name N or name CA or na \ me C or name O or name CB )) or resid 85 or (resid 86 and (name N or name CA or \ name C or name O or name CB )) or resid 87 through 90 or (resid 91 and (name N o \ r name CA or name C or name O or name CB )) or resid 92 through 97 or (resid 98 \ through 99 and (name N or name CA or name C or name O or name CB )) or resid 100 \ through 104 or (resid 105 and (name N or name CA or name C or name O or name CB \ )) or resid 115 through 141 or (resid 142 through 143 and (name N or name CA or \ name C or name O or name CB )) or resid 144 through 188 or (resid 189 through 1 \ 90 and (name N or name CA or name C or name O or name CB )) or resid 191 or (res \ id 192 through 193 and (name N or name CA or name C or name O or name CB )) or r \ esid 194 through 195 or (resid 196 and (name N or name CA or name C or name O or \ name CB )) or resid 197 through 199 or (resid 200 and (name N or name CA or nam \ e C or name O or name CB )) or resid 201 through 205 or (resid 206 through 209 a \ nd (name N or name CA or name C or name O or name CB )) or resid 210 through 217 \ or (resid 218 and (name N or name CA or name C or name O or name CB )) or resid \ 219 through 222 or (resid 223 and (name N or name CA or name C or name O or nam \ e CB )) or resid 224 through 235 or (resid 236 and (name N or name CA or name C \ or name O or name CB )) or resid 237 through 242 or (resid 243 through 244 and ( \ name N or name CA or name C or name O or name CB )) or resid 245 through 253 or \ (resid 254 and (name N or name CA or name C or name O or name CB )) or resid 255 \ through 256 or (resid 257 through 258 and (name N or name CA or name C or name \ O or name CB )) or resid 259 through 260 or (resid 261 and (name N or name CA or \ name C or name O or name CB )) or resid 262 through 267 or (resid 268 through 2 \ 69 and (name N or name CA or name C or name O or name CB )) or resid 270 through \ 271 or (resid 272 through 273 and (name N or name CA or name C or name O or nam \ e CB )) or resid 274 through 280 or (resid 281 and (name N or name CA or name C \ or name O or name CB )) or resid 282 through 287 or (resid 288 and (name N or na \ me CA or name C or name O or name CB )) or resid 289 through 293 or (resid 294 a \ nd (name N or name CA or name C or name O or name CB )) or resid 295 through 306 \ or (resid 307 through 308 and (name N or name CA or name C or name O or name CB \ )) or resid 313 through 317 or (resid 318 and (name N or name CA or name C or n \ ame O or name CB )) or resid 319 through 331 or (resid 332 and (name N or name C \ A or name C or name O or name CB )) or resid 333 through 335 or (resid 336 and ( \ name N or name CA or name C or name O or name CB )) or resid 337 through 368 or \ (resid 369 through 370 and (name N or name CA or name C or name O or name CB )) \ or resid 371 through 398 or (resid 399 and (name N or name CA or name C or name \ O or name CB )) or resid 400 or (resid 401 through 402 and (name N or name CA or \ name C or name O or name CB )) or resid 403 through 411 or (resid 412 through 4 \ 14 and (name N or name CA or name C or name O or name CB )) or resid 415 through \ 423 or (resid 424 and (name N or name CA or name C or name O or name CB )) or r \ esid 425 or (resid 426 through 427 and (name N or name CA or name C or name O or \ name CB )) or resid 428 through 429 or (resid 430 and (name N or name CA or nam \ e C or name O or name CB )))) selection = (chain 'E' and ((resid 1 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 18 or (resid 19 through 20 and (na \ me N or name CA or name C or name O or name CB )) or resid 21 through 22 or (res \ id 23 and (name N or name CA or name C or name O or name CB )) or resid 24 throu \ gh 28 or (resid 29 and (name N or name CA or name C or name O or name CB )) or r \ esid 30 through 33 or (resid 34 and (name N or name CA or name C or name O or na \ me CB )) or resid 35 through 36 or (resid 37 and (name N or name CA or name C or \ name O or name CB )) or resid 38 through 51 or (resid 52 and (name N or name CA \ or name C or name O or name CB )) or resid 53 through 64 or (resid 65 and (name \ N or name CA or name C or name O or name CB )) or resid 66 through 68 or (resid \ 69 through 70 and (name N or name CA or name C or name O or name CB )) or resid \ 71 through 73 or (resid 74 and (name N or name CA or name C or name O or name C \ B )) or resid 75 through 82 or (resid 83 through 84 and (name N or name CA or na \ me C or name O or name CB )) or resid 85 or (resid 86 and (name N or name CA or \ name C or name O or name CB )) or resid 87 through 90 or (resid 91 and (name N o \ r name CA or name C or name O or name CB )) or resid 92 through 97 or (resid 98 \ through 99 and (name N or name CA or name C or name O or name CB )) or resid 100 \ through 104 or (resid 105 and (name N or name CA or name C or name O or name CB \ )) or resid 115 through 141 or (resid 142 through 143 and (name N or name CA or \ name C or name O or name CB )) or resid 144 through 188 or (resid 189 through 1 \ 90 and (name N or name CA or name C or name O or name CB )) or resid 191 or (res \ id 192 through 193 and (name N or name CA or name C or name O or name CB )) or r \ esid 194 through 195 or (resid 196 and (name N or name CA or name C or name O or \ name CB )) or resid 197 through 199 or (resid 200 and (name N or name CA or nam \ e C or name O or name CB )) or resid 201 through 205 or (resid 206 through 209 a \ nd (name N or name CA or name C or name O or name CB )) or resid 210 through 217 \ or (resid 218 and (name N or name CA or name C or name O or name CB )) or resid \ 219 through 222 or (resid 223 and (name N or name CA or name C or name O or nam \ e CB )) or resid 224 through 235 or (resid 236 and (name N or name CA or name C \ or name O or name CB )) or resid 237 through 242 or (resid 243 through 244 and ( \ name N or name CA or name C or name O or name CB )) or resid 245 through 253 or \ (resid 254 and (name N or name CA or name C or name O or name CB )) or resid 255 \ through 256 or (resid 257 through 258 and (name N or name CA or name C or name \ O or name CB )) or resid 259 through 260 or (resid 261 and (name N or name CA or \ name C or name O or name CB )) or resid 262 through 267 or (resid 268 through 2 \ 69 and (name N or name CA or name C or name O or name CB )) or resid 270 through \ 271 or (resid 272 through 273 and (name N or name CA or name C or name O or nam \ e CB )) or resid 274 through 280 or (resid 281 and (name N or name CA or name C \ or name O or name CB )) or resid 282 through 287 or (resid 288 and (name N or na \ me CA or name C or name O or name CB )) or resid 289 through 293 or (resid 294 a \ nd (name N or name CA or name C or name O or name CB )) or resid 295 through 306 \ or (resid 307 through 308 and (name N or name CA or name C or name O or name CB \ )) or resid 313 through 317 or (resid 318 and (name N or name CA or name C or n \ ame O or name CB )) or resid 319 through 331 or (resid 332 and (name N or name C \ A or name C or name O or name CB )) or resid 333 through 335 or (resid 336 and ( \ name N or name CA or name C or name O or name CB )) or resid 337 through 368 or \ (resid 369 through 370 and (name N or name CA or name C or name O or name CB )) \ or resid 371 through 398 or (resid 399 and (name N or name CA or name C or name \ O or name CB )) or resid 400 or (resid 401 through 402 and (name N or name CA or \ name C or name O or name CB )) or resid 403 through 411 or (resid 412 through 4 \ 14 and (name N or name CA or name C or name O or name CB )) or resid 415 through \ 423 or (resid 424 and (name N or name CA or name C or name O or name CB )) or r \ esid 425 or (resid 426 through 427 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or name O or name CB )) or resid 415 through \ 423 or (resid 424 and (name N or name CA or name C or name O or name CB )) or r \ esid 425 or (resid 426 through 427 and (name N or name CA or name C or name O or \ name CB )) or resid 428 through 429 or (resid 430 and (name N or name CA or nam \ e C or name O or name CB )))) selection = (chain 'K' and ((resid 1 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 18 or (resid 19 through 20 and (na \ me N or name CA or name C or name O or name CB )) or resid 21 through 22 or (res \ id 23 and (name N or name CA or name C or name O or name CB )) or resid 24 throu \ gh 28 or (resid 29 and (name N or name CA or name C or name O or name CB )) or r \ esid 30 through 33 or (resid 34 and (name N or name CA or name C or name O or na \ me CB )) or resid 35 through 36 or (resid 37 and (name N or name CA or name C or \ name O or name CB )) or resid 38 through 51 or (resid 52 and (name N or name CA \ or name C or name O or name CB )) or resid 53 through 64 or (resid 65 and (name \ N or name CA or name C or name O or name CB )) or resid 66 through 68 or (resid \ 69 through 70 and (name N or name CA or name C or name O or name CB )) or resid \ 71 through 73 or (resid 74 and (name N or name CA or name C or name O or name C \ B )) or resid 75 through 82 or (resid 83 through 84 and (name N or name CA or na \ me C or name O or name CB )) or resid 85 or (resid 86 and (name N or name CA or \ name C or name O or name CB )) or resid 87 through 90 or (resid 91 and (name N o \ r name CA or