Starting phenix.real_space_refine on Tue Sep 15 14:41:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6dpu_7973/09_2026/6dpu_7973.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dpu_7973/09_2026/6dpu_7973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6dpu_7973/09_2026/6dpu_7973.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6dpu_7973/09_2026/6dpu_7973.cif" model { file = "/net/cci-nas-00/data/ceres_data/6dpu_7973/09_2026/6dpu_7973.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dpu_7973/09_2026/6dpu_7973.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6dpu_7973/09_2026/6dpu_7973.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dpu_7973/09_2026/6dpu_7973.map" } resolution = 3.1 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= -0.007 sd= 0.929 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 12 5.21 5 S 282 5.16 5 C 25542 2.51 5 N 6936 2.21 5 O 7842 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40650 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3353 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3353 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3353 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3353 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3353 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3353 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "K" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "L" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.85, per 1000 atoms: 0.22 Number of scatterers: 40650 At special positions: 0 Unit cell: (173.168, 85.488, 212.624, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 282 16.00 P 36 15.00 Mg 12 11.99 O 7842 8.00 N 6936 7.00 C 25542 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.83 Conformation dependent library (CDL) restraints added in 2.0 seconds 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9528 Finding SS restraints... Secondary structure from input PDB file: 252 helices and 30 sheets defined 56.7% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.612A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.573A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 162 removed outlier: 4.095A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.869A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU A 196 " --> pdb=" O HIS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 218 Processing helix chain 'A' and resid 223 through 244 removed outlier: 4.439A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.674A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N HIS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.686A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 removed outlier: 3.577A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 401 removed outlier: 3.640A pdb=" N TRP A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 4.003A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 removed outlier: 3.917A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 41 through 48 removed outlier: 4.347A pdb=" N ARG B 48 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 71 through 81 removed outlier: 4.340A pdb=" N MET B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 87 removed outlier: 3.741A pdb=" N PHE B 87 " --> pdb=" O GLY B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 109 through 129 removed outlier: 4.376A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 161 Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.566A pdb=" N GLN B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 216 Processing helix chain 'B' and resid 223 through 244 removed outlier: 3.806A pdb=" N THR B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N CYS B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N LEU B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 278 through 282 removed outlier: 3.749A pdb=" N GLN B 281 " --> pdb=" O ARG B 278 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN B 282 " --> pdb=" O GLY B 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 278 through 282' Processing helix chain 'B' and resid 287 through 297 removed outlier: 3.654A pdb=" N ASP B 297 " --> pdb=" O GLN B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 301 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 324 through 339 Processing helix chain 'B' and resid 340 through 343 Processing helix chain 'B' and resid 384 through 400 Processing helix chain 'B' and resid 404 through 411 removed outlier: 4.096A pdb=" N TYR B 408 " --> pdb=" O PHE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 437 removed outlier: 3.992A pdb=" N PHE B 418 " --> pdb=" O ASP B 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 29 Processing helix chain 'C' and resid 47 through 51 Processing helix chain 'C' and resid 72 through 81 removed outlier: 3.612A pdb=" N VAL C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 110 through 113 Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.573A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 162 removed outlier: 4.094A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 198 removed outlier: 3.869A pdb=" N THR C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU C 196 " --> pdb=" O HIS C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 218 Processing helix chain 'C' and resid 223 through 244 removed outlier: 4.439A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 277 through 284 removed outlier: 3.674A pdb=" N TYR C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N HIS C 283 " --> pdb=" O GLU C 279 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 296 removed outlier: 3.685A pdb=" N PHE C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 301 Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 324 through 338 removed outlier: 3.576A pdb=" N VAL C 328 " --> pdb=" O VAL C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 401 removed outlier: 3.639A pdb=" N TRP C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS C 401 " --> pdb=" O LEU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 removed outlier: 4.003A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 437 removed outlier: 3.917A pdb=" N PHE C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 28 Processing helix chain 'D' and resid 41 through 48 removed outlier: 4.348A pdb=" N ARG D 48 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 71 through 81 removed outlier: 4.339A pdb=" N MET D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.742A pdb=" N PHE D 87 " --> pdb=" O GLY D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 90 No H-bonds generated for 'chain 'D' and resid 88 through 90' Processing helix chain 'D' and resid 102 through 108 Processing helix chain 'D' and resid 109 through 129 removed outlier: 4.376A pdb=" N ASP D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N SER D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 161 Processing helix chain 'D' and resid 182 through 198 removed outlier: 3.560A pdb=" N GLN D 193 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU D 196 " --> pdb=" O HIS D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 216 Processing helix chain 'D' and resid 223 through 244 removed outlier: 3.809A pdb=" N THR D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N CYS D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LEU D 242 " --> pdb=" O VAL D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 278 through 282 removed outlier: 3.748A pdb=" N GLN D 281 " --> pdb=" O ARG D 278 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN D 282 " --> pdb=" O GLY D 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 278 through 282' Processing helix chain 'D' and resid 287 through 297 removed outlier: 3.654A pdb=" N ASP D 297 " --> pdb=" O GLN D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 301 Processing helix chain 'D' and resid 306 through 310 Processing helix chain 'D' and resid 324 through 339 Processing helix chain 'D' and resid 340 through 343 Processing helix chain 'D' and resid 384 through 400 Processing helix chain 'D' and resid 404 through 411 removed outlier: 4.101A pdb=" N TYR D 408 " --> pdb=" O PHE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 437 removed outlier: 3.992A pdb=" N PHE D 418 " --> pdb=" O ASP D 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 29 Processing helix chain 'E' and resid 47 through 51 Processing helix chain 'E' and resid 72 through 81 removed outlier: 3.611A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 110 through 113 Processing helix chain 'E' and resid 114 through 128 removed outlier: 3.572A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 162 removed outlier: 4.095A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 198 removed outlier: 3.869A pdb=" N THR E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU E 196 " --> pdb=" O HIS E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 218 Processing helix chain 'E' and resid 223 through 244 removed outlier: 4.440A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 260 Processing helix chain 'E' and resid 277 through 284 removed outlier: 3.673A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N HIS E 283 " --> pdb=" O GLU E 279 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU E 284 " --> pdb=" O LYS E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.687A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 301 Processing helix chain 'E' and resid 306 through 310 Processing helix chain 'E' and resid 324 through 338 removed outlier: 3.578A pdb=" N VAL E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 401 removed outlier: 3.639A pdb=" N TRP E 388 " --> pdb=" O ILE E 384 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS E 401 " --> pdb=" O LEU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 411 removed outlier: 4.003A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 437 removed outlier: 3.916A pdb=" N PHE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL E 437 " --> pdb=" O GLU E 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 28 Processing helix chain 'F' and resid 41 through 48 removed outlier: 4.349A pdb=" N ARG F 48 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 51 No H-bonds generated for 'chain 'F' and resid 49 through 51' Processing helix chain 'F' and resid 71 through 81 removed outlier: 4.339A pdb=" N MET F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.743A pdb=" N PHE F 87 " --> pdb=" O GLY F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing helix chain 'F' and resid 102 through 108 Processing helix chain 'F' and resid 109 through 129 removed outlier: 4.375A pdb=" N ASP F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N SER F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL F 118 " --> pdb=" O LEU F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 161 Processing helix chain 'F' and resid 182 through 198 removed outlier: 3.560A pdb=" N GLN F 193 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU F 196 " --> pdb=" O HIS F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 216 Processing helix chain 'F' and resid 223 through 244 removed outlier: 3.807A pdb=" N THR F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N CYS F 241 " --> pdb=" O GLY F 237 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LEU F 242 " --> pdb=" O VAL F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 260 Processing helix chain 'F' and resid 278 through 282 removed outlier: 3.749A pdb=" N GLN F 281 " --> pdb=" O ARG F 278 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN F 282 " --> pdb=" O GLY F 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 278 through 282' Processing helix chain 'F' and resid 287 through 297 removed outlier: 3.655A pdb=" N ASP F 297 " --> pdb=" O GLN F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 301 Processing helix chain 'F' and resid 306 through 310 Processing helix chain 'F' and resid 324 through 339 Processing helix chain 'F' and resid 340 through 343 Processing helix chain 'F' and resid 384 through 400 Processing helix chain 'F' and resid 404 through 411 removed outlier: 4.100A pdb=" N TYR F 408 " --> pdb=" O PHE F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 437 removed outlier: 3.991A pdb=" N PHE F 418 " --> pdb=" O ASP F 414 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 28 Processing helix chain 'G' and resid 41 through 48 removed outlier: 4.349A pdb=" N ARG G 48 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 51 No H-bonds generated for 'chain 'G' and resid 49 through 51' Processing helix chain 'G' and resid 71 through 81 removed outlier: 4.339A pdb=" N MET G 75 " --> pdb=" O GLU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.743A pdb=" N PHE G 87 " --> pdb=" O GLY G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 90 No H-bonds generated for 'chain 'G' and resid 88 through 90' Processing helix chain 'G' and resid 102 through 108 Processing helix chain 'G' and resid 109 through 129 removed outlier: 4.375A pdb=" N ASP G 116 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N SER G 117 " --> pdb=" O GLU G 113 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL G 118 " --> pdb=" O LEU G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 161 Processing helix chain 'G' and resid 182 through 198 removed outlier: 3.560A pdb=" N GLN G 193 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU G 196 " --> pdb=" O HIS G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 216 Processing helix chain 'G' and resid 223 through 244 removed outlier: 3.805A pdb=" N THR G 239 " --> pdb=" O MET G 235 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N CYS G 241 " --> pdb=" O GLY G 237 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LEU G 242 " --> pdb=" O VAL G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 260 Processing helix chain 'G' and resid 278 through 282 removed outlier: 3.747A pdb=" N GLN G 281 " --> pdb=" O ARG G 278 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN G 282 " --> pdb=" O GLY G 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 278 through 282' Processing helix chain 'G' and resid 287 through 297 removed outlier: 3.658A pdb=" N ASP G 297 " --> pdb=" O GLN G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 301 Processing helix chain 'G' and resid 306 through 310 Processing helix chain 'G' and resid 324 through 339 Processing helix chain 'G' and resid 340 through 343 Processing helix chain 'G' and resid 384 through 400 Processing helix chain 'G' and resid 404 through 411 removed outlier: 4.100A pdb=" N TYR G 408 " --> pdb=" O PHE G 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 437 removed outlier: 3.991A pdb=" N PHE G 418 " --> pdb=" O ASP G 414 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 28 Processing helix chain 'H' and resid 41 through 48 removed outlier: 4.348A pdb=" N ARG H 48 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 51 No H-bonds generated for 'chain 'H' and resid 49 through 51' Processing helix chain 'H' and resid 71 through 81 removed outlier: 4.338A pdb=" N MET H 75 " --> pdb=" O GLU H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.742A pdb=" N PHE H 87 " --> pdb=" O GLY