Starting phenix.real_space_refine on Thu Oct 29 18:54:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wd4_65882/10_2026/9wd4_65882.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wd4_65882/10_2026/9wd4_65882.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9wd4_65882/10_2026/9wd4_65882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wd4_65882/10_2026/9wd4_65882.map" model { file = "/net/cci-nas-00/data/ceres_data/9wd4_65882/10_2026/9wd4_65882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wd4_65882/10_2026/9wd4_65882.cif" } 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= -0.000 sd= 0.006 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 177 5.16 5 C 20575 2.51 5 N 5785 2.21 5 O 6158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 32695 Number of models: 1 Model: "" Number of chains: 11 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: 2785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2785 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 347} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 2765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2765 Classifications: {'peptide': 369} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 352} Chain breaks: 5 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 35 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: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2448 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 310} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "J" Number of atoms: 2940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2940 Classifications: {'peptide': 403} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 382} Chain breaks: 4 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'HIS:plan': 2, 'PHE:plan': 1, 'ASP:plan': 3, 'ARG:plan': 10, 'GLU:plan': 6, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 103 Chain: "K" 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: 6.58, per 1000 atoms: 0.20 Number of scatterers: 32695 At special positions: 0 Unit cell: (123.435, 129.132, 219.018, 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 177 16.00 O 6158 8.00 N 5785 7.00 C 20575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 38 " - pdb=" SG CYS G 38 " distance=1.93 Simple disulfide: pdb=" SG CYS B 38 " - pdb=" SG CYS H 38 " distance=2.05 Simple disulfide: pdb=" SG CYS C 38 " - pdb=" SG CYS I 38 " distance=2.04 Simple disulfide: pdb=" SG CYS E 38 " - pdb=" SG CYS J 38 " distance=2.26 Simple disulfide: pdb=" SG CYS F 38 " - pdb=" SG CYS K 38 " distance=1.88 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: 2.77 Conformation dependent library (CDL) restraints added in 1.4 seconds 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8080 Finding SS restraints... Secondary structure from input PDB file: 153 helices and 62 sheets defined 41.1% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 85 through 89 removed outlier: 3.534A pdb=" N ALA A 89 " --> pdb=" O GLU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.602A pdb=" N ARG A 130 " --> pdb=" O VAL A 127 " (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: 3.698A 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: 4.065A pdb=" N ALA A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 229 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN A 241 " --> pdb=" O TYR A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 267 removed outlier: 3.729A pdb=" N TYR A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 288 removed outlier: 3.937A 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: 3.774A pdb=" N ALA A 334 " --> pdb=" O SER A 330 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 382 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: 3.752A pdb=" N ASN A 430 " --> pdb=" O ARG A 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 89 removed outlier: 3.535A pdb=" N ALA B 89 " --> pdb=" O GLU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 130 removed outlier: 3.547A pdb=" N ARG B 130 " --> pdb=" O VAL B 127 " (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: 3.698A 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: 4.065A pdb=" N ALA B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU B 229 " --> pdb=" O CYS B 225 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN B 241 " --> pdb=" O TYR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 267 removed outlier: 3.729A pdb=" N TYR B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 288 removed outlier: 3.937A 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: 3.761A pdb=" N ALA B 334 " --> pdb=" O SER B 330 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG B 336 " --> pdb=" O GLN B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 382 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: 3.754A pdb=" N ASN B 430 " --> pdb=" O ARG B 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 89 removed outlier: 3.534A pdb=" N ALA C 89 " --> pdb=" O GLU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 130 removed outlier: 3.546A pdb=" N ARG C 130 " --> pdb=" O VAL C 127 " (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: 3.698A 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: 4.064A pdb=" N ALA C 228 " --> pdb=" O ARG C 224 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU C 229 " --> pdb=" O CYS C 225 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN C 241 " --> pdb=" O TYR C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 267 removed outlier: 3.729A pdb=" N TYR C 255 " --> pdb=" O SER C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 288 removed outlier: 3.937A 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: 3.799A pdb=" N ALA C 334 " --> pdb=" O SER C 330 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG C 336 " --> pdb=" O GLN C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 382 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: 3.753A pdb=" N ASN C 430 " --> pdb=" O ARG C 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.534A 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: 3.699A 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: 4.064A pdb=" N ALA D 228 " --> pdb=" O ARG D 224 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU D 229 " --> pdb=" O CYS D 225 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN D 241 " --> pdb=" O TYR D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 267 removed outlier: 3.729A pdb=" N TYR D 255 " --> pdb=" O SER D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 288 removed outlier: 3.937A 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 315 through 323 Processing helix chain 'D' and resid 357 through 372 Processing helix chain 'D' and resid 393 through 400 Processing helix chain 'D' and resid 400 through 409 Processing helix chain 'D' and resid 417 through 429 Processing helix chain 'E' and resid 85 through 89 removed outlier: 3.535A 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: 3.699A 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: 4.064A pdb=" N ALA E 228 " --> pdb=" O ARG E 224 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU E 229 " --> pdb=" O CYS E 225 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN E 241 " --> pdb=" O TYR E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 267 removed outlier: 3.728A pdb=" N TYR E 255 " --> pdb=" O SER E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 288 removed outlier: 3.937A 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: 3.795A pdb=" N ALA E 334 " --> pdb=" O SER E 330 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG E 336 " --> pdb=" O GLN E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 378 Processing helix chain 'E' and resid 400 through 409 Processing helix chain 'E' and resid 419 through 430 removed outlier: 3.753A pdb=" N ASN E 430 " --> pdb=" O ARG E 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.534A 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: 3.698A 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: 4.064A pdb=" N ALA F 228 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU F 229 " --> pdb=" O CYS F 225 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN F 241 " --> pdb=" O TYR F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 267 removed outlier: 3.729A pdb=" N TYR F 255 " --> pdb=" O SER F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 288 removed outlier: 3.936A 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: 3.751A pdb=" N ALA F 334 " --> pdb=" O SER F 330 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG F 336 " --> pdb=" O GLN F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 382 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: 3.760A pdb=" N ASN F 430 " --> pdb=" O ARG F 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 89 removed outlier: 3.534A pdb=" N ALA G 89 " --> pdb=" O GLU G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 130 removed outlier: 3.611A pdb=" N ARG G 130 " --> pdb=" O VAL G 127 " (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: 3.698A 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: 4.064A pdb=" N ALA G 228 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU G 229 " --> pdb=" O CYS G 225 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN G 241 " --> pdb=" O TYR G 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 267 removed outlier: 3.729A pdb=" N TYR G 255 " --> pdb=" O SER G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 276 through 288 removed outlier: 3.937A 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: 3.757A pdb=" N ALA G 334 " --> pdb=" O SER G 330 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG G 336 " --> pdb=" O GLN G 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 357 through 382 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: 3.754A pdb=" N ASN G 430 " --> pdb=" O ARG G 426 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 89 removed outlier: 3.535A 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: 3.699A 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: 4.064A pdb=" N ALA H 228 " --> pdb=" O ARG H 224 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU H 229 " --> pdb=" O CYS H 225 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN H 241 " --> pdb=" O TYR H 237 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 267 removed outlier: 3.729A pdb=" N TYR H 255 " --> pdb=" O SER H 251 " (cutoff:3.500A) Processing helix chain 'H' and resid 276 through 288 removed outlier: 3.937A 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: 3.791A pdb=" N ALA H 334 " --> pdb=" O SER H 330 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG H 336 " --> pdb=" O GLN H 332 " (cutoff:3.500A) Processing helix chain 'H' and resid 357 through 382 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: 3.761A pdb=" N ASN H 430 " --> pdb=" O ARG H 426 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 89 removed outlier: 3.725A 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: 3.653A 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: 3.958A pdb=" N ALA I 228 " --> pdb=" O ARG I 224 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU I 229 " --> pdb=" O CYS I 225 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN I 241 " --> pdb=" O TYR I 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 266 removed outlier: 3.759A pdb=" N TYR I 255 " --> pdb=" O SER I 251 " (cutoff:3.500A) Processing helix chain 'I' and resid 276 through 288 removed outlier: 3.900A 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: 3.813A pdb=" N ALA I 334 " --> pdb=" O SER I 330 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG I 336 " --> pdb=" O GLN I 332 " (cutoff:3.500A) Processing helix chain 'I' and resid 360 through 365 Processing helix chain 'J' and resid 85 through 89 removed outlier: 3.535A 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: 3.698A 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: 4.064A pdb=" N ALA J 228 " --> pdb=" O ARG J 224 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU J 229 " --> pdb=" O CYS J 225 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN J 241 " --> pdb=" O TYR J 237 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 267 removed outlier: 3.729A pdb=" N TYR J 255 " --> pdb=" O SER J 251 " (cutoff:3.500A) Processing helix chain 'J' and resid 276 through 288 removed outlier: 3.936A 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 337 removed outlier: 3.798A pdb=" N ALA J 334 " --> pdb=" O SER J 330 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG J 336 " --> pdb=" O GLN J 332 " (cutoff:3.500A) Processing helix chain 'J' and resid 357 through 379 Processing helix chain 'J' and resid 394 through 400 Processing helix chain 'J' and resid 400 through 409 Processing helix chain 'J' and resid 417 through 430 removed outlier: 3.754A pdb=" N ASN J 430 " --> pdb=" O ARG J 426 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 89 removed outlier: 3.534A 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: 3.698A 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: 4.064A pdb=" N ALA K 228 " --> pdb=" O ARG K 224 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU K 229 " --> pdb=" O CYS K 225 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN K 241 " --> pdb=" O TYR K 237 " (cutoff:3.500A) Processing helix chain 'K' and resid 251 through 267 removed outlier: 3.729A pdb=" N TYR K 255 " --> pdb=" O SER K 251 " (cutoff:3.500A) Processing helix chain 'K' and resid 276 through 288 removed outlier: 3.936A 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: 3.771A pdb=" N ALA K 334 " --> pdb=" O SER K 330 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG K 336 " --> pdb=" O GLN K 332 " (cutoff:3.500A) Processing helix chain 'K' and resid 357 through 382 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: 3.757A pdb=" N ASN K 430 " --> pdb=" O ARG K 426 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 removed outlier: 3.548A 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 61 removed outlier: 3.707A pdb=" N GLY A 50 " --> pdb=" O ILE A 57 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N SER A 59 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL A 48 " --> pdb=" O SER A 59 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ILE A 61 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ALA A 46 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N GLU A 41 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE A 33 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LYS A 45 " --> pdb=" O CYS A 31 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N CYS A 31 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLN A 47 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLU A 29 " --> pdb=" O GLN A 47 " (cutoff:3.500A) removed outlier: 7.192A 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: 6.692A pdb=" N ILE A 92 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS A 91 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 212 " --> pdb=" O LYS A 91 " (cutoff:3.500A) removed outlier: 7.476A 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: 