Starting phenix.real_space_refine on Tue Aug 26 19:38:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jat_6352/08_2025/3jat_6352.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jat_6352/08_2025/3jat_6352.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/3jat_6352/08_2025/3jat_6352.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jat_6352/08_2025/3jat_6352.map" model { file = "/net/cci-nas-00/data/ceres_data/3jat_6352/08_2025/3jat_6352.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jat_6352/08_2025/3jat_6352.cif" } resolution = 3.5 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= 0.043 sd= 0.912 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 276 5.16 5 C 25464 2.51 5 N 6918 2.21 5 O 7794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40500 Number of models: 1 Model: "" Number of chains: 24 Chain: "E" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3342 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} 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: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3342 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3342 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} 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: "G" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3342 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3342 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} 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: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3342 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3342 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} 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: "I" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3342 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3342 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} 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: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3342 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3342 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} 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: "H" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3342 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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: "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: "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: "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: "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} 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: "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: "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: "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} Time building chain proxies: 8.04, per 1000 atoms: 0.20 Number of scatterers: 40500 At special positions: 0 Unit cell: (174.24, 88.44, 211.2, 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 276 16.00 P 36 15.00 Mg 12 11.99 O 7794 8.00 N 6918 7.00 C 25464 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: 2.83 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 953.7 nanoseconds 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9492 Finding SS restraints... Secondary structure from input PDB file: 252 helices and 30 sheets defined 56.4% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... 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: 3.608A 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: 3.558A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 161 removed outlier: 4.079A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 197 removed outlier: 3.524A pdb=" N ASN E 186 " --> pdb=" O VAL E 182 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS E 192 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 218 Processing helix chain 'E' and resid 223 through 244 removed outlier: 4.405A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.260A 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: 3.995A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N HIS E 283 " --> pdb=" O GLU E 279 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU E 284 " --> pdb=" O LYS E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.602A 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 337 removed outlier: 3.592A pdb=" N VAL E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 401 removed outlier: 3.623A pdb=" N TRP E 388 " --> pdb=" O ILE E 384 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS E 401 " --> pdb=" O LEU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 411 removed outlier: 4.079A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 436 removed outlier: 3.912A pdb=" N PHE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 28 Processing helix chain 'F' and resid 41 through 48 removed outlier: 4.426A 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: 4.490A pdb=" N MET F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.741A 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: 4.295A pdb=" N ASP F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N SER F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) removed outlier: 3.994A 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: 3.546A pdb=" N GLN F 193 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 3.602A 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: 3.812A pdb=" N THR F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N CYS F 241 " --> pdb=" O GLY F 237 " (cutoff:3.500A) removed outlier: 5.736A 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: 3.600A pdb=" N GLN F 281 " --> pdb=" O ARG F 278 " (cutoff:3.500A) removed outlier: 3.852A 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: 3.546A 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 401 removed outlier: 4.206A pdb=" N ARG F 401 " --> pdb=" O ALA F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 411 removed outlier: 4.124A pdb=" N TYR F 408 " --> pdb=" O PHE F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 436 removed outlier: 4.070A pdb=" N PHE F 418 " --> pdb=" O ASP F 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: 3.608A 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: 3.559A pdb=" N GLN J 128 " --> pdb=" O LYS J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 161 removed outlier: 4.080A pdb=" N THR J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 197 removed outlier: 3.520A pdb=" N ASN J 186 " --> pdb=" O VAL J 182 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS J 192 " --> pdb=" O ILE J 188 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR J 193 " --> pdb=" O LEU J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 218 Processing helix chain 'J' and resid 223 through 244 removed outlier: 4.406A pdb=" N SER J 241 " --> pdb=" O SER J 237 " (cutoff:3.500A) removed outlier: 5.259A 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: 3.993A pdb=" N TYR J 282 " --> pdb=" O ALA J 278 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N HIS J 283 " --> pdb=" O GLU J 279 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU J 284 " --> pdb=" O LYS J 280 " (cutoff:3.500A) Processing helix chain 'J' and resid 287 through 296 removed outlier: 3.603A 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 337 removed outlier: 3.592A pdb=" N VAL J 328 " --> pdb=" O VAL J 324 " (cutoff:3.500A) Processing helix chain 'J' and resid 384 through 401 removed outlier: 3.623A pdb=" N TRP J 388 " --> pdb=" O ILE J 384 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS J 401 " --> pdb=" O LEU J 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 404 through 411 removed outlier: 4.080A pdb=" N TYR J 408 " --> pdb=" O PHE J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 414 through 436 removed outlier: 3.912A pdb=" N PHE J 418 " --> pdb=" O GLU J 414 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 28 Processing helix chain 'G' and resid 41 through 48 removed outlier: 4.429A 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: 4.488A pdb=" N MET G 75 " --> pdb=" O GLU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.744A 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: 4.293A pdb=" N ASP G 116 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N SER G 117 " --> pdb=" O GLU G 113 " (cutoff:3.500A) removed outlier: 3.994A 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: 3.545A pdb=" N GLN G 193 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 3.603A 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: 3.812A pdb=" N THR G 239 " --> pdb=" O MET G 235 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N CYS G 241 " --> pdb=" O GLY G 237 " (cutoff:3.500A) removed outlier: 5.735A 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: 3.603A pdb=" N GLN G 281 " --> pdb=" O ARG G 278 " (cutoff:3.500A) removed outlier: 3.852A 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: 3.548A 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 401 removed outlier: 4.206A pdb=" N ARG G 401 " --> pdb=" O ALA G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 411 removed outlier: 4.123A pdb=" N TYR G 408 " --> pdb=" O PHE G 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 436 removed outlier: 4.071A pdb=" N PHE G 418 " --> pdb=" O ASP G 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: 3.608A 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: 3.557A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 161 removed outlier: 4.079A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.522A pdb=" N ASN C 186 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS C 192 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 218 Processing helix chain 'C' and resid 223 through 244 removed outlier: 4.406A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.262A 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: 3.996A pdb=" N TYR C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N HIS C 283 " --> pdb=" O GLU C 279 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 296 removed outlier: 3.603A 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 337 removed outlier: 3.591A pdb=" N VAL C 328 " --> pdb=" O VAL C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 401 removed outlier: 3.623A pdb=" N TRP C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS C 401 " --> pdb=" O LEU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 removed outlier: 4.079A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 436 removed outlier: 3.912A pdb=" N PHE C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 28 Processing helix chain 'D' and resid 41 through 48 removed outlier: 4.427A 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: 4.490A 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: 4.296A pdb=" N ASP D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N SER D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 3.995A 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: 3.545A pdb=" N GLN D 193 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 3.603A 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: 3.813A pdb=" N THR D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N CYS D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 5.736A 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: 3.601A pdb=" N GLN D 281 " --> pdb=" O ARG D 278 " (cutoff:3.500A) removed outlier: 3.852A 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: 3.546A 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 401 removed outlier: 4.205A pdb=" N ARG D 401 " --> pdb=" O ALA D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 411 removed outlier: 4.124A pdb=" N TYR D 408 " --> pdb=" O PHE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 436 removed outlier: 4.070A pdb=" N PHE D 418 " --> pdb=" O ASP D 414 " (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: 3.609A 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: 3.557A pdb=" N GLN L 128 " --> pdb=" O LYS L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 161 removed outlier: 4.082A pdb=" N THR L 150 " --> pdb=" O GLY L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 197 removed outlier: 3.520A pdb=" N ASN L 186 " --> pdb=" O VAL L 182 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS L 192 " --> pdb=" O ILE L 188 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR L 193 " --> pdb=" O LEU L 189 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 218 Processing helix chain 'L' and resid 223 through 244 removed outlier: 4.406A pdb=" N SER L 241 " --> pdb=" O SER L 237 " (cutoff:3.500A) removed outlier: 5.263A 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: 3.994A pdb=" N TYR L 282 " --> pdb=" O ALA L 278 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N HIS L 283 " --> pdb=" O GLU L 279 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU L 284 " --> pdb=" O LYS L 280 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 296 removed outlier: 3.603A 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 337 removed outlier: 3.593A pdb=" N VAL L 328 " --> pdb=" O VAL L 324 " (cutoff:3.500A) Processing helix chain 'L' and resid 384 through 401 removed outlier: 3.622A pdb=" N TRP L 388 " --> pdb=" O ILE L 384 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS L 401 " --> pdb=" O LEU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 404 through 411 removed outlier: 4.079A pdb=" N TYR L 408 " --> pdb=" O PHE L 404 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 436 removed outlier: 3.912A pdb=" N PHE L 418 " --> pdb=" O GLU L 414 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 28 Processing helix chain 'I' and resid 41 through 48 removed outlier: 4.428A 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: 4.488A pdb=" N MET I 75 " --> pdb=" O GLU I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.743A 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: 4.295A pdb=" N ASP I 116 " --> pdb=" O ALA I 112 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N SER I 117 " --> pdb=" O GLU I 113 " (cutoff:3.500A) removed outlier: 3.995A 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: 3.545A pdb=" N GLN I 193 " --> pdb=" O LEU I 189 " (cutoff:3.500A) removed outlier: 3.602A 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: 3.813A pdb=" N THR I 239 " --> pdb=" O MET I 235 