H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 102 through 108 Processing helix chain 'H' and resid 109 through 129 removed outlier: 4.376A pdb=" N ASP H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N SER H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL H 118 " --> pdb=" O LEU H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 161 Processing helix chain 'H' and resid 182 through 198 removed outlier: 3.560A pdb=" N GLN H 193 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU H 196 " --> pdb=" O HIS H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 216 Processing helix chain 'H' and resid 223 through 244 removed outlier: 3.806A pdb=" N THR H 239 " --> pdb=" O MET H 235 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N CYS H 241 " --> pdb=" O GLY H 237 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LEU H 242 " --> pdb=" O VAL H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 260 Processing helix chain 'H' and resid 278 through 282 removed outlier: 3.748A pdb=" N GLN H 281 " --> pdb=" O ARG H 278 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN H 282 " --> pdb=" O GLY H 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 278 through 282' Processing helix chain 'H' and resid 287 through 297 removed outlier: 3.658A pdb=" N ASP H 297 " --> pdb=" O GLN H 293 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 301 Processing helix chain 'H' and resid 306 through 310 Processing helix chain 'H' and resid 324 through 339 Processing helix chain 'H' and resid 340 through 343 Processing helix chain 'H' and resid 384 through 400 Processing helix chain 'H' and resid 404 through 411 removed outlier: 4.100A pdb=" N TYR H 408 " --> pdb=" O PHE H 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 437 removed outlier: 3.991A pdb=" N PHE H 418 " --> pdb=" O ASP H 414 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 28 Processing helix chain 'I' and resid 41 through 48 removed outlier: 4.349A pdb=" N ARG I 48 " --> pdb=" O LEU I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'I' and resid 71 through 81 removed outlier: 4.339A pdb=" N MET I 75 " --> pdb=" O GLU I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.742A pdb=" N PHE I 87 " --> pdb=" O GLY I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 90 No H-bonds generated for 'chain 'I' and resid 88 through 90' Processing helix chain 'I' and resid 102 through 108 Processing helix chain 'I' and resid 109 through 129 removed outlier: 4.376A pdb=" N ASP I 116 " --> pdb=" O ALA I 112 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N SER I 117 " --> pdb=" O GLU I 113 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL I 118 " --> pdb=" O LEU I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 161 Processing helix chain 'I' and resid 182 through 198 removed outlier: 3.560A pdb=" N GLN I 193 " --> pdb=" O LEU I 189 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU I 196 " --> pdb=" O HIS I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 216 Processing helix chain 'I' and resid 223 through 244 removed outlier: 3.806A pdb=" N THR I 239 " --> pdb=" O MET I 235 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N CYS I 241 " --> pdb=" O GLY I 237 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LEU I 242 " --> pdb=" O VAL I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 260 Processing helix chain 'I' and resid 278 through 282 removed outlier: 3.748A pdb=" N GLN I 281 " --> pdb=" O ARG I 278 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN I 282 " --> pdb=" O GLY I 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 278 through 282' Processing helix chain 'I' and resid 287 through 297 removed outlier: 3.657A pdb=" N ASP I 297 " --> pdb=" O GLN I 293 " (cutoff:3.500A) Processing helix chain 'I' and resid 298 through 301 Processing helix chain 'I' and resid 306 through 310 Processing helix chain 'I' and resid 324 through 339 Processing helix chain 'I' and resid 340 through 343 Processing helix chain 'I' and resid 384 through 400 Processing helix chain 'I' and resid 404 through 411 removed outlier: 4.101A pdb=" N TYR I 408 " --> pdb=" O PHE I 404 " (cutoff:3.500A) Processing helix chain 'I' and resid 414 through 437 removed outlier: 3.992A pdb=" N PHE I 418 " --> pdb=" O ASP I 414 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 29 Processing helix chain 'J' and resid 47 through 51 Processing helix chain 'J' and resid 72 through 81 removed outlier: 3.610A pdb=" N VAL J 78 " --> pdb=" O VAL J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 90 No H-bonds generated for 'chain 'J' and resid 88 through 90' Processing helix chain 'J' and resid 102 through 108 Processing helix chain 'J' and resid 110 through 113 Processing helix chain 'J' and resid 114 through 128 removed outlier: 3.573A pdb=" N GLN J 128 " --> pdb=" O LYS J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 162 removed outlier: 4.094A pdb=" N THR J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 198 removed outlier: 3.871A pdb=" N THR J 193 " --> pdb=" O LEU J 189 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU J 196 " --> pdb=" O HIS J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 218 Processing helix chain 'J' and resid 223 through 244 removed outlier: 4.439A pdb=" N SER J 241 " --> pdb=" O SER J 237 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU J 242 " --> pdb=" O ILE J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 260 Processing helix chain 'J' and resid 277 through 284 removed outlier: 3.671A pdb=" N TYR J 282 " --> pdb=" O ALA J 278 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N HIS J 283 " --> pdb=" O GLU J 279 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU J 284 " --> pdb=" O LYS J 280 " (cutoff:3.500A) Processing helix chain 'J' and resid 287 through 296 removed outlier: 3.688A pdb=" N PHE J 296 " --> pdb=" O THR J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 301 Processing helix chain 'J' and resid 306 through 310 Processing helix chain 'J' and resid 324 through 338 removed outlier: 3.577A pdb=" N VAL J 328 " --> pdb=" O VAL J 324 " (cutoff:3.500A) Processing helix chain 'J' and resid 384 through 401 removed outlier: 3.639A pdb=" N TRP J 388 " --> pdb=" O ILE J 384 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS J 401 " --> pdb=" O LEU J 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 404 through 411 removed outlier: 4.004A pdb=" N TYR J 408 " --> pdb=" O PHE J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 414 through 437 removed outlier: 3.917A pdb=" N PHE J 418 " --> pdb=" O GLU J 414 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL J 437 " --> pdb=" O GLU J 433 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 29 Processing helix chain 'K' and resid 47 through 51 Processing helix chain 'K' and resid 72 through 81 removed outlier: 3.611A pdb=" N VAL K 78 " --> pdb=" O VAL K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 90 No H-bonds generated for 'chain 'K' and resid 88 through 90' Processing helix chain 'K' and resid 102 through 108 Processing helix chain 'K' and resid 110 through 113 Processing helix chain 'K' and resid 114 through 128 removed outlier: 3.573A pdb=" N GLN K 128 " --> pdb=" O LYS K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 162 removed outlier: 4.094A pdb=" N THR K 150 " --> pdb=" O GLY K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 198 removed outlier: 3.871A pdb=" N THR K 193 " --> pdb=" O LEU K 189 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU K 196 " --> pdb=" O HIS K 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 218 Processing helix chain 'K' and resid 223 through 244 removed outlier: 4.439A pdb=" N SER K 241 " --> pdb=" O SER K 237 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU K 242 " --> pdb=" O ILE K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 251 through 260 Processing helix chain 'K' and resid 277 through 284 removed outlier: 3.672A pdb=" N TYR K 282 " --> pdb=" O ALA K 278 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N HIS K 283 " --> pdb=" O GLU K 279 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU K 284 " --> pdb=" O LYS K 280 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 296 removed outlier: 3.686A pdb=" N PHE K 296 " --> pdb=" O THR K 292 " (cutoff:3.500A) Processing helix chain 'K' and resid 297 through 301 Processing helix chain 'K' and resid 306 through 310 Processing helix chain 'K' and resid 324 through 338 removed outlier: 3.577A pdb=" N VAL K 328 " --> pdb=" O VAL K 324 " (cutoff:3.500A) Processing helix chain 'K' and resid 384 through 401 removed outlier: 3.639A pdb=" N TRP K 388 " --> pdb=" O ILE K 384 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS K 401 " --> pdb=" O LEU K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 411 removed outlier: 4.004A pdb=" N TYR K 408 " --> pdb=" O PHE K 404 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 437 removed outlier: 3.917A pdb=" N PHE K 418 " --> pdb=" O GLU K 414 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL K 437 " --> pdb=" O GLU K 433 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 29 Processing helix chain 'L' and resid 47 through 51 Processing helix chain 'L' and resid 72 through 81 removed outlier: 3.611A pdb=" N VAL L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 90 No H-bonds generated for 'chain 'L' and resid 88 through 90' Processing helix chain 'L' and resid 102 through 108 Processing helix chain 'L' and resid 110 through 113 Processing helix chain 'L' and resid 114 through 128 removed outlier: 3.573A pdb=" N GLN L 128 " --> pdb=" O LYS L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 162 removed outlier: 4.094A pdb=" N THR L 150 " --> pdb=" O GLY L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 198 removed outlier: 3.870A pdb=" N THR L 193 " --> pdb=" O LEU L 189 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU L 196 " --> pdb=" O HIS L 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 218 Processing helix chain 'L' and resid 223 through 244 removed outlier: 4.438A pdb=" N SER L 241 " --> pdb=" O SER L 237 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU L 242 " --> pdb=" O ILE L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 260 Processing helix chain 'L' and resid 277 through 284 removed outlier: 3.673A pdb=" N TYR L 282 " --> pdb=" O ALA L 278 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N HIS L 283 " --> pdb=" O GLU L 279 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU L 284 " --> pdb=" O LYS L 280 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 296 removed outlier: 3.686A pdb=" N PHE L 296 " --> pdb=" O THR L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 301 Processing helix chain 'L' and resid 306 through 310 Processing helix chain 'L' and resid 324 through 338 removed outlier: 3.577A pdb=" N VAL L 328 " --> pdb=" O VAL L 324 " (cutoff:3.500A) Processing helix chain 'L' and resid 384 through 401 removed outlier: 3.639A pdb=" N TRP L 388 " --> pdb=" O ILE L 384 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS L 401 " --> pdb=" O LEU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 404 through 411 removed outlier: 4.003A pdb=" N TYR L 408 " --> pdb=" O PHE L 404 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 437 removed outlier: 3.917A pdb=" N PHE L 418 " --> pdb=" O GLU L 414 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL L 437 " --> pdb=" O GLU L 433 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.051A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.624A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 92 through 94 removed outlier: 7.886A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N GLU B 3 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY B 134 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N SER B 140 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLN B 133 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ASN B 167 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N PHE B 135 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N PHE B 169 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU B 137 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL B 171 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N HIS B 139 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N MET B 166 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N TYR B 202 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR B 168 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE B 204 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N SER B 170 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR B 201 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N CYS B 203 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 10.308A pdb=" N PHE B 272 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 13.296A pdb=" N ASP B 205 " --> pdb=" O PHE B 272 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N LYS B 352 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL B 315 " --> pdb=" O LYS B 352 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ALA B 354 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA B 317 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N CYS B 356 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE B 319 " --> pdb=" O CYS B 356 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 248 " --> pdb=" O VAL B 355 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 53 through 56 removed outlier: 3.979A pdb=" N LYS B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 92 through 94 removed outlier: 8.052A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N SER C 140 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N PHE C 135 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N PHE C 169 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL C 137 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ILE C 171 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N HIS C 139 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS C 166 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N PHE C 202 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLU C 168 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N VAL C 204 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N SER C 170 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AA8, first strand: chain 'C' and resid 269 through 273 removed outlier: 3.624A pdb=" N ALA C 314 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 92 through 94 removed outlier: 7.887A pdb=" N VAL D 93 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU D 67 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N ILE D 66 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N HIS D 6 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL D 68 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLN D 8 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N GLU D 3 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY D 134 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N SER D 140 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N GLN D 133 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N ASN D 167 