Starting phenix.real_space_refine on Tue Sep 15 14:25:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/3jat_6352/09_2026/3jat_6352.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jat_6352/09_2026/3jat_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_6352/09_2026/3jat_6352.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jat_6352/09_2026/3jat_6352.map" restraint_files = "/net/cci-nas-00/data/ceres_data/3jat_6352/09_2026/3jat_6352.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/3jat_6352/09_2026/3jat_6352.cif" model { file = "/net/cci-nas-00/data/ceres_data/3jat_6352/09_2026/3jat_6352.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jat_6352/09_2026/3jat_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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 9.02, per 1000 atoms: 0.22 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: 3.61 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.25 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: 9.84 Time building geometry restraints manager: 4.70 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: 23814 33.66 - 67.31: 654 67.31 - 100.97: 66 100.97 - 134.63: 0 134.63 - 168.29: 18 Dihedral angle restraints: 24552 sinusoidal: 9750 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 24549 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: 10.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.600 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 38.770 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.120 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 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 : 16.210 168.286 15060 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 are 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/Z covalent geometry : bond 0.00928 / 0.64 (41424) covalent geometry : angle 1.53814 / 1.05 (56292) hydrogen bonds : bond 0.19794 / 13.19 ( 2075) hydrogen bonds : angle 7.19498 / 5.29 ( 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 : 1.735 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: 0.7007 (tpp) REVERT: G 183 GLU cc_start: 0.7963 (tt0) cc_final: 0.7432 (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: 0.2786 time to fit residues: 402.6725 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 : 1.628 ------------------------------------------------------------------------------- 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... 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 = 0.087036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.073855 restraints weight = 87793.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.076711 restraints weight = 41020.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.078664 restraints weight = 24195.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.080016 restraints weight = 16383.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.080982 restraints weight = 12190.188| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 41424 Z= 0.148 Angle : 0.626 8.067 56292 Z= 0.332 Chirality : 0.045 0.218 6156 Planarity : 0.005 0.065 7320 Dihedral : 11.102 169.092 5678 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.05 % Allowed : 12.90 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.12), residues: 5088 helix: 2.19 (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 0.014 0.001 ARG D 390 TYR 0.038 0.001 TYR E 24 PHE 0.020 0.002 PHE J 255 TRP 0.024 0.002 TRP E 346 HIS 0.012 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.15 (41424) covalent geometry : angle 0.62564 / 0.33 (56292) hydrogen bonds : bond 0.05757 / 3.83 ( 2075) hydrogen bonds : angle 5.02119 / 3.63 ( 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: 89 poor density : 536 time to evaluate : 2.079 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: 0.7970 (mt-10) cc_final: 0.7746 (mt-10) REVERT: E 172 TYR cc_start: 0.8111 (t80) cc_final: 0.7638 (t80) REVERT: E 203 MET cc_start: 0.7643 (mtm) cc_final: 0.7225 (mtm) REVERT: E 205 ASP cc_start: 0.7927 (t0) cc_final: 0.7592 (t0) REVERT: E 230 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8908 (tt) REVERT: E 398 MET cc_start: 0.8918 (tpp) cc_final: 0.8339 (mmt) REVERT: F 110 GLU cc_start: 0.8058 (mp0) cc_final: 0.7063 (mp0) REVERT: J 27 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8213 (mt-10) REVERT: J 178 SER cc_start: 0.8370 (OUTLIER) cc_final: 0.8067 (p) REVERT: J 207 GLU cc_start: 0.7881 (tt0) cc_final: 0.7625 (tt0) REVERT: J 210 TYR cc_start: 0.8602 (m-80) cc_final: 0.7625 (m-80) REVERT: J 271 THR cc_start: 0.8850 (t) cc_final: 0.8109 (m) REVERT: J 413 MET cc_start: 0.7479 (OUTLIER) cc_final: 0.7194 (tpp) REVERT: G 302 MET cc_start: 0.7475 (mtt) cc_final: 0.7194 (mtt) REVERT: G 398 MET cc_start: 0.8586 (mmt) cc_final: 0.8251 (mmm) REVERT: C 313 MET cc_start: 0.8563 (mtm) cc_final: 0.8211 (mtm) REVERT: D 248 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7501 (tt) REVERT: D 301 MET cc_start: 0.8402 (mmm) cc_final: 0.8098 (mmp) REVERT: D 425 MET cc_start: 0.8676 (tpp) cc_final: 0.8271 (tpp) REVERT: L 36 MET cc_start: 0.7869 (tmm) cc_final: 0.7606 (tmm) REVERT: L 120 ASP cc_start: 0.8728 (OUTLIER) cc_final: 0.8369 (t0) REVERT: L 154 MET cc_start: 0.8981 (mmm) cc_final: 0.8780 (mmm) REVERT: L 388 TRP cc_start: 0.8369 (m-10) cc_final: 0.7892 (m-10) REVERT: I 26 ASP cc_start: 0.7381 (m-30) cc_final: 0.7018 (m-30) REVERT: I 37 HIS cc_start: 0.7945 (OUTLIER) cc_final: 0.7742 (m-70) REVERT: I 248 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7552 (tt) REVERT: I 325 MET cc_start: 0.8110 (mmm) cc_final: 0.7609 (mmm) REVERT: A 86 LEU cc_start: 0.9403 (tp) cc_final: 0.9153 (tp) REVERT: A 230 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8771 (tt) REVERT: A 276 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8586 (mm) REVERT: A 377 MET cc_start: 0.7850 (tmm) cc_final: 0.7573 (tmm) REVERT: K 109 THR cc_start: 0.8390 (m) cc_final: 0.8024 (p) REVERT: K 178 SER cc_start: 0.8441 (OUTLIER) cc_final: 0.8045 (p) REVERT: K 192 HIS cc_start: 0.7993 (t70) cc_final: 0.7770 (t70) REVERT: K 205 ASP cc_start: 0.8000 (t0) cc_final: 0.7601 (t0) REVERT: K 285 GLN cc_start: 0.7468 (tt0) cc_final: 0.6900 (pt0) REVERT: K 339 ARG cc_start: 0.7340 (mmp-170) cc_final: 0.6987 (mmp-170) REVERT: K 377 MET cc_start: 0.7761 (tmm) cc_final: 0.7502 (tmm) REVERT: H 94 PHE cc_start: 0.8693 (p90) cc_final: 0.7920 (p90) REVERT: H 120 ASP cc_start: 0.8553 (m-30) cc_final: 0.8124 (m-30) REVERT: H 200 GLU cc_start: 0.7905 (pt0) cc_final: 0.7070 (pm20) REVERT: H 325 MET cc_start: 0.7950 (mmm) cc_final: 0.7563 (mmm) REVERT: H 398 MET cc_start: 0.8408 (mmt) cc_final: 0.7874 (mmp) outliers start: 89 outliers final: 37 residues processed: 600 average time/residue: 0.2417 time to fit residues: 246.0742 Evaluate side-chains 458 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 410 time to evaluate : 1.560 ------------------------------------------------------------------------------- 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 275 VAL 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 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: 2.9990 chunk 306 optimal weight: 0.0970 chunk 232 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 422 optimal weight: 6.9990 chunk 370 optimal weight: 10.0000 chunk 170 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 441 optimal weight: 0.0770 chunk 171 optimal weight: 4.9990 overall best weight: 1.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 249 ASN F 6 HIS J 101 ASN J 192 HIS J 380 ASN J 406 HIS ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 406 HIS ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 ASN L 406 HIS I 133 GLN I 309 HIS I 406 HIS A 18 ASN A 101 ASN A 249 ASN B 6 HIS B 37 HIS K 406 HIS ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 350 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.085203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.072143 restraints weight = 88337.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.074912 restraints weight = 41365.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.076833 restraints weight = 24482.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.078139 restraints weight = 16597.