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N CYS I 241 " --> pdb=" O GLY I 237 " (cutoff:3.500A) removed outlier: 5.736A 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: 3.603A pdb=" N GLN I 281 " --> pdb=" O ARG I 278 " (cutoff:3.500A) removed outlier: 3.852A 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: 3.545A 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 401 removed outlier: 4.204A pdb=" N ARG I 401 " --> pdb=" O ALA I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 404 through 411 removed outlier: 4.123A pdb=" N TYR I 408 " --> pdb=" O PHE I 404 " (cutoff:3.500A) Processing helix chain 'I' and resid 414 through 436 removed outlier: 4.070A pdb=" N PHE I 418 " --> pdb=" O ASP I 414 " (cutoff:3.500A) 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: 3.608A 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: 3.558A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.078A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.523A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 218 Processing helix chain 'A' and resid 223 through 244 removed outlier: 4.406A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.262A 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: 3.995A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N HIS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.602A 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 337 removed outlier: 3.592A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 401 removed outlier: 3.623A pdb=" N TRP A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 4.079A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 436 removed outlier: 3.912A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 41 through 48 removed outlier: 4.427A 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: 4.490A pdb=" N MET B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 87 removed outlier: 3.742A 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: 4.295A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.994A 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: 3.545A pdb=" N GLN B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.603A 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: 3.813A pdb=" N THR B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N CYS B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 5.736A 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: 3.600A pdb=" N GLN B 281 " --> pdb=" O ARG B 278 " (cutoff:3.500A) removed outlier: 3.851A 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: 3.547A 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 401 removed outlier: 4.206A pdb=" N ARG B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 411 removed outlier: 4.123A pdb=" N TYR B 408 " --> pdb=" O PHE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 436 removed outlier: 4.070A pdb=" N PHE B 418 " --> pdb=" O ASP B 414 " (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: 3.609A 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: 3.558A pdb=" N GLN K 128 " --> pdb=" O LYS K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 161 removed outlier: 4.081A pdb=" N THR K 150 " --> pdb=" O GLY K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 197 removed outlier: 3.521A pdb=" N ASN K 186 " --> pdb=" O VAL K 182 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS K 192 " --> pdb=" O ILE K 188 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR K 193 " --> pdb=" O LEU K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 218 Processing helix chain 'K' and resid 223 through 244 removed outlier: 4.406A pdb=" N SER K 241 " --> pdb=" O SER K 237 " (cutoff:3.500A) removed outlier: 5.261A 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: 3.993A pdb=" N TYR K 282 " --> pdb=" O ALA K 278 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N HIS K 283 " --> pdb=" O GLU K 279 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU K 284 " --> pdb=" O LYS K 280 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 296 removed outlier: 3.603A 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 337 removed outlier: 3.592A pdb=" N VAL K 328 " --> pdb=" O VAL K 324 " (cutoff:3.500A) Processing helix chain 'K' and resid 384 through 401 removed outlier: 3.623A pdb=" N TRP K 388 " --> pdb=" O ILE K 384 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS K 401 " --> pdb=" O LEU K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 411 removed outlier: 4.080A pdb=" N TYR K 408 " --> pdb=" O PHE K 404 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 436 removed outlier: 3.912A pdb=" N PHE K 418 " --> pdb=" O GLU K 414 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 28 Processing helix chain 'H' and resid 41 through 48 removed outlier: 4.428A 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: 4.488A pdb=" N MET H 75 " --> pdb=" O GLU H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.744A 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: 4.295A pdb=" N ASP H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N SER H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) removed outlier: 3.995A 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: 3.545A pdb=" N GLN H 193 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 3.602A 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: 3.813A pdb=" N THR H 239 " --> pdb=" O MET H 235 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N CYS H 241 " --> pdb=" O GLY H 237 " (cutoff:3.500A) removed outlier: 5.737A 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: 3.602A pdb=" N GLN H 281 " --> pdb=" O ARG H 278 " (cutoff:3.500A) removed outlier: 3.852A 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: 3.547A 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 401 removed outlier: 4.205A pdb=" N ARG H 401 " --> pdb=" O ALA H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 411 removed outlier: 4.123A pdb=" N TYR H 408 " --> pdb=" O PHE H 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 436 removed outlier: 4.071A pdb=" N PHE H 418 " --> pdb=" O ASP H 414 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'E' and resid 92 through 94 removed outlier: 8.019A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 6.467A 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: 6.140A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N GLU E 3 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY E 134 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N SER E 140 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER E 165 " --> pdb=" O GLN E 133 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=C, first strand: chain 'E' and resid 269 through 273 removed outlier: 6.818A pdb=" N ALA E 374 " --> pdb=" O TYR E 319 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N TYR E 319 " --> pdb=" O ALA E 374 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N CYS E 376 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU E 317 " --> pdb=" O CYS E 376 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU E 378 " --> pdb=" O CYS E 315 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N CYS E 315 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASN E 380 " --> pdb=" O MET E 313 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'F' and resid 92 through 94 removed outlier: 7.910A pdb=" N VAL F 93 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU F 67 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N ILE F 66 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N HIS F 6 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL F 68 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLN F 8 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLU F 3 " --> pdb=" O LEU F 132 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY F 134 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N SER F 140 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N GLN F 133 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ASN F 167 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N PHE F 135 " --> pdb=" O ASN F 167 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N PHE F 169 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU F 137 " --> pdb=" O PHE F 169 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL F 171 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N HIS F 139 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N MET F 166 " --> pdb=" O GLU F 200 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N TYR F 202 " --> pdb=" O MET F 166 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR F 168 " --> pdb=" O TYR F 202 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ILE F 204 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER F 170 " --> pdb=" O ILE F 204 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR F 201 " --> pdb=" O PHE F 268 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N CYS F 203 " --> pdb=" O PRO F 270 " (cutoff:3.500A) removed outlier: 10.377A pdb=" N PHE F 272 " --> pdb=" O CYS F 203 " (cutoff:3.500A) removed outlier: 13.172A pdb=" N ASP F 205 " --> pdb=" O PHE F 272 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N PHE F 267 " --> pdb=" O SER F 381 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N SER F 381 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N LYS F 352 " --> pdb=" O LEU F 313 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL F 315 " --> pdb=" O LYS F 352 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ALA F 354 " --> pdb=" O VAL F 315 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA F 317 " --> pdb=" O ALA F 354 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N CYS F 356 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE F 319 " --> pdb=" O CYS F 356 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU F 248 " --> pdb=" O VAL F 355 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'F' and resid 53 through 56 removed outlier: 3.892A pdb=" N LYS F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'J' and resid 92 through 94 removed outlier: 8.017A pdb=" N ILE J 93 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE J 67 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N VAL J 66 " --> pdb=" O CYS J 4 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER J 6 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N VAL J 68 " --> pdb=" O SER J 6 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N HIS J 8 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLU J 3 " --> pdb=" O LEU J 132 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY J 134 " --> pdb=" O GLU J 3 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N SER J 140 " --> pdb=" O VAL J 9 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER J 165 " --> pdb=" O GLN J 133 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'J' and resid 53 through 55 Processing sheet with id=H, first strand: chain 'J' and resid 269 through 273 removed outlier: 6.816A pdb=" N ALA J 374 " --> pdb=" O TYR J 319 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TYR J 319 " --> pdb=" O ALA J 374 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N CYS J 376 " --> pdb=" O LEU J 317 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU J 317 " --> pdb=" O CYS J 376 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU J 378 " --> pdb=" O CYS J 315 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N CYS J 315 " --> pdb=" O LEU J 378 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASN J 380 " --> pdb=" O MET J 313 " (cutoff:3.500A) Processing sheet with id=I, first strand: chain 'G' and resid 92 through 94 removed outlier: 7.909A pdb=" N VAL G 93 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU G 67 " --> pdb=" O VAL G 93 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N ILE G 66 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N HIS G 6 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N VAL G 68 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN G 8 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLU G 3 " --> pdb=" O LEU G 132 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY G 134 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N SER G 140 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N GLN G 133 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ASN G 167 " --> pdb=" O GLN G 133 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N PHE G 135 " --> pdb=" O ASN G 167 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N PHE G 169 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU G 137 " --> pdb=" O PHE G 169 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N VAL G 171 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N HIS G 139 " --> pdb=" O VAL G 171 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N MET G 166 " --> pdb=" O GLU G 200 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N TYR G 202 " --> pdb=" O MET G 166 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N THR G 168 " --> pdb=" O TYR G 202 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ILE G 204 " --> pdb=" O THR G 168 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N SER G 170 " --> pdb=" O ILE G 204 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR G 201 " --> pdb=" O PHE G 268 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N CYS G 203 " --> pdb=" O PRO G 270 " (cutoff:3.500A) removed outlier: 10.379A pdb=" N PHE G 272 " --> pdb=" O CYS G 203 " (cutoff:3.500A) removed outlier: 13.172A pdb=" N ASP G 205 " --> pdb=" O PHE G 272 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N PHE G 267 " --> pdb=" O SER G 381 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N SER G 381 " --> pdb=" O PHE G 267 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N LYS G 352 " --> pdb=" O LEU G 313 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL G 315 " --> pdb=" O LYS G 352 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ALA G 354 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA G 317 " --> pdb=" O ALA G 354 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N CYS G 356 " --> pdb=" O ALA G 317 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N PHE G 319 " --> pdb=" O CYS G 356 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU G 248 " --> pdb=" O VAL G 355 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'G' and resid 53 through 56 removed