4.464A 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: 6.556A pdb=" N ILE A 158 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 10.088A pdb=" N HIS A 326 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N LEU A 345 " --> pdb=" O HIS A 326 " (cutoff:3.500A) removed outlier: 4.397A 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: 3.548A 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 61 removed outlier: 3.707A pdb=" N GLY B 50 " --> pdb=" O ILE B 57 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N SER B 59 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL B 48 " --> pdb=" O SER B 59 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ILE B 61 " --> pdb=" O ALA B 46 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ALA B 46 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N GLU B 41 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE B 33 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LYS B 45 " --> pdb=" O CYS B 31 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N CYS B 31 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLN B 47 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLU B 29 " --> pdb=" O GLN B 47 " (cutoff:3.500A) removed outlier: 7.192A 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: 6.680A pdb=" N ILE B 92 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS B 91 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 212 " --> pdb=" O LYS B 91 " (cutoff:3.500A) removed outlier: 7.475A 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: 4.463A 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: 6.555A pdb=" N ILE B 158 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 10.083A pdb=" N HIS B 326 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N LEU B 345 " --> pdb=" O HIS B 326 " (cutoff:3.500A) removed outlier: 4.419A 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: 3.548A 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 61 removed outlier: 3.707A pdb=" N GLY C 50 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N SER C 59 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL C 48 " --> pdb=" O SER C 59 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ILE C 61 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ALA C 46 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N GLU C 41 " --> pdb=" O ARG C 35 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE C 33 " --> pdb=" O ILE C 43 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LYS C 45 " --> pdb=" O CYS C 31 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N CYS C 31 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLN C 47 " --> pdb=" O GLU C 29 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLU C 29 " --> pdb=" O GLN C 47 " (cutoff:3.500A) removed outlier: 7.192A 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: 6.722A pdb=" N ILE C 92 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS C 91 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU C 212 " --> pdb=" O LYS C 91 " (cutoff:3.500A) removed outlier: 7.475A 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: 4.463A 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: 6.555A pdb=" N ILE C 158 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 10.139A pdb=" N HIS C 326 " --> pdb=" O LEU C 345 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N LEU C 345 " --> pdb=" O HIS C 326 " (cutoff:3.500A) removed outlier: 4.416A 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: 3.548A 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 61 removed outlier: 3.707A pdb=" N GLY D 50 " --> pdb=" O ILE D 57 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N SER D 59 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL D 48 " --> pdb=" O SER D 59 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ILE D 61 " --> pdb=" O ALA D 46 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ALA D 46 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N GLU D 41 " --> pdb=" O ARG D 35 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE D 33 " --> pdb=" O ILE D 43 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LYS D 45 " --> pdb=" O CYS D 31 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N CYS D 31 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLN D 47 " --> pdb=" O GLU D 29 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLU D 29 " --> pdb=" O GLN D 47 " (cutoff:3.500A) removed outlier: 7.191A 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 92 through 94 removed outlier: 7.475A 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: 4.463A 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 304 removed outlier: 6.555A pdb=" N ILE D 158 " --> pdb=" O VAL D 304 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 12 through 13 removed outlier: 3.548A 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 61 removed outlier: 3.708A pdb=" N GLY E 50 " --> pdb=" O ILE E 57 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N SER E 59 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N VAL E 48 " --> pdb=" O SER E 59 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ILE E 61 " --> pdb=" O ALA E 46 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ALA E 46 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N GLU E 41 " --> pdb=" O ARG E 35 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE E 33 " --> pdb=" O ILE E 43 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LYS E 45 " --> pdb=" O CYS E 31 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N CYS E 31 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLN E 47 " --> pdb=" O GLU E 29 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLU E 29 " --> pdb=" O GLN E 47 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ILE E 30 " --> pdb=" O THR E 76 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 99 through 102 removed outlier: 6.703A pdb=" N ILE E 92 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS E 91 " --> pdb=" O THR E 210 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU E 212 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL E 245 " --> pdb=" O THR E 299 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 136 through 137 removed outlier: 4.464A pdb=" N CYS E 150 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 303 through 304 removed outlier: 6.556A pdb=" N ILE E 158 " --> pdb=" O VAL E 304 " (cutoff:3.500A) removed outlier: 10.099A pdb=" N HIS E 326 " --> pdb=" O LEU E 345 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N LEU E 345 " --> pdb=" O HIS E 326 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TYR E 328 " --> pdb=" O ASP E 343 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 12 through 13 removed outlier: 3.549A pdb=" N ARG F 12 " --> pdb=" O GLU F 19 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 55 through 61 removed outlier: 3.707A pdb=" N GLY F 50 " --> pdb=" O ILE F 57 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N SER F 59 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL F 48 " --> pdb=" O SER F 59 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ILE F 61 " --> pdb=" O ALA F 46 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ALA F 46 " --> pdb=" O ILE F 61 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N GLU F 41 " --> pdb=" O ARG F 35 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE F 33 " --> pdb=" O ILE F 43 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LYS F 45 " --> pdb=" O CYS F 31 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N CYS F 31 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLN F 47 " --> pdb=" O GLU F 29 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLU F 29 " --> pdb=" O GLN F 47 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE F 30 " --> pdb=" O THR F 76 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 81 through 83 Processing sheet with id=AD6, first strand: chain 'F' and resid 99 through 102 removed outlier: 6.698A pdb=" N ILE F 92 " --> pdb=" O VAL F 100 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS F 91 " --> pdb=" O THR F 210 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU F 212 " --> pdb=" O LYS F 91 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL F 245 " --> pdb=" O THR F 299 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 136 through 137 removed outlier: 4.463A pdb=" N CYS F 150 " --> pdb=" O LEU F 137 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 303 through 305 removed outlier: 6.555A pdb=" N ILE F 158 " --> pdb=" O VAL F 304 " (cutoff:3.500A) removed outlier: 10.088A pdb=" N HIS F 326 " --> pdb=" O LEU F 345 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N LEU F 345 " --> pdb=" O HIS F 326 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TYR F 328 " --> pdb=" O ASP F 343 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 12 through 13 removed outlier: 3.548A pdb=" N ARG G 12 " --> pdb=" O GLU G 19 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 55 through 61 removed outlier: 3.707A pdb=" N GLY G 50 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N SER G 59 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL G 48 " --> pdb=" O SER G 59 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ILE G 61 " --> pdb=" O ALA G 46 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ALA G 46 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N GLU G 41 " --> pdb=" O ARG G 35 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE G 33 " --> pdb=" O ILE G 43 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LYS G 45 " --> pdb=" O CYS G 31 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N CYS G 31 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN G 47 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLU G 29 " --> pdb=" O GLN G 47 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE G 30 " --> pdb=" O THR G 76 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 81 through 83 Processing sheet with id=AE3, first strand: chain 'G' and resid 99 through 102 removed outlier: 6.727A pdb=" N ILE G 92 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS G 91 " --> pdb=" O THR G 210 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU G 212 " --> pdb=" O LYS G 91 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL G 245 " --> pdb=" O THR G 299 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 136 through 137 removed outlier: 4.463A pdb=" N CYS G 150 " --> pdb=" O LEU G 137 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 303 through 305 removed outlier: 6.555A pdb=" N ILE G 158 " --> pdb=" O VAL G 304 " (cutoff:3.500A) removed outlier: 10.139A pdb=" N HIS G 326 " --> pdb=" O LEU G 345 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N LEU G 345 " --> pdb=" O HIS G 326 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TYR G 328 " --> pdb=" O ASP G 343 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 12 through 13 removed outlier: 3.548A pdb=" N ARG H 12 " --> pdb=" O GLU H 19 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 55 through 61 removed outlier: 3.707A pdb=" N GLY H 50 " --> pdb=" O ILE H 57 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N SER H 59 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N VAL H 48 " --> pdb=" O SER H 59 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ILE H 61 " --> pdb=" O ALA H 46 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ALA H 46 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N GLU H 41 " --> pdb=" O ARG H 35 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE H 33 " --> pdb=" O ILE H 43 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LYS H 45 " --> pdb=" O CYS H 31 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N CYS H 31 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLN H 47 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLU H 29 " --> pdb=" O GLN H 47 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE H 30 " --> pdb=" O THR H 76 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 81 through 83 Processing sheet with id=AE9, first strand: chain 'H' and resid 99 through 102 removed outlier: 6.740A pdb=" N ILE H 92 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS H 91 " --> pdb=" O THR H 210 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU H 212 " --> pdb=" O LYS H 91 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL H 245 " --> pdb=" O THR H 299 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 136 through 137 removed outlier: 4.463A pdb=" N CYS H 150 " --> pdb=" O LEU H 137 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 303 through 305 removed outlier: 6.554A pdb=" N ILE H 158 " --> pdb=" O VAL H 304 " (cutoff:3.500A) removed outlier: 10.118A pdb=" N HIS H 326 " --> pdb=" O LEU H 345 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N LEU H 345 " --> pdb=" O HIS H 326 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TYR H 328 " --> pdb=" O ASP H 343 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 55 through 61 removed outlier: 3.694A pdb=" N GLY I 50 " --> pdb=" O ILE I 57 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER I 59 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N VAL I 48 " --> pdb=" O SER I 59 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ILE I 61 " --> pdb=" O ALA I 46 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ALA I 46 " --> pdb=" O ILE I 61 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ILE I 33 " --> pdb=" O ILE I 43 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LYS I 45 " --> pdb=" O CYS I 31 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N CYS I 31 " --> pdb=" O LYS I 45 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLN I 47 " --> pdb=" O GLU I 29 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLU I 29 " --> pdb=" O GLN I 47 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ILE I 30 " --> pdb=" O THR I 76 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR I 76 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 99 through 101 removed outlier: 6.683A pdb=" N ILE I 92 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N VAL I 245 " --> pdb=" O THR I 299 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 303 through 305 removed outlier: 6.563A pdb=" N ILE I 158 " --> pdb=" O VAL I 304 " (cutoff:3.500A) removed outlier: 10.216A pdb=" N HIS I 326 " --> pdb=" O LEU I 345 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N LEU I 345 " --> pdb=" O HIS I 326 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N TYR I 328 " --> pdb=" O ASP I 343 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 12 through 13 removed outlier: 3.548A pdb=" N ARG J 12 " --> pdb=" O GLU J 19 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 55 through 61 removed outlier: 3.707A pdb=" N GLY J 50 " --> pdb=" O ILE J 57 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N SER J 59 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL J 48 " --> pdb=" O SER J 59 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ILE J 61 " --> pdb=" O ALA J 46 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ALA J 46 " --> pdb=" O