name C or name O or name CB )) or resid 92 through 97 or (resid 98 \ through 99 and (name N or name CA or name C or name O or name CB )) or resid 100 \ through 104 or (resid 105 and (name N or name CA or name C or name O or name CB \ )) or resid 115 through 141 or (resid 142 through 143 and (name N or name CA or \ name C or name O or name CB )) or resid 144 through 188 or (resid 189 through 1 \ 90 and (name N or name CA or name C or name O or name CB )) or resid 191 or (res \ id 192 through 193 and (name N or name CA or name C or name O or name CB )) or r \ esid 194 through 195 or (resid 196 and (name N or name CA or name C or name O or \ name CB )) or resid 197 through 199 or (resid 200 and (name N or name CA or nam \ e C or name O or name CB )) or resid 201 through 205 or (resid 206 through 209 a \ nd (name N or name CA or name C or name O or name CB )) or resid 210 through 217 \ or (resid 218 and (name N or name CA or name C or name O or name CB )) or resid \ 219 through 222 or (resid 223 and (name N or name CA or name C or name O or nam \ e CB )) or resid 224 through 235 or (resid 236 and (name N or name CA or name C \ or name O or name CB )) or resid 237 through 242 or (resid 243 through 244 and ( \ name N or name CA or name C or name O or name CB )) or resid 245 through 253 or \ (resid 254 and (name N or name CA or name C or name O or name CB )) or resid 255 \ through 256 or (resid 257 through 258 and (name N or name CA or name C or name \ O or name CB )) or resid 259 through 260 or (resid 261 and (name N or name CA or \ name C or name O or name CB )) or resid 262 through 267 or (resid 268 through 2 \ 69 and (name N or name CA or name C or name O or name CB )) or resid 270 through \ 271 or (resid 272 through 273 and (name N or name CA or name C or name O or nam \ e CB )) or resid 274 through 280 or (resid 281 and (name N or name CA or name C \ or name O or name CB )) or resid 282 through 287 or (resid 288 and (name N or na \ me CA or name C or name O or name CB )) or resid 289 through 293 or (resid 294 a \ nd (name N or name CA or name C or name O or name CB )) or resid 295 through 306 \ or (resid 307 through 308 and (name N or name CA or name C or name O or name CB \ )) or resid 313 through 317 or (resid 318 and (name N or name CA or name C or n \ ame O or name CB )) or resid 319 through 331 or (resid 332 and (name N or name C \ A or name C or name O or name CB )) or resid 333 through 335 or (resid 336 and ( \ name N or name CA or name C or name O or name CB )) or resid 337 through 368 or \ (resid 369 through 370 and (name N or name CA or name C or name O or name CB )) \ or resid 371 through 398 or (resid 399 and (name N or name CA or name C or name \ O or name CB )) or resid 400 or (resid 401 through 402 and (name N or name CA or \ name C or name O or name CB )) or resid 403 through 411 or (resid 412 through 4 \ 14 and (name N or name CA or name C or name O or name CB )) or resid 415 through \ 423 or (resid 424 and (name N or name CA or name C or name O or name CB )) or r \ esid 425 or (resid 426 through 427 and (name N or name CA or name C or name O or \ name CB )) or resid 428 through 429 or (resid 430 and (name N or name CA or nam \ e C or name O or name CB )))) selection = (chain 'L' and ((resid 1 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 22 or (resid 23 and (name N or name \ CA or name C or name O or name CB )) or resid 24 through 28 or (resid 29 and (na \ me N or name CA or name C or name O or name CB )) or resid 30 through 33 or (res \ id 34 and (name N or name CA or name C or name O or name CB )) or resid 35 throu \ gh 51 or (resid 52 and (name N or name CA or name C or name O or name CB )) or r \ esid 53 through 62 or (resid 63 through 65 and (name N or name CA or name C or n \ ame O or name CB )) or resid 66 through 68 or (resid 69 through 70 and (name N o \ r name CA or name C or name O or name CB )) or resid 71 through 73 or (resid 74 \ and (name N or name CA or name C or name O or name CB )) or resid 75 through 90 \ or (resid 91 and (name N or name CA or name C or name O or name CB )) or resid 9 \ 2 through 98 or (resid 99 and (name N or name CA or name C or name O or name CB \ )) or resid 100 through 104 or (resid 105 and (name N or name CA or name C or na \ me O or name CB )) or resid 115 through 130 or (resid 131 and (name N or name CA \ or name C or name O or name CB )) or resid 132 through 141 or (resid 142 throug \ h 143 and (name N or name CA or name C or name O or name CB )) or resid 144 thro \ ugh 189 or (resid 190 and (name N or name CA or name C or name O or name CB )) o \ r resid 191 or (resid 192 through 193 and (name N or name CA or name C or name O \ or name CB )) or resid 194 through 195 or (resid 196 and (name N or name CA or \ name C or name O or name CB )) or resid 197 through 199 or (resid 200 and (name \ N or name CA or name C or name O or name CB )) or resid 201 through 205 or (resi \ d 206 through 209 and (name N or name CA or name C or name O or name CB )) or re \ sid 210 through 217 or (resid 218 and (name N or name CA or name C or name O or \ name CB )) or resid 219 through 222 or (resid 223 and (name N or name CA or name \ C or name O or name CB )) or resid 224 through 235 or (resid 236 and (name N or \ name CA or name C or name O or name CB )) or resid 237 through 243 or (resid 24 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 245 through \ 260 or (resid 261 and (name N or name CA or name C or name O or name CB )) or re \ sid 262 through 267 or (resid 268 through 269 and (name N or name CA or name C o \ r name O or name CB )) or resid 270 through 271 or (resid 272 through 273 and (n \ ame N or name CA or name C or name O or name CB )) or resid 274 through 280 or ( \ resid 281 and (name N or name CA or name C or name O or name CB )) or resid 282 \ through 287 or (resid 288 and (name N or name CA or name C or name O or name CB \ )) or resid 289 through 293 or (resid 294 and (name N or name CA or name C or na \ me O or name CB )) or resid 295 through 307 or (resid 308 and (name N or name CA \ or name C or name O or name CB )) or resid 313 through 317 or (resid 318 and (n \ ame N or name CA or name C or name O or name CB )) or resid 319 through 331 or ( \ resid 332 and (name N or name CA or name C or name O or name CB )) or resid 333 \ through 398 or (resid 399 and (name N or name CA or name C or name O or name CB \ )) or resid 400 or (resid 401 through 402 and (name N or name CA or name C or na \ me O or name CB )) or resid 403 through 411 or (resid 412 through 414 and (name \ N or name CA or name C or name O or name CB )) or resid 415 through 423 or (resi \ d 424 and (name N or name CA or name C or name O or name CB )) or resid 425 or ( \ resid 426 through 427 and (name N or name CA or name C or name O or name CB )) o \ r resid 428 through 429 or (resid 430 and (name N or name CA or name C or name O \ or name CB )))) } 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: 21.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.010 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 39.440 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.110 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:1.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5860 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 : 0.003 0.312 38010 Z= 0.150 Angle : 0.685 57.715 51722 Z= 0.350 Chirality : 0.042 0.207 6164 Planarity : 0.003 0.049 6823 Dihedral : 16.226 88.464 13571 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.26 % Favored : 96.70 % Rotamer: Outliers : 1.23 % Allowed : 23.72 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.13), residues: 4993 helix: 1.40 (0.12), residues: 2004 sheet: -0.83 (0.19), residues: 876 loop : -0.88 (0.13), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 69 TYR 0.031 0.001 TYR H 380 PHE 0.012 0.001 PHE B 4 HIS 0.010 0.000 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 (38004) covalent geometry : angle 0.60872 / 0.32 (51710) SS BOND : bond 0.14560 / 7.40 ( 6) SS BOND : angle 20.60140 / 14.16 ( 12) hydrogen bonds : bond 0.12616 / 8.49 ( 1608) hydrogen bonds : angle 6.21909 / 4.46 ( 4608) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 575 time to evaluate : 1.457 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: C 5 ASP cc_start: 0.1137 (OUTLIER) cc_final: 0.0056 (m-30) REVERT: C 121 ASP cc_start: 0.8302 (t0) cc_final: 0.7762 (p0) REVERT: C 166 LYS cc_start: 0.8616 (tmmt) cc_final: 0.8340 (tttp) REVERT: C 373 ARG cc_start: 0.9396 (mtt-85) cc_final: 0.9041 (mmm-85) REVERT: E 255 TYR cc_start: 0.7147 (t80) cc_final: 0.6924 (t80) REVERT: E 402 ASP cc_start: 0.8155 (m-30) cc_final: 0.7908 (m-30) REVERT: F 319 ILE cc_start: 0.9379 (mm) cc_final: 0.9139 (mt) REVERT: G 18 LEU cc_start: 0.8981 (mt) cc_final: 0.8779 (mp) REVERT: G 333 LEU cc_start: 0.9268 (mm) cc_final: 0.9032 (mm) REVERT: H 12 ARG cc_start: 0.8421 (ptp-110) cc_final: 0.7438 (ttp80) REVERT: H 18 LEU cc_start: 0.8806 (mt) cc_final: 0.8507 (mp) REVERT: H 252 MET cc_start: 0.8633 (mmm) cc_final: 0.8238 (tpp) REVERT: J 52 LYS cc_start: 0.7281 (mtpp) cc_final: 0.6438 (tppt) REVERT: J 53 GLU cc_start: 0.6483 (pm20) cc_final: 0.6168 (tp30) REVERT: J 174 MET cc_start: 0.3199 (tpt) cc_final: 0.2982 (mmm) REVERT: J 396 HIS cc_start: 0.3995 (p-80) cc_final: 0.3242 (t70) REVERT: K 394 ASN cc_start: 0.7411 (m110) cc_final: 0.7097 (m-40) REVERT: L 18 LEU cc_start: 0.8647 (mt) cc_final: 0.8419 (mp) REVERT: L 145 ASP cc_start: 0.7705 (m-30) cc_final: 0.7250 (p0) outliers start: 47 outliers final: 10 residues processed: 614 average time/residue: 0.2340 time to fit residues: 232.2367 Evaluate side-chains 376 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 365 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 38 CYS Chi-restraints excluded: chain I residue 38 CYS Chi-restraints excluded: chain J residue 38 CYS Chi-restraints excluded: chain J residue 345 LEU Chi-restraints excluded: chain L residue 38 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: [432, 197, 388, 455, 215, 20, 132, 494, 261, 248, 207] chunk 432 optimal weight: 0.9990 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 9.