Starting phenix.real_space_refine on Tue Sep 15 13:13:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5jco_8150/09_2026/5jco_8150.cif Found real_map, /net/cci-nas-00/data/ceres_data/5jco_8150/09_2026/5jco_8150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5jco_8150/09_2026/5jco_8150.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5jco_8150/09_2026/5jco_8150.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/5jco_8150/09_2026/5jco_8150.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5jco_8150/09_2026/5jco_8150.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5jco_8150/09_2026/5jco_8150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5jco_8150/09_2026/5jco_8150.map" } resolution = 4.0 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= 0.004 sd= 0.016 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 25488 2.51 5 N 6912 2.21 5 O 7788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 324 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40512 Number of models: 1 Model: "" Number of chains: 24 Chain: "K" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3341 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} 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: "H" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3345 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3341 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} 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: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3345 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "J" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3341 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} 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: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3341 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} 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: "D" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3341 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} 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: "F" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3345 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3345 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3345 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3341 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} 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: "G" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3345 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, '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: "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: "J" 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, 'G2P': 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: "F" 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: "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, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.04, per 1000 atoms: 0.20 Number of scatterers: 40512 At special positions: 0 Unit cell: (174.46, 86.62, 213.5, 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 7788 8.00 N 6912 7.00 C 25488 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.54 Conformation dependent library (CDL) restraints added in 1.8 seconds 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 56.3% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'K' and resid 10 through 28 Processing helix chain 'K' and resid 40 through 46 removed outlier: 3.529A pdb=" N LEU K 44 " --> pdb=" O SER K 40 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG K 46 " --> pdb=" O LEU K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 49 No H-bonds generated for 'chain 'K' and resid 47 through 49' Processing helix chain 'K' and resid 54 through 58 removed outlier: 3.698A pdb=" N HIS K 57 " --> pdb=" O ALA K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 79 removed outlier: 4.519A pdb=" N MET K 73 " --> pdb=" O GLU K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 85 removed outlier: 3.761A pdb=" N PHE K 85 " --> pdb=" O GLY K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 88 No H-bonds generated for 'chain 'K' and resid 86 through 88' Processing helix chain 'K' and resid 100 through 106 Processing helix chain 'K' and resid 108 through 127 removed outlier: 4.451A pdb=" N ASP K 114 " --> pdb=" O ALA K 110 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N SER K 115 " --> pdb=" O GLU K 111 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL K 116 " --> pdb=" O LEU K 112 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS K 127 " --> pdb=" O GLU K 123 " (cutoff:3.500A) Processing helix chain 'K' and resid 141 through 159 removed outlier: 3.642A pdb=" N SER K 145 " --> pdb=" O GLY K 141 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY K 148 " --> pdb=" O GLY K 144 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 196 removed outlier: 3.836A pdb=" N GLU K 194 " --> pdb=" O HIS K 190 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN K 195 " --> pdb=" O GLN K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 204 through 214 Processing helix chain 'K' and resid 221 through 237 removed outlier: 3.727A pdb=" N LEU K 228 " --> pdb=" O ASP K 224 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL K 229 " --> pdb=" O LEU K 225 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR K 237 " --> pdb=" O MET K 233 " (cutoff:3.500A) Processing helix chain 'K' and resid 237 through 242 removed outlier: 3.518A pdb=" N ARG K 241 " --> pdb=" O THR K 237 " (cutoff:3.500A) Processing helix chain 'K' and resid 249 through 258 Processing helix chain 'K' and resid 285 through 294 removed outlier: 3.500A pdb=" N PHE K 294 " --> pdb=" O THR K 290 " (cutoff:3.500A) Processing helix chain 'K' and resid 295 through 299 Processing helix chain 'K' and resid 304 through 308 removed outlier: 3.507A pdb=" N GLY K 308 " --> pdb=" O PRO K 305 " (cutoff:3.500A) Processing helix chain 'K' and resid 322 through 337 removed outlier: 3.886A pdb=" N ASN K 337 " --> pdb=" O ILE K 333 " (cutoff:3.500A) Processing helix chain 'K' and resid 338 through 341 Processing helix chain 'K' and resid 373 through 391 removed outlier: 4.231A pdb=" N LEU K 377 " --> pdb=" O ALA K 373 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE K 381 " --> pdb=" O LEU K 377 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARG K 391 " --> pdb=" O ALA K 387 " (cutoff:3.500A) Processing helix chain 'K' and resid 394 through 400 removed outlier: 4.188A pdb=" N TYR K 398 " --> pdb=" O PHE K 394 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 426 removed outlier: 3.875A pdb=" N PHE K 408 " --> pdb=" O ASP K 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 29 Processing helix chain 'H' and resid 47 through 51 removed outlier: 3.835A pdb=" N THR H 51 " --> pdb=" O SER H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 80 removed outlier: 3.575A pdb=" N GLU H 77 " --> pdb=" O THR H 73 " (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 110 through 129 removed outlier: 4.076A pdb=" N ILE H 114 " --> pdb=" O ILE H 110 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ASP H 116 " --> pdb=" O LYS H 112 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LEU H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 143 through 161 removed outlier: 4.393A pdb=" N THR H 150 " --> pdb=" O GLY H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 178 removed outlier: 3.739A pdb=" N SER H 178 " --> pdb=" O PRO H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 198 removed outlier: 4.166A pdb=" N GLU H 196 " --> pdb=" O HIS H 192 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N HIS H 197 " --> pdb=" O THR H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 217 Processing helix chain 'H' and resid 223 through 244 removed outlier: 3.592A pdb=" N ARG H 229 " --> pdb=" O THR H 225 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU H 230 " --> pdb=" O ASN H 226 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N SER H 241 " --> pdb=" O SER H 237 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU H 242 " --> pdb=" O ILE H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 260 removed outlier: 3.527A pdb=" N PHE H 255 " --> pdb=" O ASP H 251 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN H 256 " --> pdb=" O LEU H 252 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL H 260 " --> pdb=" O GLN H 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 284 removed outlier: 3.839A pdb=" N TYR H 282 " --> pdb=" O GLU H 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 287 through 296 Processing helix chain 'H' and resid 297 through 301 Processing helix chain 'H' and resid 324 through 338 Processing helix chain 'H' and resid 384 through 401 removed outlier: 3.624A pdb=" N TRP H 388 " --> pdb=" O ILE H 384 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET H 398 " --> pdb=" O LYS H 394 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS H 401 " --> pdb=" O LEU H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 410 removed outlier: 4.214A pdb=" N TYR H 408 " --> pdb=" O PHE H 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 415 through 436 removed outlier: 3.826A pdb=" N SER H 419 " --> pdb=" O GLU H 415 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 28 Processing helix chain 'I' and resid 40 through 46 removed outlier: 3.530A pdb=" N LEU I 44 " --> pdb=" O SER I 40 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG I 46 " --> pdb=" O LEU I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 49 No H-bonds generated for 'chain 'I' and resid 47 through 49' Processing helix chain 'I' and resid 54 through 58 removed outlier: 3.702A pdb=" N HIS I 57 " --> pdb=" O ALA I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 79 removed outlier: 4.519A pdb=" N MET I 73 " --> pdb=" O GLU I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 85 removed outlier: 3.760A pdb=" N PHE I 85 " --> pdb=" O GLY I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 88 No H-bonds generated for 'chain 'I' and resid 86 through 88' Processing helix chain 'I' and resid 100 through 106 Processing helix chain 'I' and resid 108 through 127 removed outlier: 4.452A pdb=" N ASP I 114 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N SER I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL I 116 " --> pdb=" O LEU I 112 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS I 127 " --> pdb=" O GLU I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 159 removed outlier: 3.643A pdb=" N SER I 145 " --> pdb=" O GLY I 141 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY I 148 " --> pdb=" O GLY I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 196 removed outlier: 3.834A pdb=" N GLU I 194 " --> pdb=" O HIS I 190 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN I 195 " --> pdb=" O GLN I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 214 Processing helix chain 'I' and resid 221 through 237 removed outlier: 3.728A pdb=" N LEU I 228 " --> pdb=" O ASP I 224 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL I 229 " --> pdb=" O LEU I 225 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR I 237 " --> pdb=" O MET I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 242 removed outlier: 3.519A pdb=" N ARG I 241 " --> pdb=" O THR I 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 258 Processing helix chain 'I' and resid 285 through 294 Processing helix chain 'I' and resid 295 through 299 Processing helix chain 'I' and resid 304 through 308 removed outlier: 3.507A pdb=" N GLY I 308 " --> pdb=" O PRO I 305 " (cutoff:3.500A) Processing helix chain 'I' and resid 322 through 337 removed outlier: 3.888A pdb=" N ASN I 337 " --> pdb=" O ILE I 333 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 341 Processing helix chain 'I' and resid 373 through 391 removed outlier: 4.230A pdb=" N LEU I 377 " --> pdb=" O