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.079080 restraints weight = 12380.361| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 41424 Z= 0.147 Angle : 0.573 9.622 56292 Z= 0.297 Chirality : 0.043 0.234 6156 Planarity : 0.004 0.051 7320 Dihedral : 10.638 170.237 5674 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.47 % Allowed : 14.47 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.12), residues: 5088 helix: 2.17 (0.11), residues: 2388 sheet: 0.65 (0.19), residues: 726 loop : -0.70 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 308 TYR 0.026 0.001 TYR D 435 PHE 0.027 0.002 PHE A 255 TRP 0.026 0.002 TRP L 346 HIS 0.011 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (41424) covalent geometry : angle 0.57350 / 0.30 (56292) hydrogen bonds : bond 0.04952 / 3.32 ( 2075) hydrogen bonds : angle 4.67671 / 3.38 ( 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 557 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 450 time to evaluate : 1.598 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: E 154 MET cc_start: 0.9116 (tpp) cc_final: 0.8867 (mmt) REVERT: E 172 TYR cc_start: 0.8111 (t80) cc_final: 0.7621 (t80) REVERT: E 203 MET cc_start: 0.7516 (mtm) cc_final: 0.7034 (mtm) REVERT: E 205 ASP cc_start: 0.7907 (t0) cc_final: 0.7574 (t0) REVERT: E 313 MET cc_start: 0.8436 (mtm) cc_final: 0.8206 (mtm) REVERT: E 398 MET cc_start: 0.9019 (tpp) cc_final: 0.8720 (mmt) REVERT: F 200 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7706 (pt0) REVERT: J 27 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8174 (mt-10) REVERT: J 101 ASN cc_start: 0.9054 (OUTLIER) cc_final: 0.8218 (t0) REVERT: J 178 SER cc_start: 0.8298 (OUTLIER) cc_final: 0.7978 (p) REVERT: J 207 GLU cc_start: 0.7907 (tt0) cc_final: 0.7635 (tt0) REVERT: J 210 TYR cc_start: 0.8567 (m-80) cc_final: 0.7610 (m-80) REVERT: J 271 THR cc_start: 0.8987 (t) cc_final: 0.8210 (m) REVERT: J 357 TYR cc_start: 0.7836 (m-80) cc_final: 0.7529 (m-80) REVERT: G 302 MET cc_start: 0.7724 (mtt) cc_final: 0.7459 (mtt) REVERT: G 416 MET cc_start: 0.8550 (tpp) cc_final: 0.8142 (tpp) REVERT: C 36 MET cc_start: 0.7623 (tmm) cc_final: 0.7384 (tmm) REVERT: C 203 MET cc_start: 0.7561 (mmm) cc_final: 0.7343 (mmm) REVERT: C 205 ASP cc_start: 0.7814 (t0) cc_final: 0.7472 (t0) REVERT: C 313 MET cc_start: 0.8644 (mtm) cc_final: 0.8186 (mtm) REVERT: D 37 HIS cc_start: 0.7446 (m170) cc_final: 0.7146 (m170) REVERT: D 75 MET cc_start: 0.8791 (mmm) cc_final: 0.8106 (mmm) REVERT: D 151 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8708 (m) REVERT: D 248 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7708 (tt) REVERT: D 301 MET cc_start: 0.8428 (mmm) cc_final: 0.8106 (mmp) REVERT: D 425 MET cc_start: 0.8674 (tpp) cc_final: 0.8230 (tpp) REVERT: L 36 MET cc_start: 0.7900 (tmm) cc_final: 0.7635 (tmm) REVERT: L 155 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8141 (tm-30) REVERT: L 243 ARG cc_start: 0.8125 (mtm110) cc_final: 0.7322 (mtm-85) REVERT: L 388 TRP cc_start: 0.8401 (m-10) cc_final: 0.7910 (m-10) REVERT: I 26 ASP cc_start: 0.7380 (m-30) cc_final: 0.7027 (m-30) REVERT: I 37 HIS cc_start: 0.7944 (OUTLIER) cc_final: 0.7704 (m-70) REVERT: I 75 MET cc_start: 0.9258 (mmt) cc_final: 0.9035 (mpp) REVERT: I 248 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7747 (tt) REVERT: A 36 MET cc_start: 0.7173 (tmm) cc_final: 0.6644 (tmm) REVERT: A 101 ASN cc_start: 0.8902 (OUTLIER) cc_final: 0.8604 (t0) REVERT: A 302 MET cc_start: 0.8844 (mmp) cc_final: 0.8362 (mmp) REVERT: A 377 MET cc_start: 0.8010 (tmm) cc_final: 0.7585 (tmm) REVERT: A 413 MET cc_start: 0.8197 (tpp) cc_final: 0.7970 (mmm) REVERT: B 149 MET cc_start: 0.8230 (tpp) cc_final: 0.8026 (ttt) REVERT: B 323 MET cc_start: 0.8166 (mtm) cc_final: 0.7942 (mtm) REVERT: K 109 THR cc_start: 0.8529 (m) cc_final: 0.8177 (p) REVERT: K 172 TYR cc_start: 0.8453 (t80) cc_final: 0.8243 (t80) REVERT: K 178 SER cc_start: 0.8433 (OUTLIER) cc_final: 0.8016 (p) REVERT: K 205 ASP cc_start: 0.8127 (t0) cc_final: 0.7798 (t0) REVERT: K 259 LEU cc_start: 0.8925 (tp) cc_final: 0.8649 (tp) REVERT: K 285 GLN cc_start: 0.7414 (tt0) cc_final: 0.6533 (pt0) REVERT: K 339 ARG cc_start: 0.7177 (mmp-170) cc_final: 0.6939 (mmp-170) REVERT: K 377 MET cc_start: 0.7940 (tmm) cc_final: 0.7717 (tmm) REVERT: H 94 PHE cc_start: 0.8700 (p90) cc_final: 0.7955 (p90) REVERT: H 120 ASP cc_start: 0.8399 (m-30) cc_final: 0.8055 (m-30) REVERT: H 200 GLU cc_start: 0.8005 (pt0) cc_final: 0.7141 (pm20) REVERT: H 325 MET cc_start: 0.8069 (mmm) cc_final: 0.7294 (mmm) REVERT: H 373 MET cc_start: 0.8261 (mtm) cc_final: 0.8051 (mtm) REVERT: H 398 MET cc_start: 0.8507 (mmt) cc_final: 0.8067 (mmp) outliers start: 107 outliers final: 44 residues processed: 529 average time/residue: 0.2351 time to fit residues: 212.4342 Evaluate side-chains 440 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 386 time to evaluate : 1.699 ------------------------------------------------------------------------------- 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 J residue 26 LEU Chi-restraints excluded: chain J residue 27 GLU 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 192 HIS Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 269 LEU 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 151 THR Chi-restraints excluded: chain D residue 241 CYS 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 122 ILE 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 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 6 SER 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 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 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 232 SER Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 235 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 285 optimal weight: 0.0030 chunk 227 optimal weight: 3.9990 chunk 382 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 200 optimal weight: 3.9990 chunk 485 optimal weight: 8.9990 chunk 392 optimal weight: 8.9990 chunk 377 optimal weight: 2.9990 chunk 181 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 237 optimal weight: 9.9990 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 101 ASN E 258 ASN J 101 ASN G 6 HIS C 31 GLN C 101 ASN C 249 ASN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 HIS L 101 ASN I 294 GLN I 309 HIS A 101 ASN B 258 ASN B 294 GLN K 249 ASN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.083209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.070176 restraints weight = 89312.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.072879 restraints weight = 42202.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.074749 restraints weight = 25078.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.076025 restraints weight = 17095.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.076949 restraints weight = 12839.417| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 41424 Z= 0.192 Angle : 0.573 8.402 56292 Z= 0.299 Chirality : 0.044 0.234 6156 Planarity : 0.004 0.051 7320 Dihedral : 10.417 168.868 5672 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.91 % Allowed : 15.77 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.12), residues: 5088 helix: 2.07 (0.10), residues: 2376 sheet: 0.58 (0.18), residues: 792 loop : -0.76 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 284 TYR 0.024 0.001 TYR D 435 PHE 0.030 0.002 PHE A 255 TRP 0.025 0.002 TRP L 346 HIS 0.019 0.001 HIS J 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (41424) covalent geometry : angle 0.57263 / 0.30 (56292) hydrogen bonds : bond 0.04944 / 3.35 ( 2075) hydrogen bonds : angle 4.62821 / 3.34 ( 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 547 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 421 time to evaluate : 1.964 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: 0.9342 (OUTLIER) cc_final: 0.9084 (p) REVERT: E 154 MET cc_start: 0.9111 (tpp) cc_final: 0.8863 (mmt) REVERT: E 172 TYR cc_start: 0.8124 (t80) cc_final: 0.7609 (t80) REVERT: E 203 MET cc_start: 0.7573 (mtm) cc_final: 0.7065 (mtm) REVERT: E 205 ASP cc_start: 0.7895 (t0) cc_final: 0.7577 (t0) REVERT: E 313 MET cc_start: 0.8500 (mtm) cc_final: 0.8227 (mtm) REVERT: E 398 MET cc_start: 0.9061 (tpp) cc_final: 0.8704 (mmt) REVERT: J 24 TYR cc_start: 0.8820 (m-80) cc_final: 0.8549 (m-80) REVERT: J 27 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8223 (mt-10) REVERT: J 101 ASN cc_start: 0.9044 (OUTLIER) cc_final: 0.8035 (t0) REVERT: J 178 SER cc_start: 0.8289 (OUTLIER) cc_final: 0.7975 (p) REVERT: J 207 GLU cc_start: 0.7940 (tt0) cc_final: 0.7657 (tt0) REVERT: J 210 TYR cc_start: 0.8608 (m-10) cc_final: 0.7669 (m-80) REVERT: J 357 TYR cc_start: 0.7946 (m-80) cc_final: 0.7578 (m-80) REVERT: J 424 ASP cc_start: 0.8574 (t70) cc_final: 0.8121 (t0) REVERT: J 425 MET cc_start: 0.9183 (mmm) cc_final: 0.8976 (tpp) REVERT: J 433 GLU cc_start: 0.7767 (pt0) cc_final: 0.7224 (pt0) REVERT: G 302 MET cc_start: 0.7809 (mtt) cc_final: 0.7547 (mtt) REVERT: G 325 MET cc_start: 0.8042 (mmm) cc_final: 0.7714 (mmm) REVERT: G 398 MET cc_start: 0.6620 (mmp) cc_final: 0.5915 (mmm) REVERT: G 416 MET cc_start: 0.8458 (tpp) cc_final: 0.8052 (tpp) REVERT: C 36 MET cc_start: 0.7547 (tmm) cc_final: 0.7332 (tmm) REVERT: C 205 ASP cc_start: 0.7824 (t0) cc_final: 0.7435 (t0) REVERT: C 313 MET cc_start: 0.8667 (mtm) cc_final: 0.8175 (mtm) REVERT: D 75 MET cc_start: 0.8993 (mmm) cc_final: 0.7907 (mmm) REVERT: D 248 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.7828 (tt) REVERT: D 301 MET cc_start: 0.8438 (mmm) cc_final: 0.7984 (mmp) REVERT: D 413 MET cc_start: 0.7913 (mtp) cc_final: 0.7659 (mtp) REVERT: D 425 MET cc_start: 0.8720 (tpp) cc_final: 0.8367 (tpp) REVERT: L 155 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8269 (tm-30) REVERT: L 388 TRP cc_start: 0.8481 (m-10) cc_final: 0.7925 (m-10) REVERT: I 26 ASP cc_start: 0.7365 (m-30) cc_final: 0.7004 (m-30) REVERT: I 37 HIS cc_start: 0.8004 (OUTLIER) cc_final: 0.7727 (m-70) REVERT: I 248 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7957 (tt) REVERT: A 123 ARG cc_start: 0.8467 (ttm-80) cc_final: 0.8255 (tpp80) REVERT: A 230 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8746 (tt) REVERT: A 302 MET cc_start: 0.8816 (mmp) cc_final: 0.8483 (mmp) REVERT: A 377 MET cc_start: 0.8178 (tmm) cc_final: 0.7726 (tmm) REVERT: B 323 MET cc_start: 0.8196 (mtm) cc_final: 0.7801 (mtm) REVERT: B 373 MET cc_start: 0.8202 (mtp) cc_final: 0.7913 (mtp) REVERT: B 398 MET cc_start: 0.8595 (tpp) cc_final: 0.8127 (mtt) REVERT: K 109 THR cc_start: 0.8600 (m) cc_final: 0.8237 (p) REVERT: K 172 TYR cc_start: 0.8213 (t80) cc_final: 0.7981 (t80) REVERT: K 178 SER cc_start: 0.8417 (OUTLIER) cc_final: 0.8011 (p) REVERT: K 205 ASP cc_start: 0.8218 (t0) cc_final: 0.7919 (t0) REVERT: K 339 ARG cc_start: 0.7252 (mmp-170) cc_final: 0.6973 (mmp-170) REVERT: K 377 MET cc_start: 0.8056 (tmm) cc_final: 0.7784 (tmm) REVERT: H 94 PHE cc_start: 0.8683 (p90) cc_final: 0.7931 (p90) REVERT: H 120 ASP cc_start: 0.8416 (m-30) cc_final: 0.8135 (m-30) REVERT: H 200 GLU cc_start: 0.8163 (pt0) cc_final: 0.7304 (pm20) REVERT: H 325 MET cc_start: 0.8116 (mmm) cc_final: 0.7518 (mmm) REVERT: H 373 MET cc_start: 0.8225 (mtm) cc_final: 0.7980 (mtm) REVERT: H 398 MET cc_start: 0.8549 (mmt) cc_final: 0.8090 (mmp) outliers start: 126 outliers final: 69 residues processed: 515 average time/residue: 0.2289 time to fit residues: 203.5585 Evaluate side-chains 456 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 378 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 SER 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 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 6 SER Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 27 GLU 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 390 ARG 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 241 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 159 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 428 LEU 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 122 ILE 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 A residue 391 LEU 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 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 225 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 503 optimal weight: 9.9990 chunk 101 optimal weight: 0.4980 chunk 367 optimal weight: 4.9990 chunk 301 optimal weight: 6.9990 chunk 457 optimal weight: 0.9990 chunk 375 optimal weight: 5.9990 chunk 311 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 450 optimal weight: 0.9990 chunk 365 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 18 ASN E 101 ASN J 101 ASN J 192 HIS C 101 ASN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS L 128 GLN A 101 ASN ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3488 r_free = 0.3488 target = 0.085363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.072254 restraints weight = 88274.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.075015 restraints weight = 41656.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.076913 restraints weight = 24699.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.078238 restraints weight = 16802.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.079137 restraints weight = 12508.331| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 41424 Z= 0.111 Angle : 0.523 9.155 56292 Z= 0.271 Chirality : 0.042 0.252 6156 Planarity : 0.004 0.044 7320 Dihedral : 10.197 166.201 5672 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.19 % Allowed : 17.29 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.12), residues: 5088 helix: 2.12 (0.11), residues: 2364 sheet: 0.52 (0.18), residues: 816 loop : -0.61 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 84 TYR 0.018 0.001 TYR E 24 PHE 0.025 0.001 PHE K 255 TRP 0.028 0.001 TRP L 346 HIS 0.007 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (41424) covalent geometry : angle 0.52282 / 0.27 (56292) hydrogen bonds : bond 0.04208 / 2.84 ( 2075) hydrogen bonds : angle 4.45223 / 3.21 ( 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 541 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 446 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 116 ASP cc_start: 0.8624 (t0) cc_final: 0.8393 (m-30) REVERT: E 154 MET cc_start: 0.9152 (tpp) cc_final: 0.8883 (mmt) REVERT: E 172 TYR cc_start: 0.8083 (t80) cc_final: 0.7588 (t80) REVERT: E 203 MET cc_start: 0.7513 (mtm) cc_final: 0.7010 (mtm) REVERT: E 205 ASP cc_start: 0.7813 (t0) cc_final: 0.7512 (t0) REVERT: E 313 MET cc_start: 0.8498 (mtm) cc_final: 0.8216 (mtm) REVERT: E 398 MET cc_start: 0.9072 (tpp) cc_final: 0.8689 (mmt) REVERT: J 88 HIS cc_start: 0.6237 (OUTLIER) cc_final: 0.5750 (m-70) REVERT: J 101 ASN cc_start: 0.8993 (OUTLIER) cc_final: 0.8355 (t0) REVERT: J 207 GLU cc_start: 0.7743 (tt0) cc_final: 0.7541 (tt0) REVERT: J 210 TYR cc_start: 0.8502 (m-80) cc_final: 0.7556 (m-80) REVERT: J 357 TYR cc_start: 0.7924 (m-80) cc_final: 0.7580 (m-80) REVERT: J 425 MET cc_start: 0.9191 (mmm) cc_final: 0.8917 (tpp) REVERT: G 176 LYS cc_start: 0.8932 (mmtm) cc_final: 0.8624 (mmmt) REVERT: G 302 MET cc_start: 0.7821 (mtt) cc_final: 0.7536 (mtt) REVERT: G 416 MET cc_start: 0.8427 (tpp) cc_final: 0.8025 (tpp) REVERT: C 36 MET cc_start: 0.7483 (tmm) cc_final: 0.7270 (tmm) REVERT: C 205 ASP cc_start: 0.7784 (t0) cc_final: 0.7362 (t0) REVERT: C 313 MET cc_start: 0.8655 (mtm) cc_final: 0.8167 (mtm) REVERT: C 377 MET cc_start: 0.7987 (tmm) cc_final: 0.7718 (tmm) REVERT: D 75 MET cc_start: 0.8882 (mmm) cc_final: 0.7941 (mmm) REVERT: D 248 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7692 (tt) REVERT: D 301 MET cc_start: 0.8326 (mmm) cc_final: 0.8081 (mmp) REVERT: L 155 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8258 (tm-30) REVERT: L 168 GLU cc_start: 0.7880 (pt0) cc_final: 0.7337 (pt0) REVERT: L 243 ARG cc_start: 0.8113 (mtm110) cc_final: 0.7353 (mtm-85) REVERT: L 388 TRP cc_start: 0.8427 (m-10) cc_final: 0.7916 (m-10) REVERT: L 420 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8198 (mm-30) REVERT: L 432 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.7853 (t80) REVERT: I 26 ASP cc_start: 0.7372 (m-30) cc_final: 0.6993 (m-30) REVERT: I 37 HIS cc_start: 0.8023 (OUTLIER) cc_final: 0.7707 (m-70) REVERT: I 211 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.8124 (t0) REVERT: I 248 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7868 (tt) REVERT: I 301 MET cc_start: 0.8194 (mmp) cc_final: 0.7947 (mmp) REVERT: A 230 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8691 (tt) REVERT: A 302 MET cc_start: 0.8820 (mmp) cc_final: 0.8543 (mmp) REVERT: A 377 MET cc_start: 0.8088 (tmm) cc_final: 0.7611 (tmm) REVERT: B 323 MET cc_start: 0.8328 (mtm) cc_final: 0.8007 (mtm) REVERT: B 373 MET cc_start: 0.8247 (mtp) cc_final: 0.7936 (mtp) REVERT: B 398 MET cc_start: 0.8611 (tpp) cc_final: 0.8136 (mtt) REVERT: B 425 MET cc_start: 0.8916 (mmm) cc_final: 0.8570 (tpp) REVERT: K 109 THR cc_start: 0.8594 (m) cc_final: 0.8216 (p) REVERT: K 178 SER cc_start: 0.8416 (OUTLIER) cc_final: 0.7979 (p) REVERT: K 205 ASP cc_start: 0.8067 (t0) cc_final: 0.7782 (t0) REVERT: K 212 ILE cc_start: 0.9167 (mt) cc_final: 0.8934 (mt) REVERT: K 285 GLN cc_start: 0.7766 (pt0) cc_final: 0.7515 (pt0) REVERT: K 302 MET cc_start: 0.8662 (mmt) cc_final: 0.8457 (mmt) REVERT: K 377 MET cc_start: 0.8038 (tmm) cc_final: 0.7771 (tmm) REVERT: H 94 PHE cc_start: 0.8778 (p90) cc_final: 0.8062 (p90) REVERT: H 120 ASP cc_start: 0.8443 (m-30) cc_final: 0.8155 (m-30) REVERT: H 200 GLU cc_start: 0.8074 (pt0) cc_final: 0.7228 (pm20) REVERT: H 325 MET cc_start: 0.8309 (mmm) cc_final: 0.7569 (mmm) REVERT: H 373 MET cc_start: 0.8163 (mtm) cc_final: 0.7868 (mtm) REVERT: H 398 MET cc_start: 0.8491 (mmt) cc_final: 0.8011 (mmp) outliers start: 95 outliers final: 45 residues processed: 515 average time/residue: 0.2294 time to fit residues: 202.8851 Evaluate side-chains 441 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 387 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 234 ILE 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 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 259 LEU Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 97 SER 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 259 LEU 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 248 LEU Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 120 ASP 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 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 211 ASP 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 101 ASN 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 130 THR Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 194 THR 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: 1.9990 chunk 165 optimal weight: 9.9990 chunk 348 optimal weight: 10.0000 chunk 307 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 354 optimal weight: 0.9990 chunk 369 optimal weight: 0.9990 chunk 139 optimal weight: 9.9990 chunk 223 optimal weight: 6.9990 chunk 490 optimal weight: 1.9990 chunk 142 optimal weight: 0.3980 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 18 ASN ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 101 ASN J 192 HIS G 294 GLN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS L 31 GLN A 31 GLN A 101 ASN A 258 ASN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 294 GLN H 349 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.085223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.072134 restraints weight = 88486.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.074866 restraints weight = 41746.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.076749 restraints weight = 24822.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.078073 restraints weight = 16951.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.079009 restraints weight = 12630.848| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 41424 Z= 0.119 Angle : 0.517 7.858 56292 Z= 0.267 Chirality : 0.042 0.241 6156 Planarity : 0.004 0.043 7320 Dihedral : 9.988 163.119 5671 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.33 % Allowed : 17.64 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.12), residues: 5088 helix: 2.08 (0.11), residues: 2364 sheet: 0.50 (0.18), residues: 816 loop : -0.56 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 284 TYR 0.045 0.001 TYR J 24 PHE 0.025 0.001 PHE A 255 TRP 0.028 0.002 TRP L 346 HIS 0.007 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (41424) covalent geometry : angle 0.51688 / 0.27 (56292) hydrogen bonds : bond 0.04124 / 2.78 ( 2075) hydrogen bonds : angle 4.41672 / 3.19 ( 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 523 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 422 time to evaluate : 1.655 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: 0.9311 (OUTLIER) cc_final: 0.9102 (p) REVERT: E 116 ASP cc_start: 0.8653 (t0) cc_final: 0.8392 (m-30) REVERT: E 154 MET cc_start: 0.9170 (tpp) cc_final: 0.8896 (mmt) REVERT: E 172 TYR cc_start: 0.8088 (t80) cc_final: 0.7555 (t80) REVERT: E 203 MET cc_start: 0.7466 (mtm) cc_final: 0.6868 (mtm) REVERT: E 205 ASP cc_start: 0.7885 (t0) cc_final: 0.7575 (t0) REVERT: E 313 MET cc_start: 0.8518 (mtm) cc_final: 0.8189 (mtm) REVERT: E 398 MET cc_start: 0.9127 (tpp) cc_final: 0.8741 (mmt) REVERT: F 398 MET cc_start: 0.8544 (mmt) cc_final: 0.8095 (mtt) REVERT: J 88 HIS cc_start: 0.6195 (OUTLIER) cc_final: 0.5716 (m-70) REVERT: J 178 SER cc_start: 0.8293 (OUTLIER) cc_final: 0.7952 (p) REVERT: J 210 TYR cc_start: 0.8506 (m-80) cc_final: 0.7589 (m-80) REVERT: J 271 THR cc_start: 0.8903 (t) cc_final: 0.8102 (m) REVERT: J 357 TYR cc_start: 0.7962 (m-80) cc_final: 0.7611 (m-80) REVERT: J 425 MET cc_start: 0.9173 (mmm) cc_final: 0.8903 (tpp) REVERT: G 75 MET cc_start: 0.9057 (mmt) cc_final: 0.8669 (mmt) REVERT: G 97 SER cc_start: 0.8976 (OUTLIER) cc_final: 0.8689 (p) REVERT: G 149 MET cc_start: 0.8883 (tpp) cc_final: 0.8543 (mmt) REVERT: G 176 LYS cc_start: 0.8920 (mmtm) cc_final: 0.8621 (mmmt) REVERT: G 302 MET cc_start: 0.7845 (mtt) cc_final: 0.7561 (mtt) REVERT: G 398 MET cc_start: 0.6556 (mmp) cc_final: 0.5924 (mmm) REVERT: G 416 MET cc_start: 0.8347 (tpp) cc_final: 0.7995 (tpp) REVERT: C 36 MET cc_start: 0.7500 (tmm) cc_final: 0.7202 (tmm) REVERT: C 205 ASP cc_start: 0.7725 (t0) cc_final: 0.7313 (t0) REVERT: C 313 MET cc_start: 0.8637 (mtm) cc_final: 0.8225 (mtm) REVERT: D 69 ASP cc_start: 0.7684 (t0) cc_final: 0.7479 (t0) REVERT: D 75 MET cc_start: 0.8923 (mmm) cc_final: 0.7906 (mmm) REVERT: D 248 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7622 (tt) REVERT: D 269 MET cc_start: 0.8700 (mtt) cc_final: 0.8455 (mtt) REVERT: D 413 MET cc_start: 0.7889 (mtp) cc_final: 0.7662 (mtp) REVERT: L 155 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8288 (tm-30) REVERT: L 168 GLU cc_start: 0.7992 (pt0) cc_final: 0.7424 (pt0) REVERT: L 243 ARG cc_start: 0.8098 (mtm110) cc_final: 0.7434 (mtm-85) REVERT: L 388 TRP cc_start: 0.8456 (m-10) cc_final: 0.7933 (m-10) REVERT: L 420 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8191 (mm-30) REVERT: L 432 TYR cc_start: 0.8547 (OUTLIER) cc_final: 0.7761 (t80) REVERT: I 26 ASP cc_start: 0.7363 (m-30) cc_final: 0.6994 (m-30) REVERT: I 37 HIS cc_start: 0.8005 (OUTLIER) cc_final: 0.7699 (m-70) REVERT: I 211 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8131 (t0) REVERT: I 213 CYS cc_start: 0.8478 (t) cc_final: 0.8132 (p) REVERT: I 248 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7791 (tt) REVERT: I 301 MET cc_start: 0.8252 (mmp) cc_final: 0.7986 (mmp) REVERT: I 325 MET cc_start: 0.8241 (mmm) cc_final: 0.8014 (mmm) REVERT: A 36 MET cc_start: 0.7501 (tmm) cc_final: 0.7092 (tmm) REVERT: A 101 ASN cc_start: 0.8956 (OUTLIER) cc_final: 0.8740 (t0) REVERT: A 230 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8725 (tt) REVERT: A 377 MET cc_start: 0.8106 (tmm) cc_final: 0.7554 (tmm) REVERT: B 323 MET cc_start: 0.8336 (mtm) cc_final: 0.7886 (mtm) REVERT: B 373 MET cc_start: 0.8278 (mtp) cc_final: 0.7991 (mtp) REVERT: B 398 MET cc_start: 0.8675 (tpp) cc_final: 0.8135 (mtt) REVERT: K 109 THR cc_start: 0.8603 (m) cc_final: 0.8222 (p) REVERT: K 178 SER cc_start: 0.8371 (OUTLIER) cc_final: 0.7927 (p) REVERT: K 205 ASP cc_start: 0.8053 (t0) cc_final: 0.7750 (t0) REVERT: K 212 ILE cc_start: 0.9180 (mt) cc_final: 0.8947 (mt) REVERT: K 313 MET cc_start: 0.9181 (mtm) cc_final: 0.8950 (mtm) REVERT: K 339 ARG cc_start: 0.7085 (mmp-170) cc_final: 0.6724 (mmp-170) REVERT: K 377 MET cc_start: 0.8075 (tmm) cc_final: 0.7771 (tmm) REVERT: K 432 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.7821 (m-80) REVERT: H 94 PHE cc_start: 0.8776 (p90) cc_final: 0.8050 (p90) REVERT: H 120 ASP cc_start: 0.8419 (m-30) cc_final: 0.8131 (m-30) REVERT: H 200 GLU cc_start: 0.8109 (pt0) cc_final: 0.7274 (pm20) REVERT: H 325 MET cc_start: 0.8275 (mmm) cc_final: 0.7631 (mmm) REVERT: H 373 MET cc_start: 0.8160 (mtm) cc_final: 0.7853 (mtm) REVERT: H 398 MET cc_start: 0.8485 (mmt) cc_final: 0.8030 (mmp) outliers start: 101 outliers final: 61 residues processed: 499 average time/residue: 0.2316 time to fit residues: 199.2264 Evaluate