outlier: 3.893A pdb=" N LYS G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'C' and resid 92 through 94 removed outlier: 8.021A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.467A 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: 6.138A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N GLU C 3 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY C 134 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N SER C 140 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER C 165 " --> pdb=" O GLN C 133 " (cutoff:3.500A) Processing sheet with id=L, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=M, first strand: chain 'C' and resid 269 through 273 removed outlier: 6.817A pdb=" N ALA C 374 " --> pdb=" O TYR C 319 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TYR C 319 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N CYS C 376 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU C 317 " --> pdb=" O CYS C 376 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU C 378 " --> pdb=" O CYS C 315 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N CYS C 315 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN C 380 " --> pdb=" O MET C 313 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain 'D' and resid 92 through 94 removed outlier: 7.909A pdb=" N VAL D 93 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU D 67 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N ILE D 66 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N HIS D 6 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL D 68 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLN D 8 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLU D 3 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY D 134 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N SER D 140 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N GLN D 133 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ASN D 167 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N PHE D 135 " --> pdb=" O ASN D 167 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N PHE D 169 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU D 137 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL D 171 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N HIS D 139 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N MET D 166 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N TYR D 202 " --> pdb=" O MET D 166 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR D 168 " --> pdb=" O TYR D 202 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE D 204 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N SER D 170 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR D 201 " --> pdb=" O PHE D 268 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N CYS D 203 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 10.377A pdb=" N PHE D 272 " --> pdb=" O CYS D 203 " (cutoff:3.500A) removed outlier: 13.173A pdb=" N ASP D 205 " --> pdb=" O PHE D 272 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N PHE D 267 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N SER D 381 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N LYS D 352 " --> pdb=" O LEU D 313 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL D 315 " --> pdb=" O LYS D 352 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ALA D 354 " --> pdb=" O VAL D 315 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA D 317 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N CYS D 356 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE D 319 " --> pdb=" O CYS D 356 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU D 248 " --> pdb=" O VAL D 355 " (cutoff:3.500A) Processing sheet with id=O, first strand: chain 'D' and resid 53 through 56 removed outlier: 3.892A pdb=" N LYS D 60 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing sheet with id=P, first strand: chain 'L' and resid 92 through 94 removed outlier: 8.020A pdb=" N ILE L 93 " --> pdb=" O ALA L 65 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N PHE L 67 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N VAL L 66 " --> pdb=" O CYS L 4 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER L 6 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL L 68 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N HIS L 8 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLU L 3 " --> pdb=" O LEU L 132 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY L 134 " --> pdb=" O GLU L 3 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N SER L 140 " --> pdb=" O VAL L 9 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER L 165 " --> pdb=" O GLN L 133 " (cutoff:3.500A) Processing sheet with id=Q, first strand: chain 'L' and resid 53 through 55 Processing sheet with id=R, first strand: chain 'L' and resid 269 through 273 removed outlier: 6.816A pdb=" N ALA L 374 " --> pdb=" O TYR L 319 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TYR L 319 " --> pdb=" O ALA L 374 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N CYS L 376 " --> pdb=" O LEU L 317 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU L 317 " --> pdb=" O CYS L 376 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU L 378 " --> pdb=" O CYS L 315 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N CYS L 315 " --> pdb=" O LEU L 378 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN L 380 " --> pdb=" O MET L 313 " (cutoff:3.500A) Processing sheet with id=S, first strand: chain 'I' and resid 92 through 94 removed outlier: 7.909A pdb=" N VAL I 93 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU I 67 " --> pdb=" O VAL I 93 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N ILE I 66 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N HIS I 6 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N VAL I 68 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLN I 8 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N GLU I 3 " --> pdb=" O LEU I 132 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY I 134 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N SER I 140 " --> pdb=" O ALA I 9 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N GLN I 133 " --> pdb=" O ILE I 165 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N ASN I 167 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N PHE I 135 " --> pdb=" O ASN I 167 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N PHE I 169 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU I 137 " --> pdb=" O PHE I 169 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL I 171 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N HIS I 139 " --> pdb=" O VAL I 171 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N MET I 166 " --> pdb=" O GLU I 200 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N TYR I 202 " --> pdb=" O MET I 166 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR I 168 " --> pdb=" O TYR I 202 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE I 204 " --> pdb=" O THR I 168 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER I 170 " --> pdb=" O ILE I 204 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR I 201 " --> pdb=" O PHE I 268 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N CYS I 203 " --> pdb=" O PRO I 270 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N PHE I 272 " --> pdb=" O CYS I 203 " (cutoff:3.500A) removed outlier: 13.172A pdb=" N ASP I 205 " --> pdb=" O PHE I 272 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N PHE I 267 " --> pdb=" O SER I 381 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N SER I 381 " --> pdb=" O PHE I 267 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N LYS I 352 " --> pdb=" O LEU I 313 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL I 315 " --> pdb=" O LYS I 352 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ALA I 354 " --> pdb=" O VAL I 315 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA I 317 " --> pdb=" O ALA I 354 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N CYS I 356 " --> pdb=" O ALA I 317 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N PHE I 319 " --> pdb=" O CYS I 356 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU I 248 " --> pdb=" O VAL I 355 " (cutoff:3.500A) Processing sheet with id=T, first strand: chain 'I' and resid 53 through 56 removed outlier: 3.891A pdb=" N LYS I 60 " --> pdb=" O ALA I 56 " (cutoff:3.500A) Processing sheet with id=U, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.020A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLU A 3 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY A 134 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER A 165 " --> pdb=" O GLN A 133 " (cutoff:3.500A) Processing sheet with id=V, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=W, first strand: chain 'A' and resid 269 through 273 removed outlier: 6.817A pdb=" N ALA A 374 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N TYR A 319 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N CYS A 376 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N CYS A 315 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) Processing sheet with id=X, first strand: chain 'B' and resid 92 through 94 removed outlier: 7.910A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N GLU B 3 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY B 134 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N SER B 140 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLN B 133 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ASN B 167 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N PHE B 135 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N PHE B 169 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU B 137 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL B 171 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N HIS B 139 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N MET B 166 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N TYR B 202 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR B 168 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE B 204 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER B 170 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR B 201 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N CYS B 203 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 10.378A pdb=" N PHE B 272 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 13.172A pdb=" N ASP B 205 " --> pdb=" O PHE B 272 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N LYS B 352 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL B 315 " --> pdb=" O LYS B 352 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ALA B 354 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA B 317 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N CYS B 356 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N PHE B 319 " --> pdb=" O CYS B 356 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 248 " --> pdb=" O VAL B 355 " (cutoff:3.500A) Processing sheet with id=Y, first strand: chain 'B' and resid 53 through 56 removed outlier: 3.893A pdb=" N LYS B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) Processing sheet with id=Z, first strand: chain 'K' and resid 92 through 94 removed outlier: 8.018A pdb=" N ILE K 93 " --> pdb=" O ALA K 65 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHE K 67 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N VAL K 66 " --> pdb=" O CYS K 4 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N VAL K 68 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N HIS K 8 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N GLU K 3 " --> pdb=" O LEU K 132 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY K 134 " --> pdb=" O GLU K 3 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N SER K 140 " --> pdb=" O VAL K 9 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER K 165 " --> pdb=" O GLN K 133 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'K' and resid 53 through 55 Processing sheet with id=AB, first strand: chain 'K' and resid 269 through 273 removed outlier: 6.816A pdb=" N ALA K 374 " --> pdb=" O TYR K 319 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TYR K 319 " --> pdb=" O ALA K 374 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N CYS K 376 " --> pdb=" O LEU K 317 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU K 317 " --> pdb=" O CYS K 376 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU K 378 " --> pdb=" O CYS K 315 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N CYS K 315 " --> pdb=" O LEU K 378 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASN K 380 " --> pdb=" O MET K 313 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain 'H' and resid 92 through 94 removed outlier: 7.910A pdb=" N VAL H 93 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU H 67 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N ILE H 66 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N HIS H 6 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL H 68 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLN H 8 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N GLU H 3 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY H 134 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N SER H 140 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N GLN H 133 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ASN H 167 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N PHE H 135 " --> pdb=" O ASN H 167 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N PHE H 169 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU H 137 " --> pdb=" O PHE H 169 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL H 171 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N HIS H 139 " --> pdb=" O VAL H 171 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N MET H 166 " --> pdb=" O GLU H 200 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N TYR H 202 " --> pdb=" O MET H 166 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR H 168 " --> pdb=" O TYR H 202 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ILE H 204 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER H 170 " --> pdb=" O ILE H 204 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR H 201 " --> pdb=" O PHE H 268 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N CYS H 203 " --> pdb=" O PRO H 270 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N PHE H 272 " --> pdb=" O CYS H 203 " (cutoff:3.500A) removed outlier: 13.170A pdb=" N ASP H 205 " --> pdb=" O PHE H 272 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N PHE H 267 " --> pdb=" O SER H 381 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N SER H 381 " --> pdb=" O PHE H 267 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER H 374 " --> pdb=" O PHE H 319 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N PHE H 319 " --> pdb=" O SER H 374 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR H 376 " --> pdb=" O ALA H 317 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ALA H 317 " --> pdb=" O THR H 376 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE H 378 " --> pdb=" O VAL H 315 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL H 315 " --> pdb=" O ILE H 378 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASN H 380 " --> pdb=" O LEU H 313 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N LYS H 352 " --> pdb=" O LEU H 313 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL H 315 " --> pdb=" O LYS H 352 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ALA H 354 " --> pdb=" O VAL H 315 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA H 317 " --> pdb=" O ALA H 354 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N CYS H 356 " --> pdb=" O ALA H 317 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N PHE H 319 " --> pdb=" O CYS H 356 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU H 248 " --> pdb=" O VAL H 355 " (cutoff:3.500A) Processing sheet with id=AD, first strand: chain 'H' and resid 53 through 56 removed outlier: 3.892A pdb=" N LYS H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) 2075 hydrogen bonds defined for protein. 