ALA I 373 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE I 381 " --> pdb=" O LEU I 377 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG I 391 " --> pdb=" O ALA I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 394 through 400 removed outlier: 4.188A pdb=" N TYR I 398 " --> pdb=" O PHE I 394 " (cutoff:3.500A) Processing helix chain 'I' and resid 404 through 426 removed outlier: 3.875A pdb=" N PHE I 408 " --> pdb=" O ASP I 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 29 Processing helix chain 'E' and resid 47 through 51 removed outlier: 3.834A pdb=" N THR E 51 " --> pdb=" O SER E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 80 removed outlier: 3.575A pdb=" N GLU E 77 " --> pdb=" O THR E 73 " (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 129 removed outlier: 4.075A pdb=" N ILE E 114 " --> pdb=" O ILE E 110 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ASP E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LEU E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 161 removed outlier: 4.395A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 178 removed outlier: 3.741A pdb=" N SER E 178 " --> pdb=" O PRO E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 198 removed outlier: 4.168A pdb=" N GLU E 196 " --> pdb=" O HIS E 192 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N HIS E 197 " --> pdb=" O THR E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 217 Processing helix chain 'E' and resid 223 through 244 removed outlier: 3.592A pdb=" N ARG E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU E 230 " --> pdb=" O ASN E 226 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 260 removed outlier: 3.528A pdb=" N PHE E 255 " --> pdb=" O ASP E 251 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL E 260 " --> pdb=" O GLN E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 284 removed outlier: 3.836A pdb=" N TYR E 282 " --> pdb=" O GLU E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 Processing helix chain 'E' and resid 297 through 301 Processing helix chain 'E' and resid 324 through 338 Processing helix chain 'E' and resid 384 through 401 removed outlier: 3.624A pdb=" N TRP E 388 " --> pdb=" O ILE E 384 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS E 401 " --> pdb=" O LEU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 410 removed outlier: 4.213A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 436 removed outlier: 3.825A pdb=" N SER E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 28 Processing helix chain 'J' and resid 40 through 46 removed outlier: 3.529A pdb=" N LEU J 44 " --> pdb=" O SER J 40 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG J 46 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 49 No H-bonds generated for 'chain 'J' and resid 47 through 49' Processing helix chain 'J' and resid 54 through 58 removed outlier: 3.703A pdb=" N HIS J 57 " --> pdb=" O ALA J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 79 removed outlier: 4.520A pdb=" N MET J 73 " --> pdb=" O GLU J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 85 removed outlier: 3.760A pdb=" N PHE J 85 " --> pdb=" O GLY J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 88 No H-bonds generated for 'chain 'J' and resid 86 through 88' Processing helix chain 'J' and resid 100 through 106 Processing helix chain 'J' and resid 108 through 127 removed outlier: 4.450A pdb=" N ASP J 114 " --> pdb=" O ALA J 110 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N SER J 115 " --> pdb=" O GLU J 111 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL J 116 " --> pdb=" O LEU J 112 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS J 127 " --> pdb=" O GLU J 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 159 removed outlier: 3.644A pdb=" N SER J 145 " --> pdb=" O GLY J 141 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY J 148 " --> pdb=" O GLY J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 196 removed outlier: 3.837A pdb=" N GLU J 194 " --> pdb=" O HIS J 190 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN J 195 " --> pdb=" O GLN J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 204 through 214 Processing helix chain 'J' and resid 221 through 237 removed outlier: 3.727A pdb=" N LEU J 228 " --> pdb=" O ASP J 224 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL J 229 " --> pdb=" O LEU J 225 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR J 237 " --> pdb=" O MET J 233 " (cutoff:3.500A) Processing helix chain 'J' and resid 237 through 242 removed outlier: 3.518A pdb=" N ARG J 241 " --> pdb=" O THR J 237 " (cutoff:3.500A) Processing helix chain 'J' and resid 249 through 258 Processing helix chain 'J' and resid 285 through 294 removed outlier: 3.501A pdb=" N PHE J 294 " --> pdb=" O THR J 290 " (cutoff:3.500A) Processing helix chain 'J' and resid 295 through 299 Processing helix chain 'J' and resid 304 through 308 removed outlier: 3.508A pdb=" N GLY J 308 " --> pdb=" O PRO J 305 " (cutoff:3.500A) Processing helix chain 'J' and resid 322 through 337 removed outlier: 3.885A pdb=" N ASN J 337 " --> pdb=" O ILE J 333 " (cutoff:3.500A) Processing helix chain 'J' and resid 338 through 341 Processing helix chain 'J' and resid 373 through 391 removed outlier: 4.231A pdb=" N LEU J 377 " --> pdb=" O ALA J 373 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE J 381 " --> pdb=" O LEU J 377 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG J 391 " --> pdb=" O ALA J 387 " (cutoff:3.500A) Processing helix chain 'J' and resid 394 through 400 removed outlier: 4.188A pdb=" N TYR J 398 " --> pdb=" O PHE J 394 " (cutoff:3.500A) Processing helix chain 'J' and resid 404 through 426 removed outlier: 3.874A pdb=" N PHE J 408 " --> pdb=" O ASP J 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 28 Processing helix chain 'C' and resid 40 through 46 removed outlier: 3.529A pdb=" N LEU C 44 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 49 No H-bonds generated for 'chain 'C' and resid 47 through 49' Processing helix chain 'C' and resid 54 through 58 removed outlier: 3.700A pdb=" N HIS C 57 " --> pdb=" O ALA C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 79 removed outlier: 4.522A pdb=" N MET C 73 " --> pdb=" O GLU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 85 removed outlier: 3.761A pdb=" N PHE C 85 " --> pdb=" O GLY C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 88 No H-bonds generated for 'chain 'C' and resid 86 through 88' Processing helix chain 'C' and resid 100 through 106 Processing helix chain 'C' and resid 108 through 127 removed outlier: 4.453A pdb=" N ASP C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N SER C 115 " --> pdb=" O GLU C 111 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N CYS C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 159 removed outlier: 3.643A pdb=" N SER C 145 " --> pdb=" O GLY C 141 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY C 148 " --> pdb=" O GLY C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 196 removed outlier: 3.837A pdb=" N GLU C 194 " --> pdb=" O HIS C 190 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN C 195 " --> pdb=" O GLN C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 214 Processing helix chain 'C' and resid 221 through 237 removed outlier: 3.727A pdb=" N LEU C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL C 229 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR C 237 " --> pdb=" O MET C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 242 removed outlier: 3.517A pdb=" N ARG C 241 " --> pdb=" O THR C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 258 Processing helix chain 'C' and resid 285 through 294 removed outlier: 3.500A pdb=" N PHE C 294 " --> pdb=" O THR C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 299 Processing helix chain 'C' and resid 304 through 308 removed outlier: 3.507A pdb=" N GLY C 308 " --> pdb=" O PRO C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 337 removed outlier: 3.888A pdb=" N ASN C 337 " --> pdb=" O ILE C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 341 Processing helix chain 'C' and resid 373 through 391 removed outlier: 4.231A pdb=" N LEU C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE C 381 " --> pdb=" O LEU C 377 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 400 removed outlier: 4.189A pdb=" N TYR C 398 " --> pdb=" O PHE C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 426 removed outlier: 3.874A pdb=" N PHE C 408 " --> pdb=" O ASP C 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 28 Processing helix chain 'D' and resid 40 through 46 removed outlier: 3.529A pdb=" N LEU D 44 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 54 through 58 removed outlier: 3.699A pdb=" N HIS D 57 " --> pdb=" O ALA D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 79 removed outlier: 4.520A pdb=" N MET D 73 " --> pdb=" O GLU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.761A pdb=" N PHE D 85 " --> pdb=" O GLY D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 100 through 106 Processing helix chain 'D' and resid 108 through 127 removed outlier: 4.451A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N SER D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N CYS D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 159 removed outlier: 3.645A pdb=" N SER D 145 " --> pdb=" O GLY D 141 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY D 148 " --> pdb=" O GLY D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 196 removed outlier: 3.836A pdb=" N GLU D 194 " --> pdb=" O HIS D 190 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN D 195 " --> pdb=" O GLN D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 214 Processing helix chain 'D' and resid 221 through 237 removed outlier: 3.727A pdb=" N LEU D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL D 229 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR D 237 " --> pdb=" O MET D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 242 removed outlier: 3.518A pdb=" N ARG D 241 " --> pdb=" O THR D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 258 Processing helix chain 'D' and resid 285 through 294 removed outlier: 3.500A pdb=" N PHE D 294 " --> pdb=" O THR D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 299 Processing helix chain 'D' and resid 304 through 308 removed outlier: 3.506A pdb=" N GLY D 308 " --> pdb=" O PRO D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 337 removed outlier: 3.888A pdb=" N ASN D 337 " --> pdb=" O ILE D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 341 Processing helix chain 'D' and resid 373 through 391 removed outlier: 4.232A pdb=" N LEU D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE D 381 " --> pdb=" O LEU D 377 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ARG D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 400 removed outlier: 4.189A pdb=" N TYR D 398 " --> pdb=" O PHE D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 426 removed outlier: 3.874A pdb=" N PHE D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 28 Processing helix chain 'F' and resid 47 through 51 removed outlier: 3.836A pdb=" N THR F 51 " --> pdb=" O SER F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 80 removed outlier: 3.575A pdb=" N GLU F 77 " --> pdb=" O THR F 73 " (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 110 through 129 removed outlier: 4.075A pdb=" N ILE F 114 " --> pdb=" O ILE F 110 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASP F 116 " --> pdb=" O LYS F 112 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LEU F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 161 removed outlier: 4.394A pdb=" N THR F 150 " --> pdb=" O GLY F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 178 removed outlier: 3.739A pdb=" N SER F 178 " --> pdb=" O PRO