Starting phenix.real_space_refine on Fri Nov 21 00:07:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dpu_7973/11_2025/6dpu_7973.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dpu_7973/11_2025/6dpu_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 { model { file = "/net/cci-nas-00/data/ceres_data/6dpu_7973/11_2025/6dpu_7973.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dpu_7973/11_2025/6dpu_7973.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6dpu_7973/11_2025/6dpu_7973.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dpu_7973/11_2025/6dpu_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-2.0-5881/lib/python3.9/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: 9.41, per 1000 atoms: 0.23 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: 3.54 Conformation dependent library (CDL) restraints added in 1.8 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: 1.46 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: 10.26 Time building geometry restraints manager: 4.65 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: 23946 33.70 - 67.41: 804 67.41 - 101.11: 54 101.11 - 134.81: 0 134.81 - 168.52: 18 Dihedral angle restraints: 24822 sinusoidal: 9966 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 24819 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: 0.14 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: 0.010 Normalize map: mean=0, sd=1: 10.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 39.350 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 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 : 16.460 168.516 15294 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 covalent geometry : bond 0.00918 (41574) covalent geometry : angle 1.53218 (56490) hydrogen bonds : bond 0.19218 ( 2076) hydrogen bonds : angle 7.24728 ( 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 : 1.644 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: 0.8142 (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: 0.2826 time to fit residues: 731.4490 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 : 1.491 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 433 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 128 GLN 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 = 0.3853 r_free = 0.3853 target = 0.135804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.116264 restraints weight = 50490.214| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.98 r_work: 0.3479 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 41574 Z= 0.162 Angle : 0.625 9.276 56490 Z= 0.331 Chirality : 0.045 0.209 6174 Planarity : 0.005 0.052 7350 Dihedral : 12.490 174.109 5903 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.49 % Allowed : 13.50 % Favored : 83.01 % 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: 1.15 (0.12), residues: 5106 helix: 2.04 (0.11), residues: 2394 sheet: 0.50 (0.17), residues: 810 loop : -0.78 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 88 TYR 0.017 0.002 TYR H 36 PHE 0.028 0.002 PHE E 255 TRP 0.023 0.002 TRP I 346 HIS 0.013 0.001 HIS F 309 Details of bonding type rmsd covalent geometry : bond 0.00346 (41574) covalent geometry : angle 0.62513 (56490) hydrogen bonds : bond 0.06313 ( 2076) hydrogen bonds : angle 5.17938 ( 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 1071 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 919 time to evaluate : 1.650 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 35 GLN cc_start: 0.8381 (mm110) cc_final: 0.8118 (tp40) REVERT: A 230 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8297 (mp) REVERT: A 290 GLU cc_start: 0.6780 (mt-10) cc_final: 0.6454 (mt-10) REVERT: B 110 GLU cc_start: 0.7000 (tt0) cc_final: 0.6752 (mt-10) REVERT: B 120 ASP cc_start: 0.7956 (m-30) cc_final: 0.7576 (m-30) REVERT: B 211 ASP cc_start: 0.8227 (m-30) cc_final: 0.7934 (m-30) REVERT: B 306 ASP cc_start: 0.7274 (t0) cc_final: 0.6697 (t0) REVERT: B 309 HIS cc_start: 0.8524 (m90) cc_final: 0.8308 (m90) REVERT: B 373 MET cc_start: 0.8791 (mtm) cc_final: 0.8561 (mtm) REVERT: C 154 MET cc_start: 0.9031 (tpp) cc_final: 0.8824 (mmt) REVERT: C 230 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8380 (mt) REVERT: C 370 LYS cc_start: 0.7869 (ttpp) cc_final: 0.7668 (ttmm) REVERT: D 306 ASP cc_start: 0.6754 (t0) cc_final: 0.6536 (t0) REVERT: E 75 ILE cc_start: 0.9090 (mm) cc_final: 0.8825 (mm) REVERT: E 91 GLN cc_start: 0.8108 (mt0) cc_final: 0.7590 (mt0) REVERT: E 123 ARG cc_start: 0.7296 (ttp80) cc_final: 0.7071 (ttp-110) REVERT: E 152 LEU cc_start: 0.8658 (tp) cc_final: 0.8457 (tp) REVERT: E 230 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8245 (mp) REVERT: F 120 ASP cc_start: 0.8173 (m-30) cc_final: 0.7953 (m-30) REVERT: F 179 ASP cc_start: 0.7756 (t70) cc_final: 0.7039 (t0) REVERT: F 325 MET cc_start: 0.8012 (mmm) cc_final: 0.7757 (mmm) REVERT: F 413 MET cc_start: 0.7909 (mtp) cc_final: 0.7625 (ttm) REVERT: G 24 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8284 (tt) REVERT: G 200 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8596 (pt0) REVERT: G 213 CYS cc_start: 0.8016 (m) cc_final: 0.7684 (m) REVERT: G 386 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7557 (mm-30) REVERT: G 422 GLU cc_start: 0.7677 (tp30) cc_final: 0.7465 (tp30) REVERT: G 426 ASN cc_start: 0.7941 (m-40) cc_final: 0.7624 (m110) REVERT: G 431 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7347 (mp0) REVERT: G 435 TYR cc_start: 0.6893 (m-80) cc_final: 0.6401 (m-10) REVERT: H 116 ASP cc_start: 0.7401 (m-30) cc_final: 0.7175 (m-30) REVERT: H 130 ASP cc_start: 0.7362 (t0) cc_final: 0.6909 (m-30) REVERT: H 207 GLU cc_start: 0.7694 (tt0) cc_final: 0.7420 (tt0) REVERT: H 211 ASP cc_start: 0.7956 (m-30) cc_final: 0.7607 (m-30) REVERT: H 213 CYS cc_start: 0.7826 (m) cc_final: 0.7408 (m) REVERT: H 309 HIS cc_start: 0.8144 (m170) cc_final: 0.7858 (m90) REVERT: H 325 MET cc_start: 0.7922 (mmm) cc_final: 0.7670 (mmm) REVERT: H 347 ILE cc_start: 0.8192 (mm) cc_final: 0.7957 (mp) REVERT: H 422 GLU cc_start: 0.7629 (tp30) cc_final: 0.7276 (tp30) REVERT: H 426 ASN cc_start: 0.7935 (m-40) cc_final: 0.7598 (m110) REVERT: H 427 ASP cc_start: 0.7649 (m-30) cc_final: 0.7189 (m-30) REVERT: H 435 TYR cc_start: 0.6809 (m-80) cc_final: 0.6029 (m-10) REVERT: I 207 GLU cc_start: 0.7521 (tt0) cc_final: 0.7234 (tt0) REVERT: I 211 ASP cc_start: 0.7998 (m-30) cc_final: 0.7558 (m-30) REVERT: I 213 CYS cc_start: 0.7993 (m) cc_final: 0.7534 (m) REVERT: I 281 GLN cc_start: 0.8402 (tt0) cc_final: 0.7990 (tm-30) REVERT: I 283 TYR cc_start: 0.8167 (m-80) cc_final: 0.7793 (m-80) REVERT: I 306 ASP cc_start: 0.6482 (t0) cc_final: 0.5837 (t70) REVERT: I 325 MET cc_start: 0.8289 (mmm) cc_final: 0.7817 (mmm) REVERT: I 422 GLU cc_start: 0.7719 (tp30) cc_final: 0.6947 (tp30) REVERT: I 426 ASN cc_start: 0.7899 (m-40) cc_final: 0.7231 (m110) REVERT: J 112 LYS cc_start: 0.8800 (mmtt) cc_final: 0.8539 (pttp) REVERT: J 128 GLN cc_start: 0.8334 (mm-40) cc_final: 0.8055 (tt0) REVERT: J 156 ARG cc_start: 0.8021 (mmt90) cc_final: 0.7735 (mmm-85) REVERT: K 120 ASP cc_start: 0.7390 (t0) cc_final: 0.7000 (t0) REVERT: K 123 ARG cc_start: 0.7723 (ttp-110) cc_final: 0.7412 (ttp-110) REVERT: K 214 ARG cc_start: 0.8209 (tmm160) cc_final: 0.7892 (ptt-90) REVERT: K 413 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7579 (ttm) REVERT: L 209 ILE cc_start: 0.8719 (mm) cc_final: 0.8400 (mt) REVERT: L 302 MET cc_start: 0.8282 (mmp) cc_final: 0.7587 (mmt) REVERT: L 413 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7881 (mtp) REVERT: L 420 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6828 (mm-30) outliers start: 152 outliers final: 70 residues processed: 1005 average time/residue: 0.2617 time to fit residues: 430.5582 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 : 1.704 ------------------------------------------------------------------------------- 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 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 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 334 ASN 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: 4.9990 chunk 384 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 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: 0.9990 chunk 32 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 436 