5973 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: 12.55 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7613 1.33 - 1.45: 10709 1.45 - 1.57: 22598 1.57 - 1.70: 60 1.70 - 1.82: 444 Bond restraints: 41424 Sorted by residual: bond pdb=" O3B G2P B 501 " pdb=" PG G2P B 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 D 501 " pdb=" PG G2P D 501 " ideal model delta sigma weight residual 1.716 1.610 0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" O3B G2P H 501 " pdb=" PG G2P H 501 " ideal model delta sigma weight residual 1.716 1.610 0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" O3B G2P I 501 " pdb=" PG G2P I 501 " ideal model delta sigma weight residual 1.716 1.611 0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" O3B G2P F 501 " pdb=" PG G2P F 501 " ideal model delta sigma weight residual 1.716 1.611 0.105 2.00e-02 2.50e+03 2.75e+01 ... (remaining 41419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 53775 3.13 - 6.26: 2286 6.26 - 9.39: 187 9.39 - 12.52: 38 12.52 - 15.65: 6 Bond angle restraints: 56292 Sorted by residual: angle pdb=" N HIS E 197 " pdb=" CA HIS E 197 " pdb=" C HIS E 197 " ideal model delta sigma weight residual 111.02 119.44 -8.42 1.52e+00 4.33e-01 3.07e+01 angle pdb=" N HIS A 197 " pdb=" CA HIS A 197 " pdb=" C HIS A 197 " ideal model delta sigma weight residual 111.02 119.40 -8.38 1.52e+00 4.33e-01 3.04e+01 angle pdb=" N HIS C 197 " pdb=" CA HIS C 197 " pdb=" C HIS C 197 " ideal model delta sigma weight residual 111.02 119.36 -8.34 1.52e+00 4.33e-01 3.01e+01 angle pdb=" N HIS J 197 " pdb=" CA HIS J 197 " pdb=" C HIS J 197 " ideal model delta sigma weight residual 111.02 119.36 -8.34 1.52e+00 4.33e-01 3.01e+01 angle pdb=" N HIS L 197 " pdb=" CA HIS L 197 " pdb=" C HIS L 197 " ideal model delta sigma weight residual 111.02 119.34 -8.32 1.52e+00 4.33e-01 3.00e+01 ... (remaining 56287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.66: 23941 33.66 - 67.31: 684 67.31 - 100.97: 77 100.97 - 134.63: 0 134.63 - 168.29: 18 Dihedral angle restraints: 24720 sinusoidal: 9918 harmonic: 14802 Sorted by residual: dihedral pdb=" C5' GTP K 501 " pdb=" O5' GTP K 501 " pdb=" PA GTP K 501 " pdb=" O3A GTP K 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.45 -168.29 1 2.00e+01 2.50e-03 4.75e+01 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 -122.53 -168.20 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' GTP C 501 " pdb=" O5' GTP C 501 " pdb=" PA GTP C 501 " pdb=" O3A GTP C 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.56 -168.17 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 24717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 4545 0.087 - 0.174: 1206 0.174 - 0.262: 344 0.262 - 0.349: 53 0.349 - 0.436: 8 Chirality restraints: 6156 Sorted by residual: chirality pdb=" C3' G2P F 501 " pdb=" C2' G2P F 501 " pdb=" C4' G2P F 501 " pdb=" O3' G2P F 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.27 -0.44 2.00e-01 2.50e+01 4.75e+00 chirality pdb=" C3' G2P G 501 " pdb=" C2' G2P G 501 " pdb=" C4' G2P G 501 " pdb=" O3' G2P G 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.28 -0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" CA HIS C 197 " pdb=" N HIS C 197 " pdb=" C HIS C 197 " pdb=" CB HIS C 197 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.93e+00 ... (remaining 6153 not shown) Planarity restraints: 7320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 288 " 0.049 5.00e-02 4.00e+02 7.46e-02 8.91e+00 pdb=" N PRO B 289 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 289 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 289 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 288 " 0.049 5.00e-02 4.00e+02 7.44e-02 8.86e+00 pdb=" N PRO D 289 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO D 289 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 289 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 288 " 0.049 5.00e-02 4.00e+02 7.42e-02 8.80e+00 pdb=" N PRO F 289 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO F 289 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 289 " 0.041 5.00e-02 4.00e+02 ... (remaining 7317 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.46: 43 2.46 - 3.07: 25821 3.07 - 3.68: 62921 3.68 - 4.29: 90358 4.29 - 4.90: 157567 Nonbonded interactions: 336710 Sorted by model distance: nonbonded pdb=" O1B GTP J 501 " pdb="MG MG J 502 " model vdw 1.855 2.170 nonbonded pdb=" O1B GTP K 501 " pdb="MG MG K 502 " model vdw 1.862 2.170 nonbonded pdb=" O1B GTP E 501 " pdb="MG MG E 502 " model vdw 1.867 2.170 nonbonded pdb=" O1B GTP L 501 " pdb="MG MG L 502 " model vdw 1.883 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 1.898 2.170 ... (remaining 336705 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 37.510 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 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 0.106 41424 Z= 0.642 Angle : 1.538 15.647 56292 Z= 1.046 Chirality : 0.089 0.436 6156 Planarity : 0.007 0.075 7320 Dihedral : 16.373 168.286 15228 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.07 % Favored : 96.82 % Rotamer: Outliers : 0.55 % Allowed : 7.13 % Favored : 92.31 % Cbeta Deviations : 0.25 % 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 aren not related in a simple way. whole: 0.14 (0.11), residues: 5088 helix: 1.05 (0.09), residues: 2304 sheet: 0.34 (0.19), residues: 822 loop : -1.13 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG F 2 TYR 0.022 0.003 TYR G 224 PHE 0.022 0.003 PHE B 377 TRP 0.019 0.003 TRP C 21 HIS 0.014 0.002 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00928 (41424) covalent geometry : angle 1.53814 (56292) hydrogen bonds : bond 0.19794 ( 2075) hydrogen bonds : angle 7.19498 ( 5973) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 875 time to evaluate : 1.160 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: E 172 TYR cc_start: 0.7591 (t80) cc_final: 0.7022 (t80) REVERT: E 398 MET cc_start: 0.7845 (tpp) cc_final: 0.7423 (mtp) REVERT: J 178 SER cc_start: 0.7599 (OUTLIER) cc_final: 0.7325 (p) REVERT: J 210 TYR cc_start: 0.7514 (m-80) cc_final: 0.6961 (m-80) REVERT: J 357 TYR cc_start: 0.7090 (m-80) cc_final: 0.6831 (m-10) REVERT: G 114 LEU cc_start: 0.8989 (tp) cc_final: 0.8723 (tp) REVERT: G 166 MET cc_start: 0.7309 (tpp) cc_final: 0.7006 (tpp) REVERT: G 183 GLU cc_start: 0.7963 (tt0) cc_final: 0.7431 (tt0) REVERT: G 302 MET cc_start: 0.7186 (mtt) cc_final: 0.6948 (mtt) REVERT: G 325 MET cc_start: 0.7264 (mmm) cc_final: 0.6844 (mmm) REVERT: G 398 MET cc_start: 0.8296 (mmt) cc_final: 0.8046 (mmp) REVERT: C 259 LEU cc_start: 0.8923 (tp) cc_final: 0.8684 (tt) REVERT: C 388 TRP cc_start: 0.8039 (m-10) cc_final: 0.7823 (m-10) REVERT: D 301 MET cc_start: 0.7872 (mmm) cc_final: 0.7627 (mmp) REVERT: D 325 MET cc_start: 0.7678 (mmm) cc_final: 0.7362 (mmm) REVERT: L 210 TYR cc_start: 0.7484 (m-80) cc_final: 0.7131 (m-80) REVERT: L 388 TRP cc_start: 0.8011 (m-10) cc_final: 0.7636 (m-10) REVERT: I 325 MET cc_start: 0.7158 (mmm) cc_final: 0.6915 (mmm) REVERT: A 172 TYR cc_start: 0.7530 (t80) cc_final: 0.6925 (t80) REVERT: A 205 ASP cc_start: 0.7033 (t0) cc_final: 0.6819 (t0) REVERT: B 325 MET cc_start: 0.7987 (mmm) cc_final: 0.7465 (mmm) REVERT: B 435 TYR cc_start: 0.8062 (m-80) cc_final: 0.7489 (m-10) REVERT: K 172 TYR cc_start: 0.7745 (t80) cc_final: 0.7543 (t80) REVERT: K 178 SER cc_start: 0.7677 (OUTLIER) cc_final: 0.7437 (p) REVERT: K 205 ASP cc_start: 0.7243 (t0) cc_final: 0.6945 (t0) REVERT: K 424 ASP cc_start: 0.7875 (t70) cc_final: 0.7477 (t0) REVERT: H 94 PHE cc_start: 0.8115 (p90) cc_final: 0.7725 (p90) REVERT: H 114 LEU cc_start: 0.8904 (tp) cc_final: 0.8495 (tp) REVERT: H 398 MET cc_start: 0.8303 (mmt) cc_final: 0.8051 (mmp) outliers start: 24 outliers final: 6 residues processed: 899 average time/residue: 0.2336 time to fit residues: 337.1390 Evaluate side-chains 468 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 460 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain K residue 178 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 432 optimal weight: 0.4980 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 0.0980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 10.0000 chunk 494 optimal weight: 0.6980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 197 HIS E 226 ASN E 228 ASN E 300 ASN E 329 ASN E 380 ASN F 101 ASN F 394 GLN F 406 HIS J 226 ASN J 228 ASN J 300 ASN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 136 GLN C 197 HIS C 226 ASN C 228 ASN C 256 GLN C 300 ASN C 329 ASN C 380 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN D 406 HIS L 226 ASN L 228 ASN L 300 ASN L 380 ASN I 136 GLN I 309 HIS A 226 ASN A 228 ASN A 256 GLN A 300 ASN A 329 ASN A 380 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN B 101 ASN B 337 ASN B 394 GLN B 406 HIS K 197 HIS K 226 ASN K 228 ASN K 300 ASN K 380 ASN H 136 GLN H 309 HIS Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.087032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.073848 restraints weight = 87785.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.076710 restraints weight = 41013.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.078684 restraints weight = 24173.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.080027 restraints weight = 16309.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.080992 restraints weight = 12135.317| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 41424 Z= 0.147 Angle : 0.626 8.062 56292 Z= 0.332 Chirality : 0.045 0.213 6156 Planarity : 0.005 0.064 7320 Dihedral : 11.994 169.152 5846 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.03 % Allowed : 12.86 % Favored : 85.11 % 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 aren not related in a simple way. whole: 1.26 (0.12), residues: 5088 helix: 2.20 (0.10), residues: 2382 sheet: 0.52 (0.18), residues: 786 loop : -0.79 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 284 TYR 0.037 0.002 TYR E 24 PHE 0.020 0.002 PHE C 255 TRP 0.025 0.002 TRP E 346 HIS 0.012 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00296 (41424) covalent geometry : angle 0.62562 (56292) hydrogen bonds : bond 0.05823 ( 2075) hydrogen bonds : angle 5.02607 ( 5973) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 537 time to evaluate : 1.728 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: E 71 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7750 (mt-10) REVERT: E 172 TYR cc_start: 0.8112 (t80) cc_final: 0.7634 (t80) REVERT: E 203 MET cc_start: 0.7647 (mtm) cc_final: 0.7229 (mtm) REVERT: E 205 ASP cc_start: 0.7926 (t0) cc_final: 0.7591 (t0) REVERT: E 230 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8722 (tt) REVERT: E 398 MET cc_start: 0.8919 (tpp) cc_final: 0.8339 (mmt) REVERT: J 27 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8211 (mt-10) REVERT: J 178 SER cc_start: 0.8373 (OUTLIER) cc_final: 0.8070 (p) REVERT: J 207 GLU cc_start: 0.7883 (tt0) cc_final: 0.7627 (tt0) REVERT: J 210 TYR cc_start: 0.8602 (m-80) cc_final: 0.7624 (m-80) REVERT: J 271 THR cc_start: 0.8852 (t) cc_final: 0.8106 (m) REVERT: J 413 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.7202 (tpp) REVERT: G 302 MET cc_start: 0.7473 (mtt) cc_final: 0.7191 (mtt) REVERT: G 398 MET cc_start: 0.8584 (mmt) cc_final: 0.8252 (mmm) REVERT: C 313 MET cc_start: 0.8540 (mtm) cc_final: 0.8186 (mtm) REVERT: D 248 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7500 (tt) REVERT: D 301 MET cc_start: 0.8403 (mmm) cc_final: 0.8097 (mmp) REVERT: D 425 MET cc_start: 0.8676 (tpp) cc_final: 0.8272 (tpp) REVERT: L 36 MET cc_start: 0.7867 (tmm) cc_final: 0.7604 (tmm) REVERT: L 120 ASP cc_start: 0.8725 (OUTLIER) cc_final: 0.8367 (t0) REVERT: L 388 TRP cc_start: 0.8368 (m-10) cc_final: 0.7893 (m-10) REVERT: I 26 ASP cc_start: 0.7374 (m-30) cc_final: 0.7011 (m-30) REVERT: I 37 HIS cc_start: 0.7945 (OUTLIER) cc_final: 0.7742 (m-70) REVERT: I 248 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7550 (tt) REVERT: I 325 MET cc_start: 0.8113 (mmm) cc_final: 0.7609 (mmm) REVERT: A 86 LEU cc_start: 0.9402 (tp) cc_final: 0.9173 (tp) REVERT: A 230 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8771 (tt) REVERT: A 276 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8585 (mm) REVERT: A 377 MET cc_start: 0.7850 (tmm) cc_final: 0.7570 (tmm) REVERT: K 109 THR cc_start: 0.8391 (m) cc_final: 0.8022 (p) REVERT: K 178 SER cc_start: 0.8441 (OUTLIER) cc_final: 0.8047 (p) REVERT: K 192 HIS cc_start: 0.7996 (t70) cc_final: 0.7775 (t70) REVERT: K 205 ASP cc_start: 0.8000 (t0) cc_final: 0.7599 (t0) REVERT: K 285 GLN cc_start: 0.7463 (tt0) cc_final: 0.6898 (pt0) REVERT: K 339 ARG cc_start: 0.7342 (mmp-170) cc_final: 0.6988 (mmp-170) REVERT: K 377 MET cc_start: 0.7764 (tmm) cc_final: 0.7504 (tmm) REVERT: H 94 PHE cc_start: 0.8694 (p90) cc_final: 0.7920 (p90) REVERT: H 120 ASP cc_start: 0.8550 (m-30) cc_final: 0.8122 (m-30) REVERT: H 200 GLU cc_start: 0.7908 (pt0) cc_final: 0.7071 (pm20) REVERT: H 325 MET cc_start: 0.7950 (mmm) cc_final: 0.7562 (mmm) REVERT: H 398 MET cc_start: 0.8408 (mmt) cc_final: 0.7872 (mmp) outliers start: 88 outliers final: 37 residues processed: 600 average time/residue: 0.2445 time to fit residues: 247.0492 Evaluate side-chains 457 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 409 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 329 ASP Chi-restraints excluded: chain F residue 434 GLN Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 413 MET Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 434 GLN Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain I residue 37 HIS Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain H residue 248 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 364 optimal weight: 0.5980 chunk 306 optimal weight: 0.8980 chunk 232 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 422 optimal weight: 6.9990 chunk 370 optimal weight: 9.9990 chunk 170 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 441 optimal weight: 0.5980 chunk 171 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 380 ASN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 309 HIS I 406 HIS A 18 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 406 HIS ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 350 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.086671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.073547 restraints weight = 87627.