ILE J 61 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N GLU J 41 " --> pdb=" O ARG J 35 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE J 33 " --> pdb=" O ILE J 43 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LYS J 45 " --> pdb=" O CYS J 31 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N CYS J 31 " --> pdb=" O LYS J 45 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLN J 47 " --> pdb=" O GLU J 29 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLU J 29 " --> pdb=" O GLN J 47 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE J 30 " --> pdb=" O THR J 76 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 81 through 83 Processing sheet with id=AF9, first strand: chain 'J' and resid 99 through 102 removed outlier: 6.708A pdb=" N ILE J 92 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS J 91 " --> pdb=" O THR J 210 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU J 212 " --> pdb=" O LYS J 91 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL J 245 " --> pdb=" O THR J 299 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 136 through 137 removed outlier: 4.463A pdb=" N CYS J 150 " --> pdb=" O LEU J 137 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 157 through 159 removed outlier: 10.059A pdb=" N HIS J 326 " --> pdb=" O LEU J 345 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N LEU J 345 " --> pdb=" O HIS J 326 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TYR J 328 " --> pdb=" O ASP J 343 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 12 through 13 removed outlier: 3.547A pdb=" N ARG K 12 " --> pdb=" O GLU K 19 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 55 through 61 removed outlier: 3.707A pdb=" N GLY K 50 " --> pdb=" O ILE K 57 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N SER K 59 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL K 48 " --> pdb=" O SER K 59 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ILE K 61 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ALA K 46 " --> pdb=" O ILE K 61 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N GLU K 41 " --> pdb=" O ARG K 35 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE K 33 " --> pdb=" O ILE K 43 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LYS K 45 " --> pdb=" O CYS K 31 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N CYS K 31 " --> pdb=" O LYS K 45 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLN K 47 " --> pdb=" O GLU K 29 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLU K 29 " --> pdb=" O GLN K 47 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE K 30 " --> pdb=" O THR K 76 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 81 through 83 Processing sheet with id=AG6, first strand: chain 'K' and resid 99 through 102 removed outlier: 6.689A pdb=" N ILE K 92 " --> pdb=" O VAL K 100 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS K 91 " --> pdb=" O THR K 210 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU K 212 " --> pdb=" O LYS K 91 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL K 245 " --> pdb=" O THR K 299 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 136 through 137 removed outlier: 4.463A pdb=" N CYS K 150 " --> pdb=" O LEU K 137 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 303 through 305 removed outlier: 6.554A pdb=" N ILE K 158 " --> pdb=" O VAL K 304 " (cutoff:3.500A) removed outlier: 10.086A pdb=" N HIS K 326 " --> pdb=" O LEU K 345 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N LEU K 345 " --> pdb=" O HIS K 326 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N TYR K 328 " --> pdb=" O ASP K 343 " (cutoff:3.500A) 1388 hydrogen bonds defined for protein. 3987 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.76 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8986 1.33 - 1.45: 5032 1.45 - 1.57: 18934 1.57 - 1.69: 0 1.69 - 1.81: 271 Bond restraints: 33223 Sorted by residual: bond pdb=" N SER G -1 " pdb=" CA SER G -1 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.17e-02 7.31e+03 8.10e+00 bond pdb=" CB GLU D 19 " pdb=" CG GLU D 19 " ideal model delta sigma weight residual 1.520 1.440 0.080 3.00e-02 1.11e+03 7.16e+00 bond pdb=" CG GLU D 19 " pdb=" CD GLU D 19 " ideal model delta sigma weight residual 1.516 1.453 0.063 2.50e-02 1.60e+03 6.34e+00 bond pdb=" CB LEU C 3 " pdb=" CG LEU C 3 " ideal model delta sigma weight residual 1.530 1.486 0.044 2.00e-02 2.50e+03 4.90e+00 bond pdb=" CB ASP D 261 " pdb=" CG ASP D 261 " ideal model delta sigma weight residual 1.516 1.471 0.045 2.50e-02 1.60e+03 3.22e+00 ... (remaining 33218 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.95: 45052 3.95 - 7.89: 92 7.89 - 11.84: 1 11.84 - 15.78: 1 15.78 - 19.73: 1 Bond angle restraints: 45147 Sorted by residual: angle pdb=" CA LEU C 3 " pdb=" CB LEU C 3 " pdb=" CG LEU C 3 " ideal model delta sigma weight residual 116.30 136.03 -19.73 3.50e+00 8.16e-02 3.18e+01 angle pdb=" CB LEU C 3 " pdb=" CG LEU C 3 " pdb=" CD2 LEU C 3 " ideal model delta sigma weight residual 110.70 98.77 11.93 3.00e+00 1.11e-01 1.58e+01 angle pdb=" C ASP D 395 " pdb=" N HIS D 396 " pdb=" CA HIS D 396 " ideal model delta sigma weight residual 121.14 114.34 6.80 1.75e+00 3.27e-01 1.51e+01 angle pdb=" C HIS H 0 " pdb=" N MET H 1 " pdb=" CA MET H 1 " ideal model delta sigma weight residual 121.54 128.90 -7.36 1.91e+00 2.74e-01 1.49e+01 angle pdb=" C ASP F 395 " pdb=" N HIS F 396 " pdb=" CA HIS F 396 " ideal model delta sigma weight residual 121.14 114.52 6.62 1.75e+00 3.27e-01 1.43e+01 ... (remaining 45142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 17587 17.79 - 35.58: 1760 35.58 - 53.37: 529 53.37 - 71.16: 100 71.16 - 88.95: 25 Dihedral angle restraints: 20001 sinusoidal: 7450 harmonic: 12551 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 180.00 143.60 36.40 0 5.00e+00 4.00e-02 5.30e+01 dihedral pdb=" CB CYS C 38 " pdb=" SG CYS C 38 " pdb=" SG CYS I 38 " pdb=" CB CYS I 38 " ideal model delta sinusoidal sigma weight residual -86.00 -146.48 60.48 1 1.00e+01 1.00e-02 4.87e+01 dihedral pdb=" CB CYS E 38 " pdb=" SG CYS E 38 " pdb=" SG CYS J 38 " pdb=" CB CYS J 38 " ideal model delta sinusoidal sigma weight residual -86.00 -137.34 51.34 1 1.00e+01 1.00e-02 3.60e+01 ... (remaining 19998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4623 0.061 - 0.121: 719 0.121 - 0.182: 21 0.182 - 0.242: 0 0.242 - 0.303: 1 Chirality restraints: 5364 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 -2.89 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CG LEU F 3 " pdb=" CB LEU F 3 " pdb=" CD1 LEU F 3 " pdb=" CD2 LEU F 3 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CA ILE A 348 " pdb=" N ILE A 348 " pdb=" C ILE A 348 " pdb=" CB ILE A 348 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 ... (remaining 5361 not shown) Planarity restraints: 5934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP G 363 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.97e+00 pdb=" CG ASP G 363 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP G 363 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP G 363 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 363 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.91e+00 pdb=" CG ASP A 363 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP A 363 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP A 363 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 363 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.89e+00 pdb=" CG ASP D 363 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP D 363 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP D 363 " 0.015 2.00e-02 2.50e+03 ... (remaining 5931 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 14413 2.94 - 3.43: 32733 3.43 - 3.92: 51527 3.92 - 4.41: 57864 4.41 - 4.90: 95922 Nonbonded interactions: 252459 Sorted by model distance: nonbonded pdb=" OD1 ASP D 261 " pdb=" N VAL D 262 " model vdw 2.451 3.120 nonbonded pdb=" O SER J 419 " pdb=" OD1 ASN J 423 " model vdw 2.458 3.040 nonbonded pdb=" O SER G 419 " pdb=" OD1 ASN G 423 " model vdw 2.458 3.040 nonbonded pdb=" O SER C 419 " pdb=" OD1 ASN C 423 " model vdw 2.458 3.040 nonbonded pdb=" O SER D 419 " pdb=" OD1 ASN D 423 " model vdw 2.459 3.040 ... (remaining 252454 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 10 or (resid 11 through 14 and (name N or name CA \ or name C or name O or name CB )) or resid 15 through 16 or (resid 17 and (name \ N or name CA or name C or name O or name CB )) or resid 18 or (resid 19 through \ 20 and (name N or name CA or name C or name O or name CB )) or resid 21 through \ 22 or (resid 23 and (name N or name CA or name C or name O or name CB )) or res \ id 24 through 33 or (resid 34 through 37 and (name N or name CA or name C or nam \ e O or name CB )) or resid 38 through 40 or (resid 41 and (name N or name CA or \ name C or name O or name CB )) or resid 42 through 44 or (resid 45 through 46 an \ d (name N or name CA or name C or name O or name CB )) or resid 47 through 50 or \ (resid 51 through 53 and (name N or name CA or name C or name O or name CB )) o \ r resid 54 through 68 or (resid 69 through 70 and (name N or name CA or name C o \ r name O or name CB )) or resid 71 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 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 132 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 159 or resid 163 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 or name CA or name C or n \ ame O or name CB )) or resid 210 through 217 or (resid 218 and (name N or name C \ A 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 267 or \ resid 274 through 287 or (resid 288 and (name N or name CA or name C or name O o \ r name CB )) or resid 289 through 305 or resid 314 through 317 or (resid 318 and \ (name N or name CA or name C or name O or name CB )) or resid 319 or (resid 320 \ and (name N or name CA or name C or name O or name CB )) or resid 321 through 3 \ 28 or resid 346 through 349 or (resid 350 and (name N or name CA or name C or na \ me 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 360 or (resid 361 throug \ h 362 and (name N or name CA or name C or name O or name CB )) or resid 363 thro \ ugh 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 372 or resid 396 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 418 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 429)) 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 10 or (resid 11 through 14 and (name N or name CA \ or name C or name O or name CB )) or resid 15 through 16 or (resid 17 and (name \ N or name CA or name C or name O or name CB )) or resid 18 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 (name N or name CA or name C or name O or name CB )) or res \ id 30 through 34 or (resid 35 through 37 and (name N or name CA or name C or nam \ e O or name CB )) or resid 38 through 40 or (resid 41 and (name N or name CA or \ name C or name O or name CB )) or resid 42 through 44 or (resid 45 through 46 an \ d (name N or name CA or name C or name O or name CB )) or resid 47 through 50 or \ (resid 51 through 53 and (name N or name CA or name C or name O or name CB )) o \ r resid 54 through 68 or (resid 69 through 70 and (name N or name CA or name C o \ r name O or name CB )) or resid 71 through 73 or (resid 74 and (name N or name C \ A 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 (resi \ d 86 and (name N or name CA or name C or name O or name CB )) or resid 87 throug \ h 90 or (resid 91 and (name N or name CA or name C or name O or name CB )) or re \ sid 92 through 97 or resid 132 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 159 or resid \ 163 through 188 or (resid 189 through 190 and (name N or name CA or name C or na \ me O or name CB )) or 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 (n \ ame 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 (resid 206 through 209 and (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 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 (resi \ d 243 through 244 and (name N or name CA or name C or name O or name CB )) or re \ sid 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 nam \ e CA or name C or name O or name CB )) or resid 259 through 260 or (resid 261 an \ d (name N or name CA or name C or name O or name CB )) or resid 262 through 267 \ or resid 274 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 name O or name CB )) or resid 295 through 305 or resid 314 through 31 \ 9 or (resid 320 and (name N or name CA or name C or name O or name CB )) or resi \ d 321 through 328 or resid 346 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 (na \ me N or name CA or name C or name O or name CB )) or resid 360 or (resid 361 thr \ ough 362 and (name N or name CA or name C or name O or name CB )) or resid 363 t \ hrough 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 372 or resid 396 through 398 or (resid 399 an \ d (name N or name CA or name C or name O or name CB )) or resid 400 or (resid 40 \ 1 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 name C or na \ me O or name CB )) or resid 418 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 (n \ ame N or name CA or name C or name O or name CB )) or resid 428 through 429)) 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 10 or (resid 11 through 14 and (name N or name CA \ or name C or name O or name CB )) or resid 15 through 16 or (resid 17 and (name \ N or name CA or name C or name O or name CB )) or resid 18 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 through 37 and (name N or name CA or name C or name O or name C \ B )) or resid 38 through 40 or (resid 41 and (name N or name CA or name C or nam \ e O or name CB )) or resid 42 through 44 or (resid 45 through 46 and (name N or \ name CA or name C or name O or name CB )) or resid 47 through 50 or (resid 51 th \ rough 53 and (name N or name CA or name C or name O or name CB )) or resid 54 th \ rough 69 or (resid 70 and (name N or name CA or name C or name O or name CB )) o \ r 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 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 na \ me CA or name C or name O or name CB )) or resid 92 through 97 or resid 132 thro \ ugh 159 or resid 163 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 na \ me CA or name C or name O or name CB )) or resid 237 through 242 or (resid 243 t \ hrough 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 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C or name O or name CB )) o \ r resid 360 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 396 \ 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 or (resid 412 through 414 and (name N or name CA or \ name C or name O or name CB )) or resid 418 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 throu \ gh 427 and (name N or name CA or name C or name O or name CB )) or resid 428 thr \ ough 429)) 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 10 or (resid 11 through 14 and (name N or name CA \ or name C or name O or name CB )) or resid 15 through 16 or (resid 17 and (name \ N or name CA or name C or name O or name CB )) or resid 18 or (resid 19 through \ 20 and (name N or name CA or name C or name O or name CB )) or resid 21 through \ 22 or (resid 23 and (name N or name CA or name C or name O or name CB )) or res \ id 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 33 or (resid 34 through 37 and (name N or name CA or \ name C or name O or name CB )) or resid 38 through 40 or (resid 41 and (name N o \ r name CA or name C or name O or name CB )) or resid 42 through 44 or (resid 45 \ through 46 and (name N or name CA or name C or name O or name CB )) or resid 47 \ through 50 or (resid 51 through 53 and (name N or name CA or name C or name O or \ name CB )) or resid 54 through 62 or (resid 63 through 65 and (name N or name C \ A 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 CB )) or resi \ d 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 na \ me 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 132 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 159 or resid 163 through 188 or (resid 189 through 190 a \ nd (name N or name CA or name C or name O or name CB )) or resid 191 or (resid 1 \ 92 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 nam \ e 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 (resid 206 through 209 and ( \ name N or name CA or name C or name O or name CB )) or resid 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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 or (resid 320 and (name N or n \ ame CA or name C or name O or name CB )) or resid 321 through 349 or (resid 350 \ and (name N or name CA or name C or name O or name CB )) or resid 351 through 35 \ 3 or (resid 354 and (name N or name CA or name C or name O or name CB )) or resi \ d 355 through 358 or (resid 359 and (name N or name CA or name C or name O or na \ me 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 363 through 365 or (resid 366 and (name N or n \ ame CA or name C or name O or name CB )) or resid 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 37 \ 2 or resid 396 through 398 or (resid 399 and (name N or name CA or name C or nam \ e 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 name C or name O or name CB )) or resid 418 throu \ gh 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 through 429)) 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 10 or (resid 11 through 14 and (name N or name CA \ or name C or name O or name CB )) or resid 15 through 16 or (resid 17 and (name \ N or name CA or name C or name O or name CB )) or resid 18 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 (name N or name CA or name C or name O or name CB )) or res \ id 30 through 33 or (resid 34 through 37 and (name N or name CA or name C or nam \ e O or name CB )) or resid 38 through 44 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(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 o \ r (resid 206 through 209 and (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 nam \ e 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 (na \ me N or name CA or name C or name O or name CB )) or resid 237 through 242 or (r \ esid 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 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through 16 or (resid 17 and (name \ N or name CA or name C or name O or name CB )) or resid 18 through 28 or (resid \ 29 and (name N or name CA or name C or name O or name CB )) or resid 30 through \ 34 or (resid 35 through 37 and (name N or name CA or name C or name O or name C \ B )) or resid 38 through 40 or (resid 41 and (name N or name CA or name C or nam \ e O or name CB )) or resid 42 through 44 or (resid 45 through 46 and (name N or \ name CA or name C or name O or name CB )) or resid 47 through 50 or (resid 51 th \ rough 53 and (name N or name CA or name C or name O or name CB )) or resid 54 th \ rough 62 or (resid 63 through 65 and (name N or name CA or name C or name O or n \ ame 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 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 resi \ d 87 through 97 or resid 132 through 141 or (resid 142 through 143 and (name N o \ r name CA or name C or name O or name CB )) or resid 144 through 159 or resid 16 \ 3 through 188 or (resid 189 through 190 and (name N or name CA or name C or name \ O or name CB )) or resid 191 or (resid 192 through 193 and (name N or name CA o \ r name C or name O or name CB )) or resid 194 through 195 or (resid 196 and (nam \ e N or name CA or name C or name O or name CB )) or resid 197 through 199 or (re \ sid 200 and (name N or name CA or name C or name O or name CB )) or resid 201 th \ rough 205 or (resid 206 through 209 and (name N or name CA or name C or name O o \ r name CB )) or resid 210 through 217 or (resid 218 and (name N or name CA or na \ me 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 throug \ h 242 or (resid 243 through 244 and (name N or name CA or name C or name O or na \ me 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 26 \ 2 through 267 or resid 274 through 305 or resid 314 through 317 or (resid 318 an \ d (name N or name CA or name C or name O or name CB )) or resid 319 or (resid 32 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 321 through \ 328 or resid 346 through 349 or (resid 350 and (name N or name CA or name C or n \ ame O or name CB )) or resid 351 through 353 or (resid 354 and (name N or name C \ A 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 t \ hrough 362 and (name N or name CA or name C or name O or name CB )) or resid 363 \ through 365 or (resid 366 and (name N or name CA or name C or name O or name CB \ )) or resid 367 or (resid 368 through 370 and (name N or name CA or name C or n \ ame O or name CB )) or resid 371 through 372 or resid 396 through 398 or (resid \ 399 and (name N or name CA or name C or name O or name CB )) or resid 400 or (re \ sid 401 through 402 and (name N or name CA or name C or name O or name CB )) or \ resid 403 through 414 or resid 418 through 429)) selection = (chain 'G' and ((resid 1 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 10 or (resid 11 through 14 and (name N or name CA \ or name C or name O or name CB )) or resid 15 through 16 or (resid 17 and (name \ N or name CA or name C or name O or name CB )) or resid 18 or (resid 19 through \ 20 and (name N or name CA or name C or name O or name CB )) or resid 21 through \ 22 or (resid 23 and (name N or name CA or name C or name O or name CB )) or res \ id 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 33 or (resid 34 through 37 and (name N or name CA or \ name C or name O or name CB )) or resid 38 through 40 or (resid 41 and (name N o \ r name CA or name C or name O or name CB )) or resid 42 through 44 or (resid 45 \ through 46 and (name N or name CA or name C or name O or name CB )) or resid 47 \ through 50 or (resid 51 through 53 and (name N or name CA or name C or name O or \ name CB )) or resid 54 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 (nam \ e N or name CA or name C or name O or name CB )) or resid 71 through 73 or (resi \ d 74 and (name N or name CA or name C or name O or name CB )) or resid 75 throug \ h 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 nam \ e 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 132 through 141 or (resid 1 \ 42 through 143 and (name N or name CA or name C or name O or name CB )) or resid \ 144 through 159 or resid 163 through 188 or (resid 189 through 190 and (name N \ or name CA or name C or name O or name CB )) or 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 throug \ h 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 o \ r name CB )) or resid 201 through 205 or (resid 206 through 209 and (name N or n \ ame 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 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314 through 317 or (resid 318 and (n \ ame N or name CA or name C or name O or name CB )) or resid 319 or (resid 320 an \ d (name N or name CA or name C or name O or name CB )) or resid 321 through 328 \ or resid 346 through 368 or (resid 369 through 370 and (name N or name CA or nam \ e C or name O or name CB )) or resid 371 through 372 or resid 396 through 398 or \ (resid 399 and (name N or name CA or name C or name O or name CB )) or resid 40 \ 0 or (resid 401 through 402 and (name N or name CA or name C or name O or name C \ B )) or resid 403 through 411 or (resid 412 through 414 and (name N or name CA o \ r name C or name O or name CB )) or resid 418 through 423 or (resid 424 and (nam \ e N or name CA or name C or name O or name CB )) or resid 425 or (resid 426 thro \ ugh 427 and (name N or name CA or name C or name O or name CB )) or resid 428 th \ rough 429)) selection = (chain 'H' and ((resid 1 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 10 or (resid 11 through 14 and (name N or name CA \ or name C or name O or name CB )) or resid 15 through 16 or (resid 17 and (name \ N or name CA or name C or name O or name CB )) or resid 18 or (resid 19 through \ 20 and (name N or name CA or name C or name O or name CB )) or resid 21 through \ 22 or (resid 23 and (name N or name CA or name C or name O or name CB )) or res \ id 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 33 or (resid 34 through 37 and (name N or name CA or \ name C or name O or name CB )) or resid 38 through 40 or (resid 41 and (name N o \ r name CA or name C or name O or name CB )) or resid 42 through 44 or (resid 45 \ through 46 and (name N or name CA or name C or name O or name CB )) or resid 47 \ through 50 or (resid 51 through 53 and (name N or name CA or name C or name O or \ name CB )) or resid 54 through 62 or (resid 63 through 65 and (name N or name C \ A 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 CB )) or resi \ d 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 na \ me 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 132 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 159 or resid 163 through 188 or (resid 189 through 190 a \ nd (name N or name CA or name C or name O or name CB )) or resid 191 or (resid 1 \ 92 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 nam \ e CB )) or resid 197 through 199 or (resid 200 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name CB )) or resid 28 \ 2 through 287 or (resid 288 and (name N or name CA or name C or name O or name C \ B )) 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 305 or resid 314 through 317 or (resid \ 318 and (name N or name CA or name C or name O or name CB )) or resid 319 or (r \ esid 320 and (name N or name CA or name C or name O or name CB )) or resid 321 t \ hrough 328 or resid 346 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 or (resid 35 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 360 or (resi \ d 361 through 362 and (name N or name CA or name C or name O or name CB )) or re \ sid 363 through 365 or (resid 366 and (name N or name CA or name C or name O or \ name CB )) or resid 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 396 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 414 and (name N or name CA or \ name C or name O or name CB )) or resid 418 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 throu \ gh 427 and (name N or name CA or name C or name O or name CB )) or resid 428 thr \ ough 429)) selection = (chain 'J' and ((resid 1 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 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 (name N or name \ CA or name C or name O or name CB )) or resid 30 through 40 or (resid 41 and (na \ me N or name CA or name C or name O or name CB )) or resid 42 through 50 or (res \ id 51 through 53 and (name N or name CA or name C or name O or name CB )) or res \ id 54 through 64 or (resid 65 and (name N or name CA or name C or name O or name \ CB )) or resid 66 through 83 or (resid 84 and (name N or name CA or name C or n \ ame 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 132 through 1 \ 41 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 190 and (name N or name CA \ or name C or name O or name CB )) or resid 191 or (resid 192 through 193 and (na \ me N or name CA or name C or name O or name CB )) or resid 194 through 195 or (r \ esid 196 and (name N or name CA or name C or name O or name CB )) or resid 197 t \ hrough 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 (resid 206 through 209 and (name N or name CA or n \ ame 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 name CB )) or resid 224 throu \ gh 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 2 \ 59 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 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 (resi \ d 288 and (name N or name CA or name C or name O or name CB )) or resid 289 thro \ ugh 293 or (resid 294 and (name N or name CA or name C or name O or name CB )) o \ r resid 295 through 305 or resid 314 through 317 or (resid 318 and (name N or na \ me CA or name C or name O or name CB )) or resid 319 through 328 or resid 346 th \ rough 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 or (resid 359 and (name N or name CA o \ r name C or name O or name CB )) or resid 360 through 361 or (resid 362 and (nam \ e N or name CA or name C or name O or name CB )) or resid 363 through 368 or (re \ sid 369 through 370 and (name N or name CA or name C or name O or name CB )) or \ resid 371 through 372 or resid 396 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 o \ r (resid 412 through 414 and (name N or name CA or name C or name O or name CB ) \ ) or resid 418 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)) 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 10 or (resid 11 through 14 and (name N or name CA \ or name C or name O or name CB )) or resid 15 through 16 or (resid 17 and (name \ N or name CA or name C or name O or name CB )) or resid 18 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 (name N or name CA or name C or name O or name CB )) or res \ id 30 through 33 or (resid 34 through 37 and (name N or name CA or name C or nam \ e O or name CB )) or resid 38 through 40 or (resid 41 and (name N or name CA or \ name C or name O or name CB )) or resid 42 through 44 or (resid 45 through 46 an \ d (name N or name CA or name C or name O or name CB )) or resid 47 through 50 or \ (resid 51 through 53 and (name N or name CA or name C or name O or name CB )) o \ r resid 54 through 62 or (resid 63 through 65 and (name N or name CA or name C o \ r 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 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 resi \ d 92 through 97 or resid 132 through 141 or (resid 142 through 143 and (name N o \ r name CA or name C or name O or name CB )) or resid 144 through 159 or resid 16 \ 3 through 189 or (resid 190 and (name N or name CA or name C or name O or name C \ B )) or 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 \ (resid 206 through 209 and (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 o \ r name C or name O or name CB )) or resid 224 through 235 or (resid 236 and (nam \ e N or name CA or name C or name O or name CB )) or resid 237 through 243 or (re \ sid 244 and (name N or name CA or name C or name O or name CB )) or resid 245 th \ rough 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 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 2 \ 93 or (resid 294 and (name N or name CA or name C or name O or name CB )) or res \ id 295 through 305 or resid 314 through 317 or (resid 318 and (name N or name CA \ or name C or name O or name CB )) or resid 319 or (resid 320 and (name N or nam \ e CA or name C or name O or name CB )) or resid 321 through 328 or resid 346 thr \ ough 372 or resid 396 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 n \ ame 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 name C or name O or name CB )) or resid 41 \ 8 through 423 or (resid 424 and (name N or name CA or name C or name O or name C \ B )) 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)) } 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: 19.600 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: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 29.370 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.080 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 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 : 0.004 0.225 33228 Z= 0.182 Angle : 0.530 19.729 45157 Z= 0.280 Chirality : 0.042 0.303 5364 Planarity : 0.003 0.083 5934 Dihedral : 16.200 88.952 11906 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.11 % Favored : 95.80 % Rotamer: Outliers : 0.72 % Allowed : 22.38 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.26 % 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: 0.12 (0.14), residues: 4332 helix: 1.37 (0.14), residues: 1724 sheet: -0.81 (0.20), residues: 826 loop : -0.69 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 131 TYR 0.022 0.001 TYR E 214 PHE 0.011 0.001 PHE B 4 HIS 0.016 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (33223) covalent geometry : angle 0.52808 / 0.28 (45147) SS BOND : bond 0.12976 / 7.42 ( 5) SS BOND : angle 3.32374 / 1.93 ( 10) hydrogen bonds : bond 0.14956 / 10.38 ( 1388) hydrogen bonds : angle 6.77279 / 4.81 ( 3987) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 698 time to evaluate : 1.217 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: A 52 LYS cc_start: 0.8024 (ttpp) cc_final: 0.7681 (tttt) REVERT: A 350 ARG cc_start: 0.8482 (ttm-80) cc_final: 0.8133 (mtt180) REVERT: A 354 LYS cc_start: 0.9121 (mttm) cc_final: 0.8888 (mtpt) REVERT: B 78 GLN cc_start: 0.8316 (mt0) cc_final: 0.8099 (pt0) REVERT: B 250 ASP cc_start: 0.7795 (t0) cc_final: 0.7480 (p0) REVERT: C 166 LYS cc_start: 0.8482 (tmmt) cc_final: 0.8274 (tttp) REVERT: C 252 MET cc_start: 0.9236 (tpt) cc_final: 0.8940 (tpt) REVERT: E 370 MET cc_start: 0.6318 (mtt) cc_final: 0.6100 (mtp) REVERT: F 84 MET cc_start: 0.7140 (mmt) cc_final: 0.6901 (mmt) REVERT: G 70 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7208 (tm-30) REVERT: H 12 ARG cc_start: 0.8340 (ptp-110) cc_final: 0.7472 (ptm-80) REVERT: H 37 LEU cc_start: 0.8936 (tp) cc_final: 0.8630 (pt) REVERT: H 68 THR cc_start: 0.8885 (OUTLIER) cc_final: 0.8620 (t) REVERT: H 99 GLU cc_start: 0.8090 (tt0) cc_final: 0.7669 (mt-10) REVERT: H 166 LYS cc_start: 0.8494 (tmmt) cc_final: 0.8164 (tttm) REVERT: H 398 LEU cc_start: 0.8244 (mt) cc_final: 0.7930 (mt) REVERT: H 400 ASN cc_start: 0.6564 (m-40) cc_final: 0.6178 (t0) REVERT: I 225 CYS cc_start: 0.8329 (t) cc_final: 0.8066 (t) REVERT: J 156 MET cc_start: 0.7165 (OUTLIER) cc_final: 0.6961 (ttm) REVERT: J 244 ASP cc_start: 0.6228 (m-30) cc_final: 0.5693 (p0) REVERT: J 402 ASP cc_start: 0.6317 (m-30) cc_final: 0.5843 (t70) REVERT: K 35 ARG cc_start: 0.8090 (tpp80) cc_final: 0.7359 (tpp80) REVERT: K 43 ILE cc_start: 0.8201 (mm) cc_final: 0.7739 (mt) REVERT: K 252 MET cc_start: 0.8498 (tpt) cc_final: 0.8063 (tpt) REVERT: K 348 ILE cc_start: 0.8574 (mm) cc_final: 0.8229 (pt) outliers start: 24 outliers final: 11 residues processed: 713 average time/residue: 0.2018 time to fit residues: 229.5379 Evaluate side-chains 380 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 367 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 156 MET Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 120 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: [432, 197, 388, 215, 20, 132, 261, 248, 207, 401, 424] chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.0980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 4.9990 chunk 424 optimal weight: 3.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 HIS ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN B 226 ASN C 226 ASN ** C 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 430 ASN D 9 HIS D 94 ASN D 359 GLN E 241 GLN E 409 GLN F 241 GLN F 378 GLN G 226 ASN G 241 GLN H 55 GLN H 175 ASN H 226 ASN H 241 GLN H 360 HIS H 423 ASN I 9 HIS ** I 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 360 HIS J 9 HIS J 55 GLN J 78 GLN J 409 GLN K 226 ASN K 430 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.153657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.094673 restraints weight = 57879.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.094683 restraints weight = 32019.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.095318 restraints weight = 24375.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.095698 restraints weight = 22661.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.095875 restraints weight = 19434.196| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33228 Z= 0.169 Angle : 0.583 11.158 45157 Z= 0.297 Chirality : 0.043 0.153 5364 Planarity : 0.004 0.052 5934 Dihedral : 4.061 37.049 4744 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.57 % Favored : 95.41 % Rotamer: Outliers : 3.48 % Allowed : 22.56 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.26 % 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: -0.12 (0.14), residues: 4332 helix: 1.37 (0.13), residues: 1683 sheet: -1.20 (0.19), residues: 862 loop : -0.82 (0.15), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 74 TYR 0.029 0.002 TYR D 237 PHE 0.017 0.001 PHE K 238 HIS 0.009 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (33223) covalent geometry : angle 0.58318 / 0.30 (45147) SS BOND : bond 0.00298 / 0.17 ( 5) SS BOND : angle 1.28075 / 0.78 ( 10) hydrogen bonds : bond 0.03735 / 2.59 ( 1388) hydrogen bonds : angle 5.14612 / 3.64 ( 3987) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 387 time to evaluate : 1.116 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: A 226 ASN cc_start: 0.8650 (OUTLIER) cc_final: 0.8040 (t0) REVERT: B 12 ARG cc_start: 0.7968 (ptp-110) cc_final: 0.7368 (ptp-110) REVERT: B 145 ASP cc_start: 0.8884 (m-30) cc_final: 0.8640 (t0) REVERT: C 36 ASP cc_start: 0.7300 (m-30) cc_final: 0.6335 (p0) REVERT: C 156 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8218 (ttm) REVERT: C 166 LYS cc_start: 0.8451 (tmmt) cc_final: 0.8228 (tttm) REVERT: C 243 LYS cc_start: 0.8104 (mttt) cc_final: 0.7824 (mtpp) REVERT: D 93 TYR cc_start: 0.2929 (m-80) cc_final: 0.2589 (m-80) REVERT: D 137 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6390 (pp) REVERT: D 170 MET cc_start: 0.8531 (mtm) cc_final: 0.8158 (mpp) REVERT: D 237 TYR cc_start: 0.8093 (t80) cc_final: 0.7810 (t80) REVERT: D 302 TYR cc_start: 0.7653 (m-80) cc_final: 0.7362 (m-10) REVERT: D 399 ASP cc_start: 0.8050 (m-30) cc_final: 0.7741 (t70) REVERT: E 166 LYS cc_start: 0.8772 (ptmm) cc_final: 0.8390 (ptmm) REVERT: E 243 LYS cc_start: 0.7426 (mttp) cc_final: 0.7036 (mttp) REVERT: E 255 TYR cc_start: 0.9190 (t80) cc_final: 0.8988 (t80) REVERT: E 259 LEU cc_start: 0.8575 (mt) cc_final: 0.8285 (mt) REVERT: E 412 MET cc_start: 0.7431 (mmp) cc_final: 0.6959 (tpp) REVERT: G 70 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7184 (tm-30) REVERT: H 18 LEU cc_start: 0.8906 (mt) cc_final: 0.8705 (mp) REVERT: H 37 LEU cc_start: 0.9038 (tp) cc_final: 0.8767 (pt) REVERT: H 144 ILE cc_start: 0.8987 (mm) cc_final: 0.8644 (tp) REVERT: H 166 LYS cc_start: 0.8014 (tmmt) cc_final: 0.7589 (tttp) REVERT: H 354 LYS cc_start: 0.8594 (ttmm) cc_final: 0.7872 (ttpp) REVERT: H 370 MET cc_start: 0.9467 (mtp) cc_final: 0.9237 (mtm) REVERT: I 45 LYS cc_start: 0.7941 (mtpp) cc_final: 0.7518 (mmmm) REVERT: J 84 MET cc_start: 0.5518 (mtt) cc_final: 0.4903 (mtm) REVERT: J 244 ASP cc_start: 0.7135 (m-30) cc_final: 0.6554 (t0) REVERT: J 402 ASP cc_start: 0.7354 (m-30) cc_final: 0.6566 (t70) REVERT: J 425 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7017 (tp) REVERT: K 18 LEU cc_start: 0.8784 (mt) cc_final: 0.8555 (mp) REVERT: K 226 ASN cc_start: 0.8804 (OUTLIER) cc_final: 0.8288 (t0) REVERT: K 348 ILE cc_start: 0.8603 (mm) cc_final: 0.8250 (pt) outliers start: 116 outliers final: 53 residues processed: 479 average time/residue: 0.1766 time to fit residues: 139.1011 Evaluate side-chains 398 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 340 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 285 LEU 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 37 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain H residue 7 CYS Chi-restraints excluded: chain H residue 78 GLN Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 317 ASP Chi-restraints excluded: chain H residue 360 HIS Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 332 GLN Chi-restraints excluded: chain I residue 338 HIS Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 425 LEU Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 216 THR Chi-restraints excluded: chain K residue 226 ASN Chi-restraints excluded: chain K residue 234 MET Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 285 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: [423, 13, 311, 274, 348, 129, 226, 147, 133, 118, 299] chunk 423 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 311 optimal weight: 8.9990 chunk 274 optimal weight: 0.9980 chunk 348 optimal weight: 20.0000 chunk 129 optimal weight: 20.0000 chunk 226 optimal weight: 4.9990 chunk 147 optimal weight: 7.9990 chunk 133 optimal weight: 20.0000 chunk 118 optimal weight: 0.9990 chunk 299 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 GLN ** E 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 396 HIS ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 376 GLN K 241 GLN ** K 338 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 = 0.4113 r_free = 0.4113 target = 0.149668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.092705 restraints weight = 58699.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.089127 restraints weight = 37608.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.090295 restraints weight = 28388.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.090812 restraints weight = 22712.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.091040 restraints weight = 20939.118| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 33228 Z= 0.248 Angle : 0.622 11.535 45157 Z= 0.314 Chirality : 0.045 0.224 5364 Planarity : 0.004 0.060 5934 Dihedral : 4.195 36.547 4734 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.31 % Favored : 94.67 % Rotamer: Outliers : 4.49 % Allowed : 22.23 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.26 % 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: -0.32 (0.13), residues: 4332 helix: 1.40 (0.13), residues: 1598 sheet: -1.71 (0.18), residues: 862 loop : -0.80 (0.15), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 426 TYR 0.020 0.002 TYR C 386 PHE 0.019 0.002 PHE A 197 HIS 0.034 0.001 HIS H 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.25 (33223) covalent geometry : angle 0.62147 / 0.31 (45147) SS BOND : bond 0.00303 / 0.18 ( 5) SS BOND : angle 1.64986 / 1.02 ( 10) hydrogen bonds : bond 0.04195 / 2.96 ( 1388) hydrogen bonds : angle 5.00864 / 3.54 ( 3987) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 337 time to evaluate : 1.014 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: A 52 LYS cc_start: 0.8254 (ttmt) cc_final: 0.7748 (tttt) REVERT: B 12 ARG cc_start: 0.8037 (ptp-110) cc_final: 0.7599 (ptp-110) REVERT: B 18 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8841 (mp) REVERT: C 98 GLU cc_start: 0.8288 (pm20) cc_final: 0.8082 (pm20) REVERT: C 156 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8244 (ttm) REVERT: C 376 GLN cc_start: 0.9463 (mm-40) cc_final: 0.8802 (tm-30) REVERT: D 137 LEU cc_start: 0.6977 (OUTLIER) cc_final: 0.6489 (pp) REVERT: D 234 MET cc_start: 0.8754 (mmm) cc_final: 0.7727 (mtm) REVERT: D 288 GLU cc_start: 0.8743 (tp30) cc_final: 0.8301 (tp30) REVERT: D 302 TYR cc_start: 0.7915 (m-80) cc_final: 0.7597 (m-10) REVERT: E 166 LYS cc_start: 0.8867 (ptmm) cc_final: 0.8653 (ptmm) REVERT: E 170 MET cc_start: 0.9270 (mtt) cc_final: 0.8734 (mtt) REVERT: E 243 LYS cc_start: 0.7642 (mttp) cc_final: 0.7106 (mttp) REVERT: E 252 MET cc_start: 0.9236 (tpt) cc_final: 0.8645 (mmt) REVERT: F 174 MET cc_start: 0.8484 (tpt) cc_final: 0.7940 (tpt) REVERT: F 401 ARG cc_start: 0.7972 (ttm-80) cc_final: 0.7598 (ttt180) REVERT: H 37 LEU cc_start: 0.9120 (tp) cc_final: 0.8819 (pt) REVERT: H 166 LYS cc_start: 0.8226 (tmmt) cc_final: 0.7868 (tttp) REVERT: H 400 ASN cc_start: 0.7253 (t0) cc_final: 0.6978 (t0) REVERT: I 45 LYS cc_start: 0.8163 (mtpp) cc_final: 0.7684 (mmmm) REVERT: I 252 MET cc_start: 0.7816 (tpp) cc_final: 0.7302 (tmm) REVERT: J 84 MET cc_start: 0.5826 (mtt) cc_final: 0.5562 (mtt) REVERT: J 181 ILE cc_start: 0.6791 (OUTLIER) cc_final: 0.6589 (pt) REVERT: J 244 ASP cc_start: 0.7464 (m-30) cc_final: 0.6001 (p0) REVERT: J 402 ASP cc_start: 0.7214 (m-30) cc_final: 0.6502 (t70) REVERT: K 129 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8940 (tt) REVERT: K 199 HIS cc_start: 0.8586 (OUTLIER) cc_final: 0.7907 (m170) REVERT: K 348 ILE cc_start: 0.8671 (mm) cc_final: 0.8360 (pt) outliers start: 150 outliers final: 84 residues processed: 461 average time/residue: 0.1730 time to fit residues: 133.2058 Evaluate side-chains 403 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 313 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 156 MET 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 345 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 156 MET 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 315 ILE Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 407 PHE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 170 MET Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 225 CYS Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain H residue 7 CYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 78 GLN Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 317 ASP Chi-restraints excluded: chain H residue 360 HIS Chi-restraints excluded: chain H residue 398 LEU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 184 ILE Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 338 HIS Chi-restraints excluded: chain J residue -1 SER Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 181 ILE Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 245 VAL Chi-restraints excluded: chain J residue 425 LEU Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 129 LEU Chi-restraints excluded: chain K residue 199 HIS Chi-restraints excluded: chain K residue 216 THR Chi-restraints excluded: chain K residue 234 MET Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 285 LEU Chi-restraints excluded: chain K residue 303 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: [240, 388, 102, 282, 383, 70, 429, 139, 85, 315, 431] chunk 240 optimal weight: 5.9990 chunk 388 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 282 optimal weight: 0.9990 chunk 383 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 429 optimal weight: 0.0170 chunk 139 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 315 optimal weight: 2.9990 chunk 431 optimal weight: 5.