F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 198 removed outlier: 4.166A pdb=" N GLU F 196 " --> pdb=" O HIS F 192 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N HIS F 197 " --> pdb=" O THR F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 217 Processing helix chain 'F' and resid 223 through 244 removed outlier: 3.593A pdb=" N ARG F 229 " --> pdb=" O THR F 225 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU F 230 " --> pdb=" O ASN F 226 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N SER F 241 " --> pdb=" O SER F 237 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N LEU F 242 " --> pdb=" O ILE F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 260 removed outlier: 3.526A pdb=" N PHE F 255 " --> pdb=" O ASP F 251 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN F 256 " --> pdb=" O LEU F 252 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL F 260 " --> pdb=" O GLN F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 284 removed outlier: 3.836A pdb=" N TYR F 282 " --> pdb=" O GLU F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 296 Processing helix chain 'F' and resid 297 through 301 Processing helix chain 'F' and resid 324 through 338 Processing helix chain 'F' and resid 384 through 401 removed outlier: 3.625A pdb=" N TRP F 388 " --> pdb=" O ILE F 384 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET F 398 " --> pdb=" O LYS F 394 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS F 401 " --> pdb=" O LEU F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 410 removed outlier: 4.214A pdb=" N TYR F 408 " --> pdb=" O PHE F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 436 removed outlier: 3.825A pdb=" N SER F 419 " --> pdb=" O GLU F 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.835A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 removed outlier: 3.576A pdb=" N GLU A 77 " --> pdb=" O THR A 73 " (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 129 removed outlier: 4.074A pdb=" N ILE A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.393A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.740A pdb=" N SER A 178 " --> pdb=" O PRO A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 198 removed outlier: 4.167A pdb=" N GLU A 196 " --> pdb=" O HIS A 192 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N HIS A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.594A pdb=" N ARG A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.527A pdb=" N PHE A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 284 removed outlier: 3.837A pdb=" N TYR A 282 " --> pdb=" O GLU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 384 through 401 removed outlier: 3.625A pdb=" N TRP A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET A 398 " --> pdb=" O LYS A 394 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.215A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 436 removed outlier: 3.826A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 47 through 51 removed outlier: 3.836A pdb=" N THR B 51 " --> pdb=" O SER B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 removed outlier: 3.574A pdb=" N GLU B 77 " --> pdb=" O THR B 73 " (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 110 through 129 removed outlier: 4.075A pdb=" N ILE B 114 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ASP B 116 " --> pdb=" O LYS B 112 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LEU B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 161 removed outlier: 4.393A pdb=" N THR B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 178 removed outlier: 3.741A pdb=" N SER B 178 " --> pdb=" O PRO B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 198 removed outlier: 4.167A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N HIS B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'B' and resid 223 through 244 removed outlier: 3.594A pdb=" N ARG B 229 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU B 230 " --> pdb=" O ASN B 226 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N SER B 241 " --> pdb=" O SER B 237 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU B 242 " --> pdb=" O ILE B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 removed outlier: 3.526A pdb=" N PHE B 255 " --> pdb=" O ASP B 251 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B 260 " --> pdb=" O GLN B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 284 removed outlier: 3.839A pdb=" N TYR B 282 " --> pdb=" O GLU B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 297 through 301 Processing helix chain 'B' and resid 324 through 338 Processing helix chain 'B' and resid 384 through 401 removed outlier: 3.625A pdb=" N TRP B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET B 398 " --> pdb=" O LYS B 394 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.214A pdb=" N TYR B 408 " --> pdb=" O PHE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 436 removed outlier: 3.826A pdb=" N SER B 419 " --> pdb=" O GLU B 415 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 28 Processing helix chain 'L' and resid 40 through 46 removed outlier: 3.530A pdb=" N LEU L 44 " --> pdb=" O SER L 40 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG L 46 " --> pdb=" O LEU L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 49 No H-bonds generated for 'chain 'L' and resid 47 through 49' Processing helix chain 'L' and resid 54 through 58 removed outlier: 3.703A pdb=" N HIS L 57 " --> pdb=" O ALA L 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 79 removed outlier: 4.518A pdb=" N MET L 73 " --> pdb=" O GLU L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.761A pdb=" N PHE L 85 " --> pdb=" O GLY L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 88 No H-bonds generated for 'chain 'L' and resid 86 through 88' Processing helix chain 'L' and resid 100 through 106 Processing helix chain 'L' and resid 108 through 127 removed outlier: 4.451A pdb=" N ASP L 114 " --> pdb=" O ALA L 110 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N SER L 115 " --> pdb=" O GLU L 111 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL L 116 " --> pdb=" O LEU L 112 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS L 127 " --> pdb=" O GLU L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 159 removed outlier: 3.643A pdb=" N SER L 145 " --> pdb=" O GLY L 141 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY L 148 " --> pdb=" O GLY L 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 180 through 196 removed outlier: 3.835A pdb=" N GLU L 194 " --> pdb=" O HIS L 190 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN L 195 " --> pdb=" O GLN L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 204 through 214 Processing helix chain 'L' and resid 221 through 237 removed outlier: 3.727A pdb=" N LEU L 228 " --> pdb=" O ASP L 224 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL L 229 " --> pdb=" O LEU L 225 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR L 237 " --> pdb=" O MET L 233 " (cutoff:3.500A) Processing helix chain 'L' and resid 237 through 242 removed outlier: 3.518A pdb=" N ARG L 241 " --> pdb=" O THR L 237 " (cutoff:3.500A) Processing helix chain 'L' and resid 249 through 258 Processing helix chain 'L' and resid 285 through 294 removed outlier: 3.500A pdb=" N PHE L 294 " --> pdb=" O THR L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 295 through 299 Processing helix chain 'L' and resid 304 through 308 removed outlier: 3.508A pdb=" N GLY L 308 " --> pdb=" O PRO L 305 " (cutoff:3.500A) Processing helix chain 'L' and resid 322 through 337 removed outlier: 3.886A pdb=" N ASN L 337 " --> pdb=" O ILE L 333 " (cutoff:3.500A) Processing helix chain 'L' and resid 338 through 341 Processing helix chain 'L' and resid 373 through 391 removed outlier: 4.231A pdb=" N LEU L 377 " --> pdb=" O ALA L 373 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE L 381 " --> pdb=" O LEU L 377 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG L 391 " --> pdb=" O ALA L 387 " (cutoff:3.500A) Processing helix chain 'L' and resid 394 through 400 removed outlier: 4.188A pdb=" N TYR L 398 " --> pdb=" O PHE L 394 " (cutoff:3.500A) Processing helix chain 'L' and resid 404 through 426 removed outlier: 3.875A pdb=" N PHE L 408 " --> pdb=" O ASP L 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 28 Processing helix chain 'G' and resid 47 through 51 removed outlier: 3.836A pdb=" N THR G 51 " --> pdb=" O SER G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 80 removed outlier: 3.575A pdb=" N GLU G 77 " --> pdb=" O THR G 73 " (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 110 through 129 removed outlier: 4.075A pdb=" N ILE G 114 " --> pdb=" O ILE G 110 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ASP G 116 " --> pdb=" O LYS G 112 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LEU G 117 " --> pdb=" O GLU G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 161 removed outlier: 4.393A pdb=" N THR G 150 " --> pdb=" O GLY G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 178 removed outlier: 3.739A pdb=" N SER G 178 " --> pdb=" O PRO G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 198 removed outlier: 4.165A pdb=" N GLU G 196 " --> pdb=" O HIS G 192 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N HIS G 197 " --> pdb=" O THR G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 217 Processing helix chain 'G' and resid 223 through 244 removed outlier: 3.593A pdb=" N ARG G 229 " --> pdb=" O THR G 225 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU G 230 " --> pdb=" O ASN G 226 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N SER G 241 " --> pdb=" O SER G 237 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N LEU G 242 " --> pdb=" O ILE G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 260 removed outlier: 3.527A pdb=" N PHE G 255 " --> pdb=" O ASP G 251 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN G 256 " --> pdb=" O LEU G 252 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL G 260 " --> pdb=" O GLN G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 284 removed outlier: 3.836A pdb=" N TYR G 282 " --> pdb=" O GLU G 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 296 Processing helix chain 'G' and resid 297 through 301 Processing helix chain 'G' and resid 324 through 338 Processing helix chain 'G' and resid 384 through 401 removed outlier: 3.626A pdb=" N TRP G 388 " --> pdb=" O ILE G 384 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET G 398 " --> pdb=" O LYS G 394 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS G 401 " --> pdb=" O LEU G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 410 removed outlier: 4.215A pdb=" N TYR G 408 " --> pdb=" O PHE G 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 415 through 436 removed outlier: 3.824A pdb=" N SER G 419 " --> pdb=" O GLU G 415 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 90 through 92 removed outlier: 8.177A pdb=" N ILE K 91 " --> pdb=" O ALA K 63 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU K 65 " --> pdb=" O ILE K 91 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ILE K 64 " --> pdb=" O ILE K 4 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N HIS K 6 " --> pdb=" O ILE K 64 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N VAL K 66 " --> pdb=" O HIS K 6 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLN K 8 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N GLU K 3 " --> pdb=" O GLN K 131 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE K 133 " --> pdb=" O GLU K 3 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL K 5 " --> pdb=" O PHE K 133 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LEU K 135 " --> pdb=" O VAL K 5 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE K 7 " --> pdb=" O LEU K 135 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N HIS K 137 " --> pdb=" O