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 8.9990 chunk 494 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 HIS A 23 HIS B 23 HIS B 362 GLN C 55 GLN C 430 ASN ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 332 GLN D 338 HIS E 14 HIS E 55 GLN E 241 GLN F 55 GLN ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 14 HIS I 55 GLN I 360 HIS I 409 GLN ** J 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 GLN J 94 ASN J 326 HIS J 409 GLN K 9 HIS K 14 HIS K 55 GLN K 394 ASN L 55 GLN ** L 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 430 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.137305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.110511 restraints weight = 124164.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.108150 restraints weight = 74437.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.108486 restraints weight = 62111.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.108321 restraints weight = 49338.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.108510 restraints weight = 45170.579| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.121 38010 Z= 0.250 Angle : 0.654 16.661 51722 Z= 0.330 Chirality : 0.044 0.285 6164 Planarity : 0.004 0.044 6823 Dihedral : 4.384 55.099 5437 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.21 % Favored : 94.77 % Rotamer: Outliers : 4.30 % Allowed : 23.69 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.13), residues: 4993 helix: 1.84 (0.13), residues: 1833 sheet: -1.08 (0.18), residues: 1011 loop : -0.67 (0.14), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 190 TYR 0.024 0.002 TYR E 302 PHE 0.020 0.002 PHE C 407 HIS 0.037 0.001 HIS D 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.25 (38004) covalent geometry : angle 0.65388 / 0.33 (51710) SS BOND : bond 0.00616 / 0.32 ( 6) SS BOND : angle 1.77106 / 1.07 ( 12) hydrogen bonds : bond 0.03704 / 2.55 ( 1608) hydrogen bonds : angle 5.08972 / 3.63 ( 4608) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 335 time to evaluate : 1.514 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: B 29 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7949 (tt0) REVERT: C 373 ARG cc_start: 0.9423 (mtt-85) cc_final: 0.8954 (mmm-85) REVERT: C 398 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8672 (mt) REVERT: D 84 MET cc_start: 0.6224 (mmt) cc_final: 0.5791 (mtt) REVERT: D 302 TYR cc_start: 0.8614 (m-80) cc_final: 0.7947 (m-10) REVERT: D 326 HIS cc_start: 0.8458 (p-80) cc_final: 0.7511 (p-80) REVERT: E 91 LYS cc_start: 0.8264 (mttp) cc_final: 0.7982 (mtpt) REVERT: E 252 MET cc_start: 0.8809 (mmm) cc_final: 0.8520 (mmt) REVERT: E 255 TYR cc_start: 0.9197 (t80) cc_final: 0.8883 (t80) REVERT: E 328 TYR cc_start: 0.8738 (t80) cc_final: 0.8381 (m-80) REVERT: E 402 ASP cc_start: 0.8934 (m-30) cc_final: 0.8687 (m-30) REVERT: F 319 ILE cc_start: 0.9451 (mm) cc_final: 0.9154 (mt) REVERT: G 156 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8332 (ttm) REVERT: H 45 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8430 (mtmm) REVERT: H 52 LYS cc_start: 0.8996 (mmmm) cc_final: 0.8748 (mmmm) REVERT: H 53 GLU cc_start: 0.8863 (pm20) cc_final: 0.8497 (pm20) REVERT: H 69 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8639 (ttt180) REVERT: H 93 TYR cc_start: 0.8638 (m-80) cc_final: 0.8058 (m-10) REVERT: H 156 MET cc_start: 0.8328 (tpp) cc_final: 0.8094 (tpp) REVERT: H 166 LYS cc_start: 0.8819 (ptmm) cc_final: 0.8592 (tttp) REVERT: H 252 MET cc_start: 0.9041 (mmm) cc_final: 0.8607 (tpp) REVERT: H 318 GLU cc_start: 0.9061 (tp30) cc_final: 0.8853 (tp30) REVERT: H 374 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.9018 (mt) REVERT: I 172 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.9000 (mmp) REVERT: I 257 ARG cc_start: 0.9356 (mtt90) cc_final: 0.9033 (mmm-85) REVERT: I 294 GLN cc_start: 0.4114 (OUTLIER) cc_final: -0.1065 (tp40) REVERT: I 315 ILE cc_start: 0.9257 (mm) cc_final: 0.9046 (pt) REVERT: I 328 TYR cc_start: 0.8185 (t80) cc_final: 0.7769 (t80) REVERT: I 412 MET cc_start: 0.5713 (mmp) cc_final: 0.5501 (mmp) REVERT: J 199 HIS cc_start: 0.5960 (m170) cc_final: 0.5625 (m-70) REVERT: J 396 HIS cc_start: 0.3989 (p-80) cc_final: 0.3337 (t70) REVERT: K 169 LEU cc_start: 0.9334 (tp) cc_final: 0.9022 (mt) REVERT: K 170 MET cc_start: 0.9342 (mtt) cc_final: 0.9029 (mpp) REVERT: K 181 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7750 (tt) REVERT: L 145 ASP cc_start: 0.7962 (m-30) cc_final: 0.7599 (p0) REVERT: L 156 MET cc_start: 0.8414 (tpt) cc_final: 0.8087 (tpt) outliers start: 164 outliers final: 75 residues processed: 481 average time/residue: 0.2180 time to fit residues: 174.5949 Evaluate side-chains 386 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 302 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 295 HIS Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 315 ILE Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 225 CYS Chi-restraints excluded: chain G residue 295 HIS Chi-restraints excluded: chain H residue 7 CYS Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 69 ARG Chi-restraints excluded: chain H residue 150 CYS Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 225 CYS Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 374 LEU Chi-restraints excluded: chain I residue 38 CYS Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 172 MET Chi-restraints excluded: chain I residue 294 GLN Chi-restraints excluded: chain I residue 427 GLU Chi-restraints excluded: chain J residue 12 ARG Chi-restraints excluded: chain J residue 23 HIS Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 38 CYS Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 94 ASN Chi-restraints excluded: chain J residue 118 CYS Chi-restraints excluded: chain J residue 326 HIS Chi-restraints excluded: chain J residue 382 ASP Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 181 ILE Chi-restraints excluded: chain K residue 304 VAL Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 225 CYS Chi-restraints excluded: chain L residue 245 VAL Chi-restraints excluded: chain L residue 425 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: [368, 357, 428, 111, 19, 0, 396, 126, 163, 402, 146] chunk 368 optimal weight: 0.0070 chunk 357 optimal weight: 20.0000 chunk 428 optimal weight: 10.0000 chunk 111 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 396 optimal weight: 20.0000 chunk 126 optimal weight: 0.0770 chunk 163 optimal weight: 5.9990 chunk 402 optimal weight: 9.9990 chunk 146 optimal weight: 6.9990 overall best weight: 1.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 241 GLN C 241 GLN D 241 GLN E 360 HIS E 409 GLN G 241 GLN ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 241 GLN I 241 GLN ** I 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 241 GLN J 326 HIS K 87 HIS K 226 ASN L 226 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.138528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.111782 restraints weight = 124844.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.109570 restraints weight = 73061.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.110294 restraints weight = 52995.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.110476 restraints weight = 40103.