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 50 ASN A 91 GLN A 101 ASN A 300 ASN B 37 HIS B 50 ASN B 192 HIS 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 15 GLN 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 6 HIS I 15 GLN I 37 HIS I 133 GLN K 91 GLN K 101 ASN K 128 GLN K 406 HIS L 128 GLN L 256 GLN L 406 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.126076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.106596 restraints weight = 51911.216| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.02 r_work: 0.3332 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 41574 Z= 0.259 Angle : 0.665 9.122 56490 Z= 0.355 Chirality : 0.048 0.229 6174 Planarity : 0.005 0.060 7350 Dihedral : 12.344 177.063 5891 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.99 % Allowed : 15.89 % Favored : 80.12 % 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 (0.11), residues: 5106 helix: 1.62 (0.10), residues: 2418 sheet: 0.52 (0.18), residues: 732 loop : -0.91 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 422 TYR 0.018 0.002 TYR L 172 PHE 0.033 0.003 PHE K 255 TRP 0.021 0.002 TRP L 21 HIS 0.011 0.002 HIS E 28 Details of bonding type rmsd covalent geometry : bond 0.00591 (41574) covalent geometry : angle 0.66487 (56490) hydrogen bonds : bond 0.06927 ( 2076) hydrogen bonds : angle 5.10287 ( 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 965 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 791 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8336 (mp) REVERT: A 332 ILE cc_start: 0.9172 (mp) cc_final: 0.8972 (mt) REVERT: A 411 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8079 (mm-30) REVERT: A 417 GLU cc_start: 0.7129 (tt0) cc_final: 0.6785 (mt-10) REVERT: B 37 HIS cc_start: 0.8289 (OUTLIER) cc_final: 0.8059 (m170) REVERT: B 120 ASP cc_start: 0.8055 (m-30) cc_final: 0.7670 (m-30) REVERT: B 211 ASP cc_start: 0.8220 (m-30) cc_final: 0.7862 (m-30) REVERT: B 213 CYS cc_start: 0.7880 (m) cc_final: 0.7664 (m) REVERT: B 306 ASP cc_start: 0.7430 (t0) cc_final: 0.6990 (t0) REVERT: B 309 HIS cc_start: 0.8420 (m170) cc_final: 0.8187 (m90) REVERT: B 311 ARG cc_start: 0.8099 (mtt-85) cc_final: 0.7816 (mtp180) REVERT: B 352 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.7540 (tmtt) REVERT: C 84 ARG cc_start: 0.8036 (ptt-90) cc_final: 0.7811 (ptt-90) REVERT: C 156 ARG cc_start: 0.8328 (mmt90) cc_final: 0.8035 (mmm-85) REVERT: C 230 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8353 (mt) REVERT: C 393 HIS cc_start: 0.8126 (t70) cc_final: 0.7559 (t-170) REVERT: D 94 PHE cc_start: 0.8917 (p90) cc_final: 0.8635 (p90) REVERT: D 308 ARG cc_start: 0.8198 (mtm180) cc_final: 0.7626 (mtm110) REVERT: D 311 ARG cc_start: 0.8191 (mtt-85) cc_final: 0.7877 (mtp180) REVERT: E 77 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7605 (mt-10) REVERT: E 230 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8401 (mp) REVERT: F 322 ARG cc_start: 0.8448 (mtp85) cc_final: 0.8233 (mmm160) REVERT: F 325 MET cc_start: 0.8272 (mmm) cc_final: 0.8037 (mmm) REVERT: F 352 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.7309 (tmtt) REVERT: G 24 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8454 (tt) REVERT: G 205 ASP cc_start: 0.8071 (t0) cc_final: 0.7864 (m-30) REVERT: G 211 ASP cc_start: 0.8093 (m-30) cc_final: 0.7794 (m-30) REVERT: G 282 GLN cc_start: 0.8069 (pt0) cc_final: 0.7680 (pm20) REVERT: G 308 ARG cc_start: 0.8067 (mtm180) cc_final: 0.7466 (mtm180) REVERT: G 426 ASN cc_start: 0.8004 (m-40) cc_final: 0.7778 (m110) REVERT: G 431 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7343 (mp0) REVERT: H 64 ARG cc_start: 0.8841 (ttm110) cc_final: 0.8627 (ttm110) REVERT: H 130 ASP cc_start: 0.7469 (t0) cc_final: 0.6982 (m-30) REVERT: H 133 GLN cc_start: 0.7434 (OUTLIER) cc_final: 0.6882 (pt0) REVERT: H 191 VAL cc_start: 0.8398 (t) cc_final: 0.8160 (t) REVERT: H 207 GLU cc_start: 0.7617 (tt0) cc_final: 0.7214 (tt0) REVERT: H 211 ASP cc_start: 0.8006 (m-30) cc_final: 0.7533 (m-30) REVERT: H 325 MET cc_start: 0.8210 (mmm) cc_final: 0.7569 (mmm) REVERT: H 416 MET cc_start: 0.7548 (mmm) cc_final: 0.7101 (mmm) REVERT: H 422 GLU cc_start: 0.7780 (tp30) cc_final: 0.7393 (tp30) REVERT: H 426 ASN cc_start: 0.8175 (m-40) cc_final: 0.7706 (m110) REVERT: H 435 TYR cc_start: 0.6959 (m-80) cc_final: 0.6333 (m-10) REVERT: I 116 ASP cc_start: 0.7534 (m-30) cc_final: 0.7237 (m-30) REVERT: I 205 ASP cc_start: 0.8103 (t0) cc_final: 0.7655 (m-30) REVERT: I 211 ASP cc_start: 0.8042 (m-30) cc_final: 0.7588 (m-30) REVERT: I 281 GLN cc_start: 0.8483 (tt0) cc_final: 0.7991 (tm-30) REVERT: I 283 TYR cc_start: 0.8218 (m-80) cc_final: 0.7844 (m-80) REVERT: I 306 ASP cc_start: 0.6585 (t0) cc_final: 0.6244 (t70) REVERT: I 402 LYS cc_start: 0.8691 (mttt) cc_final: 0.8439 (mptt) REVERT: I 413 MET cc_start: 0.7868 (mmm) cc_final: 0.7642 (mmm) REVERT: I 422 GLU cc_start: 0.7784 (tp30) cc_final: 0.6884 (tp30) REVERT: I 426 ASN cc_start: 0.7960 (m-40) cc_final: 0.7164 (m110) REVERT: J 128 GLN cc_start: 0.8480 (mm-40) cc_final: 0.8128 (tt0) REVERT: J 254 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7463 (tt0) REVERT: J 342 GLN cc_start: 0.7874 (pt0) cc_final: 0.7604 (mp10) REVERT: K 112 LYS cc_start: 0.8469 (mtmt) cc_final: 0.8266 (mttp) REVERT: K 431 ASP cc_start: 0.7391 (m-30) cc_final: 0.7108 (m-30) REVERT: L 35 GLN cc_start: 0.8330 (tt0) cc_final: 0.7976 (mm-40) REVERT: L 209 ILE cc_start: 0.8961 (mm) cc_final: 0.8686 (mt) REVERT: L 332 ILE cc_start: 0.9071 (mm) cc_final: 0.8832 (mm) REVERT: L 391 LEU cc_start: 0.8661 (tp) cc_final: 0.8414 (tt) REVERT: L 413 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8259 (mtp) outliers start: 174 outliers final: 105 residues processed: 907 average time/residue: 0.2585 time to fit residues: 384.7932 Evaluate side-chains 801 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 686 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL 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 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 200 GLU 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 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 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 193 THR 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 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 315 CYS 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 352 LYS 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 192 HIS 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 398 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 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 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 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 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 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: 4.9990 chunk 248 optimal weight: 5.9990 chunk 448 optimal weight: 0.9980 chunk 320 optimal weight: 2.9990 chunk 430 optimal weight: 3.9990 chunk 331 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 487 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 15 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN F 309 HIS H 133 GLN I 50 ASN J 406 HIS K 15 GLN K 133 GLN 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 = 0.3762 r_free = 0.3762 target = 0.128727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.108857 restraints weight = 51344.921| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.06 r_work: 0.3360 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 41574 Z= 0.183 Angle : 0.586 9.153 56490 Z= 0.309 Chirality : 0.045 0.242 6174 Planarity : 0.004 0.046 7350 Dihedral : 12.143 175.404 5884 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.09 % Allowed : 16.48 % Favored : 79.43 % 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: 0.67 (0.11), residues: 5106 helix: 1.60 (0.10), residues: 2418 sheet: 0.29 (0.18), residues: 774 loop : -0.99 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 215 TYR 0.017 0.001 TYR F 185 PHE 0.029 0.002 PHE L 255 TRP 0.030 0.002 TRP I 346 HIS 0.014 0.001 HIS F 309 Details of bonding type rmsd covalent geometry : bond 0.00423 (41574) covalent geometry : angle 0.58623 (56490) hydrogen bonds : bond 0.05924 ( 2076) hydrogen bonds : angle 4.85511 ( 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 933 