ILE K 7 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ALA K 9 " --> pdb=" O HIS K 137 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N GLN K 131 " --> pdb=" O ILE K 163 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ASN K 165 " --> pdb=" O GLN K 131 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N PHE K 133 " --> pdb=" O ASN K 165 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N PHE K 167 " --> pdb=" O PHE K 133 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU K 135 " --> pdb=" O PHE K 167 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N VAL K 169 " --> pdb=" O LEU K 135 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N HIS K 137 " --> pdb=" O VAL K 169 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N MET K 164 " --> pdb=" O GLU K 198 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N TYR K 200 " --> pdb=" O MET K 164 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR K 166 " --> pdb=" O TYR K 200 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE K 202 " --> pdb=" O THR K 166 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER K 168 " --> pdb=" O ILE K 202 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N THR K 199 " --> pdb=" O PHE K 266 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N CYS K 201 " --> pdb=" O PRO K 268 " (cutoff:3.500A) removed outlier: 10.315A pdb=" N PHE K 270 " --> pdb=" O CYS K 201 " (cutoff:3.500A) removed outlier: 13.493A pdb=" N ASP K 203 " --> pdb=" O PHE K 270 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N PHE K 265 " --> pdb=" O SER K 371 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N SER K 371 " --> pdb=" O PHE K 265 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR K 312 " --> pdb=" O ASN K 370 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N LYS K 350 " --> pdb=" O LEU K 311 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL K 313 " --> pdb=" O LYS K 350 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ALA K 352 " --> pdb=" O VAL K 313 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR K 315 " --> pdb=" O ALA K 352 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N CYS K 354 " --> pdb=" O THR K 315 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N PHE K 317 " --> pdb=" O CYS K 354 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL K 353 " --> pdb=" O GLN K 245 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 51 through 52 Processing sheet with id=AA3, first strand: chain 'H' and resid 92 through 93 removed outlier: 8.329A pdb=" N ILE H 93 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE H 67 " --> pdb=" O ILE H 93 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N VAL H 66 " --> pdb=" O CYS H 4 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N SER H 6 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL H 68 " --> pdb=" O SER H 6 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N HIS H 8 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER H 140 " --> pdb=" O VAL H 9 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS H 166 " --> pdb=" O CYS H 200 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N PHE H 202 " --> pdb=" O LYS H 166 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLU H 168 " --> pdb=" O PHE H 202 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL H 204 " --> pdb=" O GLU H 168 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N SER H 170 " --> pdb=" O VAL H 204 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 53 through 56 removed outlier: 3.791A pdb=" N LYS H 60 " --> pdb=" O THR H 56 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 269 through 273 removed outlier: 3.702A pdb=" N ALA H 314 " --> pdb=" O ASN H 380 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 90 through 92 removed outlier: 8.176A pdb=" N ILE I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU I 65 " --> pdb=" O ILE I 91 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ILE I 64 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N HIS I 6 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL I 66 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLN I 8 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LEU I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE I 7 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N HIS I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ALA I 9 " --> pdb=" O HIS I 137 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLN I 131 " --> pdb=" O ILE I 163 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N ASN I 165 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N PHE I 133 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N PHE I 167 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU I 135 " --> pdb=" O PHE I 167 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N VAL I 169 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N HIS I 137 " --> pdb=" O VAL I 169 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N MET I 164 " --> pdb=" O GLU I 198 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N TYR I 200 " --> pdb=" O MET I 164 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR I 166 " --> pdb=" O TYR I 200 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ILE I 202 " --> pdb=" O THR I 166 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N SER I 168 " --> pdb=" O ILE I 202 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N THR I 199 " --> pdb=" O PHE I 266 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N CYS I 201 " --> pdb=" O PRO I 268 " (cutoff:3.500A) removed outlier: 10.318A pdb=" N PHE I 270 " --> pdb=" O CYS I 201 " (cutoff:3.500A) removed outlier: 13.490A pdb=" N ASP I 203 " --> pdb=" O PHE I 270 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N PHE I 265 " --> pdb=" O SER I 371 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N SER I 371 " --> pdb=" O PHE I 265 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR I 312 " --> pdb=" O ASN I 370 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N LYS I 350 " --> pdb=" O LEU I 311 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL I 313 " --> pdb=" O LYS I 350 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ALA I 352 " --> pdb=" O VAL I 313 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR I 315 " --> pdb=" O ALA I 352 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N CYS I 354 " --> pdb=" O THR I 315 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N PHE I 317 " --> pdb=" O CYS I 354 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL I 353 " --> pdb=" O GLN I 245 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 51 through 52 Processing sheet with id=AA8, first strand: chain 'E' and resid 92 through 93 removed outlier: 8.325A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N PHE E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER E 140 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LYS E 166 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N PHE E 202 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER E 170 " --> pdb=" O VAL E 204 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 53 through 56 removed outlier: 3.792A pdb=" N LYS E 60 " --> pdb=" O THR E 56 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 269 through 273 removed outlier: 3.701A pdb=" N ALA E 314 " --> pdb=" O ASN E 380 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 90 through 92 removed outlier: 8.178A pdb=" N ILE J 91 " --> pdb=" O ALA J 63 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU J 65 " --> pdb=" O ILE J 91 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N ILE J 64 " --> pdb=" O ILE J 4 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N HIS J 6 " --> pdb=" O ILE J 64 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL J 66 " --> pdb=" O HIS J 6 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN J 8 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLU J 3 " --> pdb=" O GLN J 131 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE J 133 " --> pdb=" O GLU J 3 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL J 5 " --> pdb=" O PHE J 133 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LEU J 135 " --> pdb=" O VAL J 5 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE J 7 " --> pdb=" O LEU J 135 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N HIS J 137 " --> pdb=" O ILE J 7 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ALA J 9 " --> pdb=" O HIS J 137 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N GLN J 131 " --> pdb=" O ILE J 163 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ASN J 165 " --> pdb=" O GLN J 131 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N PHE J 133 " --> pdb=" O ASN J 165 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N PHE J 167 " --> pdb=" O PHE J 133 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU J 135 " --> pdb=" O PHE J 167 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N VAL J 169 " --> pdb=" O LEU J 135 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N HIS J 137 " --> pdb=" O VAL J 169 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N MET J 164 " --> pdb=" O GLU J 198 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N TYR J 200 " --> pdb=" O MET J 164 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR J 166 " --> pdb=" O TYR J 200 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ILE J 202 " --> pdb=" O THR J 166 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER J 168 " --> pdb=" O ILE J 202 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N THR J 199 " --> pdb=" O PHE J 266 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N CYS J 201 " --> pdb=" O PRO J 268 " (cutoff:3.500A) removed outlier: 10.320A pdb=" N PHE J 270 " --> pdb=" O CYS J 201 " (cutoff:3.500A) removed outlier: 13.496A pdb=" N ASP J 203 " --> pdb=" O PHE J 270 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N PHE J 265 " --> pdb=" O SER J 371 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N SER J 371 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR J 312 " --> pdb=" O ASN J 370 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N LYS J 350 " --> pdb=" O LEU J 311 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL J 313 " --> pdb=" O LYS J 350 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ALA J 352 " --> pdb=" O VAL J 313 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR J 315 " --> pdb=" O ALA J 352 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N CYS J 354 " --> pdb=" O THR J 315 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N PHE J 317 " --> pdb=" O CYS J 354 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL J 353 " --> pdb=" O GLN J 245 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 51 through 52 Processing sheet with id=AB4, first strand: chain 'C' and resid 90 through 92 removed outlier: 8.179A pdb=" N ILE C 91 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU C 65 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N ILE C 64 " --> pdb=" O ILE C 4 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N HIS C 6 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N VAL C 66 " --> pdb=" O HIS C 6 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLN C 8 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N GLU C 3 " --> pdb=" O GLN C 131 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE C 133 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL C 5 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LEU C 135 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE C 7 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N HIS C 137 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ALA C 9 " --> pdb=" O HIS C 137 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N GLN C 131 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ASN C 165 " --> pdb=" O GLN C 131 