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.110561 restraints weight = 37732.914| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 38010 Z= 0.132 Angle : 0.540 11.024 51722 Z= 0.270 Chirality : 0.042 0.156 6164 Planarity : 0.003 0.041 6823 Dihedral : 3.819 30.216 5425 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.03 % Favored : 95.95 % Rotamer: Outliers : 3.17 % Allowed : 23.74 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.13), residues: 4993 helix: 2.09 (0.13), residues: 1815 sheet: -1.17 (0.17), residues: 1056 loop : -0.58 (0.14), residues: 2122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 336 TYR 0.040 0.001 TYR H 380 PHE 0.013 0.001 PHE C 407 HIS 0.018 0.001 HIS D 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (38004) covalent geometry : angle 0.54025 / 0.27 (51710) SS BOND : bond 0.00264 / 0.13 ( 6) SS BOND : angle 1.00157 / 0.65 ( 12) hydrogen bonds : bond 0.02904 / 1.99 ( 1608) hydrogen bonds : angle 4.69253 / 3.35 ( 4608) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 324 time to evaluate : 1.478 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: C 121 ASP cc_start: 0.8077 (t0) cc_final: 0.7477 (p0) REVERT: C 373 ARG cc_start: 0.9416 (mtt-85) cc_final: 0.9016 (mmm-85) REVERT: D 156 MET cc_start: 0.8468 (tpp) cc_final: 0.7598 (tpp) REVERT: D 302 TYR cc_start: 0.8623 (m-80) cc_final: 0.8239 (m-10) REVERT: E 91 LYS cc_start: 0.8235 (mttp) cc_final: 0.8016 (mtpt) REVERT: E 193 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: E 252 MET cc_start: 0.8868 (mmm) cc_final: 0.8471 (mmt) REVERT: E 328 TYR cc_start: 0.8759 (t80) cc_final: 0.8384 (m-80) REVERT: E 402 ASP cc_start: 0.8904 (m-30) cc_final: 0.8699 (m-30) REVERT: F 319 ILE cc_start: 0.9404 (mm) cc_final: 0.9118 (mt) REVERT: G 14 HIS cc_start: 0.6803 (OUTLIER) cc_final: 0.6121 (m170) REVERT: H 52 LYS cc_start: 0.8966 (mmmm) cc_final: 0.8760 (mmmm) REVERT: H 53 GLU cc_start: 0.8759 (pm20) cc_final: 0.8349 (pm20) REVERT: H 93 TYR cc_start: 0.8513 (m-80) cc_final: 0.7850 (m-10) REVERT: H 156 MET cc_start: 0.8340 (tpp) cc_final: 0.8130 (tpp) REVERT: H 166 LYS cc_start: 0.8737 (ptmm) cc_final: 0.8399 (tttp) REVERT: I 93 TYR cc_start: 0.8512 (m-80) cc_final: 0.7991 (m-80) REVERT: I 172 MET cc_start: 0.9223 (OUTLIER) cc_final: 0.8611 (mmp) REVERT: I 257 ARG cc_start: 0.9360 (mtt90) cc_final: 0.8991 (mmm-85) REVERT: I 328 TYR cc_start: 0.8215 (t80) cc_final: 0.7745 (t80) REVERT: J 129 LEU cc_start: 0.7947 (mt) cc_final: 0.7658 (pp) REVERT: J 170 MET cc_start: 0.5199 (tmm) cc_final: 0.4994 (tpt) REVERT: J 199 HIS cc_start: 0.6090 (m170) cc_final: 0.5796 (m-70) REVERT: J 288 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7178 (tt0) REVERT: J 371 LEU cc_start: 0.2034 (OUTLIER) cc_final: 0.1119 (tt) REVERT: J 396 HIS cc_start: 0.4029 (p-80) cc_final: 0.3426 (t70) REVERT: K 170 MET cc_start: 0.9305 (mtt) cc_final: 0.9081 (mtt) REVERT: L 145 ASP cc_start: 0.8028 (m-30) cc_final: 0.7621 (p0) REVERT: L 226 ASN cc_start: 0.9111 (OUTLIER) cc_final: 0.8786 (t0) outliers start: 121 outliers final: 60 residues processed: 429 average time/residue: 0.2082 time to fit residues: 150.0180 Evaluate side-chains 371 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 306 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 295 HIS Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 315 ILE Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 225 CYS Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 295 HIS Chi-restraints excluded: chain H residue 7 CYS Chi-restraints excluded: chain H residue 150 CYS Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 345 LEU Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 172 MET Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 240 ASP Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 326 HIS Chi-restraints excluded: chain J residue 371 LEU Chi-restraints excluded: chain J residue 381 LEU Chi-restraints excluded: chain J residue 382 ASP Chi-restraints excluded: chain J residue 383 LEU Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 226 ASN Chi-restraints excluded: chain K residue 304 VAL Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 225 CYS Chi-restraints excluded: chain L residue 226 ASN Chi-restraints excluded: chain L residue 245 VAL Chi-restraints excluded: chain L residue 303 THR Chi-restraints excluded: chain L residue 425 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: [18, 195, 239, 262, 3, 287, 121, 286, 403, 320, 89] chunk 18 optimal weight: 0.7980 chunk 195 optimal weight: 0.6980 chunk 239 optimal weight: 4.9990 chunk 262 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 287 optimal weight: 1.9990 chunk 121 optimal weight: 8.9990 chunk 286 optimal weight: 6.9990 chunk 403 optimal weight: 4.9990 chunk 320 optimal weight: 0.5980 chunk 89 optimal weight: 7.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 14 HIS ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 94 ASN ** J 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 241 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.138335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.110957 restraints weight = 125787.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.109351 restraints weight = 73219.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.108992 restraints weight = 58089.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.109116 restraints weight = 43333.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.109336 restraints weight = 38214.165| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 38010 Z= 0.124 Angle : 0.531 10.743 51722 Z= 0.264 Chirality : 0.042 0.256 6164 Planarity : 0.003 0.060 6823 Dihedral : 3.661 23.670 5420 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.43 % Favored : 95.55 % Rotamer: Outliers : 3.30 % Allowed : 23.35 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.13), residues: 4993 helix: 1.92 (0.13), residues: 1857 sheet: -1.08 (0.18), residues: 1014 loop : -0.71 (0.14), residues: 2122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 12 TYR 0.041 0.001 TYR C 380 PHE 0.011 0.001 PHE C 407 HIS 0.016 0.001 HIS D 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (38004) covalent geometry : angle 0.53066 / 0.26 (51710) SS BOND : bond 0.00290 / 0.18 ( 6) SS BOND : angle 0.96260 / 0.61 ( 12) hydrogen bonds : bond 0.02727 / 1.88 ( 1608) hydrogen bonds : angle 4.56045 / 3.25 ( 4608) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 317 time to evaluate : 1.461 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: C 121 ASP cc_start: 0.8056 (t0) cc_final: 0.7499 (p0) REVERT: C 428 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8611 (tt) REVERT: D 156 MET cc_start: 0.8634 (tpp) cc_final: 0.7850 (tpp) REVERT: D 264 LEU cc_start: 0.9128 (mt) cc_final: 0.8692 (pp) REVERT: D 288 GLU cc_start: 0.9150 (tp30) cc_final: 0.8751 (tp30) REVERT: D 302 TYR cc_start: 0.8802 (m-80) cc_final: 0.8418 (m-10) REVERT: D 428 LEU cc_start: 0.6415 (OUTLIER) cc_final: 0.6003 (mm) REVERT: E 18 LEU cc_start: 0.9336 (mt) cc_final: 0.9002 (mp) REVERT: E 29 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7523 (tp30) REVERT: E 91 LYS cc_start: 0.8275 (mttp) cc_final: 0.8012 (mtpt) REVERT: E 193 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7769 (mp0) REVERT: E 252 MET cc_start: 0.8961 (mmm) cc_final: 0.8512 (mmt) REVERT: F 319 ILE cc_start: 0.9399 (mm) cc_final: 0.9135 (mt) REVERT: G 14 HIS cc_start: 0.6526 (OUTLIER) cc_final: 0.5372 (m170) REVERT: H 93 TYR cc_start: 0.8493 (m-80) cc_final: 0.7836 (m-10) REVERT: H 156 MET cc_start: 0.8335 (tpp) cc_final: 0.8113 (tpp) REVERT: H 166 LYS cc_start: 0.8662 (ptmm) cc_final: 0.8322 (tttp) REVERT: H 374 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8964 (mt) REVERT: I 93 TYR cc_start: 0.8623 (m-80) cc_final: 0.8105 (m-80) REVERT: I 252 MET cc_start: 0.8783 (tpp) cc_final: 0.8562 (tmm) REVERT: I 302 TYR cc_start: 0.7266 (m-10) cc_final: 0.6877 (m-10) REVERT: J 57 ILE cc_start: 0.2810 (OUTLIER) cc_final: 0.2381 (mt) REVERT: J 84 MET cc_start: 0.3325 (mmt) cc_final: 0.2959 (mmt) REVERT: J 129 LEU cc_start: 0.7978 (mt) cc_final: 0.7707 (mp) REVERT: J 199 HIS cc_start: 0.6114 (m170) cc_final: 0.5814 (m-70) REVERT: J 288 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7250 (tt0) REVERT: J 371 LEU cc_start: 0.2130 (OUTLIER) cc_final: 0.1222 (tt) REVERT: K 170 MET cc_start: 0.9321 (mtt) cc_final: 0.9015 (mpp) REVERT: L 121 ASP cc_start: 0.8431 (t0) cc_final: 0.7668 (p0) REVERT: L 145 ASP cc_start: 0.8074 (m-30) cc_final: 0.7660 (p0) outliers start: 126 outliers final: 84 residues processed: 422 average time/residue: 0.2105 time to fit residues: 149.7656 Evaluate side-chains 393 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 301 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 396 HIS Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 295 HIS Chi-restraints excluded: chain E residue 430 ASN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 174 MET Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 225 CYS Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 174 MET Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 295 HIS Chi-restraints excluded: chain H residue 7 CYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 345 LEU Chi-restraints excluded: chain H residue 374 LEU Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 315 ILE Chi-restraints excluded: chain J residue 12 ARG Chi-restraints excluded: chain J residue 23 HIS Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 94 ASN Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 240 ASP Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 326 HIS Chi-restraints excluded: chain J residue 371 LEU Chi-restraints excluded: chain J residue 381 LEU Chi-restraints excluded: chain J residue 382 ASP Chi-restraints excluded: chain J residue 383 LEU Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 181 ILE Chi-restraints excluded: chain K residue 225 CYS Chi-restraints excluded: chain K residue 304 VAL Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 225 CYS Chi-restraints excluded: chain L residue 245 VAL Chi-restraints excluded: chain L residue 303 THR Chi-restraints excluded: chain L residue 425 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: [339, 262, 269, 442, 256, 22, 236, 472, 487, 21, 462] chunk 339 optimal weight: 9.9990 chunk 262 optimal weight: 9.9990 chunk 269 optimal weight: 5.9990 chunk 442 optimal weight: 5.9990 chunk 256 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 236 optimal weight: 0.4980 chunk 472 optimal weight: 0.7980 chunk 487 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 462 optimal weight: 0.0570 overall best weight: 1.2702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 409 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 360 HIS G 226 ASN ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 326 HIS ** J 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.138268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.110463 restraints weight = 124839.