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.076362 restraints weight = 40965.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.078302 restraints weight = 24179.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.079665 restraints weight = 16378.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.080619 restraints weight = 12111.549| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 41424 Z= 0.124 Angle : 0.561 9.713 56292 Z= 0.290 Chirality : 0.043 0.227 6156 Planarity : 0.004 0.051 7320 Dihedral : 11.519 170.690 5842 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.17 % Allowed : 14.61 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.12), residues: 5088 helix: 2.26 (0.11), residues: 2364 sheet: 0.59 (0.18), residues: 744 loop : -0.67 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 284 TYR 0.028 0.001 TYR D 435 PHE 0.026 0.001 PHE A 255 TRP 0.027 0.002 TRP L 346 HIS 0.010 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00261 (41424) covalent geometry : angle 0.56140 (56292) hydrogen bonds : bond 0.04757 ( 2075) hydrogen bonds : angle 4.64417 ( 5973) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 473 time to evaluate : 1.447 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: E 71 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7532 (mt-10) REVERT: E 154 MET cc_start: 0.9134 (tpp) cc_final: 0.8879 (mmt) REVERT: E 172 TYR cc_start: 0.8078 (t80) cc_final: 0.7576 (t80) REVERT: E 203 MET cc_start: 0.7605 (mtm) cc_final: 0.7093 (mtm) REVERT: E 205 ASP cc_start: 0.7850 (t0) cc_final: 0.7567 (t0) REVERT: E 313 MET cc_start: 0.8419 (mtm) cc_final: 0.8201 (mtm) REVERT: E 398 MET cc_start: 0.8993 (tpp) cc_final: 0.8710 (mmt) REVERT: F 200 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7651 (pt0) REVERT: F 323 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7470 (mtp) REVERT: J 101 ASN cc_start: 0.8862 (t0) cc_final: 0.8034 (t0) REVERT: J 178 SER cc_start: 0.8307 (OUTLIER) cc_final: 0.7978 (p) REVERT: J 192 HIS cc_start: 0.7782 (t-90) cc_final: 0.7364 (m-70) REVERT: J 207 GLU cc_start: 0.7866 (tt0) cc_final: 0.7604 (tt0) REVERT: J 210 TYR cc_start: 0.8540 (m-80) cc_final: 0.7597 (m-80) REVERT: J 271 THR cc_start: 0.8981 (t) cc_final: 0.8387 (m) REVERT: G 302 MET cc_start: 0.7660 (mtt) cc_final: 0.7430 (mtt) REVERT: G 325 MET cc_start: 0.7975 (mmm) cc_final: 0.7696 (mmm) REVERT: G 416 MET cc_start: 0.8471 (tpp) cc_final: 0.8052 (tpp) REVERT: C 36 MET cc_start: 0.7534 (tmm) cc_final: 0.7310 (tmm) REVERT: C 203 MET cc_start: 0.7490 (mmm) cc_final: 0.6864 (mmm) REVERT: C 205 ASP cc_start: 0.7727 (t0) cc_final: 0.7392 (t0) REVERT: C 313 MET cc_start: 0.8611 (mtm) cc_final: 0.8277 (mtm) REVERT: D 75 MET cc_start: 0.8767 (mmm) cc_final: 0.8116 (mmm) REVERT: D 248 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7667 (tt) REVERT: D 425 MET cc_start: 0.8648 (tpp) cc_final: 0.8207 (tpp) REVERT: L 36 MET cc_start: 0.7922 (tmm) cc_final: 0.7628 (tmm) REVERT: L 155 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8155 (tm-30) REVERT: L 243 ARG cc_start: 0.8048 (mtm110) cc_final: 0.7264 (mtm-85) REVERT: L 388 TRP cc_start: 0.8371 (m-10) cc_final: 0.7900 (m-10) REVERT: I 26 ASP cc_start: 0.7367 (m-30) cc_final: 0.6993 (m-30) REVERT: I 37 HIS cc_start: 0.7968 (OUTLIER) cc_final: 0.7751 (m-70) REVERT: I 248 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7668 (tt) REVERT: A 36 MET cc_start: 0.7135 (tmm) cc_final: 0.6591 (tmm) REVERT: A 172 TYR cc_start: 0.8092 (t80) cc_final: 0.7875 (t80) REVERT: A 377 MET cc_start: 0.7835 (tmm) cc_final: 0.7433 (tmm) REVERT: B 323 MET cc_start: 0.8174 (mtm) cc_final: 0.7958 (mtm) REVERT: K 75 ILE cc_start: 0.8918 (mm) cc_final: 0.8647 (mm) REVERT: K 109 THR cc_start: 0.8468 (m) cc_final: 0.8105 (p) REVERT: K 172 TYR cc_start: 0.8422 (t80) cc_final: 0.8189 (t80) REVERT: K 178 SER cc_start: 0.8506 (OUTLIER) cc_final: 0.8097 (p) REVERT: K 205 ASP cc_start: 0.8064 (t0) cc_final: 0.7720 (t0) REVERT: K 259 LEU cc_start: 0.8901 (tp) cc_final: 0.8643 (tp) REVERT: K 339 ARG cc_start: 0.7141 (mmp-170) cc_final: 0.6914 (mmp-170) REVERT: K 377 MET cc_start: 0.7875 (tmm) cc_final: 0.7671 (tmm) REVERT: H 94 PHE cc_start: 0.8669 (p90) cc_final: 0.7912 (p90) REVERT: H 120 ASP cc_start: 0.8410 (m-30) cc_final: 0.8064 (m-30) REVERT: H 200 GLU cc_start: 0.7922 (pt0) cc_final: 0.7061 (pm20) REVERT: H 325 MET cc_start: 0.8017 (mmm) cc_final: 0.7233 (mmm) REVERT: H 398 MET cc_start: 0.8496 (mmt) cc_final: 0.8028 (mmp) outliers start: 94 outliers final: 36 residues processed: 540 average time/residue: 0.2423 time to fit residues: 221.7616 Evaluate side-chains 434 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 391 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 322 ASP Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 194 THR Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain I residue 37 HIS Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 235 MET Chi-restraints excluded: chain H residue 248 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 285 optimal weight: 0.8980 chunk 227 optimal weight: 9.9990 chunk 382 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 200 optimal weight: 1.9990 chunk 485 optimal weight: 0.8980 chunk 392 optimal weight: 4.9990 chunk 377 optimal weight: 6.9990 chunk 181 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 237 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 101 ASN E 249 ASN E 258 ASN F 6 HIS J 101 ASN J 192 HIS J 406 HIS ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN C 249 ASN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 HIS L 101 ASN L 406 HIS I 133 GLN I 294 GLN A 101 ASN A 249 ASN B 6 HIS ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 ASN K 249 ASN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.084257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.071183 restraints weight = 88821.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.073925 restraints weight = 41967.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.075812 restraints weight = 24973.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.077123 restraints weight = 17022.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.078072 restraints weight = 12713.746| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 41424 Z= 0.173 Angle : 0.563 7.699 56292 Z= 0.293 Chirality : 0.043 0.239 6156 Planarity : 0.004 0.051 7320 Dihedral : 11.288 168.244 5840 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.70 % Allowed : 15.67 % Favored : 81.63 % 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 aren not related in a simple way. whole: 1.28 (0.12), residues: 5088 helix: 2.16 (0.11), residues: 2352 sheet: 0.55 (0.18), residues: 810 loop : -0.67 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 390 TYR 0.023 0.001 TYR D 435 PHE 0.027 0.002 PHE A 255 TRP 0.027 0.002 TRP L 346 HIS 0.009 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00385 (41424) covalent geometry : angle 0.56251 (56292) hydrogen bonds : bond 0.04806 ( 2075) hydrogen bonds : angle 4.58605 ( 5973) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 424 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 154 MET cc_start: 0.9118 (tpp) cc_final: 0.8877 (mmt) REVERT: E 172 TYR cc_start: 0.8123 (t80) cc_final: 0.7574 (t80) REVERT: E 203 MET cc_start: 0.7529 (mtm) cc_final: 0.6977 (mtm) REVERT: E 205 ASP cc_start: 0.7876 (t0) cc_final: 0.7532 (t0) REVERT: E 313 MET cc_start: 0.8449 (mtm) cc_final: 0.8169 (mtm) REVERT: E 398 MET cc_start: 0.9031 (tpp) cc_final: 0.8684 (mmt) REVERT: F 151 THR cc_start: 0.8945 (OUTLIER) cc_final: 0.8498 (p) REVERT: J 24 TYR cc_start: 0.8861 (m-80) cc_final: 0.8578 (m-80) REVERT: J 101 ASN cc_start: 0.9175 (OUTLIER) cc_final: 0.8471 (t0) REVERT: J 207 GLU cc_start: 0.7907 (tt0) cc_final: 0.7639 (tt0) REVERT: J 210 TYR cc_start: 0.8584 (m-80) cc_final: 0.7575 (m-80) REVERT: J 271 THR cc_start: 0.9007 (t) cc_final: 0.8183 (m) REVERT: J 297 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7559 (tm-30) REVERT: J 425 MET cc_start: 0.9167 (mmm) cc_final: 0.8886 (tpp) REVERT: J 433 GLU cc_start: 0.7783 (pt0) cc_final: 0.7305 (pt0) REVERT: G 302 MET cc_start: 0.7785 (mtt) cc_final: 0.7541 (mtt) REVERT: G 325 MET cc_start: 0.7976 (mmm) cc_final: 0.7755 (mmm) REVERT: G 398 MET cc_start: 0.6603 (mmp) cc_final: 0.5903 (mmm) REVERT: C 36 MET cc_start: 0.7505 (tmm) cc_final: 0.7299 (tmm) REVERT: C 205 ASP cc_start: 0.7874 (t0) cc_final: 0.7515 (t0) REVERT: C 313 MET cc_start: 0.8655 (mtm) cc_final: 0.8181 (mtm) REVERT: D 75 MET cc_start: 0.8951 (mmm) cc_final: 0.7866 (mmm) REVERT: D 248 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.7943 (tt) REVERT: D 332 MET cc_start: 0.9006 (mmm) cc_final: 0.8032 (mmm) REVERT: D 413 MET cc_start: 0.7906 (mtp) cc_final: 0.7658 (mtp) REVERT: D 425 MET cc_start: 0.8704 (tpp) cc_final: 0.8344 (tpp) REVERT: L 155 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8249 (tm-30) REVERT: L 243 ARG cc_start: 0.8241 (mtm110) cc_final: 0.7476 (mtm-85) REVERT: L 388 TRP cc_start: 0.8451 (m-10) cc_final: 0.7928 (m-10) REVERT: I 26 ASP cc_start: 0.7441 (m-30) cc_final: 0.7099 (m-30) REVERT: I 37 HIS cc_start: 0.7992 (OUTLIER) cc_final: 0.7734 (m-70) REVERT: I 248 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7931 (tt) REVERT: A 36 MET cc_start: 0.7258 (tmm) cc_final: 0.6785 (tmm) REVERT: A 101 ASN cc_start: 0.8958 (OUTLIER) cc_final: 0.8679 (t0) REVERT: A 123 ARG cc_start: 0.8466 (ttm-80) cc_final: 0.8266 (tpp80) REVERT: A 230 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8800 (tt) REVERT: A 377 MET cc_start: 0.8177 (tmm) cc_final: 0.7718 (tmm) REVERT: B 398 MET cc_start: 0.8560 (tpp) cc_final: 0.8108 (mtt) REVERT: K 109 THR cc_start: 0.8560 (m) cc_final: 0.8195 (p) REVERT: K 172 TYR cc_start: 0.8345 (t80) cc_final: 0.8012 (t80) REVERT: K 178 SER cc_start: 0.8413 (OUTLIER) cc_final: 0.7998 (p) REVERT: K 205 ASP cc_start: 0.8151 (t0) cc_final: 0.7820 (t0) REVERT: K 339 ARG cc_start: 0.7221 (mmp-170) cc_final: 0.6960 (mmp-170) REVERT: K 377 MET cc_start: 0.8036 (tmm) cc_final: 0.7774 (tmm) REVERT: H 94 PHE cc_start: 0.8680 (p90) cc_final: 0.7920 (p90) REVERT: H 120 ASP cc_start: 0.8426 (m-30) cc_final: 0.8141 (m-30) REVERT: H 200 GLU cc_start: 0.8074 (pt0) cc_final: 0.7219 (pm20) REVERT: H 325 MET cc_start: 0.8091 (mmm) cc_final: 0.7886 (mmm) REVERT: H 330 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8227 (mm-30) REVERT: H 398 MET cc_start: 0.8544 (mmt) cc_final: 0.8104 (mmp) outliers start: 117 outliers final: 59 residues processed: 512 average time/residue: 0.2352 time to fit residues: 206.1194 Evaluate side-chains 446 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 379 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 101 ASN Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 192 HIS Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 428 LEU Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 194 THR Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 290 GLU Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain I residue 37 HIS Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain I residue 376 THR Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 232 SER Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 235 MET Chi-restraints excluded: chain H residue 425 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 503 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 367 optimal weight: 3.9990 chunk 301 optimal weight: 9.9990 chunk 457 optimal weight: 0.9990 chunk 375 optimal weight: 0.0570 chunk 311 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 450 optimal weight: 6.9990 chunk 365 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 101 ASN J 101 ASN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS L 101 ASN L 128 GLN A 101 ASN ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.085320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.072141 restraints weight = 88323.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.074907 restraints weight = 41792.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.076809 restraints weight = 24878.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.078126 restraints weight = 16969.