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N PHE C 133 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N PHE C 167 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU C 135 " --> pdb=" O PHE C 167 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL C 169 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N HIS C 137 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N MET C 164 " --> pdb=" O GLU C 198 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N TYR C 200 " --> pdb=" O MET C 164 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR C 166 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ILE C 202 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N SER C 168 " --> pdb=" O ILE C 202 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N THR C 199 " --> pdb=" O PHE C 266 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N CYS C 201 " --> pdb=" O PRO C 268 " (cutoff:3.500A) removed outlier: 10.321A pdb=" N PHE C 270 " --> pdb=" O CYS C 201 " (cutoff:3.500A) removed outlier: 13.494A pdb=" N ASP C 203 " --> pdb=" O PHE C 270 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N PHE C 265 " --> pdb=" O SER C 371 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N SER C 371 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR C 312 " --> pdb=" O ASN C 370 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N LYS C 350 " --> pdb=" O LEU C 311 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL C 313 " --> pdb=" O LYS C 350 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ALA C 352 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR C 315 " --> pdb=" O ALA C 352 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N CYS C 354 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N PHE C 317 " --> pdb=" O CYS C 354 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL C 353 " --> pdb=" O GLN C 245 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 51 through 52 Processing sheet with id=AB6, first strand: chain 'D' and resid 90 through 92 removed outlier: 8.177A pdb=" N ILE D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU D 65 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ILE D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N HIS D 6 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N GLU D 3 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE D 133 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL D 5 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LEU D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE D 7 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N HIS D 137 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ALA D 9 " --> pdb=" O HIS D 137 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N GLN D 131 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ASN D 165 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N PHE D 133 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N PHE D 167 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU D 135 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N VAL D 169 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N HIS D 137 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N MET D 164 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N TYR D 200 " --> pdb=" O MET D 164 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR D 166 " --> pdb=" O TYR D 200 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ILE D 202 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N SER D 168 " --> pdb=" O ILE D 202 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N THR D 199 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N CYS D 201 " --> pdb=" O PRO D 268 " (cutoff:3.500A) removed outlier: 10.318A pdb=" N PHE D 270 " --> pdb=" O CYS D 201 " (cutoff:3.500A) removed outlier: 13.495A pdb=" N ASP D 203 " --> pdb=" O PHE D 270 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N PHE D 265 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N SER D 371 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR D 312 " --> pdb=" O ASN D 370 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N LYS D 350 " --> pdb=" O LEU D 311 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL D 313 " --> pdb=" O LYS D 350 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ALA D 352 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR D 315 " --> pdb=" O ALA D 352 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N CYS D 354 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N PHE D 317 " --> pdb=" O CYS D 354 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL D 353 " --> pdb=" O GLN D 245 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 51 through 52 Processing sheet with id=AB8, first strand: chain 'F' and resid 92 through 93 removed outlier: 8.330A pdb=" N ILE F 93 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE F 67 " --> pdb=" O ILE F 93 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N VAL F 66 " --> pdb=" O CYS F 4 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER F 6 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL F 68 " --> pdb=" O SER F 6 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N HIS F 8 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N SER F 140 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS F 166 " --> pdb=" O CYS F 200 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N PHE F 202 " --> pdb=" O LYS F 166 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU F 168 " --> pdb=" O PHE F 202 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N VAL F 204 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER F 170 " --> pdb=" O VAL F 204 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 53 through 56 removed outlier: 3.501A pdb=" N THR F 56 " --> pdb=" O LYS F 60 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS F 60 " --> pdb=" O THR F 56 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 269 through 273 removed outlier: 3.700A pdb=" N ALA F 314 " --> pdb=" O ASN F 380 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 92 through 93 removed outlier: 8.328A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 53 through 56 removed outlier: 3.794A pdb=" N LYS A 60 " --> pdb=" O THR A 56 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.697A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 92 through 93 removed outlier: 8.329A pdb=" N ILE B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE B 67 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N VAL B 66 " --> pdb=" O CYS B 4 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N SER B 6 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL B 68 " --> pdb=" O SER B 6 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N HIS B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N SER B 140 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LYS B 166 " --> pdb=" O CYS B 200 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N PHE B 202 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU B 168 " --> pdb=" O PHE B 202 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL B 204 " --> pdb=" O GLU B 168 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N SER B 170 " --> pdb=" O VAL B 204 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 53 through 56 removed outlier: 3.792A pdb=" N LYS B 60 " --> pdb=" O THR B 56 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 269 through 273 removed outlier: 3.699A pdb=" N ALA B 314 " --> pdb=" O ASN B 380 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 90 through 92 removed outlier: 8.177A pdb=" N ILE L 91 " --> pdb=" O ALA L 63 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU L 65 " --> pdb=" O ILE L 91 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N ILE L 64 " --> pdb=" O ILE L 4 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N HIS L 6 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VAL L 66 " --> pdb=" O HIS L 6 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN L 8 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N GLU L 3 " --> pdb=" O GLN L 131 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE L 133 " --> pdb=" O GLU L 3 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL L 5 " --> pdb=" O PHE L 133 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LEU L 135 " --> pdb=" O VAL L 5 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE L 7 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N HIS L 137 " --> pdb=" O ILE L 7 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ALA L 9 " --> pdb=" O HIS L 137 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N GLN L 131 " --> pdb=" O ILE L 163 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ASN L 165 " --> pdb=" O GLN L 131 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N PHE L 133 " --> pdb=" O ASN L 165 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N PHE L 167 " --> pdb=" O PHE L 133 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU L 135 " --> pdb=" O PHE L 167 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N VAL L 169 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N HIS L 137 " --> pdb=" O VAL L 169 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N MET L 164 " --> pdb=" O GLU L 198 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N TYR L 200 " --> pdb=" O MET L 164 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR L 166 " --> pdb=" O TYR L 200 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ILE L 202 " --> pdb=" O THR L 166 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER L 168 " --> pdb=" O ILE L 202 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N THR L 199 " --> pdb=" O PHE L 266 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N CYS L 201 " --> pdb=" O PRO L 268 " (cutoff:3.500A) removed outlier: 10.318A pdb=" N PHE L 270 " --> pdb=" O CYS L 201 " (cutoff:3.500A) removed outlier: 13.496A pdb=" N ASP L 203 " --> pdb=" O PHE L 270 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N PHE L 265 " --> pdb=" O SER L 371 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N SER L 371 " --> pdb=" O PHE L 265 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR L 312 " --> pdb=" O ASN L 370 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N LYS L 350 " --> pdb=" O LEU L 311 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL L 313 " --> pdb=" O LYS L 350 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ALA L 352 " --> pdb=" O VAL L 313 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR L 315 " --> pdb=" O ALA L 352 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N CYS L 354 " --> pdb=" O THR L 315 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N PHE L 317 " --> pdb=" O CYS L 354 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL L 353 " --> pdb=" O GLN L 245 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 51 through 52 Processing sheet with id=AD1, first strand: chain 'G' and resid 92 through 93 removed outlier: 8.330A pdb=" N ILE G 93 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE G 67 " --> pdb=" O ILE G 93 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N VAL G 66 " --> pdb=" O CYS G 4 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N SER G 6 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N VAL G 68 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N HIS G 8 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N SER G 140 " --> pdb=" O VAL G 9 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LYS G 166 " --> pdb=" O CYS G 200 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N PHE G 202 " --> pdb=" O LYS G 166 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU G 168 " --> pdb=" O PHE G 202 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL G 204 " --> pdb=" O GLU G 168 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N SER G 170 " --> pdb=" O VAL G 204 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 53 through 56 removed outlier: 3.503A pdb=" N THR G 56 " --> pdb=" O LYS G 60 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS G 60 " --> pdb=" O THR G 56 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 269 through 273 removed outlier: 3.702A pdb=" N ALA G 314 " --> pdb=" O ASN G 380 " (cutoff:3.500A) 1959 hydrogen bonds defined for protein. 