side-chains 463 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 389 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 130 THR 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 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 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 259 LEU 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 154 ILE Chi-restraints excluded: chain D residue 248 LEU 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 275 VAL 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 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 71 GLU 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 286 LEU Chi-restraints excluded: chain B residue 434 GLN 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 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 425 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 388 optimal weight: 7.9990 chunk 458 optimal weight: 0.9990 chunk 400 optimal weight: 5.9990 chunk 246 optimal weight: 5.9990 chunk 356 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 403 optimal weight: 2.9990 chunk 276 optimal weight: 2.9990 chunk 420 optimal weight: 10.0000 chunk 211 optimal weight: 10.0000 chunk 76 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 18 ASN E 50 ASN J 31 GLN J 101 ASN J 380 ASN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 ASN K 31 GLN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.084702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.071602 restraints weight = 88849.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.074320 restraints weight = 42091.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.076202 restraints weight = 25092.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.077495 restraints weight = 17135.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.078432 restraints weight = 12874.746| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 41424 Z= 0.131 Angle : 0.523 9.752 56292 Z= 0.269 Chirality : 0.042 0.239 6156 Planarity : 0.004 0.042 7320 Dihedral : 9.807 159.202 5671 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.54 % Allowed : 17.61 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.12), residues: 5088 helix: 2.08 (0.11), residues: 2358 sheet: 0.29 (0.18), residues: 852 loop : -0.49 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 284 TYR 0.033 0.001 TYR J 24 PHE 0.029 0.001 PHE C 255 TRP 0.032 0.002 TRP L 346 HIS 0.007 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (41424) covalent geometry : angle 0.52336 / 0.27 (56292) hydrogen bonds : bond 0.04129 / 2.79 ( 2075) hydrogen bonds : angle 4.40008 / 3.17 ( 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 515 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 405 time to evaluate : 1.831 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: 0.9294 (OUTLIER) cc_final: 0.9081 (p) REVERT: E 116 ASP cc_start: 0.8664 (t0) cc_final: 0.8376 (m-30) REVERT: E 154 MET cc_start: 0.9167 (tpp) cc_final: 0.8886 (mmt) REVERT: E 172 TYR cc_start: 0.8084 (t80) cc_final: 0.7586 (t80) REVERT: E 203 MET cc_start: 0.7514 (mtm) cc_final: 0.6885 (mtm) REVERT: E 205 ASP cc_start: 0.7869 (t0) cc_final: 0.7570 (t0) REVERT: E 230 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8971 (tt) REVERT: E 313 MET cc_start: 0.8509 (mtm) cc_final: 0.8196 (mtm) REVERT: E 398 MET cc_start: 0.9141 (tpp) cc_final: 0.8707 (mmt) REVERT: F 37 HIS cc_start: 0.7782 (m-70) cc_final: 0.7466 (m170) REVERT: F 205 ASP cc_start: 0.8259 (t0) cc_final: 0.8051 (t0) REVERT: F 373 MET cc_start: 0.8327 (mmm) cc_final: 0.8086 (mmm) REVERT: F 398 MET cc_start: 0.8542 (mmt) cc_final: 0.8136 (mtt) REVERT: J 88 HIS cc_start: 0.6183 (OUTLIER) cc_final: 0.5697 (m-70) REVERT: J 178 SER cc_start: 0.8345 (OUTLIER) cc_final: 0.8009 (p) REVERT: J 210 TYR cc_start: 0.8491 (m-80) cc_final: 0.7584 (m-80) REVERT: J 271 THR cc_start: 0.8919 (t) cc_final: 0.8059 (m) REVERT: J 357 TYR cc_start: 0.7980 (m-80) cc_final: 0.7665 (m-80) REVERT: J 425 MET cc_start: 0.9176 (mmm) cc_final: 0.8897 (tpp) REVERT: G 6 HIS cc_start: 0.8523 (t-90) cc_final: 0.7779 (t70) REVERT: G 75 MET cc_start: 0.9034 (mmt) cc_final: 0.8693 (mmt) REVERT: G 97 SER cc_start: 0.8967 (OUTLIER) cc_final: 0.8683 (p) REVERT: G 149 MET cc_start: 0.8867 (tpp) cc_final: 0.8624 (mmt) REVERT: G 176 LYS cc_start: 0.8905 (mmtm) cc_final: 0.8618 (mmmt) REVERT: G 302 MET cc_start: 0.7876 (mtt) cc_final: 0.7578 (mtt) REVERT: G 398 MET cc_start: 0.6583 (mmp) cc_final: 0.5954 (mmm) REVERT: C 36 MET cc_start: 0.7529 (tmm) cc_final: 0.7240 (tmm) REVERT: C 205 ASP cc_start: 0.7777 (t0) cc_final: 0.7333 (t0) REVERT: C 302 MET cc_start: 0.8785 (mmp) cc_final: 0.8547 (mmm) REVERT: C 313 MET cc_start: 0.8630 (mtm) cc_final: 0.8145 (mtm) REVERT: D 75 MET cc_start: 0.8945 (mmm) cc_final: 0.7867 (mmm) REVERT: D 248 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7636 (tt) REVERT: D 269 MET cc_start: 0.8694 (mtt) cc_final: 0.8450 (mtt) REVERT: D 413 MET cc_start: 0.7881 (mtp) cc_final: 0.7678 (mtp) REVERT: L 155 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8327 (tm-30) REVERT: L 168 GLU cc_start: 0.7921 (pt0) cc_final: 0.7340 (pt0) REVERT: L 172 TYR cc_start: 0.8114 (t80) cc_final: 0.7862 (t80) REVERT: L 243 ARG cc_start: 0.8057 (mtm110) cc_final: 0.7408 (mtm-85) REVERT: L 388 TRP cc_start: 0.8468 (m-10) cc_final: 0.7943 (m-10) REVERT: L 432 TYR cc_start: 0.8507 (OUTLIER) cc_final: 0.7514 (t80) REVERT: I 26 ASP cc_start: 0.7350 (m-30) cc_final: 0.6991 (m-30) REVERT: I 37 HIS cc_start: 0.8026 (OUTLIER) cc_final: 0.7710 (m-70) REVERT: I 211 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.8137 (t0) REVERT: I 213 CYS cc_start: 0.8486 (t) cc_final: 0.8147 (p) REVERT: I 248 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7806 (tt) REVERT: I 301 MET cc_start: 0.8216 (mmp) cc_final: 0.7964 (mmp) REVERT: A 36 MET cc_start: 0.7471 (tmm) cc_final: 0.7041 (tmm) REVERT: A 101 ASN cc_start: 0.8901 (OUTLIER) cc_final: 0.8667 (t0) REVERT: A 172 TYR cc_start: 0.7704 (OUTLIER) cc_final: 0.7473 (t80) REVERT: A 230 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8740 (tt) REVERT: B 323 MET cc_start: 0.8361 (mtm) cc_final: 0.7932 (mtm) REVERT: B 373 MET cc_start: 0.8287 (mtp) cc_final: 0.7993 (mtp) REVERT: B 398 MET cc_start: 0.8680 (tpp) cc_final: 0.8125 (mtt) REVERT: K 109 THR cc_start: 0.8658 (m) cc_final: 0.8292 (p) REVERT: K 178 SER cc_start: 0.8394 (OUTLIER) cc_final: 0.7951 (p) REVERT: K 205 ASP cc_start: 0.8058 (t0) cc_final: 0.7735 (t0) REVERT: K 212 ILE cc_start: 0.9181 (mt) cc_final: 0.8946 (mt) REVERT: K 377 MET cc_start: 0.8125 (tmm) cc_final: 0.7798 (tmm) REVERT: K 432 TYR cc_start: 0.8617 (OUTLIER) cc_final: 0.7964 (m-80) REVERT: H 26 ASP cc_start: 0.8506 (t0) cc_final: 0.8135 (p0) REVERT: H 94 PHE cc_start: 0.8769 (p90) cc_final: 0.8076 (p90) REVERT: H 113 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8545 (pp20) REVERT: H 120 ASP cc_start: 0.8419 (m-30) cc_final: 0.8147 (m-30) REVERT: H 200 GLU cc_start: 0.8131 (pt0) cc_final: 0.7199 (pm20) REVERT: H 325 MET cc_start: 0.8274 (mmm) cc_final: 0.7738 (mmm) REVERT: H 373 MET cc_start: 0.8134 (mtm) cc_final: 0.7816 (mtm) REVERT: H 393 GLU cc_start: 0.8158 (pp20) cc_final: 0.7940 (pp20) REVERT: H 398 MET cc_start: 0.8493 (mmt) cc_final: 0.8048 (mmp) outliers start: 110 outliers final: 73 residues processed: 490 average time/residue: 0.2283 time to fit residues: 191.9751 Evaluate side-chains 471 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 383 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 18 ASN 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 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 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 275 VAL Chi-restraints excluded: chain J residue 378 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 259 LEU 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 154 ILE Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain L residue 6 SER 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 275 VAL 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 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 26 LEU Chi-restraints excluded: chain A residue 71 GLU 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 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 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 425 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 234 optimal weight: 0.0970 chunk 497 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 184 optimal weight: 4.9990 chunk 283 optimal weight: 1.9990 chunk 249 optimal weight: 0.9990 chunk 344 optimal weight: 8.9990 chunk 351 optimal weight: 10.