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.079083 restraints weight = 12687.998| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 41424 Z= 0.123 Angle : 0.530 9.506 56292 Z= 0.274 Chirality : 0.042 0.243 6156 Planarity : 0.004 0.045 7320 Dihedral : 11.091 166.130 5839 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.45 % Allowed : 17.13 % Favored : 80.42 % 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 aren not related in a simple way. whole: 1.28 (0.12), residues: 5088 helix: 2.11 (0.11), residues: 2364 sheet: 0.57 (0.18), residues: 798 loop : -0.61 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 308 TYR 0.017 0.001 TYR A 172 PHE 0.024 0.001 PHE K 255 TRP 0.028 0.002 TRP L 346 HIS 0.017 0.001 HIS J 192 Details of bonding type rmsd covalent geometry : bond 0.00270 (41424) covalent geometry : angle 0.53039 (56292) hydrogen bonds : bond 0.04327 ( 2075) hydrogen bonds : angle 4.45677 ( 5973) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 426 time to evaluate : 1.065 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: E 6 SER cc_start: 0.9309 (OUTLIER) cc_final: 0.9069 (p) REVERT: E 116 ASP cc_start: 0.8685 (t0) cc_final: 0.8463 (m-30) REVERT: E 154 MET cc_start: 0.9150 (tpp) cc_final: 0.8881 (mmt) REVERT: E 172 TYR cc_start: 0.8089 (t80) cc_final: 0.7580 (t80) REVERT: E 203 MET cc_start: 0.7471 (mtm) cc_final: 0.6917 (mtm) REVERT: E 205 ASP cc_start: 0.7788 (t0) cc_final: 0.7437 (t0) REVERT: E 313 MET cc_start: 0.8504 (mtm) cc_final: 0.8204 (mtm) REVERT: E 398 MET cc_start: 0.9049 (tpp) cc_final: 0.8679 (mmt) REVERT: J 24 TYR cc_start: 0.8831 (m-80) cc_final: 0.8606 (m-80) REVERT: J 101 ASN cc_start: 0.9020 (OUTLIER) cc_final: 0.8353 (t0) REVERT: J 178 SER cc_start: 0.8305 (OUTLIER) cc_final: 0.7962 (p) REVERT: J 205 ASP cc_start: 0.7415 (t70) cc_final: 0.7214 (t70) REVERT: J 207 GLU cc_start: 0.7859 (tt0) cc_final: 0.7569 (tt0) REVERT: J 210 TYR cc_start: 0.8521 (m-80) cc_final: 0.7571 (m-80) REVERT: J 271 THR cc_start: 0.8961 (t) cc_final: 0.8166 (m) REVERT: J 297 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7593 (tm-30) REVERT: J 424 ASP cc_start: 0.8593 (t70) cc_final: 0.8109 (t0) REVERT: J 425 MET cc_start: 0.9156 (mmm) cc_final: 0.8895 (tpp) REVERT: G 97 SER cc_start: 0.8971 (OUTLIER) cc_final: 0.8661 (p) REVERT: G 302 MET cc_start: 0.7821 (mtt) cc_final: 0.7529 (mtt) REVERT: G 416 MET cc_start: 0.8425 (tpp) cc_final: 0.7980 (tpp) REVERT: C 36 MET cc_start: 0.7453 (tmm) cc_final: 0.7238 (tmm) REVERT: C 205 ASP cc_start: 0.7696 (t0) cc_final: 0.7262 (t0) REVERT: C 313 MET cc_start: 0.8663 (mtm) cc_final: 0.8185 (mtm) REVERT: D 75 MET cc_start: 0.8893 (mmm) cc_final: 0.7924 (mmm) REVERT: D 248 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.7983 (tt) REVERT: D 269 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8384 (mtt) REVERT: D 425 MET cc_start: 0.8683 (tpp) cc_final: 0.8334 (tpp) REVERT: L 155 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8241 (tm-30) REVERT: L 168 GLU cc_start: 0.7900 (pt0) cc_final: 0.7426 (pt0) REVERT: L 243 ARG cc_start: 0.8171 (mtm110) cc_final: 0.7349 (mtm-85) REVERT: L 388 TRP cc_start: 0.8434 (m-10) cc_final: 0.7919 (m-10) REVERT: L 420 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8202 (mm-30) REVERT: I 26 ASP cc_start: 0.7360 (m-30) cc_final: 0.6981 (m-30) REVERT: I 37 HIS cc_start: 0.8015 (OUTLIER) cc_final: 0.7707 (m-70) REVERT: I 211 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.8140 (t0) REVERT: I 248 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7888 (tt) REVERT: A 36 MET cc_start: 0.7309 (tmm) cc_final: 0.6876 (tmm) REVERT: A 149 PHE cc_start: 0.9173 (t80) cc_final: 0.8902 (t80) REVERT: A 230 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8743 (tt) REVERT: A 377 MET cc_start: 0.8110 (tmm) cc_final: 0.7576 (tmm) REVERT: B 373 MET cc_start: 0.8186 (mtp) cc_final: 0.7928 (mtp) REVERT: B 398 MET cc_start: 0.8612 (tpp) cc_final: 0.8125 (mtt) REVERT: B 425 MET cc_start: 0.8913 (mmm) cc_final: 0.8557 (tpp) REVERT: K 109 THR cc_start: 0.8580 (m) cc_final: 0.8206 (p) REVERT: K 172 TYR cc_start: 0.8293 (t80) cc_final: 0.8063 (t80) REVERT: K 178 SER cc_start: 0.8424 (OUTLIER) cc_final: 0.7975 (p) REVERT: K 205 ASP cc_start: 0.8053 (t0) cc_final: 0.7743 (t0) REVERT: K 212 ILE cc_start: 0.9176 (mt) cc_final: 0.8958 (mt) REVERT: K 377 MET cc_start: 0.8041 (tmm) cc_final: 0.7788 (tmm) REVERT: H 94 PHE cc_start: 0.8766 (p90) cc_final: 0.8022 (p90) REVERT: H 120 ASP cc_start: 0.8436 (m-30) cc_final: 0.8147 (m-30) REVERT: H 200 GLU cc_start: 0.8118 (pt0) cc_final: 0.7272 (pm20) REVERT: H 325 MET cc_start: 0.8279 (mmm) cc_final: 0.7969 (mmm) REVERT: H 398 MET cc_start: 0.8504 (mmt) cc_final: 0.8038 (mmp) outliers start: 106 outliers final: 59 residues processed: 503 average time/residue: 0.1993 time to fit residues: 170.5160 Evaluate side-chains 456 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 386 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 101 ASN Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 428 LEU Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 194 THR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 290 GLU Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain I residue 37 HIS Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain I residue 211 ASP Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain I residue 376 THR Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 235 MET Chi-restraints excluded: chain H residue 425 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 358 optimal weight: 0.9980 chunk 165 optimal weight: 6.9990 chunk 348 optimal weight: 9.9990 chunk 307 optimal weight: 8.9990 chunk 129 optimal weight: 0.7980 chunk 354 optimal weight: 7.9990 chunk 369 optimal weight: 0.5980 chunk 139 optimal weight: 10.0000 chunk 223 optimal weight: 9.9990 chunk 490 optimal weight: 0.8980 chunk 142 optimal weight: 7.9990 overall best weight: 2.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 101 ASN J 192 HIS ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 294 GLN C 31 GLN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS L 31 GLN A 31 GLN A 101 ASN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.084296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.071182 restraints weight = 89112.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.073900 restraints weight = 42212.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.075768 restraints weight = 25188.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.077069 restraints weight = 17237.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.077992 restraints weight = 12917.676| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 41424 Z= 0.147 Angle : 0.532 9.180 56292 Z= 0.276 Chirality : 0.042 0.239 6156 Planarity : 0.004 0.043 7320 Dihedral : 10.913 162.716 5839 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.49 % Allowed : 17.38 % 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 aren not related in a simple way. whole: 1.24 (0.12), residues: 5088 helix: 2.06 (0.11), residues: 2364 sheet: 0.50 (0.18), residues: 798 loop : -0.59 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 84 TYR 0.023 0.001 TYR A 172 PHE 0.025 0.001 PHE A 255 TRP 0.029 0.002 TRP L 346 HIS 0.008 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00331 (41424) covalent geometry : angle 0.53244 (56292) hydrogen bonds : bond 0.04376 ( 2075) hydrogen bonds : angle 4.44725 ( 5973) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 411 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 6 SER cc_start: 0.9286 (OUTLIER) cc_final: 0.9027 (p) REVERT: E 116 ASP cc_start: 0.8672 (t0) cc_final: 0.8396 (m-30) REVERT: E 154 MET cc_start: 0.9145 (tpp) cc_final: 0.8873 (mmt) REVERT: E 172 TYR cc_start: 0.8103 (t80) cc_final: 0.7599 (t80) REVERT: E 203 MET cc_start: 0.7510 (mtm) cc_final: 0.6905 (mtm) REVERT: E 205 ASP cc_start: 0.7897 (t0) cc_final: 0.7611 (t0) REVERT: E 313 MET cc_start: 0.8535 (mtm) cc_final: 0.8199 (mtm) REVERT: E 398 MET cc_start: 0.9135 (tpp) cc_final: 0.8714 (mmt) REVERT: F 398 MET cc_start: 0.8543 (mmt) cc_final: 0.8066 (mtt) REVERT: J 24 TYR cc_start: 0.8865 (m-80) cc_final: 0.8598 (m-80) REVERT: J 88 HIS cc_start: 0.6140 (OUTLIER) cc_final: 0.5644 (m-70) REVERT: J 101 ASN cc_start: 0.9053 (OUTLIER) cc_final: 0.8546 (t0) REVERT: J 178 SER cc_start: 0.8304 (OUTLIER) cc_final: 0.7955 (p) REVERT: J 205 ASP cc_start: 0.7562 (t70) cc_final: 0.7345 (t70) REVERT: J 207 GLU cc_start: 0.7863 (tt0) cc_final: 0.7629 (tt0) REVERT: J 210 TYR cc_start: 0.8562 (m-80) cc_final: 0.7643 (m-80) REVERT: J 271 THR cc_start: 0.8973 (t) cc_final: 0.8162 (m) REVERT: J 297 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7677 (tm-30) REVERT: J 425 MET cc_start: 0.9138 (mmm) cc_final: 0.8868 (tpp) REVERT: G 6 HIS cc_start: 0.8486 (t70) cc_final: 0.7727 (t-170) REVERT: G 97 SER cc_start: 0.8924 (OUTLIER) cc_final: 0.8635 (p) REVERT: G 302 MET cc_start: 0.7871 (mtt) cc_final: 0.7579 (mtt) REVERT: G 398 MET cc_start: 0.6578 (mmp) cc_final: 0.5948 (mmm) REVERT: G 416 MET cc_start: 0.8404 (tpp) cc_final: 0.7932 (tpp) REVERT: C 36 MET cc_start: 0.7588 (tmm) cc_final: 0.7347 (tmm) REVERT: C 199 ASP cc_start: 0.7870 (t0) cc_final: 0.7657 (t0) REVERT: C 205 ASP cc_start: 0.7741 (t0) cc_final: 0.7351 (t0) REVERT: C 313 MET cc_start: 0.8651 (mtm) cc_final: 0.8152 (mtm) REVERT: D 69 ASP cc_start: 0.7766 (t0) cc_final: 0.7528 (t0) REVERT: D 75 MET cc_start: 0.8947 (mmm) cc_final: 0.7869 (mmm) REVERT: D 248 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7911 (tt) REVERT: D 269 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8375 (mtt) REVERT: D 290 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7446 (tt0) REVERT: D 413 MET cc_start: 0.7924 (mtp) cc_final: 0.7692 (mtp) REVERT: L 155 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8308 (tm-30) REVERT: L 168 GLU cc_start: 0.7978 (pt0) cc_final: 0.7434 (pt0) REVERT: L 243 ARG cc_start: 0.8215 (mtm110) cc_final: 0.7457 (mtm-85) REVERT: L 388 TRP cc_start: 0.8472 (m-10) cc_final: 0.7962 (m-10) REVERT: L 420 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8211 (mm-30) REVERT: L 432 TYR cc_start: 0.8548 (OUTLIER) cc_final: 0.7582 (t80) REVERT: I 26 ASP cc_start: 0.7363 (m-30) cc_final: 0.7012 (m-30) REVERT: I 37 HIS cc_start: 0.8007 (OUTLIER) cc_final: 0.7703 (m-70) REVERT: I 213 CYS cc_start: 0.8417 (t) cc_final: 0.8096 (p) REVERT: I 248 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7781 (tt) REVERT: A 36 MET cc_start: 0.7402 (tmm) cc_final: 0.6981 (tmm) REVERT: A 230 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8767 (tt) REVERT: B 323 MET cc_start: 0.8167 (mtm) cc_final: 0.7473 (mtp) REVERT: B 398 MET cc_start: 0.8692 (tpp) cc_final: 0.8148 (mtt) REVERT: K 109 THR cc_start: 0.8608 (m) cc_final: 0.8234 (p) REVERT: K 178 SER cc_start: 0.8378 (OUTLIER) cc_final: 0.7919 (p) REVERT: K 205 ASP cc_start: 0.8102 (t0) cc_final: 0.7777 (t0) REVERT: K 212 ILE cc_start: 0.9191 (mt) cc_final: 0.8957 (mt) REVERT: K 339 ARG cc_start: 0.7036 (mmp-170) cc_final: 0.6657 (mmp-170) REVERT: K 377 MET cc_start: 0.8115 (tmm) cc_final: 0.7821 (tmm) REVERT: K 432 TYR cc_start: 0.8621 (OUTLIER) cc_final: 0.7855 (m-80) REVERT: H 94 PHE cc_start: 0.8763 (p90) cc_final: 0.8004 (p90) REVERT: H 113 GLU cc_start: 0.8985 (tm-30) cc_final: 0.8531 (pp20) REVERT: H 120 ASP cc_start: 0.8412 (m-30) cc_final: 0.8129 (m-30) REVERT: H 200 GLU cc_start: 0.8147 (pt0) cc_final: 0.7304 (pm20) REVERT: H 325 MET cc_start: 0.8284 (mmm) cc_final: 0.7957 (mmm) REVERT: H 398 MET cc_start: 0.8496 (mmt) cc_final: 0.8032 (mmp) outliers start: 108 outliers final: 70 residues processed: 492 average time/residue: 0.2336 time to fit residues: 197.4898 Evaluate side-chains 471 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 387 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 101 ASN Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 428 LEU Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 194 THR Chi-restraints excluded: chain L residue 200 CYS Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 290 GLU Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain I residue 37 HIS Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain I residue 200 GLU Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain I residue 376 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 225 THR Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 432 TYR Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 235 MET Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 425 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 388 optimal weight: 6.9990 chunk 458 optimal weight: 6.9990 chunk 400 optimal weight: 5.9990 chunk 246 optimal weight: 3.9990 chunk 356 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 403 optimal weight: 3.9990 chunk 276 optimal weight: 3.9990 chunk 420 optimal weight: 10.0000 chunk 211 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 31 GLN E 50 ASN ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 31 GLN J 101 ASN J 380 ASN G 6 HIS ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 HIS A 101 ASN K 31 GLN K 192 HIS H 6 HIS H 294 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.082143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.069110 restraints weight = 90348.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.071757 restraints weight = 43082.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.073580 restraints weight = 25830.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.074860 restraints weight = 17771.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.075776 restraints weight = 13338.532| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 41424 Z= 0.219 Angle : 0.584 10.474 56292 Z= 0.303 Chirality : 0.044 0.224 6156 Planarity : 0.004 0.041 7320 Dihedral : 10.803 157.815 5839 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.86 % Allowed : 17.45 % Favored : 79.69 % 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 aren not related in a simple way. whole: 1.08 (0.12), residues: 5088 helix: 1.89 (0.11), residues: 2382 sheet: 0.59 (0.19), residues: 750 loop : -0.69 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 308 TYR 0.025 0.002 TYR A 172 PHE 0.027 0.002 PHE A 255 TRP 0.028 0.002 TRP L 346 HIS 0.009 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00496 (41424) covalent geometry : angle 0.58413 (56292) hydrogen bonds : bond 0.04882 ( 2075) hydrogen bonds : angle 4.56848 ( 5973) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 384 time to evaluate : 1.