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 HIS B 241 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 GLN E 23 HIS ** E 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 GLN G 396 HIS H 175 ASN H 209 GLN ** I 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 241 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.152165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.096890 restraints weight = 59489.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.093113 restraints weight = 38240.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.094484 restraints weight = 29599.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.094690 restraints weight = 25517.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.096835 restraints weight = 21764.840| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 33228 Z= 0.105 Angle : 0.530 10.859 45157 Z= 0.261 Chirality : 0.042 0.248 5364 Planarity : 0.004 0.060 5934 Dihedral : 3.846 31.469 4733 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.20 % Favored : 95.78 % Rotamer: Outliers : 2.91 % Allowed : 23.46 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.26 % 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: -0.15 (0.13), residues: 4332 helix: 1.61 (0.13), residues: 1594 sheet: -1.62 (0.18), residues: 855 loop : -0.76 (0.15), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 12 TYR 0.023 0.001 TYR E 255 PHE 0.010 0.001 PHE C 407 HIS 0.007 0.000 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (33223) covalent geometry : angle 0.53020 / 0.26 (45147) SS BOND : bond 0.00634 / 0.35 ( 5) SS BOND : angle 0.82389 / 0.52 ( 10) hydrogen bonds : bond 0.03253 / 2.27 ( 1388) hydrogen bonds : angle 4.79337 / 3.39 ( 3987) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 336 time to evaluate : 1.155 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 12 ARG cc_start: 0.7856 (ptp-110) cc_final: 0.7494 (ptp-110) REVERT: B 145 ASP cc_start: 0.8726 (OUTLIER) cc_final: 0.8264 (t0) REVERT: C 156 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.8081 (ttm) REVERT: C 376 GLN cc_start: 0.9396 (mm-40) cc_final: 0.8777 (tm-30) REVERT: C 388 ARG cc_start: 0.8520 (tpp-160) cc_final: 0.8220 (tpp80) REVERT: D 84 MET cc_start: 0.2602 (ptp) cc_final: 0.2346 (ptp) REVERT: D 137 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6562 (pp) REVERT: D 156 MET cc_start: 0.8114 (tpp) cc_final: 0.7326 (mmt) REVERT: D 170 MET cc_start: 0.8596 (mtm) cc_final: 0.8137 (mpp) REVERT: D 285 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8126 (mp) REVERT: D 288 GLU cc_start: 0.8793 (tp30) cc_final: 0.8414 (tp30) REVERT: D 302 TYR cc_start: 0.7844 (m-80) cc_final: 0.7459 (m-10) REVERT: E 166 LYS cc_start: 0.8834 (ptmm) cc_final: 0.8514 (ptmm) REVERT: E 170 MET cc_start: 0.9152 (mtt) cc_final: 0.8844 (mtt) REVERT: E 243 LYS cc_start: 0.7418 (mttp) cc_final: 0.6979 (mtmt) REVERT: E 252 MET cc_start: 0.9238 (tpt) cc_final: 0.8744 (mmt) REVERT: E 413 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7061 (tp30) REVERT: F 174 MET cc_start: 0.8427 (tpt) cc_final: 0.7942 (tpt) REVERT: F 401 ARG cc_start: 0.8032 (ttm-80) cc_final: 0.7642 (ttt180) REVERT: F 402 ASP cc_start: 0.8629 (m-30) cc_final: 0.8230 (p0) REVERT: H 14 HIS cc_start: 0.6711 (m-70) cc_final: 0.6436 (m170) REVERT: H 43 ILE cc_start: 0.8743 (mm) cc_final: 0.8525 (mt) REVERT: H 144 ILE cc_start: 0.9127 (mm) cc_final: 0.8792 (tp) REVERT: H 166 LYS cc_start: 0.8226 (tmmt) cc_final: 0.7858 (tttp) REVERT: H 209 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7793 (pm20) REVERT: H 400 ASN cc_start: 0.7339 (t0) cc_final: 0.7010 (t0) REVERT: I 45 LYS cc_start: 0.8309 (mtpp) cc_final: 0.7749 (mmmm) REVERT: I 252 MET cc_start: 0.7857 (tpp) cc_final: 0.7279 (tmm) REVERT: I 302 TYR cc_start: 0.6866 (m-10) cc_final: 0.6533 (m-10) REVERT: I 328 TYR cc_start: 0.7844 (t80) cc_final: 0.7356 (t80) REVERT: J 84 MET cc_start: 0.5837 (mtt) cc_final: 0.5252 (mtm) REVERT: J 244 ASP cc_start: 0.7359 (m-30) cc_final: 0.5873 (p0) REVERT: J 379 LEU cc_start: 0.7485 (pp) cc_final: 0.7255 (pp) REVERT: J 402 ASP cc_start: 0.7189 (m-30) cc_final: 0.6503 (t70) REVERT: K 348 ILE cc_start: 0.8686 (mm) cc_final: 0.8396 (pt) outliers start: 97 outliers final: 64 residues processed: 413 average time/residue: 0.1792 time to fit residues: 122.6014 Evaluate side-chains 385 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 315 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain B residue 7 CYS 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 120 VAL Chi-restraints excluded: chain B residue 145 ASP 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 181 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain C residue 156 MET 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 315 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 407 PHE Chi-restraints excluded: chain E residue 413 GLU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 226 ASN 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 H residue 7 CYS Chi-restraints excluded: chain H residue 78 GLN Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 209 GLN Chi-restraints excluded: chain H residue 317 ASP Chi-restraints excluded: chain H residue 333 LEU Chi-restraints excluded: chain I residue 184 ILE Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 338 HIS Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 245 VAL Chi-restraints excluded: chain J residue 425 LEU Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 216 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 319 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: [94, 76, 370, 204, 372, 243, 283, 257, 233, 49, 88] chunk 94 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 370 optimal weight: 5.9990 chunk 204 optimal weight: 4.9990 chunk 372 optimal weight: 9.9990 chunk 243 optimal weight: 5.9990 chunk 283 optimal weight: 0.1980 chunk 257 optimal weight: 0.1980 chunk 233 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 HIS A 332 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 GLN E 55 GLN ** E 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 360 HIS ** I 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.149078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.094254 restraints weight = 58048.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.090945 restraints weight = 38049.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.092260 restraints weight = 29497.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.092838 restraints weight = 23890.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.093283 restraints weight = 20850.359| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 33228 Z= 0.205 Angle : 0.575 11.358 45157 Z= 0.288 Chirality : 0.044 0.246 5364 Planarity : 0.004 0.060 5934 Dihedral : 3.999 33.520 4732 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.75 % Favored : 94.23 % Rotamer: Outliers : 4.01 % Allowed : 22.44 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.26 % 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: 4332 helix: 1.53 (0.13), residues: 1601 sheet: -1.83 (0.18), residues: 870 loop : -0.77 (0.15), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 426 TYR 0.021 0.002 TYR C 386 PHE 0.015 0.001 PHE A 197 HIS 0.005 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.21 (33223) covalent geometry : angle 0.57504 / 0.29 (45147) SS BOND : bond 0.00177 / 0.09 ( 5) SS BOND : angle 1.45492 / 0.89 ( 10) hydrogen bonds : bond 0.03637 / 2.56 ( 1388) hydrogen bonds : angle 4.79158 / 3.39 ( 3987) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 331 time to evaluate : 1.256 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 12 ARG cc_start: 0.7981 (ptp-110) cc_final: 0.7619 (ptp-110) REVERT: B 18 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8865 (mp) REVERT: B 129 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.8915 (tt) REVERT: B 145 ASP cc_start: 0.8784 (OUTLIER) cc_final: 0.8427 (t0) REVERT: B 399 ASP cc_start: 0.8577 (m-30) cc_final: 0.8306 (m-30) REVERT: C 156 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8196 (ttm) REVERT: C 388 ARG cc_start: 0.8491 (tpp-160) cc_final: 0.8164 (tpp80) REVERT: D 137 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6633 (pp) REVERT: D 225 CYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8128 (p) REVERT: D 237 TYR cc_start: 0.8266 (t80) cc_final: 0.7946 (t80) REVERT: D 285 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8285 (mp) REVERT: D 288 GLU cc_start: 0.8790 (tp30) cc_final: 0.8340 (tp30) REVERT: D 302 TYR cc_start: 0.7890 (m-80) cc_final: 0.7622 (m-10) REVERT: E 166 LYS cc_start: 0.8847 (ptmm) cc_final: 0.8506 (ptmm) REVERT: E 170 MET cc_start: 0.9116 (mtt) cc_final: 0.8729 (mtt) REVERT: E 243 LYS cc_start: 0.7362 (mttp) cc_final: 0.7008 (mttm) REVERT: E 252 MET cc_start: 0.9236 (tpt) cc_final: 0.8698 (mmt) REVERT: F 401 ARG cc_start: 0.8016 (ttm-80) cc_final: 0.7770 (ttt180) REVERT: F 402 ASP cc_start: 0.8679 (m-30) cc_final: 0.8299 (p0) REVERT: G 156 MET cc_start: 0.8931 (ttm) cc_final: 0.8681 (ttt) REVERT: H 144 ILE cc_start: 0.9174 (mm) cc_final: 0.8835 (tp) REVERT: H 166 LYS cc_start: 0.8332 (tmmt) cc_final: 0.7953 (tttp) REVERT: H 318 GLU cc_start: 0.8604 (tp30) cc_final: 0.8396 (tp30) REVERT: H 400 ASN cc_start: 0.7306 (t0) cc_final: 0.6669 (t0) REVERT: I 45 LYS cc_start: 0.8311 (mtpp) cc_final: 0.7770 (mmmm) REVERT: I 328 TYR cc_start: 0.7846 (t80) cc_final: 0.7450 (t80) REVERT: J 84 MET cc_start: 0.5879 (mtt) cc_final: 0.5358 (mtm) REVERT: J 244 ASP cc_start: 0.7571 (m-30) cc_final: 0.6092 (p0) REVERT: J 305 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.7796 (mt) REVERT: J 402 ASP cc_start: 0.7008 (m-30) cc_final: 0.6322 (t70) REVERT: K 17 LEU cc_start: 0.8213 (mm) cc_final: 0.7820 (tp) REVERT: K 156 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8045 (tpt) REVERT: K 199 HIS cc_start: 0.8563 (OUTLIER) cc_final: 0.7901 (m170) REVERT: K 348 ILE cc_start: 0.8712 (mm) cc_final: 0.8399 (pt) outliers start: 134 outliers final: 90 residues processed: 441 average time/residue: 0.1766 time to fit residues: 129.8493 Evaluate side-chains 406 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 306 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 120 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 345 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 171 SER 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 244 ASP Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 178 VAL 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 285 LEU Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 407 PHE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 225 CYS Chi-restraints excluded: chain G residue 226 ASN Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain H residue 7 CYS Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 78 GLN Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 150 CYS Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 225 CYS Chi-restraints excluded: chain H residue 234 MET Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 317 ASP Chi-restraints excluded: chain H residue 333 LEU Chi-restraints excluded: chain H residue 360 HIS Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 338 HIS Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 245 VAL Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 425 LEU Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 156 MET Chi-restraints excluded: chain K residue 199 HIS Chi-restraints excluded: chain K residue 216 THR Chi-restraints excluded: chain K residue 234 MET Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 285 LEU Chi-restraints excluded: chain K residue 303 THR Chi-restraints excluded: chain K residue 319 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: [297, 86, 239, 423, 370, 180, 14, 431, 333, 432, 63] chunk 297 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 239 optimal weight: 0.6980 chunk 423 optimal weight: 0.8980 chunk 370 optimal weight: 8.9990 chunk 180 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 431 optimal weight: 8.9990 chunk 333 optimal weight: 10.0000 chunk 432 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 23 HIS ** K 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.150390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.094112 restraints weight = 59247.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.090557 restraints weight = 36771.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.091720 restraints weight = 27684.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.092349 restraints weight = 22181.