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N PHE D 135 " --> pdb=" O ASN D 167 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N PHE D 169 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU D 137 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N VAL D 171 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N HIS D 139 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N MET D 166 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N TYR D 202 " --> pdb=" O MET D 166 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR D 168 " --> pdb=" O TYR D 202 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE D 204 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N SER D 170 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR D 201 " --> pdb=" O PHE D 268 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N CYS D 203 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 10.302A pdb=" N PHE D 272 " --> pdb=" O CYS D 203 " (cutoff:3.500A) removed outlier: 13.294A pdb=" N ASP D 205 " --> pdb=" O PHE D 272 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N PHE D 267 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N SER D 381 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N LYS D 352 " --> pdb=" O LEU D 313 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL D 315 " --> pdb=" O LYS D 352 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ALA D 354 " --> pdb=" O VAL D 315 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA D 317 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N CYS D 356 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N PHE D 319 " --> pdb=" O CYS D 356 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU D 248 " --> pdb=" O VAL D 355 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 53 through 56 removed outlier: 3.980A pdb=" N LYS D 60 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 92 through 94 removed outlier: 8.050A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N SER E 140 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N PHE E 135 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N PHE E 169 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL E 137 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ILE E 171 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N HIS E 139 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LYS E 166 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N PHE E 202 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N SER E 170 " --> pdb=" O VAL E 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'E' and resid 269 through 273 removed outlier: 3.623A pdb=" N ALA E 314 " --> pdb=" O ASN E 380 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 92 through 94 removed outlier: 7.886A pdb=" N VAL F 93 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU F 67 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N ILE F 66 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N HIS F 6 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N VAL F 68 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLN F 8 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N GLU F 3 " --> pdb=" O LEU F 132 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY F 134 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER F 140 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N GLN F 133 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ASN F 167 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N PHE F 135 " --> pdb=" O ASN F 167 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N PHE F 169 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU F 137 " --> pdb=" O PHE F 169 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N VAL F 171 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N HIS F 139 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N MET F 166 " --> pdb=" O GLU F 200 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N TYR F 202 " --> pdb=" O MET F 166 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR F 168 " --> pdb=" O TYR F 202 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ILE F 204 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N SER F 170 " --> pdb=" O ILE F 204 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR F 201 " --> pdb=" O PHE F 268 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N CYS F 203 " --> pdb=" O PRO F 270 " (cutoff:3.500A) removed outlier: 10.302A pdb=" N PHE F 272 " --> pdb=" O CYS F 203 " (cutoff:3.500A) removed outlier: 13.293A pdb=" N ASP F 205 " --> pdb=" O PHE F 272 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N PHE F 267 " --> pdb=" O SER F 381 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N SER F 381 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N LYS F 352 " --> pdb=" O LEU F 313 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL F 315 " --> pdb=" O LYS F 352 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ALA F 354 " --> pdb=" O VAL F 315 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA F 317 " --> pdb=" O ALA F 354 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N CYS F 356 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE F 319 " --> pdb=" O CYS F 356 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU F 248 " --> pdb=" O VAL F 355 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 53 through 56 removed outlier: 3.981A pdb=" N LYS F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 92 through 94 removed outlier: 7.886A pdb=" N VAL G 93 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU G 67 " --> pdb=" O VAL G 93 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N ILE G 66 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N HIS G 6 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N VAL G 68 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLN G 8 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N GLU G 3 " --> pdb=" O LEU G 132 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY G 134 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER G 140 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLN G 133 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ASN G 167 " --> pdb=" O GLN G 133 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N PHE G 135 " --> pdb=" O ASN G 167 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N PHE G 169 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU G 137 " --> pdb=" O PHE G 169 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL G 171 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N HIS G 139 " --> pdb=" O VAL G 171 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N MET G 166 " --> pdb=" O GLU G 200 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N TYR G 202 " --> pdb=" O MET G 166 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR G 168 " --> pdb=" O TYR G 202 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ILE G 204 " --> pdb=" O THR G 168 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N SER G 170 " --> pdb=" O ILE G 204 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR G 201 " --> pdb=" O PHE G 268 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N CYS G 203 " --> pdb=" O PRO G 270 " (cutoff:3.500A) removed outlier: 10.299A pdb=" N PHE G 272 " --> pdb=" O CYS G 203 " (cutoff:3.500A) removed outlier: 13.293A pdb=" N ASP G 205 " --> pdb=" O PHE G 272 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N PHE G 267 " --> pdb=" O SER G 381 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N SER G 381 " --> pdb=" O PHE G 267 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N LYS G 352 " --> pdb=" O LEU G 313 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL G 315 " --> pdb=" O LYS G 352 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ALA G 354 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA G 317 " --> pdb=" O ALA G 354 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N CYS G 356 " --> pdb=" O ALA G 317 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE G 319 " --> pdb=" O CYS G 356 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU G 248 " --> pdb=" O VAL G 355 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 53 through 56 removed outlier: 3.982A pdb=" N LYS G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 92 through 94 removed outlier: 7.886A pdb=" N VAL H 93 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU H 67 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N ILE H 66 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N HIS H 6 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL H 68 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLN H 8 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N GLU H 3 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY H 134 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER H 140 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N GLN H 133 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ASN H 167 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N PHE H 135 " --> pdb=" O ASN H 167 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N PHE H 169 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU H 137 " --> pdb=" O PHE H 169 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N VAL H 171 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N HIS H 139 " --> pdb=" O VAL H 171 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N MET H 166 " --> pdb=" O GLU H 200 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N TYR H 202 " --> pdb=" O MET H 166 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR H 168 " --> pdb=" O TYR H 202 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE H 204 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N SER H 170 " --> pdb=" O ILE H 204 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR H 201 " --> pdb=" O PHE H 268 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N CYS H 203 " --> pdb=" O PRO H 270 " (cutoff:3.500A) removed outlier: 10.300A pdb=" N PHE H 272 " --> pdb=" O CYS H 203 " (cutoff:3.500A) removed outlier: 13.293A pdb=" N ASP H 205 " --> pdb=" O PHE H 272 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N PHE H 267 " --> pdb=" O SER H 381 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N SER H 381 " --> pdb=" O PHE H 267 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N LYS H 352 " --> pdb=" O LEU H 313 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL H 315 " --> pdb=" O LYS H 352 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ALA H 354 " --> pdb=" O VAL H 315 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA H 317 " --> pdb=" O ALA H 354 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N CYS H 356 " --> pdb=" O ALA H 317 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE H 319 " --> pdb=" O CYS H 356 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU H 248 " --> pdb=" O VAL H 355 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 53 through 56 removed outlier: 3.982A pdb=" N LYS H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 92 through 94 removed outlier: 7.886A pdb=" N VAL I 93 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU I 67 " --> pdb=" O VAL I 93 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N ILE I 66 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N HIS I 6 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL I 68 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLN I 8 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N GLU I 3 " --> pdb=" O LEU I 132 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY I 134 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N SER I 140 " --> pdb=" O ALA I 9 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N GLN I 133 " --> pdb=" O ILE I 165 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ASN I 167 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N PHE I 135 " --> pdb=" O ASN I 167 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N PHE I 169 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU I 137 " --> pdb=" O PHE I 169 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL I 171 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N HIS I 139 " --> pdb=" O VAL I 171 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N MET I 166 " --> pdb=" O GLU I 200 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N TYR I 202 " --> pdb=" O MET I 166 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR I 168 " --> pdb=" O TYR I 202 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE I 204 " --> pdb=" O THR I 168 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N SER I 170 " --> pdb=" O ILE I 204 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR I 201 " --> pdb=" O PHE I 268 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N CYS I 203 " --> pdb=" O PRO I 270 " (cutoff:3.500A) removed outlier: 10.300A pdb=" N PHE I 272 " --> pdb=" O CYS I 203 " (cutoff:3.500A) removed outlier: 13.293A pdb=" N ASP I 205 " --> pdb=" O PHE I 272 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N PHE I 267 " --> pdb=" O SER I 381 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N SER I 381 " --> pdb=" O PHE I 267 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N LYS I 352 " --> pdb=" O LEU I 313 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL I 315 " --> pdb=" O LYS I 352 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ALA I 354 " --> pdb=" O VAL I 315 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA I 317 " --> pdb=" O ALA I 354 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N CYS I 356 " --> pdb=" O ALA I 317 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE I 319 " --> pdb=" O CYS I 356 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU I 248 " --> pdb=" O VAL I 355 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 53 through 56 removed outlier: 3.981A pdb=" N LYS I 60 " --> pdb=" O ALA I 56 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 92 through 94 removed outlier: 8.050A pdb=" N ILE J 93 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHE J 67 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N VAL J 66 " --> pdb=" O CYS J 4 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N SER J 6 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL J 68 " --> pdb=" O SER J 6 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N HIS J 8 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N SER J 140 " --> pdb=" O VAL J 9 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE J 135 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N PHE J 169 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL J 137 " --> pdb=" O PHE J 169 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE J 171 " --> pdb=" O VAL J 137 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N HIS J 139 " --> pdb=" O ILE J 171 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LYS J 166 " --> pdb=" O CYS J 200 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N PHE J 202 " --> pdb=" O LYS J 166 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLU J 168 " --> pdb=" O PHE J 202 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N VAL J 204 " --> pdb=" O GLU J 168 