5607 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: 9.97 Time building geometry restraints manager: 4.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7512 1.32 - 1.45: 10848 1.45 - 1.57: 22572 1.57 - 1.70: 60 1.70 - 1.82: 444 Bond restraints: 41436 Sorted by residual: bond pdb=" CA VAL C 286 " pdb=" CB VAL C 286 " ideal model delta sigma weight residual 1.537 1.569 -0.033 5.00e-03 4.00e+04 4.27e+01 bond pdb=" CA VAL J 286 " pdb=" CB VAL J 286 " ideal model delta sigma weight residual 1.537 1.569 -0.032 5.00e-03 4.00e+04 4.13e+01 bond pdb=" CA VAL D 286 " pdb=" CB VAL D 286 " ideal model delta sigma weight residual 1.537 1.569 -0.032 5.00e-03 4.00e+04 4.08e+01 bond pdb=" CA VAL L 286 " pdb=" CB VAL L 286 " ideal model delta sigma weight residual 1.537 1.568 -0.031 5.00e-03 4.00e+04 3.84e+01 bond pdb=" CA VAL I 286 " pdb=" CB VAL I 286 " ideal model delta sigma weight residual 1.537 1.568 -0.031 5.00e-03 4.00e+04 3.84e+01 ... (remaining 41431 not shown) Histogram of bond angle deviations from ideal: 0.00 - 15.39: 56292 15.39 - 30.77: 0 30.77 - 46.16: 0 46.16 - 61.54: 3 61.54 - 76.93: 3 Bond angle restraints: 56298 Sorted by residual: angle pdb=" C MET A 36 " pdb=" N PRO A 37 " pdb=" CD PRO A 37 " ideal model delta sigma weight residual 125.00 48.07 76.93 4.10e+00 5.95e-02 3.52e+02 angle pdb=" C MET E 36 " pdb=" N PRO E 37 " pdb=" CD PRO E 37 " ideal model delta sigma weight residual 125.00 52.53 72.47 4.10e+00 5.95e-02 3.12e+02 angle pdb=" C MET H 36 " pdb=" N PRO H 37 " pdb=" CD PRO H 37 " ideal model delta sigma weight residual 125.00 62.33 62.67 4.10e+00 5.95e-02 2.34e+02 angle pdb=" C MET G 36 " pdb=" N PRO G 37 " pdb=" CD PRO G 37 " ideal model delta sigma weight residual 125.00 63.75 61.25 4.10e+00 5.95e-02 2.23e+02 angle pdb=" C MET B 36 " pdb=" N PRO B 37 " pdb=" CD PRO B 37 " ideal model delta sigma weight residual 125.00 65.61 59.39 4.10e+00 5.95e-02 2.10e+02 ... (remaining 56293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.03: 23769 34.03 - 68.07: 699 68.07 - 102.10: 60 102.10 - 136.14: 6 136.14 - 170.17: 12 Dihedral angle restraints: 24546 sinusoidal: 9744 harmonic: 14802 Sorted by residual: dihedral pdb=" O3B GTP B 501 " pdb=" O3A GTP B 501 " pdb=" PB GTP B 501 " pdb=" PA GTP B 501 " ideal model delta sinusoidal sigma weight residual 291.08 120.91 170.17 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O3B GTP H 501 " pdb=" O3A GTP H 501 " pdb=" PB GTP H 501 " pdb=" PA GTP H 501 " ideal model delta sinusoidal sigma weight residual 291.08 122.17 168.91 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O3B GTP F 501 " pdb=" O3A GTP F 501 " pdb=" PB GTP F 501 " pdb=" PA GTP F 501 " ideal model delta sinusoidal sigma weight residual 291.08 122.49 168.59 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 24543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3732 0.071 - 0.142: 1702 0.142 - 0.213: 605 0.213 - 0.283: 111 0.283 - 0.354: 12 Chirality restraints: 6162 Sorted by residual: chirality pdb=" CA MET I 257 " pdb=" N MET I 257 " pdb=" C MET I 257 " pdb=" CB MET I 257 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CA MET C 257 " pdb=" N MET C 257 " pdb=" C MET C 257 " pdb=" CB MET C 257 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA MET K 257 " pdb=" N MET K 257 " pdb=" C MET K 257 " pdb=" CB MET K 257 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 6159 not shown) Planarity restraints: 7308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 36 " 0.251 5.00e-02 4.00e+02 2.78e-01 1.23e+02 pdb=" N PRO A 37 " -0.449 5.00e-02 4.00e+02 pdb=" CA PRO A 37 " 0.209 5.00e-02 4.00e+02 pdb=" CD PRO A 37 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET E 36 " 0.224 5.00e-02 4.00e+02 2.77e-01 1.23e+02 pdb=" N PRO E 37 " -0.460 5.00e-02 4.00e+02 pdb=" CA PRO E 37 " 0.211 5.00e-02 4.00e+02 pdb=" CD PRO E 37 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET H 36 " -0.186 5.00e-02 4.00e+02 2.69e-01 1.16e+02 pdb=" N PRO H 37 " 0.457 5.00e-02 4.00e+02 pdb=" CA PRO H 37 " -0.202 5.00e-02 4.00e+02 pdb=" CD PRO H 37 " -0.069 5.00e-02 4.00e+02 ... (remaining 7305 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 53 2.45 - 3.07: 26280 3.07 - 3.68: 61796 3.68 - 4.29: 90761 4.29 - 4.90: 151738 Nonbonded interactions: 330628 Sorted by model distance: nonbonded pdb=" O MET A 36 " pdb=" CD PRO A 37 " model vdw 1.843 2.752 nonbonded pdb=" O MET E 36 " pdb=" CD PRO E 37 " model vdw 1.968 2.752 nonbonded pdb=" CA MET A 36 " pdb=" CD PRO A 37 " model vdw 1.993 3.096 nonbonded pdb=" CA MET E 36 " pdb=" CD PRO E 37 " model vdw 2.040 3.096 nonbonded pdb=" O GLY K 141 " pdb=" OG SER K 145 " model vdw 2.069 3.040 ... (remaining 330623 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: 0.15 Found NCS groups: ncs_group { reference = chain 'K' selection = chain 'I' selection = chain 'J' selection = chain 'C' selection = chain 'D' selection = chain 'L' } ncs_group { reference = chain 'H' selection = chain 'E' selection = chain 'F' selection = chain 'A' selection = chain 'B' selection = chain 'G' } 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: 0.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 37.980 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.130 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 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 : 0.010 0.117 41436 Z= 0.671 Angle : 1.747 76.931 56298 Z= 1.128 Chirality : 0.089 0.354 6162 Planarity : 0.010 0.278 7308 Dihedral : 16.319 170.169 15054 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.13 % Favored : 95.75 % Rotamer: Outliers : 1.73 % Allowed : 10.60 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.01 (0.11), residues: 5088 helix: 1.23 (0.09), residues: 2268 sheet: 0.35 (0.17), residues: 750 loop : -1.54 (0.12), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 105 TYR 0.033 0.004 TYR H 108 PHE 0.030 0.004 PHE B 343 TRP 0.028 0.005 TRP C 21 HIS 0.013 0.004 HIS I 137 Details of bonding type rmsd/Z covalent geometry : bond 0.01003 / 0.67 (41436) covalent geometry : angle 1.74723 / 1.13 (56298) hydrogen bonds : bond 0.19033 / 13.33 ( 1959) hydrogen bonds : angle 5.97473 / 4.34 ( 5607) *********************** 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 1895 residues out of total 4368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 1820 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 50 TYR cc_start: 0.7853 (m-80) cc_final: 0.7151 (m-10) REVERT: K 51 TYR cc_start: 0.8411 (m-80) cc_final: 0.8200 (m-10) REVERT: K 67 ASP cc_start: 0.7424 (t0) cc_final: 0.7095 (t70) REVERT: K 88 ASP cc_start: 0.8349 (m-30) cc_final: 0.8066 (t0) REVERT: K 114 ASP cc_start: 0.7745 (m-30) cc_final: 0.7400 (t0) REVERT: K 133 PHE cc_start: 0.8669 (m-80) cc_final: 0.8218 (m-80) REVERT: K 167 PHE cc_start: 0.7868 (m-80) cc_final: 0.7538 (m-10) REVERT: K 174 LYS cc_start: 0.8208 (mttt) cc_final: 0.7824 (mmtp) REVERT: K 183 TYR cc_start: 0.7953 (m-80) cc_final: 0.7536 (m-10) REVERT: K 213 ARG cc_start: 0.7858 (ttm110) cc_final: 0.6512 (ttp80) REVERT: K 297 LYS cc_start: 0.8554 (mttt) cc_final: 0.8062 (mmmt) REVERT: K 300 MET cc_start: 0.8043 (mtt) cc_final: 0.7583 (mtt) REVERT: K 303 CYS cc_start: 0.6656 (m) cc_final: 0.5885 (m) REVERT: K 323 MET cc_start: 0.8548 (ttt) cc_final: 0.7868 (ttt) REVERT: K 406 MET cc_start: 0.7920 (ptm) cc_final: 0.5954 (mmm) REVERT: H 6 SER cc_start: 0.9390 (m) cc_final: 0.9000 (t) REVERT: H 85 GLN cc_start: 0.8096 (mt0) cc_final: 0.7690 (mt0) REVERT: H 88 HIS cc_start: 0.8418 (p-80) cc_final: 0.7262 (p90) REVERT: H 90 GLU cc_start: 0.8606 (pt0) cc_final: 0.8274 (pm20) REVERT: H 94 THR cc_start: 0.7780 (p) cc_final: 0.7496 (p) REVERT: H 96 LYS cc_start: 0.6608 (mmtm) cc_final: 0.6168 (tppt) REVERT: H 124 LYS cc_start: 0.8549 (ttpt) cc_final: 0.8031 (tptt) REVERT: H 135 PHE cc_start: 0.8702 (m-80) cc_final: 0.8393 (m-10) REVERT: H 167 LEU cc_start: 0.8908 (mp) cc_final: 0.8496 (tt) REVERT: H 191 THR cc_start: 0.8785 (p) cc_final: 0.8527 (t) REVERT: H 221 ARG cc_start: 0.7984 (ptt-90) cc_final: 0.7487 (ptt-90) REVERT: H 245 ASP cc_start: 0.8105 (m-30) cc_final: 0.7504 (p0) REVERT: H 290 GLU cc_start: 0.7832 (tt0) cc_final: 0.7549 (tp30) REVERT: H 338 LYS cc_start: 0.8193 (mmtt) cc_final: 0.7814 (mmtp) REVERT: H 356 ASN cc_start: 0.8427 (t0) cc_final: 0.7971 (m-40) REVERT: H 393 HIS cc_start: 0.8470 (t-90) cc_final: 0.8253 (t-90) REVERT: H 413 MET cc_start: 0.8659 (tpt) cc_final: 0.8268 (mmp) REVERT: H 417 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7767 (mm-30) REVERT: H 420 GLU cc_start: 0.8343 (tm-30) cc_final: 0.6267 (tp30) REVERT: I 22 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8126 (mm-30) REVERT: I 26 ASP cc_start: 0.8084 (m-30) cc_final: 0.7873 (m-30) REVERT: I 39 ASP cc_start: 0.6401 (t0) cc_final: 0.5991 (p0) REVERT: I 127 CYS cc_start: 0.6993 (p) cc_final: 0.6642 (p) REVERT: I 130 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8177 (tm) REVERT: I 133 PHE cc_start: 0.8445 (m-80) cc_final: 0.8224 (m-80) REVERT: I 136 THR cc_start: 0.9211 (m) cc_final: 0.8849 (p) REVERT: I 167 PHE cc_start: 0.8093 (m-80) cc_final: 0.7561 (m-10) REVERT: I 174 LYS cc_start: 0.8320 (mttt) cc_final: 0.7977 (mmtm) REVERT: I 183 TYR cc_start: 0.7545 (m-80) cc_final: 0.7243 (m-80) REVERT: I 297 LYS cc_start: 0.8542 (mttt) cc_final: 0.8261 (mmmt) REVERT: I 298 ASN cc_start: 0.7780 (m-40) cc_final: 0.7276 (p0) REVERT: I 300 MET cc_start: 0.7868 (mtt) cc_final: 0.7651 (mtm) REVERT: I 338 SER cc_start: 0.8167 (p) cc_final: 0.7855 (t) REVERT: I 379 LYS cc_start: 0.8431 (ttmp) cc_final: 0.8119 (tptp) REVERT: I 425 TYR cc_start: 0.7561 (m-80) cc_final: 0.7145 (m-80) REVERT: E 2 ARG cc_start: 0.7054 (mtm180) cc_final: 0.6304 (mtp-110) REVERT: E 24 TYR cc_start: 0.8320 (m-10) cc_final: 0.7726 (m-80) REVERT: E 83 TYR cc_start: 0.8002 (m-80) cc_final: 0.7364 (m-10) REVERT: E 96 LYS cc_start: 0.6267 (mmtm) cc_final: 0.5893 (tppt) REVERT: E 154 MET cc_start: 0.8281 (tpp) cc_final: 0.7464 (mtm) REVERT: E 192 HIS cc_start: 0.7805 (t70) cc_final: 0.7253 (t70) REVERT: E 193 THR cc_start: 0.8604 (p) cc_final: 0.8319 (p) REVERT: E 202 PHE cc_start: 0.8503 (m-80) cc_final: 0.8165 (m-10) REVERT: E 221 ARG cc_start: 0.8199 (ptt-90) cc_final: 0.7970 (ptt-90) REVERT: E 251 ASP cc_start: 0.8139 (m-30) cc_final: 0.7817 (m-30) REVERT: E 290 GLU cc_start: 0.7996 (tt0) cc_final: 0.7644 (tp30) REVERT: E 302 MET cc_start: 0.9070 (mmt) cc_final: 0.8580 (mmm) REVERT: E 356 ASN cc_start: 0.8281 (t0) cc_final: 0.8004 (m-40) REVERT: E 417 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7526 (mm-30) REVERT: J 19 LYS cc_start: 0.8813 (tptt) cc_final: 0.8552 (mmmm) REVERT: J 30 ILE cc_start: 0.8312 (mm) cc_final: 0.7523 (mt) REVERT: J 31 ASP cc_start: 0.8455 (m-30) cc_final: 0.8233 (m-30) REVERT: J 50 TYR cc_start: 0.7962 (m-80) cc_final: 0.7473 (m-10) REVERT: J 51 TYR cc_start: 0.8099 (m-80) cc_final: 0.7872 (m-10) REVERT: J 59 TYR cc_start: 0.7496 (m-80) cc_final: 0.6667 (m-80) REVERT: J 67 ASP cc_start: 0.7640 (t0) cc_final: 0.7192 (t70) REVERT: J 69 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7521 (tp30) REVERT: J 114 ASP cc_start: 0.8022 (m-30) cc_final: 0.7786 (p0) REVERT: J 123 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8159 (mm-30) REVERT: J 136 THR cc_start: 0.9176 (m) cc_final: 0.8789 (p) REVERT: J 159 TYR cc_start: 0.7881 (OUTLIER) cc_final: 0.7588 (m-80) REVERT: J 167 PHE cc_start: 0.7890 (m-80) cc_final: 0.7310 (m-10) REVERT: J 168 SER cc_start: 0.8168 (m) cc_final: 0.7296 (t) REVERT: J 187 LEU cc_start: 0.8684 (mt) cc_final: 