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 6 SER cc_start: 0.9285 (OUTLIER) cc_final: 0.8998 (p) REVERT: E 154 MET cc_start: 0.9244 (tpp) cc_final: 0.8983 (mmt) REVERT: E 172 TYR cc_start: 0.8139 (t80) cc_final: 0.7640 (t80) REVERT: E 203 MET cc_start: 0.7523 (mtm) cc_final: 0.6881 (mtm) REVERT: E 205 ASP cc_start: 0.7941 (t0) cc_final: 0.7654 (t0) REVERT: E 230 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8956 (tt) REVERT: E 313 MET cc_start: 0.8529 (mtm) cc_final: 0.8213 (mtm) REVERT: E 398 MET cc_start: 0.9152 (tpp) cc_final: 0.8709 (mmt) REVERT: F 398 MET cc_start: 0.8527 (mmt) cc_final: 0.8129 (mtt) REVERT: J 24 TYR cc_start: 0.8887 (m-80) cc_final: 0.8653 (m-80) REVERT: J 88 HIS cc_start: 0.6361 (OUTLIER) cc_final: 0.5896 (m-70) REVERT: J 101 ASN cc_start: 0.9169 (OUTLIER) cc_final: 0.8955 (t0) REVERT: J 169 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.6954 (m-80) REVERT: J 178 SER cc_start: 0.8305 (OUTLIER) cc_final: 0.7977 (p) REVERT: J 207 GLU cc_start: 0.7908 (tt0) cc_final: 0.7659 (tt0) REVERT: J 210 TYR cc_start: 0.8562 (m-80) cc_final: 0.7603 (m-80) REVERT: J 271 THR cc_start: 0.8970 (t) cc_final: 0.8104 (m) REVERT: J 297 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7742 (tm-30) REVERT: J 425 MET cc_start: 0.9123 (mmm) cc_final: 0.8907 (mmm) REVERT: G 6 HIS cc_start: 0.8340 (t-90) cc_final: 0.7618 (t-170) REVERT: G 302 MET cc_start: 0.7978 (mtt) cc_final: 0.7777 (mtt) REVERT: G 398 MET cc_start: 0.6768 (mmp) cc_final: 0.6247 (mmm) REVERT: G 416 MET cc_start: 0.8431 (tpp) cc_final: 0.7988 (tpp) REVERT: C 36 MET cc_start: 0.7549 (tmm) cc_final: 0.7272 (tmm) REVERT: C 203 MET cc_start: 0.7992 (mmm) cc_final: 0.7749 (mmt) REVERT: C 205 ASP cc_start: 0.7859 (t0) cc_final: 0.7413 (t0) REVERT: C 302 MET cc_start: 0.8833 (mmp) cc_final: 0.8609 (mmm) REVERT: C 313 MET cc_start: 0.8609 (mtm) cc_final: 0.8302 (mtm) REVERT: D 75 MET cc_start: 0.8972 (mmm) cc_final: 0.7845 (mmm) REVERT: D 248 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7907 (tt) REVERT: D 290 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7549 (tt0) REVERT: D 413 MET cc_start: 0.7929 (mtp) cc_final: 0.7676 (mtp) REVERT: L 155 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8370 (tm-30) REVERT: L 168 GLU cc_start: 0.7895 (pt0) cc_final: 0.7355 (pt0) REVERT: L 388 TRP cc_start: 0.8567 (m-10) cc_final: 0.7994 (m-10) REVERT: I 26 ASP cc_start: 0.7332 (m-30) cc_final: 0.6997 (m-30) REVERT: I 37 HIS cc_start: 0.8014 (OUTLIER) cc_final: 0.7706 (m-70) REVERT: I 213 CYS cc_start: 0.8478 (t) cc_final: 0.8138 (p) REVERT: I 248 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7984 (tt) REVERT: I 325 MET cc_start: 0.8166 (mmm) cc_final: 0.7903 (mmm) REVERT: A 36 MET cc_start: 0.7396 (tmm) cc_final: 0.6939 (tmm) REVERT: A 230 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8795 (tt) REVERT: A 377 MET cc_start: 0.8248 (tmm) cc_final: 0.7461 (tmm) REVERT: B 323 MET cc_start: 0.8166 (mtm) cc_final: 0.7768 (mtm) REVERT: B 373 MET cc_start: 0.7938 (mtp) cc_final: 0.7714 (mmm) REVERT: B 398 MET cc_start: 0.8697 (tpp) cc_final: 0.8169 (mtt) REVERT: K 76 ASP cc_start: 0.8771 (m-30) cc_final: 0.8460 (m-30) REVERT: K 90 GLU cc_start: 0.8000 (tt0) cc_final: 0.7522 (tt0) REVERT: K 109 THR cc_start: 0.8674 (m) cc_final: 0.8308 (p) REVERT: K 172 TYR cc_start: 0.8305 (t80) cc_final: 0.8007 (t80) REVERT: K 178 SER cc_start: 0.8398 (OUTLIER) cc_final: 0.7932 (p) REVERT: K 205 ASP cc_start: 0.8188 (t0) cc_final: 0.7781 (t70) REVERT: K 212 ILE cc_start: 0.9213 (mt) cc_final: 0.8966 (mt) REVERT: K 377 MET cc_start: 0.8180 (tmm) cc_final: 0.7871 (tmm) REVERT: K 432 TYR cc_start: 0.8648 (OUTLIER) cc_final: 0.7979 (m-80) REVERT: H 94 PHE cc_start: 0.8645 (p90) cc_final: 0.7935 (p90) REVERT: H 120 ASP cc_start: 0.8350 (m-30) cc_final: 0.8093 (m-30) REVERT: H 200 GLU cc_start: 0.8238 (pt0) cc_final: 0.7377 (pm20) REVERT: H 393 GLU cc_start: 0.8167 (pp20) cc_final: 0.7909 (pp20) REVERT: H 398 MET cc_start: 0.8526 (mmt) cc_final: 0.7981 (mmp) outliers start: 124 outliers final: 80 residues processed: 480 average time/residue: 0.2354 time to fit residues: 194.8557 Evaluate side-chains 457 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 364 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 302 MET Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 101 ASN Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 169 PHE Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 428 LEU Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 194 THR Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 290 GLU Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain I residue 37 HIS Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain I residue 376 THR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 225 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 378 LEU Chi-restraints excluded: chain K residue 432 TYR Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 235 MET Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain H residue 425 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 234 optimal weight: 0.8980 chunk 497 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 162 optimal weight: 8.9990 chunk 10 optimal weight: 0.0570 chunk 184 optimal weight: 6.9990 chunk 283 optimal weight: 0.5980 chunk 249 optimal weight: 3.9990 chunk 344 optimal weight: 6.9990 chunk 351 optimal weight: 8.9990 overall best weight: 1.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 101 ASN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 HIS A 101 ASN A 258 ASN ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 349 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.084239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.071185 restraints weight = 88645.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.073883 restraints weight = 42184.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.075741 restraints weight = 25224.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.077030 restraints weight = 17280.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.077968 restraints weight = 12986.926| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 41424 Z= 0.120 Angle : 0.533 11.335 56292 Z= 0.275 Chirality : 0.042 0.238 6156 Planarity : 0.004 0.053 7320 Dihedral : 10.516 151.834 5839 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.29 % Allowed : 18.10 % Favored : 79.62 % 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 aren not related in a simple way. whole: 1.17 (0.12), residues: 5088 helix: 1.99 (0.11), residues: 2358 sheet: 0.46 (0.19), residues: 780 loop : -0.59 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 308 TYR 0.028 0.001 TYR A 172 PHE 0.026 0.001 PHE K 255 TRP 0.025 0.002 TRP L 346 HIS 0.007 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00263 (41424) covalent geometry : angle 0.53305 (56292) hydrogen bonds : bond 0.04171 ( 2075) hydrogen bonds : angle 4.43684 ( 5973) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 415 time to evaluate : 1.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 6 SER cc_start: 0.9259 (OUTLIER) cc_final: 0.9006 (p) REVERT: E 116 ASP cc_start: 0.8685 (t0) cc_final: 0.8415 (m-30) REVERT: E 154 MET cc_start: 0.9269 (tpp) cc_final: 0.9021 (mmt) REVERT: E 172 TYR cc_start: 0.8080 (t80) cc_final: 0.7577 (t80) REVERT: E 203 MET cc_start: 0.7471 (mtm) cc_final: 0.6798 (mtm) REVERT: E 205 ASP cc_start: 0.7821 (t0) cc_final: 0.7561 (t0) REVERT: E 230 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8930 (tt) REVERT: E 313 MET cc_start: 0.8477 (mtm) cc_final: 0.8201 (mtm) REVERT: E 398 MET cc_start: 0.9138 (tpp) cc_final: 0.8687 (mmt) REVERT: F 37 HIS cc_start: 0.7783 (m-70) cc_final: 0.7460 (m170) REVERT: F 259 MET cc_start: 0.8586 (mmm) cc_final: 0.7775 (mpp) REVERT: F 398 MET cc_start: 0.8524 (mmt) cc_final: 0.8174 (mtt) REVERT: J 24 TYR cc_start: 0.8858 (m-80) cc_final: 0.8652 (m-80) REVERT: J 88 HIS cc_start: 0.6192 (OUTLIER) cc_final: 0.5755 (m-70) REVERT: J 178 SER cc_start: 0.8304 (OUTLIER) cc_final: 0.7962 (p) REVERT: J 192 HIS cc_start: 0.7794 (t-90) cc_final: 0.7582 (m-70) REVERT: J 210 TYR cc_start: 0.8476 (m-80) cc_final: 0.7506 (m-80) REVERT: J 271 THR cc_start: 0.8990 (t) cc_final: 0.8184 (m) REVERT: J 297 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7798 (tm-30) REVERT: G 6 HIS cc_start: 0.8530 (t-90) cc_final: 0.7795 (t70) REVERT: G 75 MET cc_start: 0.8976 (mmt) cc_final: 0.8625 (mmt) REVERT: G 200 GLU cc_start: 0.7766 (pt0) cc_final: 0.6603 (pm20) REVERT: G 302 MET cc_start: 0.7931 (mtt) cc_final: 0.7630 (mtt) REVERT: G 398 MET cc_start: 0.6746 (mmp) cc_final: 0.6300 (mmm) REVERT: G 416 MET cc_start: 0.8354 (tpp) cc_final: 0.7966 (tpp) REVERT: C 36 MET cc_start: 0.7560 (tmm) cc_final: 0.7284 (tmm) REVERT: C 205 ASP cc_start: 0.7711 (t0) cc_final: 0.7261 (t0) REVERT: C 313 MET cc_start: 0.8594 (mtm) cc_final: 0.8262 (mtm) REVERT: D 75 MET cc_start: 0.8954 (mmm) cc_final: 0.7937 (mmm) REVERT: D 166 MET cc_start: 0.8258 (tpp) cc_final: 0.7643 (mmm) REVERT: D 248 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8046 (tt) REVERT: D 269 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8355 (mtt) REVERT: D 290 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7469 (tt0) REVERT: D 413 MET cc_start: 0.7900 (mtp) cc_final: 0.7649 (mtp) REVERT: L 155 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8372 (tm-30) REVERT: L 168 GLU cc_start: 0.7781 (pt0) cc_final: 0.7182 (pt0) REVERT: L 243 ARG cc_start: 0.8136 (mtm110) cc_final: 0.7417 (mtm-85) REVERT: L 377 MET cc_start: 0.8285 (tmm) cc_final: 0.7738 (tmm) REVERT: L 388 TRP cc_start: 0.8506 (m-10) cc_final: 0.8004 (m-10) REVERT: L 432 TYR cc_start: 0.8400 (OUTLIER) cc_final: 0.7245 (t80) REVERT: I 26 ASP cc_start: 0.7354 (m-30) cc_final: 0.7004 (m-30) REVERT: I 37 HIS cc_start: 0.8015 (OUTLIER) cc_final: 0.7711 (m-70) REVERT: I 213 CYS cc_start: 0.8403 (t) cc_final: 0.8031 (p) REVERT: I 248 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7844 (tt) REVERT: I 325 MET cc_start: 0.8171 (mmm) cc_final: 0.7964 (mmm) REVERT: A 172 TYR cc_start: 0.8013 (OUTLIER) cc_final: 0.7613 (t80) REVERT: A 230 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8747 (tt) REVERT: A 377 MET cc_start: 0.8228 (tmm) cc_final: 0.7475 (tmm) REVERT: B 323 MET cc_start: 0.8153 (mtm) cc_final: 0.7729 (mtm) REVERT: B 398 MET cc_start: 0.8678 (tpp) cc_final: 0.8143 (mtt) REVERT: K 109 THR cc_start: 0.8654 (m) cc_final: 0.8283 (p) REVERT: K 172 TYR cc_start: 0.8244 (t80) cc_final: 0.7989 (t80) REVERT: K 178 SER cc_start: 0.8411 (OUTLIER) cc_final: 0.7936 (p) REVERT: K 205 ASP cc_start: 0.8126 (t0) cc_final: 0.7884 (t0) REVERT: K 212 ILE cc_start: 0.9197 (mt) cc_final: 0.8947 (mt) REVERT: K 377 MET cc_start: 0.8148 (tmm) cc_final: 0.7810 (tmm) REVERT: K 413 MET cc_start: 0.7937 (tpp) cc_final: 0.7500 (mpp) REVERT: K 432 TYR cc_start: 0.8574 (OUTLIER) cc_final: 0.7969 (m-80) REVERT: H 94 PHE cc_start: 0.8743 (p90) cc_final: 0.8037 (p90) REVERT: H 113 GLU cc_start: 0.8979 (tm-30) cc_final: 0.8572 (pp20) REVERT: H 120 ASP cc_start: 0.8355 (m-30) cc_final: 0.8077 (m-30) REVERT: H 200 GLU cc_start: 0.8199 (pt0) cc_final: 0.7273 (pm20) REVERT: H 378 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.9040 (mm) REVERT: H 393 GLU cc_start: 0.8152 (pp20) cc_final: 0.7912 (pp20) REVERT: H 398 MET cc_start: 0.8479 (mmt) cc_final: 0.7899 (mmp) outliers start: 99 outliers final: 73 residues processed: 492 average time/residue: 0.2340 time to fit residues: 198.3348 Evaluate side-chains 478 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 390 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 302 MET Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 101 ASN Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 225 THR Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 428 LEU Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 194 THR Chi-restraints excluded: chain L residue 200 CYS Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 290 GLU Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain I residue 37 HIS Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 432 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 235 MET Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 378 ILE Chi-restraints excluded: chain H residue 425 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 26 optimal weight: 9.9990 chunk 347 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 169 optimal weight: 0.7980 chunk 72 optimal weight: 0.0030 chunk 120 optimal weight: 0.9990 chunk 359 optimal weight: 2.9990 chunk 248 optimal weight: 8.9990 chunk 113 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 403 optimal weight: 0.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 6 HIS ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 101 ASN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 ASN ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 192 HIS K 380 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.087040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.073608 restraints weight = 87972.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.076464 restraints weight = 40981.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.078428 restraints weight = 24258.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.079803 restraints weight = 16529.