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 755 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8375 (mt) REVERT: A 417 GLU cc_start: 0.6977 (tt0) cc_final: 0.6640 (mt-10) REVERT: B 120 ASP cc_start: 0.8049 (m-30) cc_final: 0.7681 (m-30) REVERT: B 207 GLU cc_start: 0.8353 (pt0) cc_final: 0.8005 (pt0) REVERT: B 211 ASP cc_start: 0.8406 (m-30) cc_final: 0.8076 (m-30) REVERT: B 352 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7288 (tmtt) REVERT: C 156 ARG cc_start: 0.8252 (mmt90) cc_final: 0.7955 (mmm-85) REVERT: C 230 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8440 (mt) REVERT: C 393 HIS cc_start: 0.8091 (t70) cc_final: 0.7616 (t-170) REVERT: D 109 THR cc_start: 0.8657 (m) cc_final: 0.8428 (p) REVERT: D 308 ARG cc_start: 0.8024 (mtm180) cc_final: 0.7460 (mtm110) REVERT: D 311 ARG cc_start: 0.8055 (mtt-85) cc_final: 0.7486 (mtp180) REVERT: D 372 LYS cc_start: 0.8585 (mmmt) cc_final: 0.8176 (ttpt) REVERT: E 75 ILE cc_start: 0.9037 (mm) cc_final: 0.8579 (mm) REVERT: E 77 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7788 (mt-10) REVERT: E 313 MET cc_start: 0.7769 (mtt) cc_final: 0.7504 (mtm) REVERT: F 145 THR cc_start: 0.8442 (m) cc_final: 0.8083 (m) REVERT: F 301 MET cc_start: 0.8492 (mmp) cc_final: 0.8169 (mmp) REVERT: F 306 ASP cc_start: 0.7190 (t70) cc_final: 0.6809 (t0) REVERT: F 322 ARG cc_start: 0.8328 (mtp85) cc_final: 0.8090 (mmm160) REVERT: F 325 MET cc_start: 0.8452 (mmm) cc_final: 0.8022 (mmm) REVERT: G 24 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8407 (tt) REVERT: G 211 ASP cc_start: 0.8005 (m-30) cc_final: 0.7703 (m-30) REVERT: G 282 GLN cc_start: 0.8157 (pt0) cc_final: 0.7792 (pm20) REVERT: G 306 ASP cc_start: 0.7034 (t0) cc_final: 0.5666 (t0) REVERT: G 308 ARG cc_start: 0.8148 (mtm180) cc_final: 0.7674 (mtm180) REVERT: G 426 ASN cc_start: 0.7943 (m-40) cc_final: 0.7684 (m110) REVERT: H 191 VAL cc_start: 0.8423 (t) cc_final: 0.8156 (t) REVERT: H 205 ASP cc_start: 0.8154 (t0) cc_final: 0.7869 (m-30) REVERT: H 211 ASP cc_start: 0.8100 (m-30) cc_final: 0.7642 (m-30) REVERT: H 325 MET cc_start: 0.8198 (mmm) cc_final: 0.7648 (mmm) REVERT: H 398 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7788 (ttm) REVERT: H 422 GLU cc_start: 0.7653 (tp30) cc_final: 0.7308 (tp30) REVERT: H 426 ASN cc_start: 0.8083 (m-40) cc_final: 0.7656 (m110) REVERT: I 160 GLU cc_start: 0.8216 (tp30) cc_final: 0.7886 (tp30) REVERT: I 205 ASP cc_start: 0.8126 (t0) cc_final: 0.7737 (m-30) REVERT: I 211 ASP cc_start: 0.8046 (m-30) cc_final: 0.7509 (m-30) REVERT: I 281 GLN cc_start: 0.8543 (tt0) cc_final: 0.8065 (tm-30) REVERT: I 283 TYR cc_start: 0.8240 (m-80) cc_final: 0.7858 (m-80) REVERT: I 398 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7548 (ttm) REVERT: I 413 MET cc_start: 0.8047 (mmm) cc_final: 0.7806 (mmm) REVERT: I 422 GLU cc_start: 0.7897 (tp30) cc_final: 0.7011 (tp30) REVERT: I 425 MET cc_start: 0.7857 (ttp) cc_final: 0.7494 (ttt) REVERT: I 426 ASN cc_start: 0.7935 (m-40) cc_final: 0.7211 (m110) REVERT: J 128 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8185 (tt0) REVERT: J 342 GLN cc_start: 0.7831 (pt0) cc_final: 0.7579 (mp10) REVERT: K 76 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.8205 (m-30) REVERT: L 35 GLN cc_start: 0.8190 (tt0) cc_final: 0.7933 (mm-40) REVERT: L 88 HIS cc_start: 0.7276 (OUTLIER) cc_final: 0.6129 (p90) REVERT: L 332 ILE cc_start: 0.8961 (mm) cc_final: 0.8732 (mm) REVERT: L 391 LEU cc_start: 0.8639 (tp) cc_final: 0.8403 (tt) REVERT: L 413 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.8264 (mtp) outliers start: 178 outliers final: 121 residues processed: 856 average time/residue: 0.2496 time to fit residues: 352.3755 Evaluate side-chains 813 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 682 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 200 GLU 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 193 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 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 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 269 LEU 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 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 357 ASP 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 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 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 295 MET Chi-restraints excluded: chain I residue 315 VAL 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 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 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 193 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 283 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 199 optimal weight: 1.9990 chunk 336 optimal weight: 10.0000 chunk 268 optimal weight: 5.9990 chunk 219 optimal weight: 1.9990 chunk 259 optimal weight: 6.9990 chunk 342 optimal weight: 0.7980 chunk 210 optimal weight: 4.9990 chunk 307 optimal weight: 7.9990 chunk 106 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 HIS ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 GLN E 256 GLN E 406 HIS G 37 HIS L 256 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.127039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.108447 restraints weight = 51762.553| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.94 r_work: 0.3364 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 41574 Z= 0.184 Angle : 0.578 9.183 56490 Z= 0.303 Chirality : 0.045 0.262 6174 Planarity : 0.004 0.047 7350 Dihedral : 12.088 175.946 5883 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.43 % Allowed : 16.57 % Favored : 78.99 % 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: 0.60 (0.11), residues: 5106 helix: 1.49 (0.10), residues: 2436 sheet: 0.30 (0.19), residues: 762 loop : -0.98 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 422 TYR 0.018 0.001 TYR B 185 PHE 0.030 0.002 PHE K 255 TRP 0.027 0.002 TRP I 346 HIS 0.010 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00425 (41574) covalent geometry : angle 0.57755 (56490) hydrogen bonds : bond 0.05782 ( 2076) hydrogen bonds : angle 4.80321 ( 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 927 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 734 time to evaluate : 1.610 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: A 230 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8339 (mt) REVERT: A 417 GLU cc_start: 0.7100 (tt0) cc_final: 0.6764 (mt-10) REVERT: B 55 GLU cc_start: 0.8077 (tp30) cc_final: 0.7804 (tp30) REVERT: B 120 ASP cc_start: 0.7933 (m-30) cc_final: 0.7555 (m-30) REVERT: B 207 GLU cc_start: 0.8318 (pt0) cc_final: 0.7954 (pt0) REVERT: B 211 ASP cc_start: 0.8135 (m-30) cc_final: 0.7785 (m-30) REVERT: B 308 ARG cc_start: 0.7901 (mtm110) cc_final: 0.7633 (mtm110) REVERT: B 352 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7385 (tmtt) REVERT: C 156 ARG cc_start: 0.8299 (mmt90) cc_final: 0.7980 (mmm-85) REVERT: C 313 MET cc_start: 0.7752 (mtt) cc_final: 0.7507 (mtp) REVERT: C 393 HIS cc_start: 0.8087 (t70) cc_final: 0.7565 (t-170) REVERT: D 308 ARG cc_start: 0.8299 (mtm180) cc_final: 0.7771 (mtm110) REVERT: D 311 ARG cc_start: 0.8191 (mtt-85) cc_final: 0.7987 (mtp180) REVERT: D 372 LYS cc_start: 0.8495 (mmmt) cc_final: 0.8132 (ttpt) REVERT: E 75 ILE cc_start: 0.9074 (mm) cc_final: 0.8605 (mm) REVERT: E 77 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7688 (mt-10) REVERT: F 322 ARG cc_start: 0.8455 (mtp85) cc_final: 0.8177 (mmm160) REVERT: F 325 MET cc_start: 0.8357 (mmm) cc_final: 0.8027 (mmm) REVERT: G 24 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8418 (tt) REVERT: G 205 ASP cc_start: 0.7994 (t0) cc_final: 0.7727 (m-30) REVERT: G 211 ASP cc_start: 0.8027 (m-30) cc_final: 0.7653 (m-30) REVERT: G 282 GLN cc_start: 0.8047 (pt0) cc_final: 0.7693 (pm20) REVERT: G 306 ASP cc_start: 0.6938 (t0) cc_final: 0.5603 (t0) REVERT: G 308 ARG cc_start: 0.8168 (mtm180) cc_final: 0.7788 (mtm180) REVERT: G 373 MET cc_start: 0.8815 (ptp) cc_final: 0.8540 (mtm) REVERT: G 426 ASN cc_start: 0.8070 (m-40) cc_final: 0.7759 (m110) REVERT: H 211 ASP cc_start: 0.8085 (m-30) cc_final: 0.7589 (m-30) REVERT: H 325 MET cc_start: 0.8205 (mmm) cc_final: 0.7813 (mmm) REVERT: H 346 TRP cc_start: 0.8099 (p-90) cc_final: 0.7771 (p-90) REVERT: H 398 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7872 (ttm) REVERT: H 422 GLU cc_start: 0.7791 (tp30) cc_final: 0.7483 (tp30) REVERT: H 426 ASN cc_start: 0.8018 (m-40) cc_final: 0.7624 (m110) REVERT: I 47 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8279 (mt-10) REVERT: I 205 ASP cc_start: 0.8038 (t0) cc_final: 0.7731 (m-30) REVERT: I 211 ASP cc_start: 0.8066 (m-30) cc_final: 0.7485 (m-30) REVERT: I 281 GLN cc_start: 0.8474 (tt0) cc_final: 0.7931 (tm-30) REVERT: I 283 TYR cc_start: 0.8308 (m-80) cc_final: 0.7965 (m-80) REVERT: I 398 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7698 (ttm) REVERT: I 422 GLU cc_start: 0.7904 (tp30) cc_final: 0.7021 (tp30) REVERT: I 426 ASN cc_start: 0.7981 (m-40) cc_final: 0.7300 (m110) REVERT: J 128 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8202 (tt0) REVERT: J 156 ARG cc_start: 0.8405 (mmt90) cc_final: 0.7918 (mmm-85) REVERT: J 342 GLN cc_start: 0.7958 (pt0) cc_final: 0.7552 (mp10) REVERT: K 76 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.8160 (m-30) REVERT: K 431 ASP cc_start: 0.7497 (m-30) cc_final: 0.7107 (m-30) REVERT: L 35 GLN cc_start: 0.8291 (tt0) cc_final: 0.8040 (mm-40) REVERT: L 88 HIS cc_start: 0.7296 (OUTLIER) cc_final: 0.6118 (p90) REVERT: L 93 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8336 (mt) outliers start: 193 outliers final: 138 residues processed: 860 average time/residue: 0.2566 time to fit residues: 364.3778 Evaluate side-chains 826 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 678 time to evaluate : 1.600 ------------------------------------------------------------------------------- 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 159 VAL 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 269 LEU Chi-restraints excluded: chain A residue 355 ILE 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 200 GLU Chi-restraints excluded: chain B residue 213 CYS 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 349 THR 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 207 GLU Chi-restraints excluded: chain D residue 213 CYS 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 230 LEU 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 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 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 241 CYS Chi-restraints excluded: chain F residue 248 LEU 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 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 213 CYS 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 24 ILE Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 96 GLN 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 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 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 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 374 SER 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 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 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 150 THR Chi-restraints excluded: chain K residue 155 GLU 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 80 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 150 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 193 THR 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 Chi-restraints excluded: chain L residue 277 SER Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain L residue 423 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 408 optimal weight: 8.9990 chunk 435 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 148 optimal weight: 8.9990 chunk 356 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN B 37 HIS ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 GLN F 309 HIS H 349 ASN K 256 GLN L 256 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.126240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.107329 restraints weight = 52230.301| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.97 r_work: 0.3356 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 41574 Z= 0.191 Angle : 0.582 8.978 56490 Z= 0.306 Chirality : 0.045 0.263 6174 Planarity : 0.005 0.048 7350 Dihedral : 12.054 177.287 5881 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.43 % Allowed : 17.06 % Favored : 78.51 % 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: 0.50 (0.11), residues: 5106 helix: 1.37 (0.10), residues: 2472 sheet: 0.26 (0.18), residues: 816 loop : -1.05 (0.13), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 422 TYR 0.018 0.001 TYR B 185 PHE 0.034 0.002 PHE K 255 TRP 0.030 0.002 TRP I 346 HIS 0.009 0.001 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00442 (41574) covalent geometry : angle 0.58205 (56490) hydrogen bonds : bond 0.05794 ( 2076) hydrogen bonds : angle 4.77187 ( 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 913 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 720 time to evaluate : 1.612 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: 0.8628 (OUTLIER) cc_final: 0.8270 (mt) REVERT: A 417 GLU cc_start: 0.7011 (tt0) cc_final: 0.6708 (mt-10) REVERT: B 120 ASP cc_start: 0.8010 (m-30) cc_final: 0.7613 (m-30) REVERT: B 207 GLU cc_start: 0.8332 (pt0) cc_final: 0.8020 (pt0) REVERT: B 211 ASP cc_start: 0.8225 (m-30) cc_final: 0.7870 (m-30) REVERT: B 308 ARG cc_start: 0.7966 (mtm110) cc_final: 0.7602 (mtm110) REVERT: B 352 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7320 (tmtt) REVERT: C 76 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8243 (m-30) REVERT: C 393 HIS cc_start: 0.8105 (t70) cc_final: 0.7562 (t-170) REVERT: D 308 ARG cc_start: 0.8339 (mtm180) cc_final: 0.7790 (mtm110) REVERT: D 309 HIS cc_start: 0.8573 (m90) cc_final: 0.8358 (m90) REVERT: D 311 ARG cc_start: 0.8213 (mtt-85) cc_final: 0.7975 (mtp180) REVERT: D 372 LYS cc_start: 0.8506 (mmmt) cc_final: 0.8139 (ttpt) REVERT: D 413 MET cc_start: 0.8273 (mtp) cc_final: 0.7823 (ttm) REVERT: E 75 ILE cc_start: 0.9088 (mm) cc_final: 0.8624 (mm) REVERT: E 77 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7674 (mt-10) REVERT: E 313 MET cc_start: 0.8382 (mtm) cc_final: 0.8054 (mtp) REVERT: F 297 ASP cc_start: 0.7706 (t0) cc_final: 0.7501 (t0) REVERT: F 299 LYS cc_start: 0.8294 (ttpt) cc_final: 0.8015 (ptmt) REVERT: F 301 MET cc_start: 0.8448 (mmp) cc_final: 0.8205 (mmp) REVERT: F 306 ASP cc_start: 0.7044 (t0) cc_final: 0.6656 (t70) REVERT: F 308 ARG cc_start: 0.7862 (mtm110) cc_final: 0.7635 (mtm110) REVERT: F 325 MET cc_start: 0.8370 (mmm) cc_final: 0.8104 (mmm) REVERT: G 211 ASP cc_start: 0.8108 (m-30) cc_final: 0.7718 (m-30) REVERT: G 281 GLN cc_start: 0.8325 (tt0) cc_final: 0.7655 (tm-30) REVERT: G 282 GLN cc_start: 0.8073 (pt0) cc_final: 0.7798 (pm20) REVERT: G 373 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8609 (mtm) REVERT: G 426 ASN cc_start: 0.8045 (m-40) cc_final: 0.7798 (m110) REVERT: H 211 ASP cc_start: 0.8094 (m-30) cc_final: 0.7588 (m-30) REVERT: H 325 MET cc_start: 0.8200 (mmm) cc_final: 0.7794 (mmm) REVERT: H 346 TRP cc_start: 0.8138 (p-90) cc_final: 0.7772 (p-90) REVERT: H 398 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7924 (ttm) REVERT: H 422 GLU cc_start: 0.7688 (tp30) cc_final: 0.7364 (tp30) REVERT: H 426 ASN cc_start: 0.8110 (m-40) cc_final: 0.7660 (m110) REVERT: I 47 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8256 (mt-10) REVERT: I 205 ASP cc_start: 0.8035 (t0) cc_final: 0.7696 (m-30) REVERT: I 211 ASP cc_start: 0.8054 (m-30) cc_final: 0.7463 (m-30) REVERT: I 281 GLN cc_start: 0.8561 (tt0) cc_final: 0.7988 (tm-30) REVERT: I 283 TYR cc_start: 0.8254 (m-80) cc_final: 0.7869 (m-80) REVERT: I 398 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7847 (ttm) REVERT: I 422 GLU cc_start: 0.7881 (tp30) cc_final: 0.7062 (tp30) REVERT: I 426 ASN cc_start: 0.8010 (m-40) cc_final: 0.7332 (m110) REVERT: J 128 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8182 (tt0) REVERT: J 156 ARG cc_start: 0.8322 (mmt90) cc_final: 0.8025 (mmm-85) REVERT: J 342 GLN cc_start: 0.7943 (pt0) cc_final: 0.7520 (mp10) REVERT: K 76 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.8085 (m-30) REVERT: K 431 ASP cc_start: 0.7487 (m-30) cc_final: 0.7129 (m-30) REVERT: L 35 GLN cc_start: 0.8308 (tt0) cc_final: 0.8068 (mm-40) REVERT: L 88 HIS cc_start: 0.7464 (OUTLIER) cc_final: 0.6189 (p90) REVERT: L 93 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8337 (mt) REVERT: L 185 TYR cc_start: 0.8613 (m-10) cc_final: 0.8366 (m-10) outliers start: 193 outliers final: 149 residues processed: 846 average time/residue: 0.2610 time to fit residues: 363.5573 Evaluate side-chains 838 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 678 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 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 A residue 269 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 391 LEU 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 179 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 200 GLU 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 352 LYS 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 66 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 349 THR 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 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 234 ILE Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL 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 277 SER Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 334 ASN Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 419 THR 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 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 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 G residue 373 MET Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 96 GLN 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 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 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 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 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 374 SER 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 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 150 THR 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 80 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 150 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 193 THR 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 Chi-restraints excluded: chain L residue 277 SER Chi-restraints excluded: chain L residue 423 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 225 optimal weight: 9.9990 chunk 223 optimal weight: 8.9990 chunk 365 optimal weight: 8.9990 chunk 381 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 314 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 326 optimal weight: 8.9990 chunk 136 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 HIS ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 309 HIS ** H 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 434 GLN I 309 HIS K 31 GLN K 256 GLN L 256 GLN L 380 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.123096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.104113 restraints weight = 52867.954| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.03 r_work: 0.3301 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 41574 Z= 0.297 Angle : 0.668 9.681 56490 Z= 0.352 Chirality : 0.049 0.248 6174 Planarity : 0.005 0.053 7350 Dihedral : 12.247 178.855 5879 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.66 % Allowed : 17.38 % Favored : 77.96 % 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: 0.17 (0.11), residues: 5106 helix: 1.12 (0.10), residues: 2472 sheet: 0.06 (0.18), residues: 816 loop : -1.23 (0.13), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 322 TYR 0.022 0.002 TYR D 185 PHE 0.037 0.002 PHE K 255 TRP 0.027 0.002 TRP I 346 HIS 0.009 0.002 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00701 (41574) covalent geometry : angle 0.66813 (56490) hydrogen bonds : bond 0.06798 ( 2076) hydrogen bonds : angle 5.02046 ( 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 877 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 674 time to evaluate : 1.684 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: 0.8686 (OUTLIER) cc_final: 0.8312 (mt) REVERT: A 302 MET cc_start: 0.7993 (mmm) cc_final: 0.7380 (mtt) REVERT: A 398 MET cc_start: 0.8047 (mtt) cc_final: 0.7822 (mtt) REVERT: A 417 GLU cc_start: 0.7155 (tt0) cc_final: 0.6845 (mt-10) REVERT: B 120 ASP cc_start: 0.8106 (m-30) cc_final: 0.7723 (m-30) REVERT: B 207 GLU cc_start: 0.8403 (pt0) cc_final: 0.8116 (pt0) REVERT: B 211 ASP cc_start: 0.8256 (m-30) cc_final: 0.7905 (m-30) REVERT: B 308 ARG cc_start: 0.7913 (mtm110) cc_final: 0.7416 (mtm110) REVERT: B 352 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7392 (tmtt) REVERT: C 393 HIS cc_start: 0.8111 (t70) cc_final: 0.7584 (t-170) REVERT: D 281 GLN cc_start: 0.8096 (pt0) cc_final: 0.7780 (pt0) REVERT: D 308 ARG cc_start: 0.8319 (mtm180) cc_final: 0.7724 (mtm110) REVERT: D 309 HIS cc_start: 0.8633 (m90) cc_final: 0.8333 (m90) REVERT: D 311 ARG cc_start: 0.8191 (mtt-85) cc_final: 0.7753 (mtp180) REVERT: D 372 LYS cc_start: 0.8598 (mmmt) cc_final: 0.8160 (ttpt) REVERT: D 386 GLU cc_start: 0.8461 (pt0) cc_final: 0.8071 (pt0) REVERT: D 413 MET cc_start: 0.8440 (mtp) cc_final: 0.8008 (ttm) REVERT: E 77 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7690 (mt-10) REVERT: E 313 MET cc_start: 0.8461 (mtm) cc_final: 0.8035 (mtp) REVERT: F 299 LYS cc_start: 0.8354 (ttpt) cc_final: 0.8074 (ptmt) REVERT: F 301 MET cc_start: 0.8460 (mmp) cc_final: 0.8223 (mmp) REVERT: F 306 ASP cc_start: 0.6934 (t0) cc_final: 0.6694 (t0) REVERT: F 325 MET cc_start: 0.8317 (mmm) cc_final: 0.8094 (mmm) REVERT: G 113 GLU cc_start: 0.8404 (tp30) cc_final: 0.8106 (tt0) REVERT: G 211 ASP cc_start: 0.8115 (m-30) cc_final: 0.7708 (m-30) REVERT: G 281 GLN cc_start: 0.8552 (tt0) cc_final: 0.7806 (tm-30) REVERT: G 282 GLN cc_start: 0.8115 (pt0) cc_final: 0.7767 (pm20) REVERT: G 306 ASP cc_start: 0.8126 (t0) cc_final: 0.7555 (t0) REVERT: G 308 ARG cc_start: 0.8223 (mtm180) cc_final: 0.7652 (mtm-85) REVERT: G 373 MET cc_start: 0.8953 (ptp) cc_final: 0.8664 (mtm) REVERT: H 1 MET cc_start: 0.8266 (tpp) cc_final: 0.8062 (tpp) REVERT: H 211 ASP cc_start: 0.8068 (m-30) cc_final: 0.7543 (m-30) REVERT: H 308 ARG cc_start: 0.8539 (mtm180) cc_final: 0.8292 (mtm180) REVERT: H 346 TRP cc_start: 0.8173 (p-90) cc_final: 0.7764 (p-90) REVERT: H 422 GLU cc_start: 0.7702 (tp30) cc_final: 0.7346 (tp30) REVERT: H 426 ASN cc_start: 0.8107 (m-40) cc_final: 0.7608 (m110) REVERT: I 47 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8208 (mt-10) REVERT: I 113 GLU cc_start: 0.8472 (tp30) cc_final: 0.8127 (tt0) REVERT: I 211 ASP cc_start: 0.8069 (m-30) cc_final: 0.7500 (m-30) REVERT: I 283 TYR cc_start: 0.8255 (m-80) cc_final: 0.7824 (m-80) REVERT: I 398 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.7647 (ttp) REVERT: I 422 GLU cc_start: 0.7910 (tp30) cc_final: 0.7077 (tp30) REVERT: I 426 ASN cc_start: 0.8011 (m-40) cc_final: 0.7310 (m110) REVERT: J 128 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8217 (tt0) REVERT: J 156 ARG cc_start: 0.8309 (mmt90) cc_final: 0.8052 (mmm-85) REVERT: J 342 GLN cc_start: 0.7988 (pt0) cc_final: 0.7455 (mp10) REVERT: K 31 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7968 (mt0) REVERT: K 76 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8121 (m-30) REVERT: K 431 ASP cc_start: 0.7565 (m-30) cc_final: 0.7193 (m-30) REVERT: L 35 GLN cc_start: 0.8268 (tt0) cc_final: 0.8024 (mm-40) REVERT: L 71 GLU cc_start: 0.7671 (tt0) cc_final: 0.7430 (tt0) REVERT: L 76 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.8137 (m-30) REVERT: L 88 HIS cc_start: 0.7852 (OUTLIER) cc_final: 0.6528 (p90) REVERT: L 93 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8419 (mt) REVERT: L 176 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8356 (mm-40) REVERT: L 185 TYR cc_start: 0.8702 (m-10) cc_final: 0.8468 (m-10) outliers start: 203 outliers final: 161 residues processed: 810 average time/residue: 0.2583 time to fit residues: 343.4755 Evaluate side-chains 823 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 653 time to evaluate : 1.737 ------------------------------------------------------------------------------- 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 159 VAL 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 269 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain B residue 115 VAL 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 179 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 200 GLU 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 352 LYS 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 66 