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.108518 restraints weight = 70568.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.109151 restraints weight = 51452.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.108932 restraints weight = 42243.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.109088 restraints weight = 38584.636| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 38010 Z= 0.116 Angle : 0.520 11.120 51722 Z= 0.258 Chirality : 0.041 0.290 6164 Planarity : 0.003 0.045 6823 Dihedral : 3.581 23.007 5420 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.09 % Favored : 95.89 % Rotamer: Outliers : 3.43 % Allowed : 23.85 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.13), residues: 4993 helix: 1.93 (0.13), residues: 1868 sheet: -1.08 (0.18), residues: 956 loop : -0.67 (0.14), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 320 TYR 0.042 0.001 TYR C 380 PHE 0.010 0.001 PHE C 407 HIS 0.022 0.001 HIS D 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (38004) covalent geometry : angle 0.52033 / 0.26 (51710) SS BOND : bond 0.00491 / 0.26 ( 6) SS BOND : angle 0.82777 / 0.54 ( 12) hydrogen bonds : bond 0.02622 / 1.80 ( 1608) hydrogen bonds : angle 4.46409 / 3.19 ( 4608) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 318 time to evaluate : 1.444 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: C 121 ASP cc_start: 0.8042 (t0) cc_final: 0.7523 (p0) REVERT: C 428 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8619 (tt) REVERT: D 84 MET cc_start: 0.3936 (mtt) cc_final: 0.3298 (ptp) REVERT: D 156 MET cc_start: 0.8526 (tpp) cc_final: 0.8144 (tpp) REVERT: D 252 MET cc_start: 0.8930 (mmm) cc_final: 0.7949 (mmp) REVERT: D 264 LEU cc_start: 0.9160 (mt) cc_final: 0.8794 (pp) REVERT: D 288 GLU cc_start: 0.9143 (tp30) cc_final: 0.8733 (tp30) REVERT: D 302 TYR cc_start: 0.8758 (m-80) cc_final: 0.8249 (m-10) REVERT: D 428 LEU cc_start: 0.6537 (OUTLIER) cc_final: 0.6217 (mm) REVERT: E 18 LEU cc_start: 0.9343 (mt) cc_final: 0.9006 (mp) REVERT: E 29 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7531 (tp30) REVERT: E 91 LYS cc_start: 0.8271 (mttp) cc_final: 0.8009 (mtpt) REVERT: E 172 MET cc_start: 0.9349 (mtp) cc_final: 0.9011 (mpp) REVERT: E 193 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7786 (mp0) REVERT: E 252 MET cc_start: 0.8979 (mmm) cc_final: 0.8474 (mmt) REVERT: F 319 ILE cc_start: 0.9393 (mm) cc_final: 0.9138 (mt) REVERT: F 371 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9352 (mm) REVERT: H 93 TYR cc_start: 0.8444 (m-80) cc_final: 0.7624 (m-10) REVERT: H 156 MET cc_start: 0.8355 (tpp) cc_final: 0.7982 (tpp) REVERT: H 166 LYS cc_start: 0.8602 (ptmm) cc_final: 0.8208 (tttp) REVERT: H 412 MET cc_start: 0.8390 (mmp) cc_final: 0.8166 (mmp) REVERT: I 93 TYR cc_start: 0.8618 (m-80) cc_final: 0.7694 (m-80) REVERT: I 166 LYS cc_start: 0.9083 (ptmt) cc_final: 0.8863 (ptmt) REVERT: I 172 MET cc_start: 0.9097 (mmp) cc_final: 0.8774 (mmp) REVERT: I 252 MET cc_start: 0.8863 (tpp) cc_final: 0.8515 (tmm) REVERT: I 302 TYR cc_start: 0.7095 (m-10) cc_final: 0.6833 (m-10) REVERT: J 57 ILE cc_start: 0.3326 (OUTLIER) cc_final: 0.2971 (mt) REVERT: J 84 MET cc_start: 0.3992 (mmt) cc_final: 0.3242 (mmt) REVERT: J 129 LEU cc_start: 0.8005 (mt) cc_final: 0.7761 (mp) REVERT: J 199 HIS cc_start: 0.6175 (m170) cc_final: 0.5861 (m-70) REVERT: J 234 MET cc_start: -0.1516 (tmm) cc_final: -0.2997 (mmm) REVERT: J 288 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7192 (tt0) REVERT: J 371 LEU cc_start: 0.2184 (OUTLIER) cc_final: 0.1262 (tt) REVERT: J 396 HIS cc_start: 0.4368 (p-80) cc_final: 0.3648 (t70) REVERT: L 121 ASP cc_start: 0.8455 (t0) cc_final: 0.7670 (p0) REVERT: L 145 ASP cc_start: 0.8090 (m-30) cc_final: 0.7692 (p0) outliers start: 131 outliers final: 93 residues processed: 429 average time/residue: 0.2154 time to fit residues: 155.5648 Evaluate side-chains 401 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 301 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 396 HIS Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 295 HIS Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 174 MET Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 225 CYS Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 315 ILE Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 174 MET Chi-restraints excluded: chain G residue 225 CYS Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 295 HIS Chi-restraints excluded: chain H residue 7 CYS Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 150 CYS Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 225 CYS Chi-restraints excluded: chain H residue 345 LEU Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 315 ILE Chi-restraints excluded: chain J residue 12 ARG Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 172 MET Chi-restraints excluded: chain J residue 240 ASP Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 371 LEU Chi-restraints excluded: chain J residue 381 LEU Chi-restraints excluded: chain J residue 382 ASP Chi-restraints excluded: chain J residue 383 LEU Chi-restraints excluded: chain K residue 166 LYS Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 181 ILE Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 304 VAL Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 234 MET Chi-restraints excluded: chain L residue 245 VAL Chi-restraints excluded: chain L residue 285 LEU Chi-restraints excluded: chain L residue 303 THR Chi-restraints excluded: chain L residue 425 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: [232, 401, 281, 68, 137, 77, 156, 370, 19, 356, 398] chunk 232 optimal weight: 4.9990 chunk 401 optimal weight: 40.0000 chunk 281 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 156 optimal weight: 20.0000 chunk 370 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 356 optimal weight: 10.0000 chunk 398 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 GLN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 GLN ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 94 ASN J 295 HIS J 326 HIS ** J 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 87 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.135782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.108238 restraints weight = 123015.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.107322 restraints weight = 77813.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.107338 restraints weight = 59728.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.107329 restraints weight = 44587.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.107827 restraints weight = 36764.477| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 38010 Z= 0.235 Angle : 0.611 15.981 51722 Z= 0.307 Chirality : 0.043 0.279 6164 Planarity : 0.004 0.098 6823 Dihedral : 4.020 32.663 5420 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.35 % Favored : 94.63 % Rotamer: Outliers : 3.67 % Allowed : 24.03 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.13), residues: 4993 helix: 1.96 (0.13), residues: 1833 sheet: -1.26 (0.18), residues: 945 loop : -0.67 (0.13), residues: 2215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 12 TYR 0.042 0.002 TYR C 380 PHE 0.019 0.001 PHE J 280 HIS 0.046 0.001 HIS D 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.23 (38004) covalent geometry : angle 0.61115 / 0.31 (51710) SS BOND : bond 0.00522 / 0.25 ( 6) SS BOND : angle 1.38456 / 0.87 ( 12) hydrogen bonds : bond 0.03257 / 2.25 ( 1608) hydrogen bonds : angle 4.68112 / 3.34 ( 4608) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 300 time to evaluate : 1.764 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: C 121 ASP cc_start: 0.8195 (t0) cc_final: 0.7697 (p0) REVERT: C 398 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8655 (mt) REVERT: D 156 MET cc_start: 0.8304 (tpp) cc_final: 0.7945 (tpp) REVERT: D 302 TYR cc_start: 0.8653 (m-80) cc_final: 0.8317 (m-10) REVERT: E 29 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7559 (tp30) REVERT: E 172 MET cc_start: 0.9318 (mtp) cc_final: 0.9020 (mpp) REVERT: E 193 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7909 (mp0) REVERT: E 252 MET cc_start: 0.8867 (mmm) cc_final: 0.8424 (mmt) REVERT: F 319 ILE cc_start: 0.9485 (mm) cc_final: 0.9273 (mt) REVERT: H 93 TYR cc_start: 0.8607 (m-80) cc_final: 0.8096 (m-10) REVERT: I 93 TYR cc_start: 0.8575 (m-80) cc_final: 0.7707 (m-80) REVERT: I 166 LYS cc_start: 0.9113 (ptmt) cc_final: 0.8847 (ptmt) REVERT: I 252 MET cc_start: 0.8790 (tpp) cc_final: 0.8458 (tmm) REVERT: J 36 ASP cc_start: 0.5967 (OUTLIER) cc_final: 0.4169 (t70) REVERT: J 84 MET cc_start: 0.4680 (mmt) cc_final: 0.4054 (mmt) REVERT: J 129 LEU cc_start: 0.8122 (mt) cc_final: 0.7877 (mp) REVERT: J 199 HIS cc_start: 0.6122 (m170) cc_final: 0.5785 (m-70) REVERT: J 288 