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.080749 restraints weight = 12311.951| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 41424 Z= 0.112 Angle : 0.529 11.538 56292 Z= 0.273 Chirality : 0.042 0.233 6156 Planarity : 0.004 0.040 7320 Dihedral : 10.259 145.897 5839 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.31 % Allowed : 18.19 % Favored : 79.50 % 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 aren not related in a simple way. whole: 1.22 (0.12), residues: 5088 helix: 2.00 (0.11), residues: 2364 sheet: 0.52 (0.19), residues: 768 loop : -0.53 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG G 284 TYR 0.026 0.001 TYR A 172 PHE 0.027 0.001 PHE A 255 TRP 0.036 0.002 TRP L 346 HIS 0.006 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00245 (41424) covalent geometry : angle 0.52933 (56292) hydrogen bonds : bond 0.03959 ( 2075) hydrogen bonds : angle 4.40562 ( 5973) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 418 time to evaluate : 1.690 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: E 6 SER cc_start: 0.9299 (OUTLIER) cc_final: 0.9055 (p) REVERT: E 36 MET cc_start: 0.8136 (tmm) cc_final: 0.7671 (tmm) REVERT: E 116 ASP cc_start: 0.8740 (t0) cc_final: 0.8431 (m-30) REVERT: E 154 MET cc_start: 0.9167 (tpp) cc_final: 0.8909 (mmt) REVERT: E 172 TYR cc_start: 0.8106 (t80) cc_final: 0.7621 (t80) REVERT: E 203 MET cc_start: 0.7515 (mtm) cc_final: 0.6804 (mtm) REVERT: E 205 ASP cc_start: 0.7777 (t0) cc_final: 0.7485 (t0) REVERT: E 230 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8937 (tt) REVERT: E 313 MET cc_start: 0.8531 (mtm) cc_final: 0.8251 (mtm) REVERT: E 398 MET cc_start: 0.9153 (tpp) cc_final: 0.8718 (mmt) REVERT: F 145 THR cc_start: 0.7988 (m) cc_final: 0.7597 (m) REVERT: F 259 MET cc_start: 0.8559 (mmm) cc_final: 0.7952 (mpp) REVERT: F 398 MET cc_start: 0.8529 (mmt) cc_final: 0.8215 (mtt) REVERT: J 24 TYR cc_start: 0.8818 (m-80) cc_final: 0.8616 (m-80) REVERT: J 88 HIS cc_start: 0.5898 (OUTLIER) cc_final: 0.5471 (m-70) REVERT: J 178 SER cc_start: 0.8353 (OUTLIER) cc_final: 0.8008 (p) REVERT: J 192 HIS cc_start: 0.7792 (t-90) cc_final: 0.7574 (m-70) REVERT: J 194 THR cc_start: 0.8725 (m) cc_final: 0.8410 (m) REVERT: J 210 TYR cc_start: 0.8456 (m-80) cc_final: 0.7482 (m-80) REVERT: J 271 THR cc_start: 0.9011 (t) cc_final: 0.8237 (m) REVERT: J 297 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7811 (tm-30) REVERT: G 6 HIS cc_start: 0.8527 (t-90) cc_final: 0.7984 (t70) REVERT: G 97 SER cc_start: 0.8908 (OUTLIER) cc_final: 0.8631 (p) REVERT: G 200 GLU cc_start: 0.7717 (pt0) cc_final: 0.6544 (pm20) REVERT: G 302 MET cc_start: 0.7922 (mtt) cc_final: 0.7623 (mtt) REVERT: G 398 MET cc_start: 0.6749 (mmp) cc_final: 0.6228 (mmm) REVERT: C 36 MET cc_start: 0.7570 (tmm) cc_final: 0.7279 (tmm) REVERT: C 205 ASP cc_start: 0.7781 (t0) cc_final: 0.7292 (t0) REVERT: C 313 MET cc_start: 0.8599 (mtm) cc_final: 0.8261 (mtm) REVERT: D 75 MET cc_start: 0.8950 (mmm) cc_final: 0.7950 (mmm) REVERT: D 166 MET cc_start: 0.8298 (tpp) cc_final: 0.7705 (mmm) REVERT: D 248 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8038 (tt) REVERT: D 259 MET cc_start: 0.8347 (mmm) cc_final: 0.8083 (mtp) REVERT: D 269 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8344 (mtt) REVERT: D 290 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7533 (tt0) REVERT: D 413 MET cc_start: 0.7922 (mtp) cc_final: 0.7668 (mtp) REVERT: L 155 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8406 (tm-30) REVERT: L 168 GLU cc_start: 0.7805 (pt0) cc_final: 0.7155 (pt0) REVERT: L 243 ARG cc_start: 0.8107 (mtm110) cc_final: 0.7383 (mtm-85) REVERT: L 313 MET cc_start: 0.9074 (mtm) cc_final: 0.8669 (mtm) REVERT: L 377 MET cc_start: 0.8311 (tmm) cc_final: 0.7727 (tmm) REVERT: L 388 TRP cc_start: 0.8529 (m-10) cc_final: 0.8002 (m-10) REVERT: L 432 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.7304 (t80) REVERT: I 26 ASP cc_start: 0.7367 (m-30) cc_final: 0.7015 (m-30) REVERT: I 37 HIS cc_start: 0.8044 (OUTLIER) cc_final: 0.7742 (m-70) REVERT: I 213 CYS cc_start: 0.8426 (t) cc_final: 0.8021 (p) REVERT: I 248 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7798 (tt) REVERT: I 325 MET cc_start: 0.8060 (mmm) cc_final: 0.7859 (mmm) REVERT: A 172 TYR cc_start: 0.8022 (OUTLIER) cc_final: 0.7621 (t80) REVERT: A 230 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8744 (tt) REVERT: B 398 MET cc_start: 0.8686 (tpp) cc_final: 0.8131 (mtt) REVERT: K 109 THR cc_start: 0.8662 (m) cc_final: 0.8267 (p) REVERT: K 172 TYR cc_start: 0.8174 (t80) cc_final: 0.7874 (t80) REVERT: K 178 SER cc_start: 0.8421 (OUTLIER) cc_final: 0.7963 (p) REVERT: K 205 ASP cc_start: 0.8087 (t0) cc_final: 0.7819 (t0) REVERT: K 212 ILE cc_start: 0.9121 (mt) cc_final: 0.8835 (mt) REVERT: K 377 MET cc_start: 0.8197 (tmm) cc_final: 0.7839 (tmm) REVERT: K 413 MET cc_start: 0.7869 (tpp) cc_final: 0.7414 (mpp) REVERT: H 26 ASP cc_start: 0.8445 (t0) cc_final: 0.8102 (p0) REVERT: H 94 PHE cc_start: 0.8758 (p90) cc_final: 0.8055 (p90) REVERT: H 113 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8579 (pp20) REVERT: H 114 LEU cc_start: 0.9198 (tp) cc_final: 0.8953 (tt) REVERT: H 120 ASP cc_start: 0.8444 (m-30) cc_final: 0.8167 (m-30) REVERT: H 200 GLU cc_start: 0.8063 (pt0) cc_final: 0.7242 (pm20) REVERT: H 393 GLU cc_start: 0.8138 (pp20) cc_final: 0.7933 (pp20) REVERT: H 398 MET cc_start: 0.8478 (mmt) cc_final: 0.7881 (mmp) outliers start: 100 outliers final: 71 residues processed: 495 average time/residue: 0.2188 time to fit residues: 185.4909 Evaluate side-chains 483 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 398 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 101 ASN Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 391 LEU Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 194 THR Chi-restraints excluded: chain L residue 200 CYS Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 290 GLU Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain I residue 37 HIS Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain I residue 376 THR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 315 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 112 optimal weight: 0.0020 chunk 289 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 472 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 255 optimal weight: 0.9990 chunk 375 optimal weight: 1.9990 chunk 214 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 425 optimal weight: 0.0170 chunk 398 optimal weight: 0.4980 overall best weight: 0.5028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 101 ASN C 18 ASN C 139 HIS ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 ASN ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.088108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.074919 restraints weight = 86699.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.077800 restraints weight = 39934.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.079763 restraints weight = 23418.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.081096 restraints weight = 15789.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.082054 restraints weight = 11731.760| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 41424 Z= 0.105 Angle : 0.535 11.927 56292 Z= 0.273 Chirality : 0.042 0.247 6156 Planarity : 0.004 0.039 7320 Dihedral : 10.027 140.292 5839 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.89 % Allowed : 18.49 % Favored : 79.62 % 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 aren not related in a simple way. whole: 1.23 (0.12), residues: 5088 helix: 1.95 (0.11), residues: 2388 sheet: 0.57 (0.19), residues: 768 loop : -0.50 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 284 TYR 0.024 0.001 TYR A 172 PHE 0.029 0.001 PHE K 255 TRP 0.033 0.002 TRP L 346 HIS 0.006 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00224 (41424) covalent geometry : angle 0.53477 (56292) hydrogen bonds : bond 0.03716 ( 2075) hydrogen bonds : angle 4.36517 ( 5973) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 449 time to evaluate : 1.561 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: E 6 SER cc_start: 0.9320 (OUTLIER) cc_final: 0.9061 (p) REVERT: E 36 MET cc_start: 0.8134 (tmm) cc_final: 0.7682 (tmm) REVERT: E 116 ASP cc_start: 0.8720 (t0) cc_final: 0.8417 (m-30) REVERT: E 154 MET cc_start: 0.9179 (tpp) cc_final: 0.8917 (mmt) REVERT: E 172 TYR cc_start: 0.8088 (t80) cc_final: 0.7634 (t80) REVERT: E 203 MET cc_start: 0.7485 (mtm) cc_final: 0.6768 (mtm) REVERT: E 205 ASP cc_start: 0.7761 (t0) cc_final: 0.7430 (t0) REVERT: E 230 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8923 (tt) REVERT: E 313 MET cc_start: 0.8528 (mtm) cc_final: 0.8215 (mtm) REVERT: E 398 MET cc_start: 0.9145 (tpp) cc_final: 0.8666 (mmt) REVERT: F 145 THR cc_start: 0.7879 (OUTLIER) cc_final: 0.7500 (m) REVERT: F 259 MET cc_start: 0.8577 (mmm) cc_final: 0.7949 (mpp) REVERT: F 373 MET cc_start: 0.8243 (mmm) cc_final: 0.8017 (mmm) REVERT: F 398 MET cc_start: 0.8534 (mmt) cc_final: 0.8219 (mtt) REVERT: F 413 MET cc_start: 0.7784 (mmt) cc_final: 0.7242 (mmt) REVERT: J 168 GLU cc_start: 0.7823 (pt0) cc_final: 0.7438 (pt0) REVERT: J 178 SER cc_start: 0.8361 (OUTLIER) cc_final: 0.8013 (p) REVERT: J 192 HIS cc_start: 0.7687 (t-90) cc_final: 0.7477 (m-70) REVERT: J 194 THR cc_start: 0.8941 (m) cc_final: 0.8535 (m) REVERT: J 210 TYR cc_start: 0.8424 (m-80) cc_final: 0.7442 (m-80) REVERT: J 271 THR cc_start: 0.8985 (t) cc_final: 0.8246 (m) REVERT: J 297 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7785 (tm-30) REVERT: J 377 MET cc_start: 0.8257 (tmm) cc_final: 0.7970 (tmm) REVERT: G 6 HIS cc_start: 0.8465 (t-90) cc_final: 0.7763 (t-170) REVERT: G 26 ASP cc_start: 0.8319 (t0) cc_final: 0.8102 (p0) REVERT: G 75 MET cc_start: 0.9046 (mmt) cc_final: 0.8726 (mmt) REVERT: G 97 SER cc_start: 0.8866 (OUTLIER) cc_final: 0.8599 (p) REVERT: G 200 GLU cc_start: 0.7623 (pt0) cc_final: 0.6463 (pm20) REVERT: G 302 MET cc_start: 0.7904 (mtt) cc_final: 0.7615 (mtt) REVERT: G 398 MET cc_start: 0.6745 (mmp) cc_final: 0.6224 (mmm) REVERT: G 413 MET cc_start: 0.8486 (mmm) cc_final: 0.8239 (mmm) REVERT: C 36 MET cc_start: 0.7571 (tmm) cc_final: 0.7290 (tmm) REVERT: C 154 MET cc_start: 0.8951 (mmm) cc_final: 0.8682 (mmm) REVERT: C 205 ASP cc_start: 0.7798 (t0) cc_final: 0.7274 (t0) REVERT: C 313 MET cc_start: 0.8611 (mtm) cc_final: 0.8286 (mtm) REVERT: D 75 MET cc_start: 0.8935 (mmm) cc_final: 0.7938 (mmm) REVERT: D 166 MET cc_start: 0.8279 (tpp) cc_final: 0.7687 (mmm) REVERT: D 248 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8017 (tt) REVERT: D 269 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8309 (mtt) REVERT: D 290 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7508 (tt0) REVERT: D 373 MET cc_start: 0.8221 (mtp) cc_final: 0.7454 (tpp) REVERT: D 413 MET cc_start: 0.7903 (mtp) cc_final: 0.7660 (mtp) REVERT: L 155 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8410 (tm-30) REVERT: L 168 GLU cc_start: 0.7852 (pt0) cc_final: 0.7273 (pt0) REVERT: L 243 ARG cc_start: 0.8037 (mtm110) cc_final: 0.7322 (mtm-85) REVERT: L 313 MET cc_start: 0.9060 (mtm) cc_final: 0.8669 (mtm) REVERT: L 377 MET cc_start: 0.8355 (tmm) cc_final: 0.7748 (tmm) REVERT: L 388 TRP cc_start: 0.8556 (m-10) cc_final: 0.8053 (m-10) REVERT: L 424 ASP cc_start: 0.8789 (t70) cc_final: 0.8210 (t0) REVERT: L 432 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.7384 (t80) REVERT: I 26 ASP cc_start: 0.7237 (m-30) cc_final: 0.6879 (m-30) REVERT: I 37 HIS cc_start: 0.8023 (OUTLIER) cc_final: 0.7780 (m-70) REVERT: I 213 CYS cc_start: 0.8412 (t) cc_final: 0.8013 (p) REVERT: I 248 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7768 (tt) REVERT: A 101 ASN cc_start: 0.8423 (OUTLIER) cc_final: 0.7905 (t0) REVERT: A 172 TYR cc_start: 0.7998 (OUTLIER) cc_final: 0.7557 (t80) REVERT: A 377 MET cc_start: 0.8214 (tmm) cc_final: 0.7522 (tmm) REVERT: B 170 SER cc_start: 0.8897 (m) cc_final: 0.8234 (p) REVERT: B 309 HIS cc_start: 0.8330 (m170) cc_final: 0.8001 (m90) REVERT: B 398 MET cc_start: 0.8693 (tpp) cc_final: 0.8128 (mtt) REVERT: K 109 THR cc_start: 0.8659 (m) cc_final: 0.8256 (p) REVERT: K 172 TYR cc_start: 0.8194 (t80) cc_final: 0.7894 (t80) REVERT: K 178 SER cc_start: 0.8438 (OUTLIER) cc_final: 0.7985 (p) REVERT: K 205 ASP cc_start: 0.7994 (t0) cc_final: 0.7732 (t0) REVERT: K 212 ILE cc_start: 0.9045 (mt) cc_final: 0.8815 (mt) REVERT: K 237 SER cc_start: 0.8872 (m) cc_final: 0.8278 (p) REVERT: K 413 MET cc_start: 0.7775 (tpp) cc_final: 0.7387 (mpp) REVERT: K 425 MET cc_start: 0.9086 (mmm) cc_final: 0.8685 (tpp) REVERT: H 26 ASP cc_start: 0.8326 (t0) cc_final: 0.7921 (p0) REVERT: H 94 PHE cc_start: 0.8756 (p90) cc_final: 0.8080 (p90) REVERT: H 113 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8547 (pp20) REVERT: H 114 LEU cc_start: 0.9195 (tp) cc_final: 0.8916 (tt) REVERT: H 120 ASP cc_start: 0.8488 (m-30) cc_final: 0.8220 (m-30) REVERT: H 200 GLU cc_start: 0.7993 (pt0) cc_final: 0.7193 (pm20) REVERT: H 378 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.8984 (mm) REVERT: H 398 MET cc_start: 0.8457 (mmt) cc_final: 0.7883 (mmp) outliers start: 82 outliers final: 61 residues processed: 511 average time/residue: 0.2069 time to fit residues: 181.0497 Evaluate side-chains 483 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 407 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 101 ASN Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 200 CYS Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain I residue 37 HIS Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain I residue 376 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 432 TYR Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 378 ILE Chi-restraints excluded: chain H residue 425 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 318 optimal weight: 0.8980 chunk 417 optimal weight: 2.9990 chunk 332 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 396 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 chunk 300 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 168 optimal weight: 10.0000 chunk 154 optimal weight: 0.0570 chunk 490 optimal weight: 0.0020 overall best weight: 0.9910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 101 ASN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 GLN L 249 ASN A 101 ASN ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.088079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.074756 restraints weight = 87214.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.077651 restraints weight = 40467.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.079634 restraints weight = 23835.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.081005 restraints weight = 16127.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.081955 restraints weight = 11935.572| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 41424 Z= 0.112 Angle : 0.540 11.910 56292 Z= 0.276 Chirality : 0.042 0.225 6156 Planarity : 0.004 0.040 7320 Dihedral : 9.902 136.587 5839 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.94 % Allowed : 18.86 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.12), residues: 5088 helix: 2.00 (0.11), residues: 2352 sheet: 0.57 (0.19), residues: 768 loop : -0.49 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 284 TYR 0.040 0.001 TYR J 24 PHE 0.030 0.001 PHE C 255 TRP 0.032 0.002 TRP L 346 HIS 0.011 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00246 (41424) covalent geometry : angle 0.54017 (56292) hydrogen bonds : bond 0.03716 ( 2075) hydrogen bonds : angle 4.36760 ( 5973) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6694.22 seconds wall clock time: 117 minutes 12.47 seconds (7032.47 seconds total)