VAL Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 88 HIS 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 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 D residue 33 THR Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 127 GLU 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 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 374 SER Chi-restraints excluded: chain D residue 393 GLU Chi-restraints excluded: chain D residue 419 THR 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 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 275 VAL Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 371 VAL 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 126 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 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 277 SER Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 334 ASN Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 419 THR 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 26 ASP Chi-restraints excluded: chain G residue 39 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 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 115 VAL 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 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 431 GLU Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 230 LEU 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 291 LEU Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 357 ASP Chi-restraints excluded: chain I residue 374 SER 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 150 THR Chi-restraints excluded: chain J residue 159 VAL 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 361 THR Chi-restraints excluded: chain K residue 31 GLN 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 150 THR 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 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 76 ASP 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 150 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 193 THR 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 238 ILE 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 423 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 278 optimal weight: 10.0000 chunk 499 optimal weight: 6.9990 chunk 409 optimal weight: 0.8980 chunk 138 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 410 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 475 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 504 optimal weight: 0.8980 chunk 498 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 HIS ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 294 GLN G 37 HIS ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 197 ASN J 15 GLN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 256 GLN L 128 GLN L 256 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.127155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.108224 restraints weight = 51672.350| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.96 r_work: 0.3370 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 41574 Z= 0.147 Angle : 0.557 8.146 56490 Z= 0.293 Chirality : 0.044 0.243 6174 Planarity : 0.004 0.050 7350 Dihedral : 12.012 176.659 5879 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.70 % Allowed : 18.66 % 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: 0.40 (0.11), residues: 5106 helix: 1.34 (0.10), residues: 2454 sheet: 0.06 (0.18), residues: 834 loop : -1.10 (0.13), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 322 TYR 0.016 0.001 TYR D 185 PHE 0.034 0.001 PHE K 255 TRP 0.034 0.002 TRP I 346 HIS 0.008 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00332 (41574) covalent geometry : angle 0.55732 (56490) hydrogen bonds : bond 0.05236 ( 2076) hydrogen bonds : angle 4.70026 ( 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 872 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 711 time to evaluate : 1.557 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: 0.8634 (OUTLIER) cc_final: 0.8282 (mt) REVERT: A 313 MET cc_start: 0.8161 (mtp) cc_final: 0.7811 (mtm) REVERT: B 37 HIS cc_start: 0.7973 (m-70) cc_final: 0.7672 (m170) REVERT: B 120 ASP cc_start: 0.7949 (m-30) cc_final: 0.7559 (m-30) REVERT: B 207 GLU cc_start: 0.8339 (pt0) cc_final: 0.8031 (pt0) REVERT: B 211 ASP cc_start: 0.8210 (m-30) cc_final: 0.7846 (m-30) REVERT: B 308 ARG cc_start: 0.7945 (mtm110) cc_final: 0.7552 (mtm110) REVERT: C 76 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.8197 (m-30) REVERT: C 393 HIS cc_start: 0.8097 (t70) cc_final: 0.7590 (t-170) REVERT: D 47 GLU cc_start: 0.8183 (tt0) cc_final: 0.7962 (tt0) REVERT: D 281 GLN cc_start: 0.8115 (pt0) cc_final: 0.7812 (pt0) REVERT: D 308 ARG cc_start: 0.8376 (mtm180) cc_final: 0.7958 (mtm110) REVERT: D 309 HIS cc_start: 0.8498 (m90) cc_final: 0.8264 (m90) REVERT: D 311 ARG cc_start: 0.8143 (mtt-85) cc_final: 0.7817 (mtp180) REVERT: D 372 LYS cc_start: 0.8546 (mmmt) cc_final: 0.8150 (ttpt) REVERT: D 413 MET cc_start: 0.8330 (mtp) cc_final: 0.7916 (ttm) REVERT: E 77 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7669 (mt-10) REVERT: E 91 GLN cc_start: 0.8054 (mt0) cc_final: 0.7534 (mt0) REVERT: E 313 MET cc_start: 0.8382 (mtm) cc_final: 0.8010 (mtp) REVERT: F 55 GLU cc_start: 0.8051 (tp30) cc_final: 0.7634 (tp30) REVERT: F 145 THR cc_start: 0.8184 (m) cc_final: 0.7836 (m) REVERT: F 301 MET cc_start: 0.8357 (mmp) cc_final: 0.8019 (mmp) REVERT: G 1 MET cc_start: 0.8524 (mmm) cc_final: 0.7892 (tpt) REVERT: G 113 GLU cc_start: 0.8370 (tp30) cc_final: 0.8135 (tt0) REVERT: G 211 ASP cc_start: 0.8089 (m-30) cc_final: 0.7739 (m-30) REVERT: G 281 GLN cc_start: 0.8528 (tt0) cc_final: 0.7815 (tm-30) REVERT: G 282 GLN cc_start: 0.8108 (pt0) cc_final: 0.7836 (pm20) REVERT: G 308 ARG cc_start: 0.8228 (mtm180) cc_final: 0.7772 (mtm-85) REVERT: H 211 ASP cc_start: 0.8108 (m-30) cc_final: 0.7588 (m-30) REVERT: H 308 ARG cc_start: 0.8441 (mtm180) cc_final: 0.8199 (mtm180) REVERT: H 346 TRP cc_start: 0.8133 (p-90) cc_final: 0.7764 (p-90) REVERT: H 398 MET cc_start: 0.8167 (mtm) cc_final: 0.7957 (ttm) REVERT: H 422 GLU cc_start: 0.7687 (tp30) cc_final: 0.7348 (tp30) REVERT: H 426 ASN cc_start: 0.8066 (m-40) cc_final: 0.7593 (m110) REVERT: I 47 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8138 (mt-10) REVERT: I 211 ASP cc_start: 0.8053 (m-30) cc_final: 0.7464 (m-30) REVERT: I 283 TYR cc_start: 0.8239 (m-80) cc_final: 0.7846 (m-80) REVERT: I 284 ARG cc_start: 0.7521 (ttt-90) cc_final: 0.7162 (ttt90) REVERT: I 398 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7609 (ttp) REVERT: I 422 GLU cc_start: 0.7892 (tp30) cc_final: 0.7189 (tp30) REVERT: I 426 ASN cc_start: 0.7995 (m-40) cc_final: 0.7299 (m110) REVERT: J 128 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8166 (tt0) REVERT: J 156 ARG cc_start: 0.8262 (mmt90) cc_final: 0.7934 (mmm-85) REVERT: J 342 GLN cc_start: 0.7907 (pt0) cc_final: 0.7405 (mp10) REVERT: K 76 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.7997 (m-30) REVERT: K 357 TYR cc_start: 0.8645 (m-80) cc_final: 0.8394 (m-80) REVERT: K 431 ASP cc_start: 0.7455 (m-30) cc_final: 0.7135 (m-30) REVERT: L 71 GLU cc_start: 0.7545 (tt0) cc_final: 0.7314 (tt0) REVERT: L 88 HIS cc_start: 0.7464 (OUTLIER) cc_final: 0.6133 (p90) REVERT: L 93 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8351 (mt) REVERT: L 185 TYR cc_start: 0.8666 (m-10) cc_final: 0.8389 (m-10) outliers start: 161 outliers final: 127 residues processed: 813 average time/residue: 0.2556 time to fit residues: 341.5415 Evaluate side-chains 815 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 680 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 159 VAL 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 269 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 115 VAL 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 194 LEU 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 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 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 393 GLU 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 241 SER Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 371 VAL 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 165 ILE 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 315 VAL 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 39 ASP 