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 18 ASN E 31 GLN J 192 HIS ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 258 ASN A 101 ASN H 6 HIS H 349 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.084101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.071098 restraints weight = 88770.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.073774 restraints weight = 42228.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.075640 restraints weight = 25242.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.076930 restraints weight = 17245.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.077846 restraints weight = 12898.221| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 41424 Z= 0.144 Angle : 0.536 11.340 56292 Z= 0.276 Chirality : 0.042 0.238 6156 Planarity : 0.004 0.052 7320 Dihedral : 9.599 152.769 5671 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.40 % Allowed : 18.05 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.12), residues: 5088 helix: 2.05 (0.11), residues: 2358 sheet: 0.48 (0.18), residues: 798 loop : -0.52 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 308 TYR 0.027 0.001 TYR J 24 PHE 0.032 0.001 PHE C 255 TRP 0.032 0.002 TRP L 346 HIS 0.007 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (41424) covalent geometry : angle 0.53626 / 0.28 (56292) hydrogen bonds : bond 0.04207 / 2.84 ( 2075) hydrogen bonds : angle 4.41962 / 3.18 ( 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 512 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 408 time to evaluate : 1.704 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: 0.9281 (OUTLIER) cc_final: 0.9058 (p) REVERT: E 116 ASP cc_start: 0.8661 (t0) cc_final: 0.8356 (m-30) REVERT: E 154 MET cc_start: 0.9174 (tpp) cc_final: 0.8913 (mmt) REVERT: E 172 TYR cc_start: 0.8090 (t80) cc_final: 0.7603 (t80) REVERT: E 203 MET cc_start: 0.7531 (mtm) cc_final: 0.6898 (mtm) REVERT: E 205 ASP cc_start: 0.7807 (t0) cc_final: 0.7511 (t0) REVERT: E 313 MET cc_start: 0.8490 (mtm) cc_final: 0.8223 (mtm) REVERT: E 398 MET cc_start: 0.9146 (tpp) cc_final: 0.8706 (mmt) REVERT: F 205 ASP cc_start: 0.8196 (t0) cc_final: 0.7909 (t0) REVERT: F 373 MET cc_start: 0.8285 (mmm) cc_final: 0.8047 (mmm) REVERT: F 398 MET cc_start: 0.8515 (mmt) cc_final: 0.8137 (mtt) REVERT: J 24 TYR cc_start: 0.8759 (m-80) cc_final: 0.8463 (m-80) REVERT: J 88 HIS cc_start: 0.6085 (OUTLIER) cc_final: 0.5636 (m-70) REVERT: J 101 ASN cc_start: 0.8952 (OUTLIER) cc_final: 0.7936 (t0) REVERT: J 168 GLU cc_start: 0.7787 (pt0) cc_final: 0.7367 (pt0) REVERT: J 178 SER cc_start: 0.8354 (OUTLIER) cc_final: 0.8009 (p) REVERT: J 194 THR cc_start: 0.8696 (m) cc_final: 0.8299 (m) REVERT: J 210 TYR cc_start: 0.8488 (m-80) cc_final: 0.7581 (m-80) REVERT: J 271 THR cc_start: 0.8927 (t) cc_final: 0.8020 (m) REVERT: J 357 TYR cc_start: 0.8007 (m-80) cc_final: 0.7685 (m-80) REVERT: J 425 MET cc_start: 0.9177 (mmm) cc_final: 0.8900 (tpp) REVERT: G 6 HIS cc_start: 0.8562 (t-90) cc_final: 0.7880 (t70) REVERT: G 75 MET cc_start: 0.9026 (mmt) cc_final: 0.8651 (mmt) REVERT: G 97 SER cc_start: 0.8945 (OUTLIER) cc_final: 0.8662 (p) REVERT: G 200 GLU cc_start: 0.7894 (pt0) cc_final: 0.7076 (pm20) REVERT: G 302 MET cc_start: 0.7904 (mtt) cc_final: 0.7601 (mtt) REVERT: G 398 MET cc_start: 0.6713 (mmp) cc_final: 0.6204 (mmm) REVERT: C 36 MET cc_start: 0.7543 (tmm) cc_final: 0.7263 (tmm) REVERT: C 205 ASP cc_start: 0.7822 (t0) cc_final: 0.7382 (t0) REVERT: C 313 MET cc_start: 0.8587 (mtm) cc_final: 0.8290 (mtm) REVERT: D 75 MET cc_start: 0.8940 (mmm) cc_final: 0.7868 (mmm) REVERT: D 166 MET cc_start: 0.8264 (tpp) cc_final: 0.7644 (mmm) REVERT: D 248 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7837 (tt) REVERT: D 413 MET cc_start: 0.7922 (mtp) cc_final: 0.7710 (mtp) REVERT: L 155 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8347 (tm-30) REVERT: L 168 GLU cc_start: 0.7847 (pt0) cc_final: 0.7250 (pt0) REVERT: L 243 ARG cc_start: 0.8100 (mtm110) cc_final: 0.7425 (mtm-85) REVERT: L 388 TRP cc_start: 0.8544 (m-10) cc_final: 0.8047 (m-10) REVERT: L 432 TYR cc_start: 0.8509 (OUTLIER) cc_final: 0.7540 (t80) REVERT: I 26 ASP cc_start: 0.7353 (m-30) cc_final: 0.7011 (m-30) REVERT: I 37 HIS cc_start: 0.7973 (OUTLIER) cc_final: 0.7658 (m-70) REVERT: I 211 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8078 (t0) REVERT: I 213 CYS cc_start: 0.8414 (t) cc_final: 0.8049 (p) REVERT: I 248 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7897 (tt) REVERT: I 301 MET cc_start: 0.8230 (mmp) cc_final: 0.7984 (mmp) REVERT: A 230 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8746 (tt) REVERT: A 377 MET cc_start: 0.8196 (tmm) cc_final: 0.7439 (tmm) REVERT: B 323 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7909 (mtp) REVERT: B 373 MET cc_start: 0.8287 (mtp) cc_final: 0.7991 (mtp) REVERT: B 398 MET cc_start: 0.8698 (tpp) cc_final: 0.8136 (mtt) REVERT: K 109 THR cc_start: 0.8684 (m) cc_final: 0.8315 (p) REVERT: K 178 SER cc_start: 0.8409 (OUTLIER) cc_final: 0.7944 (p) REVERT: K 205 ASP cc_start: 0.8094 (t0) cc_final: 0.7784 (t0) REVERT: K 212 ILE cc_start: 0.9167 (mt) cc_final: 0.8919 (mt) REVERT: K 377 MET cc_start: 0.8155 (tmm) cc_final: 0.7809 (tmm) REVERT: K 413 MET cc_start: 0.7868 (tpp) cc_final: 0.7385 (mpp) REVERT: K 432 TYR cc_start: 0.8595 (OUTLIER) cc_final: 0.7972 (m-80) REVERT: H 26 ASP cc_start: 0.8481 (t0) cc_final: 0.8042 (p0) REVERT: H 94 PHE cc_start: 0.8752 (p90) cc_final: 0.8037 (p90) REVERT: H 120 ASP cc_start: 0.8410 (m-30) cc_final: 0.8144 (m-30) REVERT: H 200 GLU cc_start: 0.8038 (pt0) cc_final: 0.7189 (pm20) REVERT: H 325 MET cc_start: 0.8223 (mmm) cc_final: 0.7660 (mmm) REVERT: H 373 MET cc_start: 0.8132 (mtm) cc_final: 0.7810 (mtm) REVERT: H 378 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.9005 (mm) REVERT: H 398 MET cc_start: 0.8493 (mmt) cc_final: 0.7931 (mmp) outliers start: 104 outliers final: 78 residues processed: 490 average time/residue: 0.2384 time to fit residues: 200.4867 Evaluate side-chains 485 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 392 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 18 ASN 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 220 THR 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 259 LEU Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 378 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 259 LEU 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 220 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain L residue 6 SER 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 271 THR Chi-restraints excluded: chain L residue 275 VAL 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 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 26 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 71 GLU 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 286 LEU Chi-restraints excluded: chain B residue 323 MET 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 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 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 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: 2.9990 chunk 174 optimal weight: 5.9990 chunk 169 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 359 optimal weight: 10.0000 chunk 248 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 163 optimal weight: 10.0000 chunk 403 optimal weight: 0.4980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 18 ASN F 6 HIS F 434 GLN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 ASN K 380 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.083933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.070905 restraints weight = 89601.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.073589 restraints weight = 42576.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.075469 restraints weight = 25445.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.076719 restraints weight = 17351.