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7061 (tt0) REVERT: J 396 HIS cc_start: 0.4431 (p-80) cc_final: 0.3857 (t70) REVERT: L 121 ASP cc_start: 0.8584 (t0) cc_final: 0.7894 (p0) REVERT: L 145 ASP cc_start: 0.8091 (m-30) cc_final: 0.7840 (p0) outliers start: 140 outliers final: 110 residues processed: 415 average time/residue: 0.2107 time to fit residues: 149.1294 Evaluate side-chains 403 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 289 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 396 HIS Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 295 HIS Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 430 ASN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 174 MET Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 225 CYS Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 315 ILE Chi-restraints excluded: chain F residue 370 MET Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain G residue 170 MET Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 174 MET Chi-restraints excluded: chain G residue 225 CYS Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain G residue 295 HIS Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain H residue 7 CYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 150 CYS Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 225 CYS Chi-restraints excluded: chain H residue 345 LEU Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 184 ILE Chi-restraints excluded: chain I residue 189 GLU Chi-restraints excluded: chain I residue 315 ILE Chi-restraints excluded: chain J residue 12 ARG Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 240 ASP Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 357 THR Chi-restraints excluded: chain J residue 381 LEU Chi-restraints excluded: chain J residue 382 ASP Chi-restraints excluded: chain J residue 383 LEU Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 166 LYS Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 181 ILE Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 304 VAL Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 225 CYS Chi-restraints excluded: chain L residue 234 MET Chi-restraints excluded: chain L residue 245 VAL Chi-restraints excluded: chain L residue 285 LEU Chi-restraints excluded: chain L residue 303 THR Chi-restraints excluded: chain L residue 319 ILE Chi-restraints excluded: chain L residue 357 THR Chi-restraints excluded: chain L residue 425 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: [16, 213, 25, 456, 174, 390, 33, 54, 492, 273, 270] chunk 16 optimal weight: 0.8980 chunk 213 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 456 optimal weight: 30.0000 chunk 174 optimal weight: 2.9990 chunk 390 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 492 optimal weight: 1.9990 chunk 273 optimal weight: 3.9990 chunk 270 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 GLN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 GLN J 94 ASN ** J 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 360 HIS L 241 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.137802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.111228 restraints weight = 124274.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.109149 restraints weight = 69934.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.110109 restraints weight = 49681.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.109727 restraints weight = 39247.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.110229 restraints weight = 35638.733| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 38010 Z= 0.113 Angle : 0.535 13.127 51722 Z= 0.263 Chirality : 0.041 0.198 6164 Planarity : 0.003 0.098 6823 Dihedral : 3.663 20.636 5420 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.21 % Favored : 95.77 % Rotamer: Outliers : 3.01 % Allowed : 25.05 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.13), residues: 4993 helix: 2.11 (0.13), residues: 1821 sheet: -1.04 (0.19), residues: 900 loop : -0.62 (0.13), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 12 TYR 0.044 0.001 TYR C 380 PHE 0.010 0.001 PHE C 407 HIS 0.013 0.001 HIS D 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (38004) covalent geometry : angle 0.53511 / 0.26 (51710) SS BOND : bond 0.00160 / 0.08 ( 6) SS BOND : angle 0.95820 / 0.63 ( 12) hydrogen bonds : bond 0.02620 / 1.80 ( 1608) hydrogen bonds : angle 4.44519 / 3.19 ( 4608) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 302 time to evaluate : 1.498 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: C 121 ASP cc_start: 0.8060 (t0) cc_final: 0.7609 (p0) REVERT: C 398 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8856 (mt) REVERT: D 156 MET cc_start: 0.8323 (tpp) cc_final: 0.7972 (tpp) REVERT: D 252 MET cc_start: 0.8780 (mmm) cc_final: 0.7629 (mmp) REVERT: D 302 TYR cc_start: 0.8644 (m-80) cc_final: 0.8329 (m-10) REVERT: E 193 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: E 252 MET cc_start: 0.8968 (mmm) cc_final: 0.8475 (mmt) REVERT: F 319 ILE cc_start: 0.9419 (mm) cc_final: 0.9206 (mt) REVERT: H 93 TYR cc_start: 0.8477 (m-80) cc_final: 0.7829 (m-10) REVERT: H 156 MET cc_start: 0.8437 (tpp) cc_final: 0.8228 (tpp) REVERT: H 166 LYS cc_start: 0.8664 (ptmt) cc_final: 0.8451 (tttp) REVERT: H 412 MET cc_start: 0.8398 (mmp) cc_final: 0.8173 (mmp) REVERT: I 93 TYR cc_start: 0.8450 (m-80) cc_final: 0.7559 (m-80) REVERT: I 166 LYS cc_start: 0.9128 (ptmt) cc_final: 0.8877 (ptmt) REVERT: I 252 MET cc_start: 0.8836 (tpp) cc_final: 0.8405 (tmm) REVERT: J 84 MET cc_start: 0.3617 (mmt) cc_final: 0.3208 (mmt) REVERT: J 129 LEU cc_start: 0.8080 (mt) cc_final: 0.7865 (mp) REVERT: J 199 HIS cc_start: 0.6156 (m170) cc_final: 0.5883 (m170) REVERT: J 262 VAL cc_start: 0.4361 (OUTLIER) cc_final: 0.4104 (t) REVERT: J 288 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7083 (tt0) REVERT: J 320 ARG cc_start: 0.5549 (mmm-85) cc_final: 0.4985 (mmm-85) REVERT: J 326 HIS cc_start: 0.2405 (p-80) cc_final: 0.1422 (p90) REVERT: J 396 HIS cc_start: 0.4441 (p-80) cc_final: 0.3837 (t70) REVERT: K 29 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7418 (tp30) REVERT: K 169 LEU cc_start: 0.9277 (tp) cc_final: 0.9020 (mt) REVERT: L 121 ASP cc_start: 0.8539 (t0) cc_final: 0.7849 (p0) REVERT: L 145 ASP cc_start: 0.8176 (m-30) cc_final: 0.7771 (p0) outliers start: 115 outliers final: 91 residues processed: 401 average time/residue: 0.2053 time to fit residues: 139.6384 Evaluate side-chains 386 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 291 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 396 HIS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 295 HIS Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 174 MET Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 225 CYS Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 315 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain G residue 170 MET Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 174 MET Chi-restraints excluded: chain G residue 225 CYS Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 295 HIS Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain H residue 7 CYS Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 218 ASP Chi-restraints excluded: chain H residue 225 CYS Chi-restraints excluded: chain H residue 345 LEU Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 184 ILE Chi-restraints excluded: chain I residue 315 ILE Chi-restraints excluded: chain J residue 12 ARG Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 94 ASN Chi-restraints excluded: chain J residue 240 ASP Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 360 HIS Chi-restraints excluded: chain J residue 381 LEU Chi-restraints excluded: chain J residue 382 ASP Chi-restraints excluded: chain J residue 383 LEU Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 166 LYS Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 181 ILE Chi-restraints excluded: chain K residue 225 CYS Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 304 VAL Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 225 CYS Chi-restraints excluded: chain L residue 245 VAL Chi-restraints excluded: chain L residue 285 LEU Chi-restraints excluded: chain L residue 303 THR Chi-restraints excluded: chain L residue 425 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: [169, 171, 118, 442, 386, 355, 173, 16, 163, 343, 322] chunk 169 optimal weight: 6.9990 chunk 171 optimal weight: 8.9990 chunk 118 optimal weight: 7.9990 chunk 442 optimal weight: 10.0000 chunk 386 optimal weight: 9.9990 chunk 355 optimal weight: 20.0000 chunk 173 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 343 optimal weight: 10.0000 chunk 322 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 2 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 HIS ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 241 GLN H 378 GLN I 9 HIS ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 94 ASN ** J 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.132910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.105951 restraints weight = 120173.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.104153 restraints weight = 77272.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.104469 restraints weight = 63659.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.104314 restraints weight = 46849.