0.8135 (mt) REVERT: J 190 HIS cc_start: 0.7976 (t70) cc_final: 0.7277 (t-170) REVERT: J 213 ARG cc_start: 0.8048 (ttm110) cc_final: 0.7651 (ttp80) REVERT: J 297 LYS cc_start: 0.8697 (mttt) cc_final: 0.8155 (mmmt) REVERT: J 298 ASN cc_start: 0.7992 (m-40) cc_final: 0.7343 (p0) REVERT: J 307 HIS cc_start: 0.7831 (m-70) cc_final: 0.7463 (m90) REVERT: J 312 THR cc_start: 0.7652 (p) cc_final: 0.7203 (t) REVERT: J 313 VAL cc_start: 0.8195 (OUTLIER) cc_final: 0.6984 (p) REVERT: J 320 ARG cc_start: 0.8118 (mtm-85) cc_final: 0.7737 (mtm-85) REVERT: J 323 MET cc_start: 0.8559 (ttt) cc_final: 0.7791 (ttt) REVERT: J 379 LYS cc_start: 0.8786 (ttmp) cc_final: 0.8480 (tptp) REVERT: J 391 ARG cc_start: 0.8069 (mmm-85) cc_final: 0.7460 (tmm160) REVERT: J 406 MET cc_start: 0.8127 (ptm) cc_final: 0.5795 (mmm) REVERT: C 8 GLN cc_start: 0.7936 (mt0) cc_final: 0.7333 (mt0) REVERT: C 22 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8188 (mm-30) REVERT: C 83 HIS cc_start: 0.7921 (m-70) cc_final: 0.7712 (m-70) REVERT: C 130 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8179 (tm) REVERT: C 136 THR cc_start: 0.9300 (m) cc_final: 0.9064 (p) REVERT: C 247 ASN cc_start: 0.8098 (m-40) cc_final: 0.7316 (t0) REVERT: C 253 LEU cc_start: 0.8873 (mp) cc_final: 0.8658 (mp) REVERT: C 279 GLN cc_start: 0.8708 (tt0) cc_final: 0.8020 (mt0) REVERT: C 295 ASP cc_start: 0.8141 (t0) cc_final: 0.7936 (t0) REVERT: C 299 MET cc_start: 0.8456 (mmm) cc_final: 0.8256 (mmt) REVERT: C 383 GLU cc_start: 0.8295 (tt0) cc_final: 0.7857 (tp30) REVERT: C 425 TYR cc_start: 0.7413 (m-80) cc_final: 0.7106 (m-80) REVERT: D 26 ASP cc_start: 0.8075 (m-30) cc_final: 0.7849 (m-30) REVERT: D 67 ASP cc_start: 0.7320 (t0) cc_final: 0.6900 (t70) REVERT: D 114 ASP cc_start: 0.8038 (m-30) cc_final: 0.7668 (t0) REVERT: D 133 PHE cc_start: 0.8753 (m-80) cc_final: 0.8327 (m-80) REVERT: D 183 TYR cc_start: 0.7913 (m-80) cc_final: 0.7590 (m-10) REVERT: D 208 TYR cc_start: 0.7933 (m-80) cc_final: 0.7721 (m-80) REVERT: D 213 ARG cc_start: 0.7829 (ttm110) cc_final: 0.7335 (tmm-80) REVERT: D 247 ASN cc_start: 0.8316 (m-40) cc_final: 0.7627 (t0) REVERT: D 303 CYS cc_start: 0.6573 (m) cc_final: 0.5559 (m) REVERT: D 306 ARG cc_start: 0.8033 (mmt90) cc_final: 0.7617 (mtt-85) REVERT: D 321 MET cc_start: 0.8035 (mtm) cc_final: 0.7730 (mtm) REVERT: D 383 GLU cc_start: 0.8279 (tt0) cc_final: 0.7783 (tm-30) REVERT: D 406 MET cc_start: 0.7891 (ptm) cc_final: 0.5895 (mmm) REVERT: D 412 GLU cc_start: 0.8640 (tt0) cc_final: 0.8386 (tt0) REVERT: D 425 TYR cc_start: 0.7585 (m-80) cc_final: 0.7254 (m-80) REVERT: F 2 ARG cc_start: 0.7954 (mtm180) cc_final: 0.7556 (mtp-110) REVERT: F 85 GLN cc_start: 0.8089 (mt0) cc_final: 0.7695 (mp10) REVERT: F 94 THR cc_start: 0.7716 (p) cc_final: 0.7329 (p) REVERT: F 96 LYS cc_start: 0.6461 (mmtm) cc_final: 0.6070 (tppt) REVERT: F 108 TYR cc_start: 0.7536 (m-80) cc_final: 0.6620 (m-80) REVERT: F 124 LYS cc_start: 0.8486 (ttpt) cc_final: 0.8210 (tptt) REVERT: F 191 THR cc_start: 0.9076 (p) cc_final: 0.8837 (t) REVERT: F 205 ASP cc_start: 0.7132 (t0) cc_final: 0.6574 (t0) REVERT: F 210 TYR cc_start: 0.7588 (m-10) cc_final: 0.7169 (m-10) REVERT: F 251 ASP cc_start: 0.7669 (m-30) cc_final: 0.7351 (m-30) REVERT: F 269 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7710 (mt) REVERT: F 279 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7202 (tp30) REVERT: F 290 GLU cc_start: 0.8247 (tt0) cc_final: 0.8004 (tp30) REVERT: F 302 MET cc_start: 0.8778 (mmt) cc_final: 0.8367 (mmm) REVERT: F 326 LYS cc_start: 0.8712 (ttmt) cc_final: 0.8451 (tppt) REVERT: F 356 ASN cc_start: 0.8475 (t0) cc_final: 0.8263 (m-40) REVERT: F 399 TYR cc_start: 0.7034 (t80) cc_final: 0.5924 (t80) REVERT: F 413 MET cc_start: 0.8730 (tpt) cc_final: 0.8152 (tpt) REVERT: F 417 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8014 (mm-30) REVERT: F 418 PHE cc_start: 0.8450 (m-80) cc_final: 0.8156 (m-80) REVERT: F 420 GLU cc_start: 0.8199 (tm-30) cc_final: 0.6517 (tp30) REVERT: F 425 MET cc_start: 0.8848 (mmm) cc_final: 0.8507 (mmp) REVERT: F 430 LYS cc_start: 0.8394 (ttpt) cc_final: 0.8188 (ttpp) REVERT: F 431 ASP cc_start: 0.7225 (m-30) cc_final: 0.6664 (t0) REVERT: A 6 SER cc_start: 0.9322 (m) cc_final: 0.8979 (t) REVERT: A 24 TYR cc_start: 0.8332 (m-10) cc_final: 0.7787 (m-80) REVERT: A 83 TYR cc_start: 0.7839 (m-80) cc_final: 0.7187 (m-10) REVERT: A 88 HIS cc_start: 0.8630 (p-80) cc_final: 0.8094 (p90) REVERT: A 124 LYS cc_start: 0.8333 (ttpt) cc_final: 0.7929 (tptt) REVERT: A 251 ASP cc_start: 0.7787 (m-30) cc_final: 0.7554 (m-30) REVERT: A 262 TYR cc_start: 0.8063 (m-80) cc_final: 0.7822 (m-10) REVERT: A 290 GLU cc_start: 0.7992 (tt0) cc_final: 0.7545 (tp30) REVERT: A 302 MET cc_start: 0.8972 (mmt) cc_final: 0.8594 (mmm) REVERT: A 317 LEU cc_start: 0.9277 (mt) cc_final: 0.9058 (mt) REVERT: A 326 LYS cc_start: 0.8728 (ttmt) cc_final: 0.8313 (tppt) REVERT: A 356 ASN cc_start: 0.8536 (t0) cc_final: 0.8169 (m-40) REVERT: A 417 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7867 (mm-30) REVERT: B 2 ARG cc_start: 0.8060 (mtm180) cc_final: 0.7643 (mtm110) REVERT: B 6 SER cc_start: 0.9281 (m) cc_final: 0.8891 (t) REVERT: B 85 GLN cc_start: 0.8103 (mt0) cc_final: 0.7545 (mp10) REVERT: B 88 HIS cc_start: 0.8510 (p-80) cc_final: 0.8053 (p90) REVERT: B 94 THR cc_start: 0.8038 (p) cc_final: 0.7638 (p) REVERT: B 96 LYS cc_start: 0.6514 (mmtm) cc_final: 0.5706 (tppt) REVERT: B 221 ARG cc_start: 0.8012 (ptt-90) cc_final: 0.7524 (ptt-90) REVERT: B 245 ASP cc_start: 0.7877 (m-30) cc_final: 0.7561 (p0) REVERT: B 250 VAL cc_start: 0.8885 (t) cc_final: 0.8566 (t) REVERT: B 265 ILE cc_start: 0.8171 (mm) cc_final: 0.7944 (tt) REVERT: B 302 MET cc_start: 0.8853 (mmt) cc_final: 0.8160 (mmt) REVERT: B 356 ASN cc_start: 0.8222 (t0) cc_final: 0.7923 (t0) REVERT: B 399 TYR cc_start: 0.6920 (t80) cc_final: 0.6616 (t80) REVERT: B 413 MET cc_start: 0.8607 (tpt) cc_final: 0.8097 (mmp) REVERT: B 417 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7890 (mm-30) REVERT: B 420 GLU cc_start: 0.8100 (tm-30) cc_final: 0.6153 (tp30) REVERT: B 431 ASP cc_start: 0.7359 (m-30) cc_final: 0.6859 (m-30) REVERT: L 22 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8238 (mm-30) REVERT: L 25 SER cc_start: 0.8475 (m) cc_final: 0.8189 (p) REVERT: L 30 ILE cc_start: 0.8474 (mm) cc_final: 0.8258 (mt) REVERT: L 53 GLU cc_start: 0.8265 (pm20) cc_final: 0.7992 (pm20) REVERT: L 69 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7342 (tt0) REVERT: L 114 ASP cc_start: 0.7755 (m-30) cc_final: 0.7389 (t0) REVERT: L 122 LYS cc_start: 0.7933 (mtpm) cc_final: 0.7727 (mtmm) REVERT: L 167 PHE cc_start: 0.7957 (m-80) cc_final: 0.7736 (m-80) REVERT: L 190 HIS cc_start: 0.7805 (t70) cc_final: 0.7290 (t-170) REVERT: L 217 LEU cc_start: 0.6720 (OUTLIER) cc_final: 0.6502 (mt) REVERT: L 225 LEU cc_start: 0.8275 (mp) cc_final: 0.7815 (mp) REVERT: L 233 MET cc_start: 0.8330 (mtp) cc_final: 0.8064 (mtt) REVERT: L 247 ASN cc_start: 0.8216 (m-40) cc_final: 0.7615 (t0) REVERT: L 307 HIS cc_start: 0.7948 (m-70) cc_final: 0.7692 (m-70) REVERT: L 321 MET cc_start: 0.8004 (mtm) cc_final: 0.7785 (mtp) REVERT: L 343 GLU cc_start: 0.7919 (pm20) cc_final: 0.7559 (pm20) REVERT: L 379 LYS cc_start: 0.8669 (ttmp) cc_final: 0.8381 (tptp) REVERT: G 25 CYS cc_start: 0.9099 (m) cc_final: 0.8795 (m) REVERT: G 85 GLN cc_start: 0.8088 (mt0) cc_final: 0.7740 (mp10) REVERT: G 86 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8043 (mm) REVERT: G 94 THR cc_start: 0.7895 (p) cc_final: 0.7309 (p) REVERT: G 96 LYS cc_start: 0.6492 (mmtm) cc_final: 0.6192 (tppt) REVERT: G 108 TYR cc_start: 0.7653 (m-80) cc_final: 0.6874 (m-80) REVERT: G 124 LYS cc_start: 0.8364 (ttpt) cc_final: 0.8087 (tptt) REVERT: G 205 ASP cc_start: 0.6977 (t0) cc_final: 0.6548 (t0) REVERT: G 210 TYR cc_start: 0.7613 (m-10) cc_final: 0.6946 (m-80) REVERT: G 224 TYR cc_start: 0.7607 (OUTLIER) cc_final: 0.7253 (m-10) REVERT: G 262 TYR cc_start: 0.7839 (m-80) cc_final: 0.7610 (m-10) REVERT: G 356 ASN cc_start: 0.8471 (t0) cc_final: 0.8238 (m-40) REVERT: G 357 TYR cc_start: 0.8574 (m-80) cc_final: 0.8315 (m-80) REVERT: G 378 LEU cc_start: 0.8119 (mt) cc_final: 0.7703 (mt) REVERT: G 396 ASP cc_start: 0.8595 (t0) cc_final: 0.8142 (m-30) REVERT: G 399 TYR cc_start: 0.7015 (t80) cc_final: 0.6144 (t80) REVERT: G 411 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.7069 (mm-30) REVERT: G 413 MET cc_start: 0.8746 (tpt) cc_final: 0.8110 (mmp) REVERT: G 417 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7924 (mm-30) REVERT: G 420 GLU cc_start: 0.8534 (tm-30) cc_final: 0.6940 (tp30) REVERT: G 425 MET cc_start: 0.8400 (mmm) cc_final: 0.8162 (mmp) REVERT: G 431 ASP cc_start: 0.7064 (m-30) cc_final: 0.6723 (t0) outliers start: 75 outliers final: 22 residues processed: 1852 average time/residue: 0.2920 time to fit residues: 849.5239 Evaluate side-chains 1210 residues out of total 4368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 1179 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 313 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 269 LEU Chi-restraints excluded: chain H residue 411 GLU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 159 TYR Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain J residue 159 TYR Chi-restraints excluded: chain J residue 313 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 159 TYR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 159 TYR Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 411 GLU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 224 TYR Chi-restraints excluded: chain G residue 411 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 10.0000 chunk 455 optimal weight: 40.0000 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.0970 chunk 494 optimal weight: 0.0570 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 overall best weight: 3.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 15 GLN K 28 HIS K 57 HIS ** K 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 131 GLN K 279 GLN K 375 GLN K 423 GLN H 197 HIS H 228 ASN I 6 HIS I 15 GLN I 28 HIS I 131 GLN I 137 HIS ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 GLN I 396 HIS ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 HIS E 258 ASN J 15 GLN J 28 HIS J 191 GLN J 227 HIS J 347 ASN C 15 GLN C 28 HIS C 131 GLN C 191 GLN C 396 HIS D 15 GLN D 28 HIS D 57 HIS D 105 HIS D 131 GLN D 396 HIS D 423 GLN F 197 HIS F 228 ASN F 301 GLN F 393 HIS B 228 ASN L 6 HIS L 15 GLN L 28 HIS ** L 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 227 HIS L 347 ASN L 396 HIS G 228 ASN G 258 ASN G 393 HIS Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.133259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.122823 restraints weight = 74063.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.126019 restraints weight = 39182.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.128109 restraints weight = 23043.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.129497 restraints weight = 14616.