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 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 47 GLU Chi-restraints excluded: chain H residue 96 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 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 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 277 SER 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 159 VAL 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 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 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 Chi-restraints excluded: chain L residue 277 SER Chi-restraints excluded: chain L residue 423 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 102 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 278 optimal weight: 6.9990 chunk 338 optimal weight: 9.9990 chunk 176 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 chunk 301 optimal weight: 8.9990 chunk 305 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 GLN G 37 HIS ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 192 HIS K 256 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 = 0.3714 r_free = 0.3714 target = 0.125232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.106714 restraints weight = 52298.249| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.93 r_work: 0.3343 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 41574 Z= 0.210 Angle : 0.602 9.262 56490 Z= 0.316 Chirality : 0.046 0.244 6174 Planarity : 0.005 0.051 7350 Dihedral : 12.065 178.963 5877 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.67 % Allowed : 18.99 % Favored : 77.34 % 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: 0.28 (0.11), residues: 5106 helix: 1.23 (0.10), residues: 2472 sheet: 0.02 (0.18), residues: 834 loop : -1.15 (0.13), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 322 TYR 0.018 0.001 TYR D 185 PHE 0.027 0.002 PHE K 255 TRP 0.037 0.002 TRP F 346 HIS 0.007 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00494 (41574) covalent geometry : angle 0.60168 (56490) hydrogen bonds : bond 0.05931 ( 2076) hydrogen bonds : angle 4.80969 ( 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 836 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 676 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8317 (mt) REVERT: A 302 MET cc_start: 0.7751 (mmm) cc_final: 0.7296 (mtt) REVERT: A 313 MET cc_start: 0.8210 (mtp) cc_final: 0.7856 (mtm) REVERT: A 342 GLN cc_start: 0.7278 (mp10) cc_final: 0.7052 (mp10) REVERT: B 120 ASP cc_start: 0.8042 (m-30) cc_final: 0.7733 (m-30) REVERT: B 207 GLU cc_start: 0.8375 (pt0) cc_final: 0.8090 (pt0) REVERT: B 211 ASP cc_start: 0.8239 (m-30) cc_final: 0.7892 (m-30) REVERT: B 308 ARG cc_start: 0.7920 (mtm110) cc_final: 0.7492 (mtm110) REVERT: C 76 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.8234 (m-30) REVERT: C 393 HIS cc_start: 0.8123 (t70) cc_final: 0.7607 (t-170) REVERT: D 47 GLU cc_start: 0.8217 (tt0) cc_final: 0.7983 (tt0) REVERT: D 281 GLN cc_start: 0.8204 (pt0) cc_final: 0.7946 (pt0) REVERT: D 308 ARG cc_start: 0.8296 (mtm180) cc_final: 0.7776 (mtm110) REVERT: D 309 HIS cc_start: 0.8615 (m90) cc_final: 0.8343 (m90) REVERT: D 311 ARG cc_start: 0.8182 (mtt-85) cc_final: 0.7872 (mtp180) REVERT: D 372 LYS cc_start: 0.8543 (mmmt) cc_final: 0.8139 (ttpt) REVERT: D 386 GLU cc_start: 0.8506 (pt0) cc_final: 0.8283 (pt0) REVERT: D 413 MET cc_start: 0.8395 (mtp) cc_final: 0.7942 (ttm) REVERT: E 75 ILE cc_start: 0.9016 (mm) cc_final: 0.8659 (mm) REVERT: E 77 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7728 (mt-10) REVERT: E 313 MET cc_start: 0.8417 (mtm) cc_final: 0.8016 (mtp) REVERT: F 55 GLU cc_start: 0.8074 (tp30) cc_final: 0.7731 (tp30) REVERT: G 26 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.8270 (m-30) REVERT: G 113 GLU cc_start: 0.8347 (tp30) cc_final: 0.8118 (tt0) REVERT: G 211 ASP cc_start: 0.8112 (m-30) cc_final: 0.7714 (m-30) REVERT: G 281 GLN cc_start: 0.8625 (tt0) cc_final: 0.7858 (tm-30) REVERT: G 282 GLN cc_start: 0.8119 (pt0) cc_final: 0.7848 (pm20) REVERT: G 308 ARG cc_start: 0.8249 (mtm180) cc_final: 0.7688 (mtm-85) REVERT: H 211 ASP cc_start: 0.8110 (m-30) cc_final: 0.7585 (m-30) REVERT: H 308 ARG cc_start: 0.8444 (mtm180) cc_final: 0.8171 (mtm180) REVERT: H 346 TRP cc_start: 0.8154 (p-90) cc_final: 0.7768 (p-90) REVERT: H 398 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7958 (ttm) REVERT: H 422 GLU cc_start: 0.7673 (tp30) cc_final: 0.7311 (tp30) REVERT: H 426 ASN cc_start: 0.8064 (m-40) cc_final: 0.7588 (m110) REVERT: I 47 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8198 (mt-10) REVERT: I 211 ASP cc_start: 0.8076 (m-30) cc_final: 0.7490 (m-30) REVERT: I 283 TYR cc_start: 0.8256 (m-80) cc_final: 0.7853 (m-80) REVERT: I 284 ARG cc_start: 0.7544 (ttt-90) cc_final: 0.7197 (ttt90) REVERT: I 398 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.7664 (ttp) REVERT: I 422 GLU cc_start: 0.7905 (tp30) cc_final: 0.7202 (tp30) REVERT: I 426 ASN cc_start: 0.7925 (m-40) cc_final: 0.7251 (m110) REVERT: J 128 GLN cc_start: 0.8499 (mm-40) cc_final: 0.8202 (tt0) REVERT: J 156 ARG cc_start: 0.8261 (mmt90) cc_final: 0.8048 (mmm-85) REVERT: J 342 GLN cc_start: 0.7907 (pt0) cc_final: 0.7391 (mp10) REVERT: K 76 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.8037 (m-30) REVERT: K 431 ASP cc_start: 0.7521 (m-30) cc_final: 0.7189 (m-30) REVERT: L 71 GLU cc_start: 0.7622 (tt0) cc_final: 0.7392 (tt0) REVERT: L 88 HIS cc_start: 0.7630 (OUTLIER) cc_final: 0.6310 (p90) REVERT: L 93 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8361 (mt) REVERT: L 185 TYR cc_start: 0.8746 (m-10) cc_final: 0.8505 (m-10) outliers start: 160 outliers final: 136 residues processed: 775 average time/residue: 0.2581 time to fit residues: 327.2038 Evaluate side-chains 806 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 661 time to evaluate : 1.862 ------------------------------------------------------------------------------- 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 159 VAL 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 269 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 433 GLU 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 194 LEU 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 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 159 VAL 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 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 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 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 159 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 230 LEU 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 371 VAL 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 132 LEU Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 165 ILE 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 315 VAL Chi-restraints excluded: chain F residue 334 ASN Chi-restraints excluded: chain F residue 357 ASP 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 26 ASP Chi-restraints excluded: chain G residue 39 ASP 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 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 47 GLU Chi-restraints excluded: chain H residue 96 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 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 277 SER Chi-restraints excluded: chain I residue 291 LEU 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 159 VAL 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 361 THR 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 255 PHE 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 423 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 222 optimal weight: 2.9990 chunk 310 optimal weight: 5.9990 chunk 487 optimal weight: 0.7980 chunk 353 optimal weight: 8.9990 chunk 218 optimal weight: 0.8980 chunk 436 optimal weight: 2.9990 chunk 284 optimal weight: 0.9990 chunk 272 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 473 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 HIS ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 HIS ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 256 GLN L 256 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.127263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.107723 restraints weight = 51864.798| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.06 