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.092562 restraints weight = 20409.432| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33228 Z= 0.136 Angle : 0.550 11.780 45157 Z= 0.269 Chirality : 0.043 0.293 5364 Planarity : 0.004 0.059 5934 Dihedral : 3.846 30.240 4732 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.59 % Favored : 95.38 % Rotamer: Outliers : 3.33 % Allowed : 23.43 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.26 % 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: -0.13 (0.13), residues: 4332 helix: 1.68 (0.13), residues: 1586 sheet: -1.74 (0.18), residues: 846 loop : -0.74 (0.15), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 12 TYR 0.023 0.001 TYR C 386 PHE 0.012 0.001 PHE B 4 HIS 0.005 0.000 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (33223) covalent geometry : angle 0.55021 / 0.27 (45147) SS BOND : bond 0.00153 / 0.09 ( 5) SS BOND : angle 1.03552 / 0.64 ( 10) hydrogen bonds : bond 0.03179 / 2.23 ( 1388) hydrogen bonds : angle 4.67147 / 3.30 ( 3987) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 326 time to evaluate : 1.110 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 12 ARG cc_start: 0.7962 (ptp-110) cc_final: 0.7541 (ptp-110) REVERT: B 145 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8394 (t0) REVERT: C 156 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8106 (ttm) REVERT: C 388 ARG cc_start: 0.8481 (tpp-160) cc_final: 0.8160 (tpp80) REVERT: D 137 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6662 (pp) REVERT: D 170 MET cc_start: 0.8520 (mtm) cc_final: 0.8076 (mpp) REVERT: D 225 CYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8108 (p) REVERT: D 237 TYR cc_start: 0.8251 (t80) cc_final: 0.7904 (t80) REVERT: D 285 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8320 (mp) REVERT: D 288 GLU cc_start: 0.8752 (tp30) cc_final: 0.8283 (tp30) REVERT: D 320 ARG cc_start: 0.8462 (ttp-110) cc_final: 0.7804 (ptp-170) REVERT: D 399 ASP cc_start: 0.7808 (m-30) cc_final: 0.7529 (t70) REVERT: E 166 LYS cc_start: 0.8796 (ptmm) cc_final: 0.8470 (ptmm) REVERT: E 170 MET cc_start: 0.9142 (mtt) cc_final: 0.8735 (mtt) REVERT: E 243 LYS cc_start: 0.7226 (mttp) cc_final: 0.6815 (mtmt) REVERT: E 252 MET cc_start: 0.9274 (tpt) cc_final: 0.8739 (mmt) REVERT: F 52 LYS cc_start: 0.8913 (ttpp) cc_final: 0.8497 (ttpp) REVERT: F 53 GLU cc_start: 0.9022 (pm20) cc_final: 0.8766 (pm20) REVERT: F 402 ASP cc_start: 0.8673 (m-30) cc_final: 0.8345 (p0) REVERT: G 174 MET cc_start: 0.8419 (tpp) cc_final: 0.8162 (mmm) REVERT: H 19 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7660 (mt-10) REVERT: H 43 ILE cc_start: 0.8774 (mm) cc_final: 0.8567 (mt) REVERT: H 144 ILE cc_start: 0.9099 (mm) cc_final: 0.8766 (tp) REVERT: H 166 LYS cc_start: 0.8213 (tmmt) cc_final: 0.7784 (tttp) REVERT: H 318 GLU cc_start: 0.8581 (tp30) cc_final: 0.8358 (tp30) REVERT: H 357 THR cc_start: 0.5999 (OUTLIER) cc_final: 0.5781 (m) REVERT: H 400 ASN cc_start: 0.7306 (t0) cc_final: 0.6648 (t0) REVERT: H 426 ARG cc_start: 0.9002 (tpm170) cc_final: 0.8652 (tpm170) REVERT: I 45 LYS cc_start: 0.8194 (mtpp) cc_final: 0.7657 (mmmm) REVERT: I 328 TYR cc_start: 0.7821 (t80) cc_final: 0.7389 (t80) REVERT: J 84 MET cc_start: 0.5887 (mtt) cc_final: 0.5374 (mtm) REVERT: J 244 ASP cc_start: 0.7551 (m-30) cc_final: 0.6019 (p0) REVERT: J 305 LEU cc_start: 0.8694 (tt) cc_final: 0.7820 (mt) REVERT: J 402 ASP cc_start: 0.7244 (m-30) cc_final: 0.6509 (t70) REVERT: K 156 MET cc_start: 0.8353 (ttm) cc_final: 0.8044 (tpt) REVERT: K 199 HIS cc_start: 0.8585 (OUTLIER) cc_final: 0.7904 (m170) REVERT: K 348 ILE cc_start: 0.8689 (mm) cc_final: 0.8342 (pt) outliers start: 111 outliers final: 87 residues processed: 417 average time/residue: 0.1743 time to fit residues: 121.5064 Evaluate side-chains 403 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 309 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 120 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 303 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain B residue 7 CYS 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 120 VAL Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 171 SER 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 404 ILE Chi-restraints excluded: chain C residue 156 MET 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 315 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 407 PHE Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 225 CYS Chi-restraints excluded: chain G residue 226 ASN Chi-restraints excluded: chain G residue 269 LEU 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 H residue 7 CYS Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 78 GLN Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 225 CYS Chi-restraints excluded: chain H residue 234 MET Chi-restraints excluded: chain H residue 317 ASP Chi-restraints excluded: chain H residue 333 LEU Chi-restraints excluded: chain H residue 357 THR Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 184 ILE Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 338 HIS Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 245 VAL Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 346 HIS Chi-restraints excluded: chain J residue 425 LEU Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 199 HIS Chi-restraints excluded: chain K residue 216 THR Chi-restraints excluded: chain K residue 225 CYS Chi-restraints excluded: chain K residue 234 MET Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 285 LEU Chi-restraints excluded: chain K residue 319 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: [183, 72, 248, 338, 179, 435, 15, 196, 224, 311, 214] chunk 183 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 338 optimal weight: 8.9990 chunk 179 optimal weight: 9.9990 chunk 435 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 196 optimal weight: 20.0000 chunk 224 optimal weight: 2.9990 chunk 311 optimal weight: 6.9990 chunk 214 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 396 HIS I 9 HIS I 14 HIS I 346 HIS K 87 HIS ** K 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.147985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.093183 restraints weight = 59686.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.088365 restraints weight = 38480.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.089584 restraints weight = 30606.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.089925 restraints weight = 25813.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.090294 restraints weight = 22272.262| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 33228 Z= 0.229 Angle : 0.607 11.634 45157 Z= 0.303 Chirality : 0.044 0.288 5364 Planarity : 0.004 0.059 5934 Dihedral : 4.130 33.556 4732 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.89 % Favored : 94.09 % Rotamer: Outliers : 4.04 % Allowed : 23.01 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.26 % 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: -0.30 (0.13), residues: 4332 helix: 1.51 (0.13), residues: 1597 sheet: -1.84 (0.18), residues: 830 loop : -0.83 (0.15), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 12 TYR 0.024 0.002 TYR C 386 PHE 0.017 0.001 PHE A 197 HIS 0.005 0.001 HIS G 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.23 (33223) covalent geometry : angle 0.60712 / 0.30 (45147) SS BOND : bond 0.00226 / 0.14 ( 5) SS BOND : angle 1.55191 / 0.95 ( 10) hydrogen bonds : bond 0.03771 / 2.66 ( 1388) hydrogen bonds : angle 4.77657 / 3.38 ( 3987) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 312 time to evaluate : 1.204 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: A 129 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8689 (tt) REVERT: B 12 ARG cc_start: 0.8054 (ptp-110) cc_final: 0.7685 (ptp-110) REVERT: B 18 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8904 (mp) REVERT: B 129 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.8946 (tt) REVERT: B 145 ASP cc_start: 0.8764 (OUTLIER) cc_final: 0.8457 (t0) REVERT: C 156 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8171 (ttm) REVERT: C 388 ARG cc_start: 0.8447 (tpp-160) cc_final: 0.8114 (tpp80) REVERT: D 137 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6764 (pp) REVERT: D 156 MET cc_start: 0.8066 (tpp) cc_final: 0.7407 (mmt) REVERT: D 170 MET cc_start: 0.8498 (mtm) cc_final: 0.8047 (mpp) REVERT: D 225 CYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8048 (p) REVERT: D 237 TYR cc_start: 0.8123 (t80) cc_final: 0.7845 (t80) REVERT: D 285 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8444 (mp) REVERT: D 320 ARG cc_start: 0.8486 (ttp-110) cc_final: 0.7730 (ptp90) REVERT: E 166 LYS cc_start: 0.8895 (ptmm) cc_final: 0.8603 (ptmm) REVERT: E 243 LYS cc_start: 0.7311 (mttp) cc_final: 0.6958 (mttm) REVERT: E 252 MET cc_start: 0.9210 (tpt) cc_final: 0.8654 (mmt) REVERT: F 401 ARG cc_start: 0.8073 (ttm-80) cc_final: 0.7702 (ttt180) REVERT: F 402 ASP cc_start: 0.8656 (m-30) cc_final: 0.8296 (p0) REVERT: H 43 ILE cc_start: 0.8809 (mm) cc_final: 0.8598 (mt) REVERT: H 144 ILE cc_start: 0.9175 (mm) cc_final: 0.8850 (tp) REVERT: H 166 LYS cc_start: 0.8347 (tmmt) cc_final: 0.7903 (tttp) REVERT: H 400 ASN cc_start: 0.7283 (t0) cc_final: 0.6658 (t0) REVERT: H 426 ARG cc_start: 0.8973 (tpm170) cc_final: 0.8578 (tpm170) REVERT: I 328 TYR cc_start: 0.7668 (t80) cc_final: 0.7242 (t80) REVERT: J 84 MET cc_start: 0.6008 (mtt) cc_final: 0.5463 (mtm) REVERT: J 181 ILE cc_start: 0.7187 (OUTLIER) cc_final: 0.6878 (tt) REVERT: J 244 ASP cc_start: 0.7606 (m-30) cc_final: 0.6149 (p0) REVERT: J 252 MET cc_start: 0.7264 (mmm) cc_final: 0.7061 (mmm) REVERT: J 402 ASP cc_start: 0.7066 (m-30) cc_final: 0.6344 (t70) REVERT: K 156 MET cc_start: 0.8415 (ttm) cc_final: 0.8120 (tpt) REVERT: K 199 HIS cc_start: 0.8625 (OUTLIER) cc_final: 0.7923 (m170) REVERT: K 348 ILE cc_start: 0.8708 (mm) cc_final: 0.8367 (pt) outliers start: 135 outliers final: 99 residues processed: 427 average time/residue: 0.1748 time to fit residues: 124.2437 Evaluate side-chains 403 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 294 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 129 LEU 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 357 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 18 LEU 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 120 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 171 SER 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 404 ILE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 178 VAL 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 285 LEU Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 407 PHE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 225 CYS Chi-restraints excluded: chain G residue 226 ASN Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain H residue 7 CYS Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 78 GLN Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 225 CYS Chi-restraints excluded: chain H residue 234 MET Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 317 ASP Chi-restraints excluded: chain H residue 333 LEU Chi-restraints excluded: chain H residue 360 HIS Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 184 ILE Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 338 HIS Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 181 ILE Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 216 THR Chi-restraints excluded: chain J residue 245 VAL Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 346 HIS Chi-restraints excluded: chain J residue 425 LEU Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 199 HIS Chi-restraints excluded: chain K residue 216 THR Chi-restraints excluded: chain K residue 225 CYS Chi-restraints excluded: chain K residue 234 MET Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 285 LEU Chi-restraints excluded: chain K residue 303 THR Chi-restraints excluded: chain K residue 319 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: [2, 328, 404, 71, 296, 59, 129, 8, 199, 269, 211] chunk 2 optimal weight: 0.9980 chunk 328 optimal weight: 5.9990 chunk 404 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 296 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 199 optimal weight: 4.9990 chunk 269 optimal weight: 4.9990 chunk 211 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 HIS E 378 GLN G 332 GLN ** I 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 226 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.149512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.094121 restraints weight = 59877.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.091637 restraints weight = 36279.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.092132 restraints weight = 30450.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.093298 restraints weight = 23933.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.093354 restraints weight = 20921.340| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 33228 Z= 0.175 Angle : 0.575 12.428 45157 Z= 0.282 Chirality : 0.043 0.302 5364 Planarity : 0.004 0.059 5934 Dihedral : 4.006 30.006 4732 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.94 % Favored : 95.04 % Rotamer: Outliers : 3.74 % Allowed : 23.64 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.26 % 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: -0.20 (0.13), residues: 4332 helix: 1.62 (0.13), residues: 1571 sheet: -1.77 (0.18), residues: 824 loop : -0.78 (0.15), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 12 TYR 0.022 0.001 TYR C 386 PHE 0.020 0.001 PHE C 197 HIS 0.004 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.17 (33223) covalent geometry : angle 0.57478 / 0.28 (45147) SS BOND : bond 0.00182 / 0.11 ( 5) SS BOND : angle 1.20860 / 0.75 ( 10) hydrogen bonds : bond 0.03328 / 2.33 ( 1388) hydrogen bonds : angle 4.70835 / 3.32 ( 3987) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 317 time to evaluate : 1.195 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: A 174 MET cc_start: 0.8153 (tpt) cc_final: 0.7909 (tpt) REVERT: B 12 ARG cc_start: 0.7950 (ptp-110) cc_final: 0.7643 (ptp-110) REVERT: B 18 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8868 (mp) REVERT: B 145 ASP cc_start: 0.8718 (OUTLIER) cc_final: 0.8400 (t0) REVERT: C 129 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9153 (tt) REVERT: C 156 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8121 (ttm) REVERT: C 388 ARG cc_start: 0.8458 (tpp-160) cc_final: 0.8093 (tpp80) REVERT: D 137 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6872 (pp) REVERT: D 156 MET cc_start: 0.8083 (tpp) cc_final: 0.7444 (mmt) REVERT: D 170 MET cc_start: 0.8477 (mtm) cc_final: 0.8031 (mpp) REVERT: D 225 CYS cc_start: 0.8258 (OUTLIER) cc_final: 0.8028 (p) REVERT: D 237 TYR cc_start: 0.8096 (t80) cc_final: 0.7849 (t80) REVERT: D 320 ARG cc_start: 0.8504 (ttp-110) cc_final: 0.8105 (ptp90) REVERT: D 399 ASP cc_start: 0.7589 (m-30) cc_final: 0.7319 (t70) REVERT: E 166 LYS cc_start: 0.8833 (ptmm) cc_final: 0.8535 (ptmm) REVERT: E 243 LYS cc_start: 0.7271 (mttp) cc_final: 0.6928 (mttm) REVERT: E 252 MET cc_start: 0.9212 (tpt) cc_final: 0.8625 (mmt) REVERT: F 32 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8915 (mt) REVERT: F 238 PHE cc_start: 0.8782 (m-80) cc_final: 0.8534 (m-10) REVERT: F 401 ARG cc_start: 0.8091 (ttm-80) cc_final: 0.7772 (ttt180) REVERT: F 402 ASP cc_start: 0.8671 (m-30) cc_final: 0.8310 (p0) REVERT: G 174 MET cc_start: 0.8460 (tpp) cc_final: 0.8200 (mmm) REVERT: H 43 ILE cc_start: 0.8818 (mm) cc_final: 0.8601 (mt) REVERT: H 144 ILE cc_start: 0.9196 (mm) cc_final: 0.8888 (tp) REVERT: H 166 LYS cc_start: 0.8343 (tmmt) cc_final: 0.7895 (tttp) REVERT: H 318 GLU cc_start: 0.8453 (tp30) cc_final: 0.8233 (tp30) REVERT: H 400 ASN cc_start: 0.7224 (t0) cc_final: 0.6571 (t0) REVERT: H 426 ARG cc_start: 0.8969 (tpm170) cc_final: 0.8683 (tpm170) REVERT: I 328 TYR cc_start: 0.7750 (t80) cc_final: 0.7315 (t80) REVERT: J 244 ASP cc_start: 0.7452 (m-30) cc_final: 0.5893 (p0) REVERT: J 379 LEU cc_start: 0.7474 (pp) cc_final: 0.7038 (mp) REVERT: J 402 ASP cc_start: 0.7006 (m-30) cc_final: 0.6318 (t70) REVERT: K 199 HIS cc_start: 0.8607 (OUTLIER) cc_final: 0.7940 (m170) REVERT: K 348 ILE cc_start: 0.8701 (mm) cc_final: 0.8371 (pt) outliers start: 125 outliers final: 95 residues processed: 416 average time/residue: 0.1747 time to fit residues: 121.9232 Evaluate side-chains 409 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 306 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 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 357 THR Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 171 SER 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 404 ILE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 156 MET 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 303 THR Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 182 CYS Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 378 GLN Chi-restraints excluded: chain E residue 407 PHE Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 225 CYS Chi-restraints excluded: chain G residue 226 ASN Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 332 GLN Chi-restraints excluded: chain H residue 7 CYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 78 GLN Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 225 CYS Chi-restraints excluded: chain H residue 234 MET Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 317 ASP Chi-restraints excluded: chain H residue 333 LEU Chi-restraints excluded: chain H residue 398 LEU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 184 ILE Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 338 HIS Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 216 THR Chi-restraints excluded: chain J residue 245 VAL Chi-restraints excluded: chain J residue 346 HIS Chi-restraints excluded: chain J residue 425 LEU Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 199 HIS Chi-restraints excluded: chain K residue 216 THR Chi-restraints excluded: chain K residue 225 CYS Chi-restraints excluded: chain K residue 234 MET Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 285 LEU Chi-restraints excluded: chain K residue 303 THR Chi-restraints excluded: chain K residue 319 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: [391, 138, 384, 251, 152, 211, 271, 51, 31, 298, 212] chunk 391 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 384 optimal weight: 10.0000 chunk 251 optimal weight: 0.1980 chunk 152 optimal weight: 6.9990 chunk 211 optimal weight: 4.9990 chunk 271 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 298 optimal weight: 8.9990 chunk 212 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 409 GLN ** G 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 226 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.150624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.096100 restraints weight = 59401.