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N SER J 170 " --> pdb=" O VAL J 204 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 53 through 55 Processing sheet with id=AC6, first strand: chain 'J' and resid 269 through 273 removed outlier: 3.624A pdb=" N ALA J 314 " --> pdb=" O ASN J 380 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 92 through 94 removed outlier: 8.050A pdb=" N ILE K 93 " --> pdb=" O ALA K 65 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE K 67 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N VAL K 66 " --> pdb=" O CYS K 4 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL K 68 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N HIS K 8 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N SER K 140 " --> pdb=" O VAL K 9 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE K 135 " --> pdb=" O LEU K 167 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N PHE K 169 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL K 137 " --> pdb=" O PHE K 169 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE K 171 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N HIS K 139 " --> pdb=" O ILE K 171 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS K 166 " --> pdb=" O CYS K 200 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N PHE K 202 " --> pdb=" O LYS K 166 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLU K 168 " --> pdb=" O PHE K 202 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N VAL K 204 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N SER K 170 " --> pdb=" O VAL K 204 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 53 through 55 Processing sheet with id=AC9, first strand: chain 'K' and resid 269 through 273 removed outlier: 3.624A pdb=" N ALA K 314 " --> pdb=" O ASN K 380 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 92 through 94 removed outlier: 8.051A pdb=" N ILE L 93 " --> pdb=" O ALA L 65 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE L 67 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N VAL L 66 " --> pdb=" O CYS L 4 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N SER L 6 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL L 68 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N HIS L 8 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N SER L 140 " --> pdb=" O VAL L 9 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE L 135 " --> pdb=" O LEU L 167 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N PHE L 169 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL L 137 " --> pdb=" O PHE L 169 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE L 171 " --> pdb=" O VAL L 137 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N HIS L 139 " --> pdb=" O ILE L 171 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS L 166 " --> pdb=" O CYS L 200 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N PHE L 202 " --> pdb=" O LYS L 166 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLU L 168 " --> pdb=" O PHE L 202 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N VAL L 204 " --> pdb=" O GLU L 168 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N SER L 170 " --> pdb=" O VAL L 204 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 53 through 55 Processing sheet with id=AD3, first strand: chain 'L' and resid 269 through 273 removed outlier: 3.624A pdb=" N ALA L 314 " --> pdb=" O ASN L 380 " (cutoff:3.500A) 2076 hydrogen bonds defined for protein. 5994 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.20 Time building geometry restraints manager: 5.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7421 1.32 - 1.45: 10794 1.45 - 1.57: 22838 1.57 - 1.69: 65 1.69 - 1.81: 456 Bond restraints: 41574 Sorted by residual: bond pdb=" O3B G2P F 501 " pdb=" PG G2P F 501 " ideal model delta sigma weight residual 1.716 1.605 0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" O3B G2P B 501 " pdb=" PG G2P B 501 " ideal model delta sigma weight residual 1.716 1.607 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" O3B G2P D 501 " pdb=" PG G2P D 501 " ideal model delta sigma weight residual 1.716 1.609 0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" O3B G2P G 501 " pdb=" PG G2P G 501 " ideal model delta sigma weight residual 1.716 1.610 0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" O3B G2P H 501 " pdb=" PG G2P H 501 " ideal model delta sigma weight residual 1.716 1.612 0.104 2.00e-02 2.50e+03 2.70e+01 ... (remaining 41569 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 54079 3.20 - 6.40: 2240 6.40 - 9.60: 130 9.60 - 12.80: 35 12.80 - 16.00: 6 Bond angle restraints: 56490 Sorted by residual: angle pdb=" C3' G2P B 501 " pdb=" C2' G2P B 501 " pdb=" O2' G2P B 501 " ideal model delta sigma weight residual 116.29 100.29 16.00 3.00e+00 1.11e-01 2.84e+01 angle pdb=" N THR L 73 " pdb=" CA THR L 73 " pdb=" C THR L 73 " ideal model delta sigma weight residual 111.11 117.50 -6.39 1.20e+00 6.94e-01 2.84e+01 angle pdb=" N THR K 73 " pdb=" CA THR K 73 " pdb=" C THR K 73 " ideal model delta sigma weight residual 111.11 117.49 -6.38 1.20e+00 6.94e-01 2.83e+01 angle pdb=" N THR J 73 " pdb=" CA THR J 73 " pdb=" C THR J 73 " ideal model delta sigma weight residual 111.11 117.49 -6.38 1.20e+00 6.94e-01 2.82e+01 angle pdb=" C3' G2P D 501 " pdb=" C2' G2P D 501 " pdb=" O2' G2P D 501 " ideal model delta sigma weight residual 116.29 100.38 15.91 3.00e+00 1.11e-01 2.81e+01 ... (remaining 56485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.70: 23820 33.70 - 67.41: 774 67.41 - 101.11: 42 101.11 - 134.81: 0 134.81 - 168.52: 18 Dihedral angle restraints: 24654 sinusoidal: 9798 harmonic: 14856 Sorted by residual: dihedral pdb=" C5' GTP E 501 " pdb=" O5' GTP E 501 " pdb=" PA GTP E 501 " pdb=" O3A GTP E 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.21 -168.52 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.60 -168.13 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' GTP L 501 " pdb=" O5' GTP L 501 " pdb=" PA GTP L 501 " pdb=" O3A GTP L 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.67 -168.07 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 24651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 4429 0.085 - 0.169: 1372 0.169 - 0.254: 301 0.254 - 0.338: 70 0.338 - 0.423: 2 Chirality restraints: 6174 Sorted by residual: chirality pdb=" C3' G2P B 501 " pdb=" C2' G2P B 501 " pdb=" C4' G2P B 501 " pdb=" O3' G2P B 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.28 -0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" C3' G2P D 501 " pdb=" C2' G2P D 501 " pdb=" C4' G2P D 501 " pdb=" O3' G2P D 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.29 -0.42 2.00e-01 2.50e+01 4.36e+00 chirality pdb=" CA LEU L 269 " pdb=" N LEU L 269 " pdb=" C LEU L 269 " pdb=" CB LEU L 269 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 6171 not shown) Planarity restraints: 7350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GTP C 501 " 0.025 2.00e-02 2.50e+03 1.21e-02 4.39e+00 pdb=" C2 GTP C 501 " -0.010 2.00e-02 2.50e+03 pdb=" C4 GTP C 501 " -0.000 2.00e-02 2.50e+03 pdb=" C5 GTP C 501 " -0.001 2.00e-02 2.50e+03 pdb=" C6 GTP C 501 " 0.005 2.00e-02 2.50e+03 pdb=" C8 GTP C 501 " 0.002 2.00e-02 2.50e+03 pdb=" N1 GTP C 501 " 0.009 2.00e-02 2.50e+03 pdb=" N2 GTP C 501 " 0.000 2.00e-02 2.50e+03 pdb=" N3 GTP C 501 " -0.002 2.00e-02 2.50e+03 pdb=" N7 GTP C 501 " -0.001 2.00e-02 2.50e+03 pdb=" N9 GTP C 501 " -0.030 2.00e-02 2.50e+03 pdb=" O6 GTP C 501 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GTP L 501 " 0.025 2.00e-02 2.50e+03 1.20e-02 4.33e+00 pdb=" C2 GTP L 501 " -0.007 2.00e-02 2.50e+03 pdb=" C4 GTP L 501 " -0.001 2.00e-02 2.50e+03 pdb=" C5 GTP L 501 " -0.001 2.00e-02 2.50e+03 pdb=" C6 GTP L 501 " 0.004 2.00e-02 2.50e+03 pdb=" C8 GTP L 501 " 0.004 2.00e-02 2.50e+03 pdb=" N1 GTP L 501 " 0.007 2.00e-02 2.50e+03 pdb=" N2 GTP L 501 " 0.000 2.00e-02 2.50e+03 pdb=" N3 GTP L 501 " -0.004 2.00e-02 2.50e+03 pdb=" N7 GTP L 501 " -0.002 2.00e-02 2.50e+03 pdb=" N9 GTP L 501 " -0.031 2.00e-02 2.50e+03 pdb=" O6 GTP L 501 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GTP K 501 " -0.023 2.00e-02 2.50e+03 1.16e-02 4.06e+00 pdb=" C2 GTP K 501 " 0.007 2.00e-02 2.50e+03 pdb=" C4 GTP K 501 " -0.001 2.00e-02 2.50e+03 pdb=" C5 GTP K 501 " 0.001 2.00e-02 2.50e+03 pdb=" C6 GTP K 501 " -0.005 2.00e-02 2.50e+03 pdb=" C8 GTP K 501 " -0.004 2.00e-02 2.50e+03 pdb=" N1 GTP K 501 " -0.007 2.00e-02 2.50e+03 pdb=" N2 GTP K 501 " -0.001 2.00e-02 2.50e+03 pdb=" N3 GTP K 501 " 0.004 2.00e-02 2.50e+03 pdb=" N7 GTP K 501 " 0.001 2.00e-02 2.50e+03 pdb=" N9 GTP K 501 " 0.030 2.00e-02 2.50e+03 pdb=" O6 GTP K 501 " -0.003 2.00e-02 2.50e+03 ... (remaining 7347 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 69 2.51 - 3.11: 28304 3.11 - 3.71: 64622 3.71 - 4.30: 92883 4.30 - 4.90: 158613 Nonbonded interactions: 344491 Sorted by model distance: nonbonded pdb=" O3G GTP J 501 " pdb="MG MG J 502 " model vdw 1.913 2.170 nonbonded pdb=" O1B GTP E 501 " pdb="MG MG E 502 " model vdw 1.960 2.170 nonbonded pdb=" O1B GTP J 501 " pdb="MG MG J 502 " model vdw 1.969 2.170 nonbonded pdb=" O3G GTP E 501 " pdb="MG MG E 502 " model vdw 1.971 2.170 nonbonded pdb=" O2B G2P G 501 " pdb="MG MG G 502 " model vdw 1.972 2.170 ... (remaining 344486 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 40.750 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.200 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: 0.020 Load rotamer database and sin/cos tables:1.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 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 : 0.009 0.111 41574 Z= 0.640 Angle : 1.532 16.001 56490 Z= 1.036 Chirality : 0.087 0.423 6174 Planarity : 0.006 0.055 7350 Dihedral : 16.279 168.516 15126 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.47 % Favored : 97.30 % Rotamer: Outliers : 3.17 % Allowed : 8.26 % Favored : 88.57 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.11), residues: 5106 helix: 0.72 (0.09), residues: 2334 sheet: 0.55 (0.18), residues: 792 loop : -1.18 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG B 2 TYR 0.022 0.003 TYR D 224 PHE 0.026 0.003 PHE F 92 TRP 0.027 0.004 TRP L 21 HIS 0.007 0.002 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00918 / 0.64 (41574) covalent geometry : angle 1.53218 / 1.04 (56490) hydrogen bonds : bond 0.19218 / 12.91 ( 2076) hydrogen bonds : angle 7.24728 / 5.27 ( 5994) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1684 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 1546 time to evaluate : 1.543 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: A 280 LYS cc_start: 0.8195 (ttmm) cc_final: 0.7989 (ttmt) REVERT: D 5 VAL cc_start: 0.7844 (OUTLIER) cc_final: 0.7625 (t) REVERT: D 120 ASP cc_start: 0.7444 (m-30) cc_final: 0.7189 (m-30) REVERT: D 306 ASP cc_start: 0.6300 (t0) cc_final: 0.5979 (t0) REVERT: E 91 GLN cc_start: 0.7347 (mt0) cc_final: 0.6896 (mt0) REVERT: E 110 ILE cc_start: 0.8835 (mm) cc_final: 0.8607 (mm) REVERT: E 280 LYS cc_start: 0.8316 (ttmm) cc_final: 0.7935 (ttmt) REVERT: G 156 LYS cc_start: 0.8419 (mmtm) cc_final: 0.8141 (mmtt) REVERT: G 414 ASP cc_start: 0.7440 (t0) cc_final: 0.7044 (m-30) REVERT: G 426 ASN cc_start: 0.7809 (m-40) cc_final: 0.7582 (m110) REVERT: G 435 TYR cc_start: 0.7432 (m-80) cc_final: 0.7064 (m-80) REVERT: H 156 LYS cc_start: 0.8439 (mmtm) cc_final: 0.8199 (mmtt) REVERT: H 199 ASP cc_start: 0.7570 (m-30) cc_final: 0.7365 (m-30) REVERT: H 300 ASN cc_start: 0.7907 (OUTLIER) cc_final: 0.7700 (t0) REVERT: H 325 MET cc_start: 0.7600 (mmm) cc_final: 0.7161 (mmm) REVERT: H 414 ASP cc_start: 0.7171 (t0) cc_final: 0.6849 (m-30) REVERT: H 426 ASN cc_start: 0.7797 (m-40) cc_final: 0.7572 (m110) REVERT: H 427 ASP cc_start: 0.7441 (m-30) cc_final: 0.7220 (m-30) REVERT: H 435 TYR cc_start: 0.7387 (m-80) cc_final: 0.7073 (m-10) REVERT: I 207 GLU cc_start: 0.6914 (tt0) cc_final: 0.6518 (tt0) REVERT: I 283 TYR cc_start: 0.8274 (m-80) cc_final: 0.7873 (m-80) REVERT: I 306 ASP cc_start: 0.6456 (t0) cc_final: 0.5909 (t70) REVERT: I 426 ASN cc_start: 0.7913 (m-40) cc_final: 0.7493 (m110) REVERT: J 91 GLN cc_start: 0.7425 (mt0) cc_final: 0.7125 (mt0) REVERT: J 123 ARG cc_start: 0.7142 (ttp-110) cc_final: 0.6892 (ttp-110) REVERT: K 120 ASP cc_start: 0.5999 (t0) cc_final: 0.5683 (t0) REVERT: K 123 ARG cc_start: 0.7037 (ttp-110) cc_final: 0.6787 (ttp-110) REVERT: K 211 ASP cc_start: 0.7001 (m-30) cc_final: 0.6799 (m-30) REVERT: L 209 ILE cc_start: 0.8583 (mm) cc_final: 0.7919 (mp) REVERT: L 302 MET cc_start: 0.7787 (mmp) cc_final: 0.7160 (mmt) outliers start: 138 outliers final: 32 residues processed: 1633 average time/residue: 0.2791 time to fit residues: 727.7173 Evaluate side-chains 849 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 815 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 180 THR Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 300 ASN Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 192 HIS Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 276 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 1.9990 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 494 optimal weight: 0.7980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 HIS A 226 ASN A 228 ASN A 258 ASN A 300 ASN A 393 HIS B 6 HIS B 28 HIS B 85 GLN B 101 ASN B 133 GLN B 136 GLN B 385 GLN B 436 GLN ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN C 107 HIS C 228 ASN ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 HIS D 28 HIS D 101 ASN D 133 GLN D 136 GLN D 385 GLN D 436 GLN E 101 ASN E 107 HIS E 216 ASN E 228 ASN E 258 ASN E 300 ASN F 6 HIS F 28 HIS F 37 HIS F 85 GLN F 101 ASN F 133 GLN F 136 GLN F 300 ASN ** F 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 385 GLN F 436 GLN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 HIS G 133 GLN G 136 GLN G 247 GLN G 436 GLN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 HIS H 85 GLN H 133 GLN H 136 GLN ** H 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 HIS H 334 ASN H 436 GLN I 6 HIS I 15 GLN I 28 HIS I 133 GLN I 136 GLN I 247 GLN I 300 ASN I 434 GLN I 436 GLN J 101 ASN J 107 HIS J 133 GLN J 226 ASN J 228 ASN J 300 ASN J 393 HIS K 18 ASN K 91 GLN K 107 HIS K 133 GLN K 226 ASN K 228 ASN K 300 ASN K 393 HIS L 18 ASN L 101 ASN L 107 HIS L 133 GLN L 228 ASN L 256 GLN L 300 ASN L 380 ASN L 393 HIS Total number of N/Q/H flips: 85 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.135871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.116352 restraints weight = 50466.851| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.98 r_work: 0.3472 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 41574 Z= 0.167 Angle : 0.637 9.510 56490 Z= 0.338 Chirality : 0.045 0.195 6174 Planarity : 0.005 0.051 7350 Dihedral : 11.647 174.067 5735 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.44 % Allowed : 13.64 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.12), residues: 5106 helix: 2.02 (0.11), residues: 2394 sheet: 0.49 (0.17), residues: 810 loop : -0.80 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 308 TYR 0.016 0.002 TYR H 36 PHE 0.027 0.002 PHE E 255 TRP 0.024 0.003 TRP I 346 HIS 0.015 0.001 HIS F 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (41574) covalent geometry : angle 0.63745 / 0.34 (56490) hydrogen bonds : bond 0.06418 / 4.33 ( 2076) hydrogen bonds : angle 5.22114 / 3.77 ( 5994) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1068 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 918 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.8373 (mm110) cc_final: 0.8083 (tp40) REVERT: A 230 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8298 (mp) REVERT: A 290 GLU cc_start: 0.6774 (mt-10) cc_final: 0.6448 (mt-10) REVERT: B 120 ASP cc_start: 0.7952 (m-30) cc_final: 0.7573 (m-30) REVERT: B 211 ASP cc_start: 0.8224 (m-30) cc_final: 0.7932 (m-30) REVERT: B 306 ASP cc_start: 0.7154 (t0) cc_final: 0.6625 (t0) REVERT: B 309 HIS cc_start: 0.8520 (m90) cc_final: 0.8304 (m90) REVERT: B 373 MET cc_start: 0.8782 (mtm) cc_final: 0.8553 (mtm) REVERT: C 154 MET cc_start: 0.9016 (tpp) cc_final: 0.8812 (mmt) REVERT: C 230 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8389 (mt) REVERT: D 74 THR cc_start: 0.8807 (p) cc_final: 0.8606 (t) REVERT: D 306 ASP cc_start: 0.6748 (t0) cc_final: 0.6336 (t0) REVERT: E 75 ILE cc_start: 0.9098 (mm) cc_final: 0.8833 (mm) REVERT: E 91 GLN cc_start: 0.8108 (mt0) cc_final: 0.7576 (mt0) REVERT: E 123 ARG cc_start: 0.7285 (ttp80) cc_final: 0.7066 (ttp-110) REVERT: E 152 LEU cc_start: 0.8671 (tp) cc_final: 0.8467 (tp) REVERT: E 230 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8250 (mp) REVERT: F 325 MET cc_start: 0.8022 (mmm) cc_final: 0.7765 (mmm) REVERT: F 413 MET cc_start: 0.7930 (mtp) cc_final: 0.7647 (ttm) REVERT: G 24 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8302 (tt) REVERT: G 200 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8592 (pt0) REVERT: G 213 CYS cc_start: 0.8002 (m) cc_final: 0.7681 (m) REVERT: G 386 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7536 (mm-30) REVERT: G 422 GLU cc_start: 0.7661 (tp30) cc_final: 0.7452 (tp30) REVERT: G 426 ASN cc_start: 0.7936 (m-40) cc_final: 0.7625 (m110) REVERT: G 431 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7345 (mp0) REVERT: G 435 TYR cc_start: 0.6897 (m-80) cc_final: 0.6337 (m-10) REVERT: H 116 ASP cc_start: 0.7407 (m-30) cc_final: 0.7180 (m-30) REVERT: H 130 ASP cc_start: 0.7353 (t0) cc_final: 0.6917 (m-30) REVERT: H 207 GLU cc_start: 0.7697 (tt0) cc_final: 0.7429 (tt0) REVERT: H 211 ASP cc_start: 0.7961 (m-30) cc_final: 0.7614 (m-30) REVERT: H 213 CYS cc_start: 0.7806 (m) cc_final: 0.7468 (m) REVERT: H 309 HIS cc_start: 0.8153 (m170) cc_final: 0.7909 (m170) REVERT: H 325 MET cc_start: 0.7954 (mmm) cc_final: 0.7675 (mmm) REVERT: H 422 GLU cc_start: 0.7625 (tp30) cc_final: 0.7273 (tp30) REVERT: H 426 ASN cc_start: 0.7934 (m-40) cc_final: 0.7600 (m110) REVERT: H 427 ASP cc_start: 0.7649 (m-30) cc_final: 0.7190 (m-30) REVERT: H 435 TYR cc_start: 0.6823 (m-80) cc_final: 0.6030 (m-10) REVERT: I 207 GLU cc_start: 0.7517 (tt0) cc_final: 0.7245 (tt0) REVERT: I 211 ASP cc_start: 0.7994 (m-30) cc_final: 0.7572 (m-30) REVERT: I 213 CYS cc_start: 0.8009 (m) cc_final: 0.7562 (m) REVERT: I 281 GLN cc_start: 0.8398 (tt0) cc_final: 0.7994 (tm-30) REVERT: I 283 TYR cc_start: 0.8170 (m-80) cc_final: 0.7797 (m-80) REVERT: I 422 GLU cc_start: 0.7711 (tp30) cc_final: 0.6938 (tp30) REVERT: I 426 ASN cc_start: 0.7896 (m-40) cc_final: 0.7229 (m110) REVERT: J 112 LYS cc_start: 0.8775 (mmtt) cc_final: 0.8535 (pttp) REVERT: J 128 GLN cc_start: 0.8330 (mm-40) cc_final: 0.8051 (tt0) REVERT: J 156 ARG cc_start: 0.8038 (mmt90) cc_final: 0.7744 (mmm-85) REVERT: K 91 GLN cc_start: 0.7977 (mt0) cc_final: 0.7769 (mt0) REVERT: K 120 ASP cc_start: 0.7403 (t0) cc_final: 0.7026 (t0) REVERT: K 123 ARG cc_start: 0.7724 (ttp-110) cc_final: 0.7413 (ttp-110) REVERT: K 214 ARG cc_start: 0.8207 (tmm160) cc_final: 0.7968 (ptt-90) REVERT: K 380 ASN cc_start: 0.8115 (t0) cc_final: 0.7746 (t0) REVERT: K 413 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7547 (ttm) REVERT: L 209 ILE cc_start: 0.8702 (mm) cc_final: 0.8375 (mt) REVERT: L 302 MET cc_start: 0.8250 (mmp) cc_final: 0.7560 (mmt) REVERT: L 413 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7846 (mtp) REVERT: L 420 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6808 (mm-30) outliers start: 150 outliers final: 70 residues processed: 1004 average time/residue: 0.2515 time to fit residues: 415.9882 Evaluate side-chains 817 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 740 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 334 ASN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 200 GLU Chi-restraints excluded: chain G residue 269 MET Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 192 HIS Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 338 LYS Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain K residue 71 GLU Chi-restraints excluded: chain K residue 225 THR Chi-restraints excluded: chain K residue 241 SER Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 413 MET Chi-restraints excluded: chain L residue 241 SER Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 276 ILE Chi-restraints excluded: chain L residue 413 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 264 optimal weight: 7.9990 chunk 384 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 340 optimal weight: 8.9990 chunk 140 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 chunk 439 optimal weight: 7.9990 chunk 489 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 436 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN A 50 ASN A 91 GLN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN B 37 HIS B 50 ASN B 192 HIS B 433 GLN C 15 GLN C 18 ASN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN C 256 GLN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN D 50 ASN E 18 ASN F 309 HIS G 6 HIS G 37 HIS H 6 HIS H 15 GLN H 37 HIS H 50 ASN H 133 GLN ** H 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 HIS I 133 GLN K 128 GLN K 406 HIS L 256 GLN L 406 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.126637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.106916 restraints weight = 51842.925| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.01 r_work: 0.3353 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 41574 Z= 0.233 Angle : 0.638 8.495 56490 Z= 0.338 Chirality : 0.047 0.228 6174 Planarity : 0.005 0.060 7350 Dihedral : 11.331 176.336 5723 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.88 % Allowed : 15.89 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.11), residues: 5106 helix: 1.69 (0.10), residues: 2412 sheet: 0.50 (0.18), residues: 744 loop : -0.89 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 422 TYR 0.017 0.002 TYR L 172 PHE 0.031 0.002 PHE K 255 TRP 0.021 0.002 TRP I 346 HIS 0.010 0.002 HIS E 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.23 (41574) covalent geometry : angle 0.63830 / 0.34 (56490) hydrogen bonds : bond 0.06640 / 4.49 ( 2076) hydrogen bonds : angle 5.04185 / 3.65 ( 5994) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 963 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 794 time to evaluate : 1.630 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 96 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8127 (mttp) REVERT: A 230 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8314 (mp) REVERT: A 332 ILE cc_start: 0.9126 (mp) cc_final: 0.8905 (mt) REVERT: A 417 GLU cc_start: 0.7092 (tt0) cc_final: 0.6680 (mt-10) REVERT: B 37 HIS cc_start: 0.8246 (OUTLIER) cc_final: 0.8024 (m170) REVERT: B 120 ASP cc_start: 0.7961 (m-30) cc_final: 0.7577 (m-30) REVERT: B 211 ASP cc_start: 0.8211 (m-30) cc_final: 0.7854 (m-30) REVERT: B 213 CYS cc_start: 0.7853 (m) cc_final: 0.7647 (m) REVERT: B 308 ARG cc_start: 0.8036 (mtm180) cc_final: 0.7660 (mtm180) REVERT: B 311 ARG cc_start: 0.8092 (mtt-85) cc_final: 0.7797 (mtp180) REVERT: B 352 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7439 (tmtt) REVERT: C 156 ARG cc_start: 0.8291 (mmt90) cc_final: 0.8035 (mmm-85) REVERT: C 230 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8327 (mt) REVERT: C 393 HIS cc_start: 0.8124 (t70) cc_final: 0.7547 (t-170) REVERT: D 74 THR cc_start: 0.8813 (p) cc_final: 0.8613 (t) REVERT: D 94 PHE cc_start: 0.8918 (p90) cc_final: 0.8674 (p90) REVERT: D 308 ARG cc_start: 0.8143 (mtm110) cc_final: 0.7466 (mtm110) REVERT: D 311 ARG cc_start: 0.8112 (mtt-85) cc_final: 0.7746 (mtp180) REVERT: E 77 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7584 (mt-10) REVERT: E 230 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8408 (mp) REVERT: F 322 ARG cc_start: 0.8450 (mtp85) cc_final: 0.8235 (mmm160) REVERT: F 325 MET cc_start: 0.8272 (mmm) cc_final: 0.8025 (mmm) REVERT: G 24 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8492 (tt) REVERT: G 160 GLU cc_start: 0.8248 (tp30) cc_final: 0.8024 (tp30) REVERT: G 205 ASP cc_start: 0.7999 (t0) cc_final: 0.7797 (t0) REVERT: G 207 GLU cc_start: 0.7525 (tt0) cc_final: 0.7292 (tt0) REVERT: G 211 ASP cc_start: 0.8058 (m-30) cc_final: 0.7764 (m-30) REVERT: G 282 GLN cc_start: 0.8056 (pt0) cc_final: 0.7672 (pm20) REVERT: G 308 ARG cc_start: 0.8074 (mtm180) cc_final: 0.7524 (mtm180) REVERT: G 426 ASN cc_start: 0.7996 (m-40) cc_final: 0.7772 (m110) REVERT: G 431 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7323 (mp0) REVERT: H 64 ARG cc_start: 0.8822 (ttm110) cc_final: 0.8594 (ttm110) REVERT: H 130 ASP cc_start: 0.7455 (t0) cc_final: 0.6964 (m-30) REVERT: H 133 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.6857 (pt0) REVERT: H 191 VAL cc_start: 0.8373 (t) cc_final: 0.8118 (t) REVERT: H 207 GLU cc_start: 0.7599 (tt0) cc_final: 0.7205 (tt0) REVERT: H 211 ASP cc_start: 0.7987 (m-30) cc_final: 0.7525 (m-30) REVERT: H 283 TYR cc_start: 0.8378 (m-80) cc_final: 0.8163 (m-10) REVERT: H 325 MET cc_start: 0.8104 (mmm) cc_final: 0.7405 (mmm) REVERT: H 346 TRP cc_start: 0.8184 (p-90) cc_final: 0.7703 (p-90) REVERT: H 416 MET cc_start: 0.7554 (mmm) cc_final: 0.6811 (mmm) REVERT: H 422 GLU cc_start: 0.7767 (tp30) cc_final: 0.7385 (tp30) REVERT: H 426 ASN cc_start: 0.8156 (m-40) cc_final: 0.7700 (m110) REVERT: H 435 TYR cc_start: 0.6885 (m-80) cc_final: 0.6297 (m-10) REVERT: I 211 ASP cc_start: 0.8033 (m-30) cc_final: 0.7585 (m-30) REVERT: I 281 GLN cc_start: 0.8449 (tt0) cc_final: 0.7965 (tm-30) REVERT: I 283 TYR cc_start: 0.8214 (m-80) cc_final: 0.7823 (m-80) REVERT: I 398 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7621 (ttp) REVERT: I 402 LYS cc_start: 0.8695 (mttt) cc_final: 0.8399 (mptt) REVERT: I 422 GLU cc_start: 0.7768 (tp30) cc_final: 0.6860 (tp30) REVERT: I 426 ASN cc_start: 0.7939 (m-40) cc_final: 0.7146 (m110) REVERT: J 128 GLN cc_start: 0.8461 (mm-40) cc_final: 0.8102 (tt0) REVERT: J 254 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7422 (tt0) REVERT: J 342 GLN cc_start: 0.7875 (pt0) cc_final: 0.7600 (mp10) REVERT: K 302 MET cc_start: 0.8250 (mmm) cc_final: 0.8046 (mtt) REVERT: L 35 GLN cc_start: 0.8311 (tt0) cc_final: 0.7960 (mm-40) REVERT: L 209 ILE cc_start: 0.8920 (mm) cc_final: 0.8617 (mt) REVERT: L 332 ILE cc_start: 0.9052 (mm) cc_final: 0.8826 (mm) REVERT: L 391 LEU cc_start: 0.8595 (tp) cc_final: 0.8341 (tt) REVERT: L 413 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8153 (mtp) outliers start: 169 outliers final: 99 residues processed: 905 average time/residue: 0.2556 time to fit residues: 380.6246 Evaluate side-chains 801 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 691 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 393 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 269 MET Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 133 GLN Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 277 SER Chi-restraints excluded: chain H residue 295 MET Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 373 MET Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 105 LYS Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 277 SER Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 398 MET Chi-restraints excluded: chain I residue 425 MET Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 198 SER Chi-restraints excluded: chain J residue 254 GLU Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain K residue 241 SER Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 211 ASP Chi-restraints excluded: chain L residue 241 SER Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 276 ILE Chi-restraints excluded: chain L residue 277 SER Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain L residue 413 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 366 optimal weight: 0.7980 chunk 461 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 448 optimal weight: 0.8980 chunk 320 optimal weight: 4.9990 chunk 430 optimal weight: 7.9990 chunk 331 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 487 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 HIS ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN E 256 GLN F 309 HIS H 133 GLN H 309 HIS I 50 ASN J 31 GLN J 406 HIS K 15 GLN K 101 ASN K 256 GLN L 256 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.128527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.108615 restraints weight = 51332.092| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.06 r_work: 0.3359 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 41574 Z= 0.202 Angle : 0.596 9.418 56490 Z= 0.314 Chirality : 0.045 0.240 6174 Planarity : 0.005 0.049 7350 Dihedral : 11.171 175.395 5717 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.20 % Allowed : 16.57 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.11), residues: 5106 helix: 1.59 (0.10), residues: 2418 sheet: 0.28 (0.18), residues: 774 loop : -0.98 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 215 TYR 0.017 0.002 TYR F 185 PHE 0.029 0.002 PHE L 255 TRP 0.028 0.002 TRP I 346 HIS 0.018 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 (41574) covalent geometry : angle 0.59591 / 0.31 (56490) hydrogen bonds : bond 0.06082 / 4.11 ( 2076) hydrogen bonds : angle 4.87687 / 3.54 ( 5994) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 747 time to evaluate : 1.634 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: A 230 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8368 (mp) REVERT: A 417 GLU cc_start: 0.6963 (tt0) cc_final: 0.6654 (mt-10) REVERT: B 120 ASP cc_start: 0.8102 (m-30) cc_final: 0.7715 (m-30) REVERT: B 207 GLU cc_start: 0.8423 (pt0) cc_final: 0.8128 (pt0) REVERT: B 211 ASP cc_start: 0.8421 (m-30) cc_final: 0.8083 (m-30) REVERT: B 213 CYS cc_start: 0.7646 (m) cc_final: 0.7415 (m) REVERT: B 308 ARG cc_start: 0.8020 (mtm180) cc_final: 0.7630 (mtm180) REVERT: B 311 ARG cc_start: 0.8088 (mtt-85) cc_final: 0.7770 (mtp180) REVERT: B 352 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7318 (tmtt) REVERT: C 84 ARG cc_start: 0.8003 (ptt-90) cc_final: 0.7789 (ptt-90) REVERT: C 156 ARG cc_start: 0.8277 (mmt90) cc_final: 0.7956 (mmm-85) REVERT: C 230 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8439 (mt) REVERT: C 393 HIS cc_start: 0.8096 (t70) cc_final: 0.7618 (t-170) REVERT: D 308 ARG cc_start: 0.7974 (mtm110) cc_final: 0.7309 (mtm110) REVERT: D 311 ARG cc_start: 0.8028 (mtt-85) cc_final: 0.7450 (mtp180) REVERT: D 372 LYS cc_start: 0.8631 (mmmt) cc_final: 0.8195 (ttpt) REVERT: E 75 ILE cc_start: 0.9053 (mm) cc_final: 0.8598 (mm) REVERT: E 77 