r_work: 0.3370 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.5208 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= 0.145 Angle : 0.560 8.514 56490 Z= 0.294 Chirality : 0.044 0.244 6174 Planarity : 0.004 0.050 7350 Dihedral : 11.920 177.456 5877 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.31 % Allowed : 19.61 % Favored : 77.09 % 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: 0.48 (0.11), residues: 5106 helix: 1.43 (0.10), residues: 2418 sheet: 0.10 (0.18), residues: 834 loop : -1.03 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 278 TYR 0.015 0.001 TYR G 283 PHE 0.025 0.001 PHE K 255 TRP 0.036 0.002 TRP I 346 HIS 0.008 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00327 (41574) covalent geometry : angle 0.55987 (56490) hydrogen bonds : bond 0.05089 ( 2076) hydrogen bonds : angle 4.65832 ( 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 847 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 703 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.8060 (m-30) REVERT: A 230 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8371 (mt) REVERT: A 302 MET cc_start: 0.7685 (mmm) cc_final: 0.7339 (mtt) REVERT: A 313 MET cc_start: 0.8138 (mtp) cc_final: 0.7771 (mtm) REVERT: A 342 GLN cc_start: 0.7138 (mp10) cc_final: 0.6919 (mp10) REVERT: B 120 ASP cc_start: 0.7944 (m-30) cc_final: 0.7552 (m-30) REVERT: B 207 GLU cc_start: 0.8347 (pt0) cc_final: 0.7976 (pt0) REVERT: B 211 ASP cc_start: 0.8226 (m-30) cc_final: 0.7883 (m-30) REVERT: B 308 ARG cc_start: 0.7938 (mtm110) cc_final: 0.7466 (mtm110) REVERT: C 76 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.8167 (m-30) REVERT: C 411 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7956 (mm-30) REVERT: D 47 GLU cc_start: 0.8189 (tt0) cc_final: 0.7959 (tt0) REVERT: D 281 GLN cc_start: 0.8246 (pt0) cc_final: 0.7988 (pt0) REVERT: D 308 ARG cc_start: 0.8386 (mtm180) cc_final: 0.7948 (mtm110) REVERT: D 309 HIS cc_start: 0.8586 (m90) cc_final: 0.8328 (m90) REVERT: D 372 LYS cc_start: 0.8560 (mmmt) cc_final: 0.8137 (ttpt) REVERT: D 413 MET cc_start: 0.8253 (mtp) cc_final: 0.7770 (ttm) REVERT: D 433 GLN cc_start: 0.8572 (tp40) cc_final: 0.8297 (tp40) REVERT: E 75 ILE cc_start: 0.8963 (mm) cc_final: 0.8620 (mm) REVERT: E 77 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7646 (mt-10) REVERT: E 91 GLN cc_start: 0.7931 (mt0) cc_final: 0.7462 (mt0) REVERT: E 313 MET cc_start: 0.8428 (mtm) cc_final: 0.8074 (mtp) REVERT: E 392 ASP cc_start: 0.8268 (m-30) cc_final: 0.7912 (m-30) REVERT: F 55 GLU cc_start: 0.8006 (tp30) cc_final: 0.7621 (tp30) REVERT: G 113 GLU cc_start: 0.8416 (tp30) cc_final: 0.8167 (tt0) REVERT: G 211 ASP cc_start: 0.8118 (m-30) cc_final: 0.7718 (m-30) REVERT: G 281 GLN cc_start: 0.8621 (tt0) cc_final: 0.7843 (tm-30) REVERT: G 282 GLN cc_start: 0.8119 (pt0) cc_final: 0.7674 (pm20) REVERT: G 308 ARG cc_start: 0.8304 (mtm180) cc_final: 0.7780 (mtm-85) REVERT: G 398 MET cc_start: 0.7937 (mtp) cc_final: 0.7387 (ttm) REVERT: G 414 ASP cc_start: 0.6916 (t0) cc_final: 0.6218 (m-30) REVERT: H 211 ASP cc_start: 0.8097 (m-30) cc_final: 0.7557 (m-30) REVERT: H 308 ARG cc_start: 0.8408 (mtm180) cc_final: 0.8052 (mtm180) REVERT: H 323 MET cc_start: 0.8538 (mtm) cc_final: 0.8260 (ptp) REVERT: H 346 TRP cc_start: 0.8152 (p-90) cc_final: 0.7753 (p-90) REVERT: H 398 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7981 (ttm) REVERT: H 422 GLU cc_start: 0.7671 (tp30) cc_final: 0.7278 (tp30) REVERT: H 426 ASN cc_start: 0.8028 (m-40) cc_final: 0.7524 (m110) REVERT: I 47 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8115 (mt-10) REVERT: I 113 GLU cc_start: 0.8388 (tp30) cc_final: 0.8082 (tt0) REVERT: I 211 ASP cc_start: 0.8042 (m-30) cc_final: 0.7448 (m-30) REVERT: I 283 TYR cc_start: 0.8229 (m-80) cc_final: 0.7827 (m-80) REVERT: I 284 ARG cc_start: 0.7453 (ttt-90) cc_final: 0.7135 (ttt90) REVERT: I 398 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7660 (ttp) REVERT: I 422 GLU cc_start: 0.7806 (tp30) cc_final: 0.7075 (tp30) REVERT: I 426 ASN cc_start: 0.7909 (m-40) cc_final: 0.7221 (m110) REVERT: J 128 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8171 (tt0) REVERT: J 156 ARG cc_start: 0.8290 (mmt90) cc_final: 0.8003 (mmm-85) REVERT: J 342 GLN cc_start: 0.7874 (pt0) cc_final: 0.7311 (mp10) REVERT: K 76 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.8000 (m-30) REVERT: K 357 TYR cc_start: 0.8681 (m-80) cc_final: 0.8462 (m-80) REVERT: K 431 ASP cc_start: 0.7440 (m-30) cc_final: 0.7111 (m-30) REVERT: L 71 GLU cc_start: 0.7538 (tt0) cc_final: 0.7284 (tt0) REVERT: L 88 HIS cc_start: 0.7417 (OUTLIER) cc_final: 0.6092 (p90) REVERT: L 93 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8352 (mt) REVERT: L 185 TYR cc_start: 0.8692 (m-10) cc_final: 0.8434 (m-10) outliers start: 144 outliers final: 122 residues processed: 792 average time/residue: 0.2628 time to fit residues: 340.3701 Evaluate side-chains 802 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 670 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 88 HIS 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 238 ILE Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 269 LEU 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 334 ASN 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 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 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 207 GLU 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 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 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 349 THR Chi-restraints excluded: chain E residue 371 VAL 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 132 LEU Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 165 ILE 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 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 39 ASP 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 277 SER Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain H residue 96 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 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 398 MET Chi-restraints excluded: chain H residue 431 GLU Chi-restraints excluded: chain I residue 47 GLU 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 159 VAL 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 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 238 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 88 HIS Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 150 THR 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 Chi-restraints excluded: chain L residue 277 SER Chi-restraints excluded: chain L residue 423 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 26 optimal weight: 0.9980 chunk 261 optimal weight: 3.9990 chunk 295 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 chunk 154 optimal weight: 5.9990 chunk 352 optimal weight: 6.9990 chunk 359 optimal weight: 5.9990 chunk 191 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 GLN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 HIS ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 256 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.126758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.107184 restraints weight = 52034.625| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.06 r_work: 0.3361 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.5239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 41574 Z= 0.164 Angle : 0.573 8.242 56490 Z= 0.301 Chirality : 0.045 0.242 6174 Planarity : 0.004 0.051 7350 Dihedral : 11.871 178.316 5874 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.54 % Allowed : 19.58 % Favored : 76.88 % 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: 0.48 (0.11), residues: 5106 helix: 1.43 (0.10), residues: 2418 sheet: 0.10 (0.18), residues: 834 loop : -1.03 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 322 TYR 0.015 0.001 TYR D 185 PHE 0.023 0.002 PHE L 255 TRP 0.036 0.002 TRP I 346 HIS 0.008 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00378 (41574) covalent geometry : angle 0.57310 (56490) hydrogen bonds : bond 0.05293 ( 2076) hydrogen bonds : angle 4.68427 ( 5994) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12725.01 seconds wall clock time: 218 minutes 11.26 seconds (13091.26 seconds total)