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.104820 restraints weight = 37676.959| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.5045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.284 38010 Z= 0.419 Angle : 0.800 30.522 51722 Z= 0.403 Chirality : 0.047 0.373 6164 Planarity : 0.005 0.104 6823 Dihedral : 4.741 40.283 5420 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.81 % Favored : 93.13 % Rotamer: Outliers : 4.01 % Allowed : 24.06 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.12), residues: 4993 helix: 1.53 (0.12), residues: 1835 sheet: -1.40 (0.19), residues: 882 loop : -0.93 (0.13), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 69 TYR 0.042 0.002 TYR C 380 PHE 0.024 0.002 PHE J 280 HIS 0.058 0.002 HIS D 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00930 / 0.42 (38004) covalent geometry : angle 0.79924 / 0.40 (51710) SS BOND : bond 0.00675 / 0.45 ( 6) SS BOND : angle 1.68014 / 1.06 ( 12) hydrogen bonds : bond 0.04068 / 2.81 ( 1608) hydrogen bonds : angle 5.09604 / 3.64 ( 4608) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 286 time to evaluate : 1.353 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: C 121 ASP cc_start: 0.8354 (t0) cc_final: 0.7932 (p0) REVERT: D 69 ARG cc_start: 0.1567 (OUTLIER) cc_final: -0.4318 (ttt180) REVERT: D 156 MET cc_start: 0.8290 (tpp) cc_final: 0.7746 (tpp) REVERT: D 214 TYR cc_start: 0.8653 (p90) cc_final: 0.8443 (p90) REVERT: D 287 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9036 (mm) REVERT: D 302 TYR cc_start: 0.8750 (m-80) cc_final: 0.8492 (m-10) REVERT: E 93 TYR cc_start: 0.8669 (m-10) cc_final: 0.8346 (m-10) REVERT: E 252 MET cc_start: 0.8862 (mmm) cc_final: 0.8410 (mmt) REVERT: G 319 ILE cc_start: 0.9405 (mm) cc_final: 0.9141 (mt) REVERT: H 93 TYR cc_start: 0.8716 (m-80) cc_final: 0.8377 (m-10) REVERT: I 93 TYR cc_start: 0.8607 (m-80) cc_final: 0.7716 (m-80) REVERT: J 23 HIS cc_start: 0.5984 (OUTLIER) cc_final: 0.5781 (p-80) REVERT: J 36 ASP cc_start: 0.6979 (OUTLIER) cc_final: 0.3459 (t70) REVERT: J 84 MET cc_start: 0.5299 (mmt) cc_final: 0.4775 (mmt) REVERT: J 152 GLN cc_start: 0.6402 (mm-40) cc_final: 0.5802 (mp10) REVERT: J 199 HIS cc_start: 0.6265 (m170) cc_final: 0.6031 (m170) REVERT: J 262 VAL cc_start: 0.4822 (OUTLIER) cc_final: 0.4562 (t) REVERT: J 320 ARG cc_start: 0.5751 (mmm-85) cc_final: 0.5478 (mmm-85) REVERT: J 396 HIS cc_start: 0.4830 (p-80) cc_final: 0.4229 (t70) REVERT: K 29 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7934 (tp30) REVERT: K 84 MET cc_start: 0.6411 (OUTLIER) cc_final: 0.5522 (mtt) REVERT: K 169 LEU cc_start: 0.9295 (tp) cc_final: 0.9054 (mt) REVERT: K 170 MET cc_start: 0.9303 (mtt) cc_final: 0.9047 (mtt) REVERT: L 121 ASP cc_start: 0.8661 (t0) cc_final: 0.8121 (p0) outliers start: 153 outliers final: 124 residues processed: 419 average time/residue: 0.2058 time to fit residues: 147.7413 Evaluate side-chains 402 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 271 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 396 HIS Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 295 HIS Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 430 ASN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 174 MET Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 225 CYS Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 315 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 174 MET Chi-restraints excluded: chain G residue 225 CYS Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 295 HIS Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 430 ASN Chi-restraints excluded: chain H residue 7 CYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 150 CYS Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 218 ASP Chi-restraints excluded: chain H residue 225 CYS Chi-restraints excluded: chain H residue 357 THR Chi-restraints excluded: chain H residue 399 ASP Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 184 ILE Chi-restraints excluded: chain I residue 315 ILE Chi-restraints excluded: chain J residue 12 ARG Chi-restraints excluded: chain J residue 23 HIS Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 94 ASN Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 198 ILE Chi-restraints excluded: chain J residue 240 ASP Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 357 THR Chi-restraints excluded: chain J residue 381 LEU Chi-restraints excluded: chain J residue 382 ASP Chi-restraints excluded: chain J residue 383 LEU Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 166 LYS Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 181 ILE Chi-restraints excluded: chain K residue 225 CYS Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 304 VAL Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 225 CYS Chi-restraints excluded: chain L residue 234 MET Chi-restraints excluded: chain L residue 245 VAL Chi-restraints excluded: chain L residue 285 LEU Chi-restraints excluded: chain L residue 303 THR Chi-restraints excluded: chain L residue 357 THR Chi-restraints excluded: chain L residue 425 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: [394, 425, 35, 45, 379, 193, 420, 166, 421, 301, 338] chunk 394 optimal weight: 30.0000 chunk 425 optimal weight: 8.9990 chunk 35 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 chunk 379 optimal weight: 6.9990 chunk 193 optimal weight: 10.0000 chunk 420 optimal weight: 20.0000 chunk 166 optimal weight: 3.9990 chunk 421 optimal weight: 6.9990 chunk 301 optimal weight: 0.8980 chunk 338 optimal weight: 8.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 241 GLN J 39 GLN ** J 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 94 ASN ** J 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 360 HIS ** L 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.134363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.107808 restraints weight = 122451.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.105656 restraints weight = 80426.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.105997 restraints weight = 66440.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.105702 restraints weight = 50240.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.105936 restraints weight = 44601.497| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.176 38010 Z= 0.270 Angle : 0.668 19.655 51722 Z= 0.332 Chirality : 0.044 0.227 6164 Planarity : 0.004 0.096 6823 Dihedral : 4.367 35.479 5420 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.99 % Favored : 93.97 % Rotamer: Outliers : 3.64 % Allowed : 24.40 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.12), residues: 4993 helix: 1.77 (0.13), residues: 1815 sheet: -1.51 (0.19), residues: 858 loop : -0.92 (0.13), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 142 TYR 0.043 0.002 TYR C 380 PHE 0.021 0.001 PHE J 280 HIS 0.038 0.001 HIS D 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.27 (38004) covalent geometry : angle 0.66814 / 0.33 (51710) SS BOND : bond 0.00258 / 0.13 ( 6) SS BOND : angle 1.56236 / 0.97 ( 12) hydrogen bonds : bond 0.03399 / 2.34 ( 1608) hydrogen bonds : angle 4.83698 / 3.46 ( 4608) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 289 time to evaluate : 1.429 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: C 121 ASP cc_start: 0.8247 (t0) cc_final: 0.7809 (p0) REVERT: D 129 LEU cc_start: 0.8850 (mt) cc_final: 0.8606 (tt) REVERT: D 156 MET cc_start: 0.8402 (tpp) cc_final: 0.7823 (tpp) REVERT: D 214 TYR cc_start: 0.8761 (p90) cc_final: 0.8528 (p90) REVERT: D 302 TYR cc_start: 0.8856 (m-80) cc_final: 0.8628 (m-10) REVERT: E 93 TYR cc_start: 0.8661 (m-10) cc_final: 0.8361 (m-10) REVERT: E 166 LYS cc_start: 0.9013 (ptmm) cc_final: 0.8634 (ptmm) REVERT: E 170 MET cc_start: 0.9062 (mpp) cc_final: 0.8650 (mpp) REVERT: E 252 MET cc_start: 0.8994 (mmm) cc_final: 0.8525 (mmt) REVERT: G 156 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8224 (ttm) REVERT: H 93 TYR cc_start: 0.8684 (m-80) cc_final: 0.8285 (m-10) REVERT: H 166 LYS cc_start: 0.8776 (ptmt) cc_final: 0.8337 (tttp) REVERT: I 93 TYR cc_start: 0.8549 (m-80) cc_final: 0.7580 (m-80) REVERT: I 252 MET cc_start: 0.8871 (tpp) cc_final: 0.8321 (tmm) REVERT: J 36 ASP cc_start: 0.6611 (OUTLIER) cc_final: 0.3868 (t70) REVERT: J 70 GLU cc_start: 0.4289 (OUTLIER) cc_final: 0.0424 (mt-10) REVERT: J 199 HIS cc_start: 0.6536 (m170) cc_final: 0.6203 (m170) REVERT: J 262 VAL cc_start: 0.5104 (OUTLIER) cc_final: 0.4854 (t) REVERT: J 285 LEU cc_start: 0.3020 (OUTLIER) cc_final: 0.2721 (tt) REVERT: J 320 ARG cc_start: 0.5837 (mmm-85) cc_final: 0.5632 (mmm-85) REVERT: J 396 HIS cc_start: 0.4965 (p-80) cc_final: 0.4392 (t70) REVERT: K 29 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7779 (tp30) REVERT: K 84 MET cc_start: 0.6206 (OUTLIER) cc_final: 0.5409 (mtt) REVERT: L 121 ASP cc_start: 0.8654 (t0) cc_final: 0.8118 (p0) REVERT: L 374 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8811 (mm) outliers start: 139 outliers final: 112 residues processed: 410 average time/residue: 0.2038 time to fit residues: 143.2741 Evaluate side-chains 401 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 281 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 396 HIS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 295 HIS Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 174 