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.077666 restraints weight = 13075.610| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 41424 Z= 0.145 Angle : 0.542 11.727 56292 Z= 0.279 Chirality : 0.042 0.246 6156 Planarity : 0.004 0.042 7320 Dihedral : 9.427 146.444 5671 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.42 % Allowed : 18.21 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.12), residues: 5088 helix: 2.00 (0.11), residues: 2382 sheet: 0.45 (0.18), residues: 798 loop : -0.55 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 308 TYR 0.029 0.001 TYR L 172 PHE 0.032 0.001 PHE C 255 TRP 0.033 0.002 TRP L 346 HIS 0.007 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (41424) covalent geometry : angle 0.54175 / 0.28 (56292) hydrogen bonds : bond 0.04208 / 2.84 ( 2075) hydrogen bonds : angle 4.43195 / 3.19 ( 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 513 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 408 time to evaluate : 1.609 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 6 SER cc_start: 0.9277 (OUTLIER) cc_final: 0.9050 (p) REVERT: E 24 TYR cc_start: 0.9046 (m-80) cc_final: 0.8815 (m-80) REVERT: E 116 ASP cc_start: 0.8657 (t0) cc_final: 0.8354 (m-30) REVERT: E 154 MET cc_start: 0.9253 (tpp) cc_final: 0.9020 (mmt) REVERT: E 172 TYR cc_start: 0.8107 (t80) cc_final: 0.7644 (t80) REVERT: E 203 MET cc_start: 0.7499 (mtm) cc_final: 0.6821 (mtm) REVERT: E 205 ASP cc_start: 0.7786 (t0) cc_final: 0.7513 (t0) REVERT: E 313 MET cc_start: 0.8486 (mtm) cc_final: 0.8234 (mtm) REVERT: E 398 MET cc_start: 0.9145 (tpp) cc_final: 0.8698 (mmt) REVERT: F 205 ASP cc_start: 0.8206 (t0) cc_final: 0.7874 (t0) REVERT: F 259 MET cc_start: 0.8615 (mmm) cc_final: 0.7718 (mpp) REVERT: F 373 MET cc_start: 0.8295 (mmm) cc_final: 0.8053 (mmm) REVERT: F 398 MET cc_start: 0.8515 (mmt) cc_final: 0.8159 (mtt) REVERT: J 24 TYR cc_start: 0.8660 (m-80) cc_final: 0.8362 (m-80) REVERT: J 88 HIS cc_start: 0.6126 (OUTLIER) cc_final: 0.5726 (m-70) REVERT: J 101 ASN cc_start: 0.9042 (OUTLIER) cc_final: 0.8032 (t0) REVERT: J 168 GLU cc_start: 0.7860 (pt0) cc_final: 0.7485 (pt0) REVERT: J 178 SER cc_start: 0.8364 (OUTLIER) cc_final: 0.8024 (p) REVERT: J 194 THR cc_start: 0.8747 (m) cc_final: 0.8328 (m) REVERT: J 210 TYR cc_start: 0.8465 (m-80) cc_final: 0.7533 (m-80) REVERT: J 271 THR cc_start: 0.8920 (t) cc_final: 0.8020 (m) REVERT: J 357 TYR cc_start: 0.8017 (m-80) cc_final: 0.7691 (m-80) REVERT: J 425 MET cc_start: 0.9176 (mmm) cc_final: 0.8947 (tpp) REVERT: G 6 HIS cc_start: 0.8485 (t-90) cc_final: 0.7836 (t70) REVERT: G 75 MET cc_start: 0.9010 (mmt) cc_final: 0.8700 (mmt) REVERT: G 97 SER cc_start: 0.8906 (OUTLIER) cc_final: 0.8619 (p) REVERT: G 200 GLU cc_start: 0.7966 (pt0) cc_final: 0.6868 (pm20) REVERT: G 302 MET cc_start: 0.7937 (mtt) cc_final: 0.7638 (mtt) REVERT: G 398 MET cc_start: 0.6740 (mmp) cc_final: 0.6302 (mmm) REVERT: C 36 MET cc_start: 0.7576 (tmm) cc_final: 0.7297 (tmm) REVERT: C 205 ASP cc_start: 0.7808 (t0) cc_final: 0.7347 (t0) REVERT: C 313 MET cc_start: 0.8576 (mtm) cc_final: 0.8284 (mtm) REVERT: D 75 MET cc_start: 0.8949 (mmm) cc_final: 0.7847 (mmm) REVERT: D 166 MET cc_start: 0.8290 (tpp) cc_final: 0.7724 (mmm) REVERT: D 248 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.7876 (tt) REVERT: D 259 MET cc_start: 0.8329 (mmm) cc_final: 0.8083 (mtp) REVERT: D 413 MET cc_start: 0.7927 (mtp) cc_final: 0.7702 (mtp) REVERT: L 155 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8357 (tm-30) REVERT: L 168 GLU cc_start: 0.7852 (pt0) cc_final: 0.7232 (pt0) REVERT: L 243 ARG cc_start: 0.8150 (mtm110) cc_final: 0.7439 (mtm-85) REVERT: L 388 TRP cc_start: 0.8540 (m-10) cc_final: 0.8021 (m-10) REVERT: L 432 TYR cc_start: 0.8417 (OUTLIER) cc_final: 0.7305 (t80) REVERT: I 26 ASP cc_start: 0.7226 (m-30) cc_final: 0.6897 (m-30) REVERT: I 37 HIS cc_start: 0.7984 (OUTLIER) cc_final: 0.7662 (m-70) REVERT: I 211 ASP cc_start: 0.8633 (OUTLIER) cc_final: 0.8086 (t0) REVERT: I 213 CYS cc_start: 0.8361 (t) cc_final: 0.7956 (p) REVERT: I 248 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7898 (tt) REVERT: I 301 MET cc_start: 0.8232 (mmp) cc_final: 0.7919 (mmp) REVERT: A 230 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8753 (tt) REVERT: B 170 SER cc_start: 0.8919 (m) cc_final: 0.8253 (p) REVERT: B 323 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7883 (mtm) REVERT: B 373 MET cc_start: 0.8277 (mtp) cc_final: 0.7976 (mtp) REVERT: B 398 MET cc_start: 0.8703 (tpp) cc_final: 0.8152 (mtt) REVERT: K 109 THR cc_start: 0.8653 (m) cc_final: 0.8276 (p) REVERT: K 178 SER cc_start: 0.8425 (OUTLIER) cc_final: 0.7964 (p) REVERT: K 203 MET cc_start: 0.7574 (mtm) cc_final: 0.7360 (mtp) REVERT: K 205 ASP cc_start: 0.8087 (t0) cc_final: 0.7777 (t0) REVERT: K 212 ILE cc_start: 0.9155 (mt) cc_final: 0.8903 (mt) REVERT: K 377 MET cc_start: 0.8201 (tmm) cc_final: 0.7838 (tmm) REVERT: K 413 MET cc_start: 0.7916 (tpp) cc_final: 0.7493 (mpp) REVERT: K 432 TYR cc_start: 0.8633 (OUTLIER) cc_final: 0.8038 (m-80) REVERT: H 26 ASP cc_start: 0.8513 (t0) cc_final: 0.7989 (p0) REVERT: H 94 PHE cc_start: 0.8742 (p90) cc_final: 0.8030 (p90) REVERT: H 113 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8531 (pp20) REVERT: H 120 ASP cc_start: 0.8356 (m-30) cc_final: 0.8086 (m-30) REVERT: H 200 GLU cc_start: 0.7997 (pt0) cc_final: 0.7182 (pm20) REVERT: H 325 MET cc_start: 0.8229 (mmm) cc_final: 0.7724 (mmm) REVERT: H 373 MET cc_start: 0.8217 (mtm) cc_final: 0.7891 (mtm) REVERT: H 378 ILE cc_start: 0.9295 (OUTLIER) cc_final: 0.9003 (mm) REVERT: H 393 GLU cc_start: 0.8060 (pp20) cc_final: 0.7706 (pp20) REVERT: H 398 MET cc_start: 0.8491 (mmt) cc_final: 0.7943 (mmp) outliers start: 105 outliers final: 76 residues processed: 490 average time/residue: 0.2325 time to fit residues: 196.6011 Evaluate side-chains 489 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 398 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 130 THR 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 302 MET 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 259 LEU Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 378 LEU Chi-restraints excluded: chain J residue 432 TYR 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 259 LEU 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 154 ILE Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 6 SER 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 271 THR Chi-restraints excluded: chain L residue 275 VAL 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 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 26 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 71 GLU 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 286 LEU Chi-restraints excluded: chain B residue 323 MET 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 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 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 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 112 optimal weight: 8.9990 chunk 289 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 472 optimal weight: 10.0000 chunk 96 optimal weight: 0.0970 chunk 255 optimal weight: 0.5980 chunk 375 optimal weight: 0.0070 chunk 214 optimal weight: 0.9990 chunk 123 optimal weight: 7.9990 chunk 425 optimal weight: 0.0010 chunk 398 optimal weight: 1.9990 overall best weight: 0.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 18 ASN C 18 ASN C 139 HIS ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 249 ASN A 101 ASN H 350 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.089305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.076115 restraints weight = 86440.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.079014 restraints weight = 40074.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.080983 restraints weight = 23519.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.082330 restraints weight = 15886.