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7792 (mt-10) REVERT: F 301 MET cc_start: 0.8530 (mmp) cc_final: 0.8219 (mmp) REVERT: F 306 ASP cc_start: 0.7155 (t70) cc_final: 0.6747 (t0) REVERT: F 322 ARG cc_start: 0.8320 (mtp85) cc_final: 0.8064 (mmm160) REVERT: F 325 MET cc_start: 0.8405 (mmm) cc_final: 0.8002 (mmm) REVERT: G 24 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8374 (tt) REVERT: G 160 GLU cc_start: 0.8292 (tp30) cc_final: 0.8070 (tp30) REVERT: G 211 ASP cc_start: 0.8016 (m-30) cc_final: 0.7726 (m-30) REVERT: G 282 GLN cc_start: 0.8165 (pt0) cc_final: 0.7800 (pm20) REVERT: G 306 ASP cc_start: 0.7044 (t0) cc_final: 0.5718 (t0) REVERT: G 308 ARG cc_start: 0.8158 (mtm180) cc_final: 0.7670 (mtm180) REVERT: G 426 ASN cc_start: 0.7956 (m-40) cc_final: 0.7564 (m110) REVERT: H 191 VAL cc_start: 0.8424 (t) cc_final: 0.8170 (t) REVERT: H 205 ASP cc_start: 0.8125 (t0) cc_final: 0.7883 (m-30) REVERT: H 211 ASP cc_start: 0.8105 (m-30) cc_final: 0.7658 (m-30) REVERT: H 325 MET cc_start: 0.8192 (mmm) cc_final: 0.7598 (mmm) REVERT: H 398 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7762 (ttm) REVERT: H 422 GLU cc_start: 0.7669 (tp30) cc_final: 0.7321 (tp30) REVERT: H 426 ASN cc_start: 0.8067 (m-40) cc_final: 0.7641 (m110) REVERT: I 160 GLU cc_start: 0.8223 (tp30) cc_final: 0.7886 (tp30) REVERT: I 205 ASP cc_start: 0.8162 (t0) cc_final: 0.7762 (m-30) REVERT: I 211 ASP cc_start: 0.8057 (m-30) cc_final: 0.7524 (m-30) REVERT: I 281 GLN cc_start: 0.8533 (tt0) cc_final: 0.8031 (tm-30) REVERT: I 283 TYR cc_start: 0.8233 (m-80) cc_final: 0.7857 (m-80) REVERT: I 398 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7544 (ttm) REVERT: I 413 MET cc_start: 0.8073 (mmm) cc_final: 0.7843 (mmm) REVERT: I 422 GLU cc_start: 0.7883 (tp30) cc_final: 0.7002 (tp30) REVERT: I 426 ASN cc_start: 0.7940 (m-40) cc_final: 0.7209 (m110) REVERT: J 128 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8143 (tt0) REVERT: J 342 GLN cc_start: 0.7850 (pt0) cc_final: 0.7582 (mp10) REVERT: K 76 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8264 (m-30) REVERT: L 35 GLN cc_start: 0.8147 (tt0) cc_final: 0.7892 (mm-40) REVERT: L 88 HIS cc_start: 0.7271 (OUTLIER) cc_final: 0.6181 (p90) REVERT: L 332 ILE cc_start: 0.8967 (mm) cc_final: 0.8734 (mm) REVERT: L 391 LEU cc_start: 0.8621 (tp) cc_final: 0.8381 (tt) outliers start: 183 outliers final: 122 residues processed: 854 average time/residue: 0.2629 time to fit residues: 369.5712 Evaluate side-chains 821 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 690 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 393 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 334 ASN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 269 MET Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 415 GLU Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 277 SER Chi-restraints excluded: chain H residue 295 MET Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 372 LYS Chi-restraints excluded: chain H residue 398 MET Chi-restraints excluded: chain H residue 431 GLU Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 105 LYS Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 357 ASP Chi-restraints excluded: chain I residue 398 MET Chi-restraints excluded: chain I residue 425 MET Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 128 GLN Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 155 GLU Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 198 SER Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 361 THR Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 88 HIS Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain K residue 225 THR Chi-restraints excluded: chain K residue 241 SER Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 88 HIS Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 198 SER Chi-restraints excluded: chain L residue 211 ASP Chi-restraints excluded: chain L residue 241 SER Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 276 ILE Chi-restraints excluded: chain L residue 277 SER Chi-restraints excluded: chain L residue 349 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 283 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 199 optimal weight: 0.4980 chunk 336 optimal weight: 10.0000 chunk 268 optimal weight: 6.9990 chunk 219 optimal weight: 0.8980 chunk 259 optimal weight: 5.9990 chunk 342 optimal weight: 0.0670 chunk 210 optimal weight: 0.7980 chunk 307 optimal weight: 5.9990 chunk 106 optimal weight: 0.0570 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 GLN B 37 HIS ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 ASN E 15 GLN J 15 GLN L 256 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.132227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.112506 restraints weight = 50931.259| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.08 r_work: 0.3432 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 41574 Z= 0.111 Angle : 0.521 7.659 56490 Z= 0.272 Chirality : 0.042 0.264 6174 Planarity : 0.004 0.043 7350 Dihedral : 10.799 173.967 5713 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.08 % Allowed : 16.97 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.11), residues: 5106 helix: 1.76 (0.10), residues: 2388 sheet: 0.48 (0.18), residues: 774 loop : -0.81 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 215 TYR 0.014 0.001 TYR B 185 PHE 0.029 0.001 PHE K 255 TRP 0.025 0.002 TRP I 346 HIS 0.009 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (41574) covalent geometry : angle 0.52076 / 0.27 (56490) hydrogen bonds : bond 0.04467 / 3.03 ( 2076) hydrogen bonds : angle 4.57094 / 3.31 ( 5994) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 942 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 808 time to evaluate : 1.634 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: A 230 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8333 (mt) REVERT: A 370 LYS cc_start: 0.8247 (ttpp) cc_final: 0.8038 (ttmm) REVERT: A 417 GLU cc_start: 0.6868 (tt0) cc_final: 0.6627 (mt-10) REVERT: B 120 ASP cc_start: 0.7961 (m-30) cc_final: 0.7539 (m-30) REVERT: B 207 GLU cc_start: 0.8232 (pt0) cc_final: 0.7811 (pt0) REVERT: B 211 ASP cc_start: 0.8293 (m-30) cc_final: 0.7899 (m-30) REVERT: B 308 ARG cc_start: 0.8133 (mtm180) cc_final: 0.7893 (mtm180) REVERT: B 311 ARG cc_start: 0.7980 (mtt-85) cc_final: 0.7719 (mtp180) REVERT: B 325 MET cc_start: 0.8110 (mmm) cc_final: 0.7558 (mmm) REVERT: B 357 ASP cc_start: 0.8384 (m-30) cc_final: 0.8116 (m-30) REVERT: C 393 HIS cc_start: 0.8043 (t70) cc_final: 0.7595 (t-170) REVERT: D 179 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.6920 (t70) REVERT: D 308 ARG cc_start: 0.8364 (mtm110) cc_final: 0.7922 (mtm110) REVERT: D 311 ARG cc_start: 0.7969 (mtt-85) cc_final: 0.7717 (mtp180) REVERT: D 372 LYS cc_start: 0.8498 (mmmt) cc_final: 0.8154 (ttpt) REVERT: D 433 GLN cc_start: 0.8420 (tp40) cc_final: 0.8148 (tp40) REVERT: E 77 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7630 (mt-10) REVERT: E 91 GLN cc_start: 0.8007 (mt0) cc_final: 0.7471 (mt0) REVERT: F 55 GLU cc_start: 0.7997 (tp30) cc_final: 0.7585 (tp30) REVERT: F 306 ASP cc_start: 0.6887 (t70) cc_final: 0.6637 (t70) REVERT: F 322 ARG cc_start: 0.8375 (mtp85) cc_final: 0.8114 (mmm160) REVERT: F 325 MET cc_start: 0.8427 (mmm) cc_final: 0.8122 (mmm) REVERT: G 24 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8422 (tt) REVERT: G 160 GLU cc_start: 0.8305 (tp30) cc_final: 0.8073 (tp30) REVERT: G 205 ASP cc_start: 0.7906 (t0) cc_final: 0.7658 (m-30) REVERT: G 211 ASP cc_start: 0.8033 (m-30) cc_final: 0.7701 (m-30) REVERT: G 282 GLN cc_start: 0.8050 (pt0) cc_final: 0.7693 (pm20) REVERT: G 306 ASP cc_start: 0.6837 (t0) cc_final: 0.6526 (t0) REVERT: G 308 ARG cc_start: 0.8344 (mtm180) cc_final: 0.7737 (mtm-85) REVERT: G 398 MET cc_start: 0.7779 (mtp) cc_final: 0.7196 (ttm) REVERT: G 426 ASN cc_start: 0.7986 (m-40) cc_final: 0.7726 (m110) REVERT: H 191 VAL cc_start: 0.8389 (t) cc_final: 0.8089 (t) REVERT: H 207 GLU cc_start: 0.7492 (tt0) cc_final: 0.6771 (tt0) REVERT: H 211 ASP cc_start: 0.8057 (m-30) cc_final: 0.7565 (m-30) REVERT: H 325 MET cc_start: 0.8197 (mmm) cc_final: 0.7841 (mmm) REVERT: H 398 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7793 (ttm) REVERT: H 422 GLU cc_start: 0.7579 (tp30) cc_final: 0.7297 (tp30) REVERT: H 426 ASN cc_start: 0.7975 (m-40) cc_final: 0.7544 (m110) REVERT: I 160 GLU cc_start: 0.8245 (tp30) cc_final: 0.7938 (tp30) REVERT: I 205 ASP cc_start: 0.7960 (t0) cc_final: 0.7669 (m-30) REVERT: I 207 GLU cc_start: 0.7853 (tt0) cc_final: 0.7296 (tt0) REVERT: I 211 ASP cc_start: 0.7982 (m-30) cc_final: 0.7386 (m-30) REVERT: I 281 GLN cc_start: 0.8439 (tt0) cc_final: 0.8018 (tm-30) REVERT: I 283 TYR cc_start: 0.8187 (m-80) cc_final: 0.7781 (m-80) REVERT: I 398 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7876 (ttm) REVERT: I 422 GLU cc_start: 0.7859 (tp30) cc_final: 0.7040 (tp30) REVERT: I 426 ASN cc_start: 0.8024 (m-40) cc_final: 0.7324 (m110) REVERT: I 435 TYR cc_start: 0.6760 (m-80) cc_final: 0.6470 (m-10) REVERT: J 128 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8104 (tt0) REVERT: J 156 ARG cc_start: 0.8252 (mmt90) cc_final: 0.8035 (mmm-85) REVERT: J 342 GLN cc_start: 0.7899 (pt0) cc_final: 0.7563 (mp10) REVERT: J 396 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7686 (m-30) REVERT: K 76 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.8073 (m-30) REVERT: L 35 GLN cc_start: 0.8250 (tt0) cc_final: 0.8038 (mm-40) REVERT: L 391 LEU cc_start: 0.8563 (tp) cc_final: 0.8347 (tt) outliers start: 134 outliers final: 82 residues processed: 880 average time/residue: 0.2607 time to fit residues: 379.5076 Evaluate side-chains 805 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 715 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 128 GLN Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 334 ASN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 269 MET Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 213 CYS Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 295 MET Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 398 MET Chi-restraints excluded: chain H residue 428 LEU Chi-restraints excluded: chain H residue 431 GLU Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 295 MET Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 357 ASP Chi-restraints excluded: chain I residue 398 MET Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 128 GLN Chi-restraints excluded: chain J residue 198 SER Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 361 THR Chi-restraints excluded: chain J residue 396 ASP Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 194 THR Chi-restraints excluded: chain L residue 211 ASP Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 276 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 408 optimal weight: 10.0000 chunk 435 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 356 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 100 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 182 optimal weight: 5.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 HIS E 15 GLN ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 GLN E 256 GLN E 406 HIS ** F 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 GLN G 37 HIS ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 309 HIS ** H 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 256 GLN L 256 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.124932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.105742 restraints weight = 52403.126| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.02 r_work: 0.3326 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.4768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 41574 Z= 0.251 Angle : 0.634 8.420 56490 Z= 0.331 Chirality : 0.047 0.252 6174 Planarity : 0.005 0.049 7350 Dihedral : 10.957 178.173 5709 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.22 % Allowed : 17.77 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.11), residues: 5106 helix: 1.45 (0.10), residues: 2430 sheet: 0.30 (0.18), residues: 816 loop : -0.97 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 215 TYR 0.019 0.002 TYR B 185 PHE 0.028 0.002 PHE C 255 TRP 0.027 0.002 TRP I 346 HIS 0.011 0.002 HIS F 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.25 (41574) covalent geometry : angle 0.63365 / 0.33 (56490) hydrogen bonds : bond 0.06369 / 4.31 ( 2076) hydrogen bonds : angle 4.86579 / 3.53 ( 5994) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 706 time to evaluate : 1.689 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: A 230 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8289 (mt) REVERT: A 417 GLU cc_start: 0.7069 (tt0) cc_final: 0.6782 (mt-10) REVERT: B 120 ASP cc_start: 0.8010 (m-30) cc_final: 0.7663 (m-30) REVERT: B 207 GLU cc_start: 0.8363 (pt0) cc_final: 0.8052 (pt0) REVERT: B 211 ASP cc_start: 0.8284 (m-30) cc_final: 0.7935 (m-30) REVERT: B 308 ARG cc_start: 0.8095 (mtm180) cc_final: 0.7837 (mtm180) REVERT: B 311 ARG cc_start: 0.8247 (mtt-85) cc_final: 0.7920 (mtp180) REVERT: B 352 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.7446 (tmtt) REVERT: C 393 HIS cc_start: 0.8155 (t70) cc_final: 0.7614 (t-170) REVERT: D 308 ARG cc_start: 0.8266 (mtm110) cc_final: 0.7628 (mtm110) REVERT: D 311 ARG cc_start: 0.8192 (mtt-85) cc_final: 0.7892 (mtp85) REVERT: D 372 LYS cc_start: 0.8557 (mmmt) cc_final: 0.8143 (ttpt) REVERT: D 386 GLU cc_start: 0.8403 (pt0) cc_final: 0.8140 (pt0) REVERT: E 77 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7666 (mt-10) REVERT: F 55 GLU cc_start: 0.8130 (tp30) cc_final: 0.7734 (tp30) REVERT: F 145 THR cc_start: 0.8196 (m) cc_final: 0.7859 (m) REVERT: F 301 MET cc_start: 0.8480 (mmp) cc_final: 0.8226 (mmp) REVERT: F 306 ASP cc_start: 0.7103 (t70) cc_final: 0.6725 (t0) REVERT: F 325 MET cc_start: 0.8345 (mmm) cc_final: 0.8044 (mmm) REVERT: G 24 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8379 (tt) REVERT: G 160 GLU cc_start: 0.8294 (tp30) cc_final: 0.8072 (tp30) REVERT: G 211 ASP cc_start: 0.8140 (m-30) cc_final: 0.7757 (m-30) REVERT: G 282 GLN cc_start: 0.8048 (pt0) cc_final: 0.7656 (pm20) REVERT: G 426 ASN cc_start: 0.8028 (m-40) cc_final: 0.7779 (m110) REVERT: H 211 ASP cc_start: 0.8116 (m-30) cc_final: 0.7606 (m-30) REVERT: H 325 MET cc_start: 0.8252 (mmm) cc_final: 0.7844 (mmm) REVERT: H 398 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7873 (ttm) REVERT: H 422 GLU cc_start: 0.7680 (tp30) cc_final: 0.7320 (tp30) REVERT: H 426 ASN cc_start: 0.8121 (m-40) cc_final: 0.7642 (m110) REVERT: I 47 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8280 (mt-10) REVERT: I 160 GLU cc_start: 0.8316 (tp30) cc_final: 0.8061 (tp30) REVERT: I 205 ASP cc_start: 0.8102 (t0) cc_final: 0.7729 (m-30) REVERT: I 211 ASP cc_start: 0.8130 (m-30) cc_final: 0.7590 (m-30) REVERT: I 283 TYR cc_start: 0.8161 (m-80) cc_final: 0.7799 (m-80) REVERT: I 308 ARG cc_start: 0.8332 (mtm180) cc_final: 0.8061 (mmt180) REVERT: I 398 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7710 (ttm) REVERT: I 422 GLU cc_start: 0.7882 (tp30) cc_final: 0.7004 (tp30) REVERT: I 426 ASN cc_start: 0.7989 (m-40) cc_final: 0.7267 (m110) REVERT: J 128 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8174 (tt0) REVERT: J 156 ARG cc_start: 0.8332 (mmt90) cc_final: 0.7970 (mmm-85) REVERT: J 342 GLN cc_start: 0.7952 (pt0) cc_final: 0.7490 (mp10) REVERT: K 76 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.8110 (m-30) REVERT: L 35 GLN cc_start: 0.8238 (tt0) cc_final: 0.7977 (mm-40) REVERT: L 88 HIS cc_start: 0.7426 (OUTLIER) cc_final: 0.6273 (p90) REVERT: L 93 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8387 (mt) REVERT: L 176 GLN cc_start: 0.8553 (mm-40) cc_final: 0.8296 (mm-40) outliers start: 184 outliers final: 126 residues processed: 816 average time/residue: 0.2616 time to fit residues: 353.1555 Evaluate side-chains 799 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 663 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 413 MET Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 334 ASN Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 269 MET Chi-restraints excluded: chain G residue 277 SER Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 204 ILE Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 295 MET Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 372 LYS Chi-restraints excluded: chain H residue 398 MET Chi-restraints excluded: chain H residue 428 LEU Chi-restraints excluded: chain H residue 431 GLU Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 105 LYS Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 357 ASP Chi-restraints excluded: chain I residue 398 MET Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 128 GLN Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 155 GLU Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 198 SER Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 361 THR Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 88 HIS Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 241 SER Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 88 HIS Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 194 THR Chi-restraints excluded: chain L residue 198 SER Chi-restraints excluded: chain L residue 211 ASP Chi-restraints excluded: chain L residue 241 SER Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 276 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 225 optimal weight: 5.9990 chunk 223 optimal weight: 1.9990 chunk 365 optimal weight: 5.9990 chunk 381 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 141 optimal weight: 4.9990 chunk 314 optimal weight: 0.4980 chunk 21 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 326 optimal weight: 0.5980 chunk 136 optimal weight: 4.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 GLN B 37 HIS ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 GLN F 309 HIS G 37 HIS ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 HIS H 349 ASN K 256 GLN L 128 GLN L 256 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.126453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.107706 restraints weight = 52159.960| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.95 r_work: 0.3364 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 41574 Z= 0.181 Angle : 0.575 7.643 56490 Z= 0.302 Chirality : 0.045 0.244 6174 Planarity : 0.004 0.047 7350 Dihedral : 10.853 177.325 5707 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.76 % Allowed : 18.37 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.11), residues: 5106 helix: 1.44 (0.10), residues: 2430 sheet: 0.19 (0.18), residues: 834 loop : -0.97 (0.13), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 422 TYR 0.015 0.001 TYR B 185 PHE 0.033 0.002 PHE K 255 TRP 0.020 0.002 TRP F 346 HIS 0.011 0.001 HIS F 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (41574) covalent geometry : angle 0.57511 / 0.30 (56490) hydrogen bonds : bond 0.05589 / 3.79 ( 2076) hydrogen bonds : angle 4.73130 / 3.43 ( 5994) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 690 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8286 (mt) REVERT: A 302 MET cc_start: 0.7770 (mmm) cc_final: 0.7438 (mtt) REVERT: A 417 GLU cc_start: 0.7029 (tt0) cc_final: 0.6765 (mt-10) REVERT: B 37 HIS cc_start: 0.8199 (OUTLIER) cc_final: 0.7938 (m170) REVERT: B 120 ASP cc_start: 0.7974 (m-30) cc_final: 0.7582 (m-30) REVERT: B 207 GLU cc_start: 0.8350 (pt0) cc_final: 0.7997 (pt0) REVERT: B 211 ASP cc_start: 0.8228 (m-30) cc_final: 0.7852 (m-30) REVERT: B 308 ARG cc_start: 0.8080 (mtm180) cc_final: 0.7857 (mtm180) REVERT: C 76 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.8179 (m-30) REVERT: C 393 HIS cc_start: 0.8138 (t70) cc_final: 0.7603 (t-170) REVERT: C 419 SER cc_start: 0.7893 (m) cc_final: 0.7659 (p) REVERT: D 44 LEU cc_start: 0.8671 (mt) cc_final: 0.8453 (mt) REVERT: D 281 GLN cc_start: 0.7987 (pt0) cc_final: 0.7629 (pt0) REVERT: D 308 ARG cc_start: 0.8306 (mtm110) cc_final: 0.7738 (mtm110) REVERT: D 311 ARG cc_start: 0.8182 (mtt-85) cc_final: 0.7855 (mtp85) REVERT: D 372 LYS cc_start: 0.8524 (mmmt) cc_final: 0.8164 (ttpt) REVERT: E 77 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7675 (mt-10) REVERT: F 55 GLU cc_start: 0.8101 (tp30) cc_final: 0.7703 (tp30) REVERT: F 301 MET cc_start: 0.8419 (mmp) cc_final: 0.8155 (mmp) REVERT: F 306 ASP cc_start: 0.6914 (t70) cc_final: 0.6651 (t0) REVERT: F 325 MET cc_start: 0.8398 (mmm) cc_final: 0.8174 (mmm) REVERT: G 24 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8345 (tt) REVERT: G 96 GLN cc_start: 0.7263 (pm20) cc_final: 0.7032 (mm110) REVERT: G 113 GLU cc_start: 0.8339 (tp30) cc_final: 0.8067 (tt0) REVERT: G 160 GLU cc_start: 0.8287 (tp30) cc_final: 0.8059 (tp30) REVERT: G 211 ASP cc_start: 0.8115 (m-30) cc_final: 0.7727 (m-30) REVERT: G 282 GLN cc_start: 0.8047 (pt0) cc_final: 0.7680 (pm20) REVERT: G 306 ASP cc_start: 0.7949 (m-30) cc_final: 0.7600 (t0) REVERT: G 308 ARG cc_start: 0.8415 (mtm180) cc_final: 0.7762 (mtm-85) REVERT: G 426 ASN cc_start: 0.8018 (m-40) cc_final: 0.7757 (m110) REVERT: H 211 ASP cc_start: 0.8088 (m-30) cc_final: 0.7566 (m-30) REVERT: H 398 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7938 (ttm) REVERT: H 422 GLU cc_start: 0.7653 (tp30) cc_final: 0.7310 (tp30) REVERT: H 426 ASN cc_start: 0.8106 (m-40) cc_final: 0.7627 (m110) REVERT: I 1 MET cc_start: 0.8332 (tpt) cc_final: 0.8104 (tpt) REVERT: I 47 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8239 (mt-10) REVERT: I 113 GLU cc_start: 0.8394 (tp30) cc_final: 0.8080 (tt0) REVERT: I 160 GLU cc_start: 0.8310 (tp30) cc_final: 0.8071 (tp30) REVERT: I 205 ASP cc_start: 0.8036 (t0) cc_final: 0.7690 (m-30) REVERT: I 211 ASP cc_start: 0.8035 (m-30) cc_final: 0.7446 (m-30) REVERT: I 283 TYR cc_start: 0.8150 (m-80) cc_final: 0.7766 (m-80) REVERT: I 398 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7823 (ttm) REVERT: I 422 GLU cc_start: 0.7902 (tp30) cc_final: 0.7151 (tp30) REVERT: I 426 ASN cc_start: 0.8018 (m-40) cc_final: 0.7291 (m110) REVERT: J 128 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8133 (tt0) REVERT: J 156 ARG cc_start: 0.8246 (mmt90) cc_final: 0.7880 (mmm-85) REVERT: J 342 GLN cc_start: 0.7950 (pt0) cc_final: 0.7472 (mp10) REVERT: J 396 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7661 (m-30) REVERT: K 76 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.8049 (m-30) REVERT: L 35 GLN cc_start: 0.8259 (tt0) cc_final: 0.8007 (mm-40) REVERT: L 71 GLU cc_start: 0.7492 (tt0) cc_final: 0.7279 (tt0) REVERT: L 88 HIS cc_start: 0.7333 (OUTLIER) cc_final: 0.6175 (p90) REVERT: L 93 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8375 (mt) outliers start: 164 outliers final: 127 residues processed: 788 average time/residue: 0.2615 time to fit residues: 340.5285 Evaluate side-chains 799 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 660 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 413 MET Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 269 MET Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 334 ASN Chi-restraints excluded: chain F residue 425 MET Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 277 SER Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 133 GLN Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 277 SER Chi-restraints excluded: chain H residue 295 MET Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 398 MET Chi-restraints excluded: chain H residue 431 GLU Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 133 GLN Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 291 LEU Chi-restraints excluded: chain I residue 295 MET Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 357 ASP Chi-restraints excluded: chain I residue 398 MET Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 128 GLN Chi-restraints excluded: chain J residue 155 GLU Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 396 ASP Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 88 HIS Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain K residue 241 SER Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 88 HIS Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 194 THR Chi-restraints excluded: chain L residue 198 SER Chi-restraints excluded: chain L residue 211 ASP Chi-restraints excluded: chain L residue 241 SER Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 276 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 278 optimal weight: 8.9990 chunk 499 optimal weight: 7.9990 chunk 409 optimal weight: 0.9990 chunk 138 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 410 optimal weight: 0.9990 chunk 205 optimal weight: 0.4980 chunk 475 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 504 optimal weight: 0.7980 chunk 498 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 294 GLN G 37 HIS ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 ASN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 256 GLN L 256 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.129874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.110289 restraints weight = 51358.336| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.06 r_work: 0.3404 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 41574 Z= 0.117 Angle : 0.532 7.023 56490 Z= 0.278 Chirality : 0.043 0.251 6174 Planarity : 0.004 0.046 7350 Dihedral : 10.664 176.088 5707 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.21 % Allowed : 19.15 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.12), residues: 5106 helix: 1.61 (0.10), residues: 2418 sheet: 0.31 (0.18), residues: 834 loop : -0.88 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 278 TYR 0.020 0.001 TYR B 36 PHE 0.028 0.001 PHE K 255 TRP 0.028 0.002 TRP I 346 HIS 0.034 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (41574) covalent geometry : angle 0.53248 / 0.28 (56490) hydrogen bonds : bond 0.04564 / 3.10 ( 2076) hydrogen bonds : angle 4.54947 / 3.29 ( 5994) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 733 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8387 (mt) REVERT: A 417 GLU cc_start: 0.6919 (tt0) cc_final: 0.6656 (mt-10) REVERT: B 120 ASP cc_start: 0.7955 (m-30) cc_final: 0.7543 (m-30) REVERT: B 207 GLU cc_start: 0.8312 (pt0) cc_final: 0.7875 (pt0) REVERT: B 211 ASP cc_start: 0.8219 (m-30) cc_final: 0.7878 (m-30) REVERT: B 325 MET cc_start: 0.8189 (mmm) cc_final: 0.7806 (mmm) REVERT: B 357 ASP cc_start: 0.8382 (m-30) cc_final: 0.8031 (m-30) REVERT: C 393 HIS cc_start: 0.8126 (t70) cc_final: 0.7645 (t-170) REVERT: D 44 LEU cc_start: 0.8595 (mt) cc_final: 0.8344 (mt) REVERT: D 94 PHE cc_start: 0.8852 (p90) cc_final: 0.8529 (p90) REVERT: D 281 GLN cc_start: 0.8006 (pt0) cc_final: 0.7669 (pt0) REVERT: D 311 ARG cc_start: 0.8193 (mtt-85) cc_final: 0.7854 (mtp180) REVERT: D 372 LYS cc_start: 0.8540 (mmmt) cc_final: 0.8175 (ttpt) REVERT: D 433 GLN cc_start: 0.8558 (tp40) cc_final: 0.8279 (tp40) REVERT: E 77 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7673 (mt-10) REVERT: E 91 GLN cc_start: 0.8030 (mt0) cc_final: 0.7503 (mt0) REVERT: F 55 GLU cc_start: 0.8015 (tp30) cc_final: 0.7613 (tp30) REVERT: F 309 HIS cc_start: 0.8455 (m90) cc_final: 0.8246 (m-70) REVERT: G 1 MET cc_start: 0.8491 (mmm) cc_final: 0.7878 (tpt) REVERT: G 24 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8351 (tt) REVERT: G 160 GLU cc_start: 0.8311 (tp30) cc_final: 0.8108 (tp30) REVERT: G 211 ASP cc_start: 0.8110 (m-30) cc_final: 0.7721 (m-30) REVERT: G 282 GLN cc_start: 0.8103 (pt0) cc_final: 0.7769 (pm20) REVERT: G 308 ARG cc_start: 0.8444 (mtm180) cc_final: 0.7734 (mtm180) REVERT: G 373 MET cc_start: 0.8795 (ptp) cc_final: 0.8480 (ptm) REVERT: G 398 MET cc_start: 0.7840 (mtp) cc_final: 0.7340 (ttm) REVERT: G 414 ASP cc_start: 0.6745 (t0) cc_final: 0.6340 (m-30) REVERT: G 426 ASN cc_start: 0.8011 (m-40) cc_final: 0.7777 (m110) REVERT: G 431 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7403 (mp0) REVERT: H 211 ASP cc_start: 0.8089 (m-30) cc_final: 0.7582 (m-30) REVERT: H 422 GLU cc_start: 0.7614 (tp30) cc_final: 0.7283 (tp30) REVERT: H 426 ASN cc_start: 0.8029 (m-40) cc_final: 0.7538 (m110) REVERT: I 1 MET cc_start: 0.8268 (tpt) cc_final: 0.8005 (tpt) REVERT: I 47 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8188 (mt-10) REVERT: I 113 GLU cc_start: 0.8436 (tp30) cc_final: 0.8065 (mp0) REVERT: I 205 ASP cc_start: 0.7982 (t0) cc_final: 0.7756 (m-30) REVERT: I 211 ASP cc_start: 0.8050 (m-30) cc_final: 0.7465 (m-30) REVERT: I 281 GLN cc_start: 0.8490 (tt0) cc_final: 0.7822 (tm-30) REVERT: I 283 TYR cc_start: 0.8125 (m-80) cc_final: 0.7757 (m-10) REVERT: I 398 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7920 (ttm) REVERT: I 422 GLU cc_start: 0.7857 (tp30) cc_final: 0.7169 (tp30) REVERT: I 426 ASN cc_start: 0.8001 (m-40) cc_final: 0.7310 (m110) REVERT: J 128 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8123 (tt0) REVERT: J 156 ARG cc_start: 0.8316 (mmt90) cc_final: 0.8038 (mmm-85) REVERT: J 342 GLN cc_start: 0.7929 (pt0) cc_final: 0.7445 (mp10) REVERT: J 396 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7580 (m-30) REVERT: K 76 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.7943 (m-30) REVERT: L 35 GLN cc_start: 0.8291 (tt0) cc_final: 0.8065 (mm-40) REVERT: L 71 GLU cc_start: 0.7284 (tt0) cc_final: 0.7050 (tt0) REVERT: L 88 HIS cc_start: 0.7022 (OUTLIER) cc_final: 0.5904 (p90) REVERT: L 93 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8379 (mt) outliers start: 140 outliers final: 97 residues processed: 810 average time/residue: 0.2630 time to fit residues: 352.3994 Evaluate side-chains 798 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 692 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 213 CYS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 277 SER Chi-restraints excluded: chain H residue 295 MET Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 431 GLU Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 133 GLN Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 291 LEU Chi-restraints excluded: chain I residue 295 MET Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 357 ASP Chi-restraints excluded: chain I residue 398 MET Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 128 GLN Chi-restraints excluded: chain J residue 155 GLU Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 396 ASP Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 88 HIS Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain K residue 241 SER Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 