MET Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 225 CYS Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 315 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 174 MET Chi-restraints excluded: chain G residue 225 CYS Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 430 ASN Chi-restraints excluded: chain H residue 7 CYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 218 ASP Chi-restraints excluded: chain H residue 225 CYS Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 357 THR Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 315 ILE Chi-restraints excluded: chain J residue 12 ARG Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 70 GLU Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 198 ILE Chi-restraints excluded: chain J residue 240 ASP Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 345 LEU Chi-restraints excluded: chain J residue 357 THR Chi-restraints excluded: chain J residue 360 HIS Chi-restraints excluded: chain J residue 381 LEU Chi-restraints excluded: chain J residue 382 ASP Chi-restraints excluded: chain J residue 383 LEU Chi-restraints excluded: chain J residue 422 LEU Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 135 THR Chi-restraints excluded: chain K residue 166 LYS Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 181 ILE Chi-restraints excluded: chain K residue 225 CYS Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 304 VAL Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 225 CYS Chi-restraints excluded: chain L residue 234 MET Chi-restraints excluded: chain L residue 245 VAL Chi-restraints excluded: chain L residue 285 LEU Chi-restraints excluded: chain L residue 303 THR Chi-restraints excluded: chain L residue 374 LEU Chi-restraints excluded: chain L residue 425 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: [370, 72, 465, 59, 409, 47, 461, 397, 136, 82, 90] chunk 370 optimal weight: 30.0000 chunk 72 optimal weight: 0.7980 chunk 465 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 409 optimal weight: 30.0000 chunk 47 optimal weight: 0.7980 chunk 461 optimal weight: 0.0970 chunk 397 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 94 ASN ** J 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 338 HIS J 360 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.137220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.109289 restraints weight = 125648.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.108038 restraints weight = 73593.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.108640 restraints weight = 53602.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.108516 restraints weight = 42177.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.108516 restraints weight = 38051.055| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 38010 Z= 0.101 Angle : 0.573 13.319 51722 Z= 0.280 Chirality : 0.042 0.209 6164 Planarity : 0.003 0.080 6823 Dihedral : 3.793 22.721 5420 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.37 % Favored : 95.61 % Rotamer: Outliers : 2.25 % Allowed : 25.63 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.13), residues: 4993 helix: 2.04 (0.13), residues: 1811 sheet: -1.28 (0.19), residues: 896 loop : -0.69 (0.13), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 142 TYR 0.047 0.001 TYR C 380 PHE 0.017 0.001 PHE C 197 HIS 0.017 0.001 HIS D 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (38004) covalent geometry : angle 0.57308 / 0.28 (51710) SS BOND : bond 0.00234 / 0.15 ( 6) SS BOND : angle 0.78737 / 0.58 ( 12) hydrogen bonds : bond 0.02627 / 1.79 ( 1608) hydrogen bonds : angle 4.54864 / 3.27 ( 4608) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 299 time to evaluate : 1.569 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: B 121 ASP cc_start: 0.8572 (t0) cc_final: 0.8167 (p0) REVERT: C 121 ASP cc_start: 0.8077 (t0) cc_final: 0.7647 (p0) REVERT: D 31 CYS cc_start: 0.8102 (m) cc_final: 0.7611 (p) REVERT: D 39 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7344 (mp10) REVERT: D 129 LEU cc_start: 0.8860 (mt) cc_final: 0.8577 (tt) REVERT: D 156 MET cc_start: 0.8457 (tpp) cc_final: 0.7859 (tpp) REVERT: D 252 MET cc_start: 0.8697 (mmm) cc_final: 0.7510 (mmp) REVERT: D 264 LEU cc_start: 0.9448 (mt) cc_final: 0.9109 (pp) REVERT: D 302 TYR cc_start: 0.8924 (m-80) cc_final: 0.8688 (m-10) REVERT: E 93 TYR cc_start: 0.8579 (m-10) cc_final: 0.8264 (m-10) REVERT: E 166 LYS cc_start: 0.8882 (ptmm) cc_final: 0.8490 (ptmm) REVERT: E 170 MET cc_start: 0.9065 (mpp) cc_final: 0.8763 (mpp) REVERT: E 252 MET cc_start: 0.9102 (mmm) cc_final: 0.8633 (mmt) REVERT: G 156 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8155 (ttm) REVERT: G 174 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7489 (mmm) REVERT: H 84 MET cc_start: 0.6456 (ptp) cc_final: 0.5034 (ptp) REVERT: H 93 TYR cc_start: 0.8493 (m-80) cc_final: 0.7984 (m-10) REVERT: H 166 LYS cc_start: 0.8670 (ptmt) cc_final: 0.8161 (tttp) REVERT: H 425 LEU cc_start: 0.9397 (tp) cc_final: 0.9144 (pp) REVERT: I 93 TYR cc_start: 0.8467 (m-80) cc_final: 0.7510 (m-80) REVERT: I 252 MET cc_start: 0.8952 (tpp) cc_final: 0.8229 (tmm) REVERT: J 70 GLU cc_start: 0.3545 (OUTLIER) cc_final: 0.1315 (mm-30) REVERT: J 199 HIS cc_start: 0.6528 (m170) cc_final: 0.6218 (m170) REVERT: J 262 VAL cc_start: 0.5039 (OUTLIER) cc_final: 0.4793 (t) REVERT: J 285 LEU cc_start: 0.2972 (OUTLIER) cc_final: 0.2700 (tt) REVERT: K 84 MET cc_start: 0.6149 (OUTLIER) cc_final: 0.5355 (mtt) REVERT: L 121 ASP cc_start: 0.8559 (t0) cc_final: 0.7957 (p0) REVERT: L 374 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8791 (mm) outliers start: 86 outliers final: 70 residues processed: 370 average time/residue: 0.2074 time to fit residues: 129.1850 Evaluate side-chains 362 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 284 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 396 HIS Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain E residue 295 HIS Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 174 MET Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 225 CYS Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 174 MET Chi-restraints excluded: chain G residue 225 CYS Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 150 CYS Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 225 CYS Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 315 ILE Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 70 GLU Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 240 ASP Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 345 LEU Chi-restraints excluded: chain J residue 360 HIS Chi-restraints excluded: chain J residue 381 LEU Chi-restraints excluded: chain J residue 383 LEU Chi-restraints excluded: chain J residue 422 LEU Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 166 LYS Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 181 ILE Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 304 VAL Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain L residue 225 CYS Chi-restraints excluded: chain L residue 234 MET Chi-restraints excluded: chain L residue 374 LEU Chi-restraints excluded: chain L residue 425 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: [440, 406, 369, 382, 416, 137, 154, 133, 194, 286, 69] chunk 440 optimal weight: 5.9990 chunk 406 optimal weight: 20.0000 chunk 369 optimal weight: 10.0000 chunk 382 optimal weight: 0.5980 chunk 416 optimal weight: 1.9990 chunk 137 optimal weight: 9.9990 chunk 154 optimal weight: 20.0000 chunk 133 optimal weight: 10.0000 chunk 194 optimal weight: 20.0000 chunk 286 optimal weight: 0.0670 chunk 69 optimal weight: 0.0970 overall best weight: 1.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN ** J 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 282 GLN J 326 HIS J 360 HIS ** L 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.136244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.109722 restraints weight = 122842.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.108037 restraints weight = 75256.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.108702 restraints weight = 54637.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.108539 restraints weight = 41065.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.109061 restraints weight = 35812.237| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.124 38010 Z= 0.149 Angle : 0.600 15.837 51722 Z= 0.293 Chirality : 0.042 0.191 6164 Planarity : 0.004 0.072 6823 Dihedral : 3.834 24.215 5420 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.41 % Favored : 94.55 % Rotamer: Outliers : 2.28 % Allowed : 25.89 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.13), residues: 4993 helix: 2.00 (0.13), residues: 1831 sheet: -1.19 (0.19), residues: 893 loop : -0.69 (0.13), residues: 2269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 69 TYR 0.047 0.001 TYR C 380 PHE 0.011 0.001 PHE C 407 HIS 0.021 0.001 HIS D 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (38004) covalent geometry : angle 0.60014 / 0.29 (51710) SS BOND : bond 0.00117 / 0.06 ( 6) SS BOND : angle 1.02163 / 0.69 ( 12) hydrogen bonds : bond 0.02852 / 1.96 ( 1608) hydrogen bonds : angle 4.56551 / 3.28 ( 4608) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7263.30 seconds wall clock time: 125 minutes 35.13 seconds (7535.13 seconds total)