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.092179 restraints weight = 37231.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.094107 restraints weight = 30068.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.094511 restraints weight = 23511.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.094879 restraints weight = 20312.751| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33228 Z= 0.120 Angle : 0.558 12.494 45157 Z= 0.271 Chirality : 0.043 0.307 5364 Planarity : 0.004 0.059 5934 Dihedral : 3.837 26.969 4731 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.99 % Favored : 94.99 % Rotamer: Outliers : 2.97 % Allowed : 24.18 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.26 % 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: -0.07 (0.13), residues: 4332 helix: 1.73 (0.13), residues: 1569 sheet: -1.66 (0.19), residues: 827 loop : -0.72 (0.15), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 12 TYR 0.024 0.001 TYR J 237 PHE 0.013 0.001 PHE B 4 HIS 0.005 0.000 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (33223) covalent geometry : angle 0.55820 / 0.27 (45147) SS BOND : bond 0.00392 / 0.27 ( 5) SS BOND : angle 0.95519 / 0.57 ( 10) hydrogen bonds : bond 0.03060 / 2.14 ( 1388) hydrogen bonds : angle 4.62871 / 3.26 ( 3987) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 318 time to evaluate : 1.289 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: A 174 MET cc_start: 0.8095 (tpt) cc_final: 0.7871 (tpt) REVERT: B 12 ARG cc_start: 0.7922 (ptp-110) cc_final: 0.7551 (ptp-110) REVERT: B 121 ASP cc_start: 0.8671 (t0) cc_final: 0.7963 (p0) REVERT: B 145 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8383 (t0) REVERT: C 129 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9134 (tt) REVERT: C 156 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8114 (ttm) REVERT: C 388 ARG cc_start: 0.8446 (tpp-160) cc_final: 0.8080 (tpp80) REVERT: D 137 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6933 (pp) REVERT: D 156 MET cc_start: 0.8095 (tpp) cc_final: 0.7395 (mmt) REVERT: D 225 CYS cc_start: 0.8308 (OUTLIER) cc_final: 0.8017 (p) REVERT: D 237 TYR cc_start: 0.8103 (t80) cc_final: 0.7835 (t80) REVERT: D 320 ARG cc_start: 0.8728 (ttp-110) cc_final: 0.8092 (ptp90) REVERT: D 399 ASP cc_start: 0.7642 (m-30) cc_final: 0.7360 (t70) REVERT: E 166 LYS cc_start: 0.8817 (ptmm) cc_final: 0.8524 (ptmm) REVERT: E 243 LYS cc_start: 0.7218 (mttp) cc_final: 0.6882 (mttm) REVERT: E 252 MET cc_start: 0.9219 (tpt) cc_final: 0.8629 (mmt) REVERT: F 402 ASP cc_start: 0.8679 (m-30) cc_final: 0.8390 (p0) REVERT: G 174 MET cc_start: 0.8424 (tpp) cc_final: 0.8185 (mmm) REVERT: H 144 ILE cc_start: 0.9169 (mm) cc_final: 0.8865 (tp) REVERT: H 166 LYS cc_start: 0.8277 (tmmt) cc_final: 0.7835 (tttp) REVERT: H 240 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7724 (t0) REVERT: H 357 THR cc_start: 0.6064 (OUTLIER) cc_final: 0.5849 (m) REVERT: H 400 ASN cc_start: 0.7243 (t0) cc_final: 0.6606 (t0) REVERT: H 426 ARG cc_start: 0.8978 (tpm170) cc_final: 0.8675 (tpm170) REVERT: I 328 TYR cc_start: 0.7755 (t80) cc_final: 0.7318 (t80) REVERT: J 84 MET cc_start: 0.6088 (mtt) cc_final: 0.5853 (mtm) REVERT: J 244 ASP cc_start: 0.7426 (m-30) cc_final: 0.5831 (p0) REVERT: J 402 ASP cc_start: 0.7071 (m-30) cc_final: 0.6360 (t70) REVERT: K 199 HIS cc_start: 0.8610 (OUTLIER) cc_final: 0.7941 (m170) REVERT: K 348 ILE cc_start: 0.8680 (mm) cc_final: 0.8390 (pt) outliers start: 99 outliers final: 85 residues processed: 399 average time/residue: 0.1763 time to fit residues: 116.5870 Evaluate side-chains 399 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 306 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 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 303 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 171 SER 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 357 THR Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 178 VAL 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 285 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 407 PHE Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 225 CYS Chi-restraints excluded: chain G residue 226 ASN Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain H residue 7 CYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 78 GLN Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 225 CYS Chi-restraints excluded: chain H residue 234 MET Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 317 ASP Chi-restraints excluded: chain H residue 333 LEU Chi-restraints excluded: chain H residue 357 THR Chi-restraints excluded: chain H residue 398 LEU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 184 ILE Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 338 HIS Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 216 THR Chi-restraints excluded: chain J residue 245 VAL Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 346 HIS Chi-restraints excluded: chain J residue 425 LEU Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 199 HIS Chi-restraints excluded: chain K residue 216 THR Chi-restraints excluded: chain K residue 234 MET Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: [117, 103, 361, 55, 373, 170, 390, 407, 90, 306, 365] chunk 117 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 361 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 373 optimal weight: 10.0000 chunk 170 optimal weight: 7.9990 chunk 390 optimal weight: 8.9990 chunk 407 optimal weight: 0.0770 chunk 90 optimal weight: 0.9990 chunk 306 optimal weight: 0.9990 chunk 365 optimal weight: 30.0000 overall best weight: 1.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 332 GLN ** J 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.150354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.095072 restraints weight = 59542.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.092245 restraints weight = 37100.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.092798 restraints weight = 30254.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.094201 restraints weight = 23782.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.094219 restraints weight = 20428.129| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33228 Z= 0.131 Angle : 0.566 12.710 45157 Z= 0.276 Chirality : 0.043 0.299 5364 Planarity : 0.004 0.057 5934 Dihedral : 3.790 26.483 4730 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.99 % Favored : 94.99 % Rotamer: Outliers : 3.15 % Allowed : 24.33 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.26 % 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: -0.00 (0.13), residues: 4332 helix: 1.79 (0.13), residues: 1559 sheet: -1.61 (0.19), residues: 818 loop : -0.69 (0.15), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 12 TYR 0.024 0.001 TYR J 237 PHE 0.012 0.001 PHE B 4 HIS 0.005 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (33223) covalent geometry : angle 0.56587 / 0.28 (45147) SS BOND : bond 0.00169 / 0.10 ( 5) SS BOND : angle 0.96874 / 0.61 ( 10) hydrogen bonds : bond 0.03073 / 2.15 ( 1388) hydrogen bonds : angle 4.60816 / 3.25 ( 3987) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 319 time to evaluate : 1.165 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: B 12 ARG cc_start: 0.7914 (ptp-110) cc_final: 0.7647 (ptp-110) REVERT: B 121 ASP cc_start: 0.8701 (t0) cc_final: 0.8000 (p0) REVERT: B 145 ASP cc_start: 0.8725 (OUTLIER) cc_final: 0.8390 (t0) REVERT: B 193 GLU cc_start: 0.8335 (tp30) cc_final: 0.8102 (tp30) REVERT: B 285 LEU cc_start: 0.9261 (mm) cc_final: 0.9017 (mp) REVERT: C 129 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9134 (tt) REVERT: C 156 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.8104 (ttm) REVERT: C 388 ARG cc_start: 0.8421 (tpp-160) cc_final: 0.8098 (tpp80) REVERT: D 156 MET cc_start: 0.8084 (tpp) cc_final: 0.7294 (mmt) REVERT: D 170 MET cc_start: 0.8429 (mtm) cc_final: 0.8027 (mpp) REVERT: D 225 CYS cc_start: 0.8321 (OUTLIER) cc_final: 0.8020 (p) REVERT: D 237 TYR cc_start: 0.8052 (t80) cc_final: 0.7781 (t80) REVERT: D 288 GLU cc_start: 0.8634 (tp30) cc_final: 0.8147 (tp30) REVERT: D 320 ARG cc_start: 0.8748 (ttp-110) cc_final: 0.8093 (ptp90) REVERT: D 399 ASP cc_start: 0.7583 (m-30) cc_final: 0.7327 (t70) REVERT: E 166 LYS cc_start: 0.8824 (ptmm) cc_final: 0.8546 (ptmm) REVERT: E 243 LYS cc_start: 0.7202 (mttp) cc_final: 0.6866 (mttm) REVERT: E 252 MET cc_start: 0.9216 (tpt) cc_final: 0.8634 (mmt) REVERT: F 401 ARG cc_start: 0.8069 (ttm-80) cc_final: 0.7792 (ttt180) REVERT: F 402 ASP cc_start: 0.8651 (m-30) cc_final: 0.8318 (p0) REVERT: G 174 MET cc_start: 0.8402 (tpp) cc_final: 0.8173 (mmm) REVERT: H 144 ILE cc_start: 0.9183 (mm) cc_final: 0.8884 (tp) REVERT: H 166 LYS cc_start: 0.8304 (tmmt) cc_final: 0.7854 (tttp) REVERT: H 240 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7731 (t0) REVERT: H 288 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7923 (mt-10) REVERT: H 357 THR cc_start: 0.6053 (OUTLIER) cc_final: 0.5822 (m) REVERT: H 400 ASN cc_start: 0.7220 (t0) cc_final: 0.6582 (t0) REVERT: H 426 ARG cc_start: 0.8947 (tpm170) cc_final: 0.8668 (tpm170) REVERT: I 328 TYR cc_start: 0.7750 (t80) cc_final: 0.7437 (t80) REVERT: J 244 ASP cc_start: 0.7446 (m-30) cc_final: 0.5912 (p0) REVERT: J 402 ASP cc_start: 0.7020 (m-30) cc_final: 0.6332 (t70) REVERT: K 199 HIS cc_start: 0.8609 (OUTLIER) cc_final: 0.7963 (m170) REVERT: K 348 ILE cc_start: 0.8719 (mm) cc_final: 0.8428 (pt) outliers start: 105 outliers final: 89 residues processed: 407 average time/residue: 0.1784 time to fit residues: 120.9265 Evaluate side-chains 405 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 309 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 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 303 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 171 SER 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 244 ASP Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 178 VAL 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 285 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 150 CYS Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 127 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 371 LEU Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 225 CYS Chi-restraints excluded: chain G residue 226 ASN Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain H residue 7 CYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 78 GLN Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 225 CYS Chi-restraints excluded: chain H residue 234 MET Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 317 ASP Chi-restraints excluded: chain H residue 333 LEU Chi-restraints excluded: chain H residue 357 THR Chi-restraints excluded: chain H residue 398 LEU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 184 ILE Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 338 HIS Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 216 THR Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 346 HIS Chi-restraints excluded: chain J residue 425 LEU Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 199 HIS Chi-restraints excluded: chain K residue 216 THR Chi-restraints excluded: chain K residue 234 MET Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: [256, 285, 89, 272, 309, 214, 71, 191, 332, 196, 131] chunk 256 optimal weight: 5.9990 chunk 285 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 272 optimal weight: 0.8980 chunk 309 optimal weight: 7.9990 chunk 214 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 191 optimal weight: 30.0000 chunk 332 optimal weight: 20.0000 chunk 196 optimal weight: 30.0000 chunk 131 optimal weight: 8.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 HIS F 55 GLN ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 GLN ** I 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.147322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.091796 restraints weight = 60439.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.089186 restraints weight = 36668.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.089987 restraints weight = 28598.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.090770 restraints weight = 24181.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.090890 restraints weight = 21569.587| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 33228 Z= 0.337 Angle : 0.722 15.604 45157 Z= 0.364 Chirality : 0.048 0.273 5364 Planarity : 0.005 0.059 5934 Dihedral : 4.491 30.849 4730 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.23 % Favored : 92.75 % Rotamer: Outliers : 3.27 % Allowed : 24.45 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.26 % 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: -0.53 (0.13), residues: 4332 helix: 1.25 (0.13), residues: 1592 sheet: -1.94 (0.18), residues: 826 loop : -0.91 (0.15), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 273 TYR 0.027 0.002 TYR I 255 PHE 0.031 0.002 PHE F 238 HIS 0.006 0.001 HIS B 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00808 / 0.34 (33223) covalent geometry : angle 0.72193 / 0.36 (45147) SS BOND : bond 0.00260 / 0.16 ( 5) SS BOND : angle 1.93235 / 1.18 ( 10) hydrogen bonds : bond 0.04360 / 3.08 ( 1388) hydrogen bonds : angle 4.96585 / 3.50 ( 3987) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6256.61 seconds wall clock time: 108 minutes 15.50 seconds (6495.50 seconds total)