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.083302 restraints weight = 11775.498| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 41424 Z= 0.100 Angle : 0.523 12.080 56292 Z= 0.267 Chirality : 0.041 0.250 6156 Planarity : 0.004 0.043 7320 Dihedral : 9.048 138.626 5671 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.59 % Allowed : 18.88 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.12), residues: 5088 helix: 2.02 (0.11), residues: 2370 sheet: 0.41 (0.18), residues: 834 loop : -0.40 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 308 TYR 0.029 0.001 TYR J 24 PHE 0.033 0.001 PHE C 255 TRP 0.032 0.002 TRP L 346 HIS 0.005 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (41424) covalent geometry : angle 0.52280 / 0.27 (56292) hydrogen bonds : bond 0.03553 / 2.40 ( 2075) hydrogen bonds : angle 4.33415 / 3.12 ( 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 552 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 483 time to evaluate : 1.648 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 36 MET cc_start: 0.8120 (tmm) cc_final: 0.7682 (tmm) REVERT: E 116 ASP cc_start: 0.8741 (t0) cc_final: 0.8369 (m-30) REVERT: E 154 MET cc_start: 0.9194 (tpp) cc_final: 0.8942 (mmt) REVERT: E 172 TYR cc_start: 0.8095 (t80) cc_final: 0.7631 (t80) REVERT: E 203 MET cc_start: 0.7535 (mtm) cc_final: 0.6857 (mtm) REVERT: E 205 ASP cc_start: 0.7717 (t0) cc_final: 0.7372 (t0) REVERT: E 313 MET cc_start: 0.8550 (mtm) cc_final: 0.8215 (mtm) REVERT: E 398 MET cc_start: 0.9156 (tpp) cc_final: 0.8702 (mmt) REVERT: F 145 THR cc_start: 0.7755 (m) cc_final: 0.7369 (m) REVERT: F 205 ASP cc_start: 0.8109 (t0) cc_final: 0.7707 (t0) REVERT: F 259 MET cc_start: 0.8636 (mmm) cc_final: 0.7880 (mpp) REVERT: F 398 MET cc_start: 0.8524 (mmt) cc_final: 0.8226 (mtt) REVERT: J 24 TYR cc_start: 0.8644 (m-80) cc_final: 0.8305 (m-80) REVERT: J 101 ASN cc_start: 0.8990 (OUTLIER) cc_final: 0.7941 (t0) REVERT: J 168 GLU cc_start: 0.7893 (pt0) cc_final: 0.7479 (pt0) REVERT: J 178 SER cc_start: 0.8378 (OUTLIER) cc_final: 0.8043 (p) REVERT: J 194 THR cc_start: 0.8871 (m) cc_final: 0.8434 (m) REVERT: J 210 TYR cc_start: 0.8424 (m-80) cc_final: 0.7481 (m-80) REVERT: J 271 THR cc_start: 0.8915 (t) cc_final: 0.8362 (m) REVERT: J 357 TYR cc_start: 0.8103 (m-80) cc_final: 0.7793 (m-80) REVERT: J 376 CYS cc_start: 0.8677 (t) cc_final: 0.8347 (t) REVERT: J 377 MET cc_start: 0.8181 (tmm) cc_final: 0.7930 (tmm) REVERT: J 425 MET cc_start: 0.9164 (mmm) cc_final: 0.8946 (tpp) REVERT: G 6 HIS cc_start: 0.8436 (t-90) cc_final: 0.7882 (t-170) REVERT: G 75 MET cc_start: 0.8976 (mmt) cc_final: 0.8698 (mmt) REVERT: G 97 SER cc_start: 0.8864 (OUTLIER) cc_final: 0.8602 (p) REVERT: G 302 MET cc_start: 0.7874 (mtt) cc_final: 0.7596 (mtt) REVERT: G 398 MET cc_start: 0.6687 (mmp) cc_final: 0.6089 (mmm) REVERT: G 413 MET cc_start: 0.8506 (mmm) cc_final: 0.8271 (mmm) REVERT: C 36 MET cc_start: 0.7529 (tmm) cc_final: 0.7237 (tmm) REVERT: C 154 MET cc_start: 0.8969 (mmm) cc_final: 0.8705 (mmm) REVERT: C 205 ASP cc_start: 0.7724 (t0) cc_final: 0.7270 (t0) REVERT: D 69 ASP cc_start: 0.7803 (t0) cc_final: 0.7526 (t0) REVERT: D 75 MET cc_start: 0.8870 (mmm) cc_final: 0.7978 (mmm) REVERT: D 166 MET cc_start: 0.8111 (tpp) cc_final: 0.7675 (mmm) REVERT: D 248 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7768 (tt) REVERT: D 413 MET cc_start: 0.7909 (mtp) cc_final: 0.7667 (mtp) REVERT: L 155 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8374 (tm-30) REVERT: L 168 GLU cc_start: 0.7854 (pt0) cc_final: 0.7183 (pt0) REVERT: L 243 ARG cc_start: 0.7933 (mtm110) cc_final: 0.7329 (mtm-85) REVERT: L 313 MET cc_start: 0.9137 (mtm) cc_final: 0.8833 (mtm) REVERT: L 377 MET cc_start: 0.8356 (tmm) cc_final: 0.7800 (tmm) REVERT: L 388 TRP cc_start: 0.8482 (m-10) cc_final: 0.7982 (m-10) REVERT: L 424 ASP cc_start: 0.8763 (t70) cc_final: 0.8183 (t0) REVERT: L 432 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.7473 (t80) REVERT: I 26 ASP cc_start: 0.7226 (m-30) cc_final: 0.6765 (m-30) REVERT: I 37 HIS cc_start: 0.8002 (OUTLIER) cc_final: 0.7763 (m-70) REVERT: I 211 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.8062 (t0) REVERT: I 213 CYS cc_start: 0.8388 (t) cc_final: 0.7922 (p) REVERT: I 248 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7695 (tt) REVERT: I 301 MET cc_start: 0.8177 (mmp) cc_final: 0.7891 (mmp) REVERT: A 149 PHE cc_start: 0.9009 (t80) cc_final: 0.8666 (t80) REVERT: A 313 MET cc_start: 0.8491 (mtm) cc_final: 0.8248 (mtm) REVERT: B 170 SER cc_start: 0.8930 (m) cc_final: 0.8317 (p) REVERT: B 309 HIS cc_start: 0.8462 (m170) cc_final: 0.8141 (m90) REVERT: B 323 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7799 (mtm) REVERT: B 373 MET cc_start: 0.8343 (mtp) cc_final: 0.8037 (mtp) REVERT: B 398 MET cc_start: 0.8666 (tpp) cc_final: 0.8104 (mtt) REVERT: K 109 THR cc_start: 0.8641 (m) cc_final: 0.8226 (p) REVERT: K 178 SER cc_start: 0.8458 (OUTLIER) cc_final: 0.7989 (p) REVERT: K 203 MET cc_start: 0.7484 (mtm) cc_final: 0.7260 (mtp) REVERT: K 205 ASP cc_start: 0.7980 (t0) cc_final: 0.7693 (t0) REVERT: K 212 ILE cc_start: 0.9018 (mt) cc_final: 0.8797 (mt) REVERT: K 237 SER cc_start: 0.8809 (m) cc_final: 0.8241 (p) REVERT: K 413 MET cc_start: 0.7676 (tpp) cc_final: 0.7309 (mpp) REVERT: K 432 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.8049 (m-80) REVERT: H 26 ASP cc_start: 0.8389 (t0) cc_final: 0.7856 (m-30) REVERT: H 94 PHE cc_start: 0.8773 (p90) cc_final: 0.8082 (p90) REVERT: H 113 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8565 (pp20) REVERT: H 114 LEU cc_start: 0.9186 (tp) cc_final: 0.8913 (tt) REVERT: H 120 ASP cc_start: 0.8518 (m-30) cc_final: 0.8235 (m-30) REVERT: H 200 GLU cc_start: 0.7883 (pt0) cc_final: 0.6890 (pm20) REVERT: H 325 MET cc_start: 0.8246 (mmm) cc_final: 0.7686 (mmm) REVERT: H 378 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8943 (mm) REVERT: H 393 GLU cc_start: 0.8094 (pp20) cc_final: 0.7712 (pp20) REVERT: H 398 MET cc_start: 0.8503 (mmt) cc_final: 0.7901 (mmp) outliers start: 69 outliers final: 44 residues processed: 535 average time/residue: 0.2379 time to fit residues: 218.2702 Evaluate side-chains 475 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 419 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain J residue 66 VAL 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 432 TYR 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 150 THR Chi-restraints excluded: chain C residue 259 LEU 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 L residue 4 CYS Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 200 CYS 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 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 71 GLU Chi-restraints excluded: chain A residue 182 VAL 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 323 MET Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain K residue 66 VAL 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 432 TYR Chi-restraints excluded: chain H residue 5 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: 3.9990 chunk 417 optimal weight: 3.9990 chunk 332 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 396 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 300 optimal weight: 0.0070 chunk 88 optimal weight: 0.0670 chunk 168 optimal weight: 10.0000 chunk 154 optimal weight: 4.9990 chunk 490 optimal weight: 0.9990 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 28 HIS ** G 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 ASN D 133 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.088416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.075153 restraints weight = 87172.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.078042 restraints weight = 40673.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.079999 restraints weight = 23937.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.081335 restraints weight = 16216.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.082296 restraints weight = 12068.806| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 41424 Z= 0.111 Angle : 0.535 12.381 56292 Z= 0.273 Chirality : 0.042 0.234 6156 Planarity : 0.004 0.052 7320 Dihedral : 8.942 135.848 5671 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.62 % Allowed : 19.09 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.12), residues: 5088 helix: 2.02 (0.11), residues: 2370 sheet: 0.55 (0.19), residues: 798 loop : -0.44 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 284 TYR 0.047 0.001 TYR E 24 PHE 0.032 0.001 PHE C 255 TRP 0.032 0.002 TRP L 346 HIS 0.007 0.001 HIS A 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (41424) covalent geometry : angle 0.53453 / 0.27 (56292) hydrogen bonds : bond 0.03685 / 2.49 ( 2075) hydrogen bonds : angle 4.33260 / 3.11 ( 5973) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6894.94 seconds wall clock time: 120 minutes 40.15 seconds (7240.15 seconds total)