88 HIS Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 194 THR Chi-restraints excluded: chain L residue 211 ASP Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 276 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 102 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 278 optimal weight: 5.9990 chunk 338 optimal weight: 7.9990 chunk 176 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 149 optimal weight: 7.9990 chunk 301 optimal weight: 8.9990 chunk 305 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 37 HIS B 309 HIS ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 GLN C 197 HIS D 59 ASN ** D 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 GLN G 37 HIS ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 GLN H 197 ASN J 31 GLN J 192 HIS K 50 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.128581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.109116 restraints weight = 51767.620| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.02 r_work: 0.3397 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 41574 Z= 0.137 Angle : 0.548 7.676 56490 Z= 0.285 Chirality : 0.044 0.253 6174 Planarity : 0.004 0.046 7350 Dihedral : 10.606 176.466 5707 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.10 % Allowed : 19.70 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.12), residues: 5106 helix: 1.62 (0.10), residues: 2418 sheet: 0.30 (0.18), residues: 834 loop : -0.87 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 278 TYR 0.017 0.001 TYR I 435 PHE 0.025 0.001 PHE K 255 TRP 0.027 0.002 TRP H 346 HIS 0.008 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (41574) covalent geometry : angle 0.54753 / 0.29 (56490) hydrogen bonds : bond 0.04836 / 3.28 ( 2076) hydrogen bonds : angle 4.57083 / 3.31 ( 5994) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 705 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 GLU cc_start: 0.6912 (tt0) cc_final: 0.6634 (mt-10) REVERT: B 120 ASP cc_start: 0.7989 (m-30) cc_final: 0.7587 (m-30) REVERT: B 207 GLU cc_start: 0.8313 (pt0) cc_final: 0.7904 (pt0) REVERT: B 211 ASP cc_start: 0.8263 (m-30) cc_final: 0.7950 (m-30) REVERT: B 308 ARG cc_start: 0.7970 (mtm180) cc_final: 0.7719 (mtm110) REVERT: B 357 ASP cc_start: 0.8356 (m-30) cc_final: 0.8009 (m-30) REVERT: C 393 HIS cc_start: 0.8118 (t70) cc_final: 0.7652 (t-170) REVERT: D 44 LEU cc_start: 0.8561 (mt) cc_final: 0.8328 (mt) REVERT: D 94 PHE cc_start: 0.8766 (p90) cc_final: 0.8459 (p90) REVERT: D 281 GLN cc_start: 0.8001 (pt0) cc_final: 0.7662 (pt0) REVERT: D 290 GLU cc_start: 0.6802 (mm-30) cc_final: 0.6423 (mm-30) REVERT: D 306 ASP cc_start: 0.7648 (t0) cc_final: 0.6245 (t0) REVERT: D 308 ARG cc_start: 0.8435 (mtm180) cc_final: 0.7920 (mtm110) REVERT: D 311 ARG cc_start: 0.8143 (mtt-85) cc_final: 0.7834 (mtp180) REVERT: D 372 LYS cc_start: 0.8534 (mmmt) cc_final: 0.8164 (ttpt) REVERT: D 433 GLN cc_start: 0.8542 (tp40) cc_final: 0.8268 (tp40) REVERT: E 77 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7621 (mt-10) REVERT: E 91 GLN cc_start: 0.8030 (mt0) cc_final: 0.7530 (mt0) REVERT: E 313 MET cc_start: 0.8079 (mtm) cc_final: 0.7857 (mtt) REVERT: F 55 GLU cc_start: 0.8086 (tp30) cc_final: 0.7565 (tp30) REVERT: G 1 MET cc_start: 0.8516 (mmm) cc_final: 0.7913 (tpt) REVERT: G 24 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8363 (tt) REVERT: G 113 GLU cc_start: 0.8378 (tp30) cc_final: 0.8018 (tt0) REVERT: G 160 GLU cc_start: 0.8339 (tp30) cc_final: 0.8126 (tp30) REVERT: G 211 ASP cc_start: 0.8107 (m-30) cc_final: 0.7719 (m-30) REVERT: G 282 GLN cc_start: 0.8099 (pt0) cc_final: 0.7792 (pm20) REVERT: G 306 ASP cc_start: 0.7977 (t0) cc_final: 0.7246 (t0) REVERT: G 308 ARG cc_start: 0.8295 (mtm180) cc_final: 0.7751 (mtm-85) REVERT: G 373 MET cc_start: 0.8770 (ptp) cc_final: 0.8564 (mtm) REVERT: G 398 MET cc_start: 0.7824 (mtp) cc_final: 0.7334 (ttm) REVERT: G 414 ASP cc_start: 0.6655 (t0) cc_final: 0.6248 (m-30) REVERT: G 426 ASN cc_start: 0.7997 (m-40) cc_final: 0.7739 (m110) REVERT: H 211 ASP cc_start: 0.8038 (m-30) cc_final: 0.7540 (m-30) REVERT: H 422 GLU cc_start: 0.7569 (tp30) cc_final: 0.7182 (tp30) REVERT: H 426 ASN cc_start: 0.8014 (m-40) cc_final: 0.7506 (m110) REVERT: I 1 MET cc_start: 0.8251 (tpt) cc_final: 0.8011 (tpt) REVERT: I 47 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8151 (mt-10) REVERT: I 113 GLU cc_start: 0.8450 (tp30) cc_final: 0.8068 (mp0) REVERT: I 159 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8124 (pt0) REVERT: I 211 ASP cc_start: 0.8030 (m-30) cc_final: 0.7450 (m-30) REVERT: I 281 GLN cc_start: 0.8484 (tt0) cc_final: 0.7815 (tm-30) REVERT: I 283 TYR cc_start: 0.8121 (m-80) cc_final: 0.7737 (m-80) REVERT: I 422 GLU cc_start: 0.7843 (tp30) cc_final: 0.7126 (tp30) REVERT: I 426 ASN cc_start: 0.7910 (m-40) cc_final: 0.7205 (m110) REVERT: J 128 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8131 (tt0) REVERT: J 156 ARG cc_start: 0.8311 (mmt90) cc_final: 0.8032 (mmm-85) REVERT: J 342 GLN cc_start: 0.7906 (pt0) cc_final: 0.7398 (mp10) REVERT: J 396 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7641 (m-30) REVERT: K 76 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.7962 (m-30) REVERT: L 71 GLU cc_start: 0.7402 (tt0) cc_final: 0.7190 (tt0) REVERT: L 88 HIS cc_start: 0.7037 (OUTLIER) cc_final: 0.5908 (p90) REVERT: L 93 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8359 (mt) REVERT: L 380 ASN cc_start: 0.8707 (t160) cc_final: 0.8408 (t0) outliers start: 135 outliers final: 106 residues processed: 785 average time/residue: 0.2605 time to fit residues: 337.9028 Evaluate side-chains 792 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 679 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 213 CYS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 133 GLN Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 213 CYS Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 295 MET Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 431 GLU Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 133 GLN Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 291 LEU Chi-restraints excluded: chain I residue 295 MET Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain I residue 357 ASP Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 128 GLN Chi-restraints excluded: chain J residue 155 GLU Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 396 ASP Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 88 HIS Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain K residue 241 SER Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 338 LYS Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 88 HIS Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 194 THR Chi-restraints excluded: chain L residue 211 ASP Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 276 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 222 optimal weight: 10.0000 chunk 310 optimal weight: 9.9990 chunk 487 optimal weight: 0.0000 chunk 353 optimal weight: 20.0000 chunk 218 optimal weight: 4.9990 chunk 436 optimal weight: 0.9980 chunk 284 optimal weight: 3.9990 chunk 272 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 473 optimal weight: 0.6980 chunk 50 optimal weight: 10.0000 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 37 HIS ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN D 309 HIS ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 HIS G 37 HIS G 197 ASN ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 GLN I 229 HIS J 31 GLN K 50 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.130780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.111516 restraints weight = 51335.803| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.05 r_work: 0.3423 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.5198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 41574 Z= 0.116 Angle : 0.536 10.069 56490 Z= 0.279 Chirality : 0.043 0.252 6174 Planarity : 0.004 0.046 7350 Dihedral : 10.463 174.237 5706 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.73 % Allowed : 20.22 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.12), residues: 5106 helix: 1.66 (0.11), residues: 2418 sheet: 0.38 (0.18), residues: 834 loop : -0.81 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 278 TYR 0.014 0.001 TYR D 185 PHE 0.022 0.001 PHE L 255 TRP 0.025 0.002 TRP H 346 HIS 0.007 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (41574) covalent geometry : angle 0.53628 / 0.28 (56490) hydrogen bonds : bond 0.04389 / 2.98 ( 2076) hydrogen bonds : angle 4.50962 / 3.26 ( 5994) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10212 Ramachandran restraints generated. 5106 Oldfield, 0 Emsley, 5106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 724 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 HIS cc_start: 0.8066 (OUTLIER) cc_final: 0.7818 (m170) REVERT: B 120 ASP cc_start: 0.7991 (m-30) cc_final: 0.7579 (m-30) REVERT: B 166 MET cc_start: 0.8767 (tpt) cc_final: 0.8539 (tpp) REVERT: B 207 GLU cc_start: 0.8263 (pt0) cc_final: 0.7833 (pt0) REVERT: B 211 ASP cc_start: 0.8286 (m-30) cc_final: 0.7965 (m-30) REVERT: B 308 ARG cc_start: 0.8001 (mtm180) cc_final: 0.7603 (mtm110) REVERT: B 357 ASP cc_start: 0.8335 (m-30) cc_final: 0.7972 (m-30) REVERT: C 377 MET cc_start: 0.8524 (tmm) cc_final: 0.8129 (tpt) REVERT: D 94 PHE cc_start: 0.8756 (p90) cc_final: 0.8491 (p90) REVERT: D 281 GLN cc_start: 0.8008 (pt0) cc_final: 0.7672 (pt0) REVERT: D 290 GLU cc_start: 0.6754 (mm-30) cc_final: 0.6401 (mm-30) REVERT: D 306 ASP cc_start: 0.7672 (t0) cc_final: 0.6270 (t0) REVERT: D 308 ARG cc_start: 0.8497 (mtm180) cc_final: 0.8007 (mtm110) REVERT: D 311 ARG cc_start: 0.8144 (mtt-85) cc_final: 0.7906 (mtp85) REVERT: D 372 LYS cc_start: 0.8559 (mmmt) cc_final: 0.8191 (ttpt) REVERT: D 433 GLN cc_start: 0.8536 (tp40) cc_final: 0.8256 (tp40) REVERT: E 77 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7639 (mt-10) REVERT: E 91 GLN cc_start: 0.7977 (mt0) cc_final: 0.7467 (mt0) REVERT: F 55 GLU cc_start: 0.8036 (tp30) cc_final: 0.7507 (tp30) REVERT: G 1 MET cc_start: 0.8534 (mmm) cc_final: 0.7939 (tpt) REVERT: G 24 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8411 (tt) REVERT: G 113 GLU cc_start: 0.8410 (tp30) cc_final: 0.8064 (tt0) REVERT: G 160 GLU cc_start: 0.8389 (tp30) cc_final: 0.8179 (tp30) REVERT: G 211 ASP cc_start: 0.8104 (m-30) cc_final: 0.7724 (m-30) REVERT: G 282 GLN cc_start: 0.8138 (pt0) cc_final: 0.7837 (pm20) REVERT: G 306 ASP cc_start: 0.7975 (t0) cc_final: 0.7314 (t0) REVERT: G 308 ARG cc_start: 0.8296 (mtm180) cc_final: 0.7736 (mtm-85) REVERT: G 398 MET cc_start: 0.7748 (mtp) cc_final: 0.7301 (ttm) REVERT: G 414 ASP cc_start: 0.6635 (t0) cc_final: 0.6175 (m-30) REVERT: G 426 ASN cc_start: 0.7968 (m-40) cc_final: 0.7736 (m110) REVERT: H 211 ASP cc_start: 0.8013 (m-30) cc_final: 0.7519 (m-30) REVERT: H 422 GLU cc_start: 0.7653 (tp30) cc_final: 0.7262 (tp30) REVERT: H 426 ASN cc_start: 0.7859 (m-40) cc_final: 0.7394 (m110) REVERT: H 431 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.5902 (mt-10) REVERT: I 1 MET cc_start: 0.8204 (tpt) cc_final: 0.7944 (tpt) REVERT: I 47 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8088 (mt-10) REVERT: I 211 ASP cc_start: 0.8021 (m-30) cc_final: 0.7428 (m-30) REVERT: I 281 GLN cc_start: 0.8511 (tt0) cc_final: 0.7774 (tm-30) REVERT: I 283 TYR cc_start: 0.8096 (m-80) cc_final: 0.7803 (m-10) REVERT: I 398 MET cc_start: 0.8081 (ttm) cc_final: 0.7869 (ttp) REVERT: I 422 GLU cc_start: 0.7832 (tp30) cc_final: 0.7108 (tp30) REVERT: I 426 ASN cc_start: 0.7875 (m-40) cc_final: 0.7092 (m110) REVERT: J 128 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8122 (tt0) REVERT: J 156 ARG cc_start: 0.8296 (mmt90) cc_final: 0.8063 (mmm-85) REVERT: J 342 GLN cc_start: 0.7889 (pt0) cc_final: 0.7378 (mp10) REVERT: J 396 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7629 (m-30) REVERT: K 76 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.7905 (m-30) REVERT: K 302 MET cc_start: 0.7653 (mtp) cc_final: 0.7377 (mtp) REVERT: K 357 TYR cc_start: 0.8637 (m-80) cc_final: 0.8410 (m-80) REVERT: L 88 HIS cc_start: 0.6931 (OUTLIER) cc_final: 0.5789 (p90) REVERT: L 93 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8376 (mt) REVERT: L 176 GLN cc_start: 0.8544 (mm-40) cc_final: 0.8327 (mm-40) REVERT: L 380 ASN cc_start: 0.8666 (t160) cc_final: 0.8367 (t0) outliers start: 119 outliers final: 94 residues processed: 791 average time/residue: 0.2616 time to fit residues: 340.6201 Evaluate side-chains 790 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 687 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 213 CYS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 213 CYS Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 295 MET Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 431 GLU Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 133 GLN Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 291 LEU Chi-restraints excluded: chain I residue 295 MET Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 357 ASP Chi-restraints excluded: chain I residue 378 ILE Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 128 GLN Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 396 ASP Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 88 HIS Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 241 SER Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 88 HIS Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 194 THR Chi-restraints excluded: chain L residue 211 ASP Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 276 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 26 optimal weight: 7.9990 chunk 261 optimal weight: 1.9990 chunk 295 optimal weight: 5.9990 chunk 190 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 352 optimal weight: 9.9990 chunk 359 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 37 HIS ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 HIS D 59 ASN ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 HIS G 197 ASN ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 GLN I 229 HIS K 50 ASN L 192 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.129591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.110171 restraints weight = 51645.088| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.01 r_work: 0.3400 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 41574 Z= 0.137 Angle : 0.546 8.045 56490 Z= 0.284 Chirality : 0.043 0.246 6174 Planarity : 0.004 0.045 7350 Dihedral : 10.433 174.448 5704 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.89 % Allowed : 20.06 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.12), residues: 5106 helix: 1.68 (0.11), residues: 2412 sheet: 0.37 (0.18), residues: 834 loop : -0.84 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 278 TYR 0.016 0.001 TYR D 185 PHE 0.022 0.001 PHE L 255 TRP 0.025 0.002 TRP G 346 HIS 0.011 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (41574) covalent geometry : angle 0.54622 / 0.28 (56490) hydrogen bonds : bond 0.04674 / 3.17 ( 2076) hydrogen bonds : angle 4.54320 / 3.29 ( 5994) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12412.56 seconds wall clock time: 213 minutes 27.89 seconds (12807.89 seconds total)