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.130427 restraints weight = 9821.953| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 41436 Z= 0.173 Angle : 0.749 13.950 56298 Z= 0.381 Chirality : 0.048 0.378 6162 Planarity : 0.006 0.093 7308 Dihedral : 10.760 170.501 5730 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.30 % Allowed : 19.30 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.91 (0.12), residues: 5088 helix: 2.01 (0.10), residues: 2388 sheet: 0.54 (0.18), residues: 840 loop : -1.28 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 318 TYR 0.024 0.002 TYR E 103 PHE 0.033 0.002 PHE K 294 TRP 0.023 0.002 TRP H 346 HIS 0.012 0.002 HIS H 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (41436) covalent geometry : angle 0.74857 / 0.38 (56298) hydrogen bonds : bond 0.05613 / 3.88 ( 1959) hydrogen bonds : angle 4.87358 / 3.52 ( 5607) *********************** 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 1437 residues out of total 4368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 1294 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 50 TYR cc_start: 0.7321 (m-80) cc_final: 0.6838 (m-10) REVERT: K 99 ASN cc_start: 0.8281 (m-40) cc_final: 0.7871 (m-40) REVERT: K 130 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8289 (tm) REVERT: K 133 PHE cc_start: 0.8362 (m-80) cc_final: 0.8112 (m-80) REVERT: K 167 PHE cc_start: 0.8222 (m-80) cc_final: 0.7314 (m-10) REVERT: K 208 TYR cc_start: 0.7250 (m-10) cc_final: 0.6876 (m-10) REVERT: K 222 TYR cc_start: 0.8057 (OUTLIER) cc_final: 0.6615 (m-10) REVERT: H 26 LEU cc_start: 0.8167 (tt) cc_final: 0.7959 (tt) REVERT: H 88 HIS cc_start: 0.7573 (p-80) cc_final: 0.6791 (p90) REVERT: H 176 GLN cc_start: 0.6990 (OUTLIER) cc_final: 0.6744 (pm20) REVERT: H 177 VAL cc_start: 0.8192 (t) cc_final: 0.7979 (m) REVERT: H 191 THR cc_start: 0.8565 (p) cc_final: 0.8036 (t) REVERT: H 239 THR cc_start: 0.7710 (p) cc_final: 0.6973 (p) REVERT: H 302 MET cc_start: 0.8410 (mmt) cc_final: 0.8006 (mmm) REVERT: H 356 ASN cc_start: 0.8276 (t0) cc_final: 0.7641 (m-40) REVERT: H 420 GLU cc_start: 0.7472 (tm-30) cc_final: 0.5542 (tp30) REVERT: H 429 GLU cc_start: 0.6532 (mt-10) cc_final: 0.6188 (pp20) REVERT: I 8 GLN cc_start: 0.8283 (mt0) cc_final: 0.7372 (mt0) REVERT: I 51 TYR cc_start: 0.8326 (m-80) cc_final: 0.8067 (m-10) REVERT: I 127 CYS cc_start: 0.6479 (p) cc_final: 0.6138 (p) REVERT: I 130 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8219 (tm) REVERT: I 136 THR cc_start: 0.8942 (m) cc_final: 0.8643 (p) REVERT: I 167 PHE cc_start: 0.8121 (m-80) cc_final: 0.7853 (m-10) REVERT: I 222 TYR cc_start: 0.8121 (OUTLIER) cc_final: 0.7777 (m-80) REVERT: I 233 MET cc_start: 0.7557 (mtp) cc_final: 0.6914 (mtp) REVERT: I 299 MET cc_start: 0.8110 (mmt) cc_final: 0.7742 (mmm) REVERT: I 383 GLU cc_start: 0.7560 (tt0) cc_final: 0.7198 (tm-30) REVERT: E 24 TYR cc_start: 0.7873 (m-10) cc_final: 0.7489 (m-80) REVERT: E 83 TYR cc_start: 0.7081 (m-80) cc_final: 0.6233 (m-10) REVERT: E 156 ARG cc_start: 0.7683 (mmp-170) cc_final: 0.7265 (mmt-90) REVERT: E 193 THR cc_start: 0.8080 (p) cc_final: 0.7854 (p) REVERT: E 207 GLU cc_start: 0.6659 (tp30) cc_final: 0.6253 (tp30) REVERT: E 302 MET cc_start: 0.8258 (mmt) cc_final: 0.8000 (mmm) REVERT: E 356 ASN cc_start: 0.7743 (t0) cc_final: 0.7405 (m-40) REVERT: J 50 TYR cc_start: 0.7606 (m-80) cc_final: 0.7114 (m-10) REVERT: J 59 TYR cc_start: 0.6846 (m-80) cc_final: 0.6372 (m-80) REVERT: J 103 LYS cc_start: 0.9047 (mtpt) cc_final: 0.8838 (mtpt) REVERT: J 127 CYS cc_start: 0.7383 (p) cc_final: 0.7100 (p) REVERT: J 136 THR cc_start: 0.8817 (m) cc_final: 0.8371 (p) REVERT: J 187 LEU cc_start: 0.8239 (mt) cc_final: 0.8016 (mt) REVERT: J 213 ARG cc_start: 0.7154 (ttm110) cc_final: 0.6428 (ttp80) REVERT: J 222 TYR cc_start: 0.8164 (OUTLIER) cc_final: 0.6962 (m-80) REVERT: J 383 GLU cc_start: 0.7678 (tt0) cc_final: 0.7084 (tm-30) REVERT: J 406 MET cc_start: 0.6889 (ptm) cc_final: 0.4948 (mmm) REVERT: C 8 GLN cc_start: 0.8122 (mt0) cc_final: 0.7175 (mt0) REVERT: C 130 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8459 (tm) REVERT: C 136 THR cc_start: 0.9102 (m) cc_final: 0.8823 (p) REVERT: C 164 MET cc_start: 0.7053 (mmt) cc_final: 0.6735 (mmt) REVERT: C 222 TYR cc_start: 0.8186 (OUTLIER) cc_final: 0.6616 (m-10) REVERT: C 257 MET cc_start: 0.7399 (mmm) cc_final: 0.6942 (mmm) REVERT: C 312 THR cc_start: 0.8838 (p) cc_final: 0.8631 (p) REVERT: C 377 LEU cc_start: 0.8147 (mp) cc_final: 0.7914 (mt) REVERT: C 383 GLU cc_start: 0.7411 (tt0) cc_final: 0.7183 (tm-30) REVERT: D 99 ASN cc_start: 0.7531 (m-40) cc_final: 0.7301 (m110) REVERT: D 130 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8150 (tm) REVERT: D 133 PHE cc_start: 0.8607 (m-80) cc_final: 0.8393 (m-80) REVERT: D 213 ARG cc_start: 0.7139 (ttm110) cc_final: 0.6795 (ptm-80) REVERT: D 222 TYR cc_start: 0.8273 (OUTLIER) cc_final: 0.7488 (m-80) REVERT: D 379 LYS cc_start: 0.7955 (mtpp) cc_final: 0.7657 (ttmm) REVERT: F 157 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8486 (mp) REVERT: F 191 THR cc_start: 0.8597 (p) cc_final: 0.8045 (t) REVERT: F 210 TYR cc_start: 0.7202 (m-10) cc_final: 0.6759 (m-10) REVERT: F 269 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7765 (mp) REVERT: F 356 ASN cc_start: 0.7899 (t0) cc_final: 0.7587 (m-40) REVERT: F 376 CYS cc_start: 0.8651 (t) cc_final: 0.8265 (t) REVERT: F 420 GLU cc_start: 0.7251 (tm-30) cc_final: 0.5535 (tp30) REVERT: F 429 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6903 (mt-10) REVERT: F 430 LYS cc_start: 0.8041 (ttpt) cc_final: 0.7827 (ttpp) REVERT: A 24 TYR cc_start: 0.7867 (m-10) cc_final: 0.7308 (m-80) REVERT: A 83 TYR cc_start: 0.6985 (m-80) cc_final: 0.6069 (m-10) REVERT: A 176 GLN cc_start: 0.7228 (OUTLIER) cc_final: 0.6907 (pm20) REVERT: A 191 THR cc_start: 0.8476 (p) cc_final: 0.8113 (t) REVERT: A 265 ILE cc_start: 0.7910 (mm) cc_final: 0.7239 (tt) REVERT: A 276 ILE cc_start: 0.8599 (mt) cc_final: 0.8381 (tt) REVERT: A 356 ASN cc_start: 0.7919 (t0) cc_final: 0.7657 (m-40) REVERT: A 377 MET cc_start: 0.7032 (ttp) cc_final: 0.6359 (ttp) REVERT: A 382 THR cc_start: 0.6665 (p) cc_final: 0.5749 (t) REVERT: A 417 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7150 (mm-30) REVERT: A 431 ASP cc_start: 0.5765 (t70) cc_final: 0.5390 (t70) REVERT: B 85 GLN cc_start: 0.7696 (mt0) cc_final: 0.7481 (mp10) REVERT: B 167 LEU cc_start: 0.8639 (mp) cc_final: 0.8434 (mp) REVERT: B 265 ILE cc_start: 0.7685 (mm) cc_final: 0.7341 (tt) REVERT: B 302 MET cc_start: 0.8235 (mmt) cc_final: 0.7975 (mmm) REVERT: B 356 ASN cc_start: 0.7927 (t0) cc_final: 0.7472 (m-40) REVERT: B 399 TYR cc_start: 0.6656 (t80) cc_final: 0.6346 (t80) REVERT: B 415 GLU cc_start: 0.8043 (tt0) cc_final: 0.7075 (tm-30) REVERT: B 420 GLU cc_start: 0.7020 (tm-30) cc_final: 0.5815 (tp30) REVERT: L 11 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7631 (pt0) REVERT: L 133 PHE cc_start: 0.8476 (m-80) cc_final: 0.8209 (m-10) REVERT: L 167 PHE cc_start: 0.7965 (m-80) cc_final: 0.7463 (m-10) REVERT: L 216 LYS cc_start: 0.6686 (mptt) cc_final: 0.6249 (ptmm) REVERT: L 222 TYR cc_start: 0.7975 (OUTLIER) cc_final: 0.6612 (m-80) REVERT: L 225 LEU cc_start: 0.8509 (mp) cc_final: 0.7947 (tt) REVERT: L 257 MET cc_start: 0.7251 (mmm) cc_final: 0.6919 (mmt) REVERT: L 321 MET cc_start: 0.7197 (mtm) cc_final: 0.6988 (mtp) REVERT: G 207 GLU cc_start: 0.6973 (tp30) cc_final: 0.6769 (tp30) REVERT: G 210 TYR cc_start: 0.6984 (m-10) cc_final: 0.6698 (m-80) REVERT: G 251 ASP cc_start: 0.6419 (m-30) cc_final: 0.5815 (m-30) REVERT: G 254 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7821 (mt-10) REVERT: G 290 GLU cc_start: 0.6895 (tm-30) cc_final: 0.6297 (tm-30) REVERT: G 302 MET cc_start: 0.8112 (mmt) cc_final: 0.7711 (mmm) REVERT: G 356 ASN cc_start: 0.7968 (t0) cc_final: 0.7623 (m-40) REVERT: G 382 THR cc_start: 0.7010 (p) cc_final: 0.6500 (t) REVERT: G 413 MET cc_start: 0.8283 (tpt) cc_final: 0.7880 (mmp) REVERT: G 420 GLU cc_start: 0.7509 (tm-30) cc_final: 0.6316 (tp30) REVERT: G 429 GLU cc_start: 0.7334 (mt-10) cc_final: 0.6898 (mt-10) REVERT: G 430 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7515 (ttpp) outliers start: 143 outliers final: 70 residues processed: 1368 average time/residue: 0.2758 time to fit residues: 603.5184 Evaluate side-chains 1153 residues out of total 4368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 1066 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 GLN Chi-restraints excluded: chain K residue 57 HIS Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 163 ILE Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 222 TYR Chi-restraints excluded: chain K residue 293 MET Chi-restraints excluded: chain K residue 338 SER Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 176 GLN Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 328 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 222 TYR Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 347 ASN Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 222 TYR Chi-restraints excluded: chain J residue 371 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 222 TYR Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain L residue 11 GLN Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 222 TYR Chi-restraints excluded: chain L residue 371 SER Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 224 TYR Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 328 VAL Chi-restraints excluded: chain G residue 430 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 64 optimal weight: 20.0000 chunk 466 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 chunk 464 optimal weight: 10.0000 chunk 335 optimal weight: 5.9990 chunk 455 optimal weight: 9.9990 chunk 249 optimal weight: 0.0170 chunk 63 optimal weight: 7.9990 chunk 79 optimal weight: 20.0000 chunk 500 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 overall best weight: 6.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 105 HIS H 285 GLN H 301 GLN ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 384 GLN I 423 GLN E 128 GLN E 228 ASN ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 GLN D 105 HIS F 31 GLN F 301 GLN F 393 HIS A 128 GLN A 228 ASN A 393 HIS B 285 GLN B 393 HIS L 57 HIS L 131 GLN L 347 ASN G 258 ASN G 301 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.128809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.118523 restraints weight = 74866.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.121598 restraints weight = 39467.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.123612 restraints weight = 23259.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.124921 restraints weight = 14805.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.125836 restraints weight = 10027.447| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 41436 Z= 0.222 Angle : 0.754 17.590 56298 Z= 0.381 Chirality : 0.048 0.228 6162 Planarity : 0.006 0.090 7308 Dihedral : 10.301 166.392 5697 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 5.36 % Allowed : 21.38 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.69 (0.12), residues: 5088 helix: 1.75 (0.10), residues: 2352 sheet: 0.47 (0.18), residues: 798 loop : -1.19 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 380 TYR 0.032 0.002 TYR E 103 PHE 0.022 0.002 PHE A 149 TRP 0.018 0.002 TRP H 388 HIS 0.022 0.002 HIS K 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.22 (41436) covalent geometry : angle 0.75353 / 0.38 (56298) hydrogen bonds : bond 0.05322 / 3.70 ( 1959) hydrogen bonds : angle 4.87963 / 3.52 ( 5607) *********************** 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 1332 residues out of total 4368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 1100 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 50 TYR cc_start: 0.7527 (m-80) cc_final: 0.7041 (m-10) REVERT: K 99 ASN cc_start: 0.8291 (m-40) cc_final: 0.7897 (m-40) REVERT: K 130 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8063 (tm) REVERT: K 158 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6893 (mt-10) REVERT: K 209 ASP cc_start: 0.7483 (t0) cc_final: 0.7022 (t0) REVERT: K 213 ARG cc_start: 0.7310 (ttp80) cc_final: 0.6023 (ttp80) REVERT: K 222 TYR cc_start: 0.8402 (OUTLIER) cc_final: 0.7160 (m-10) REVERT: K 247 ASN cc_start: 0.7567 (m-40) cc_final: 0.7280 (p0) REVERT: K 257 MET cc_start: 0.7159 (mmm) cc_final: 0.6614 (mmt) REVERT: K 312 THR cc_start: 0.8503 (p) cc_final: 0.8263 (p) REVERT: K 323 MET cc_start: 0.8531 (ttt) cc_final: 0.7846 (ttt) REVERT: K 355 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7189 (t70) REVERT: H 26 LEU cc_start: 0.8334 (tt) cc_final: 0.8115 (tt) REVERT: H 93 ILE cc_start: 0.8497 (mp) cc_final: 0.8292 (mt) REVERT: H 154 MET cc_start: 0.7650 (mmp) cc_final: 0.7449 (tpt) REVERT: H 191 THR cc_start: 0.8430 (p) cc_final: 0.8187 (t) REVERT: H 302 MET cc_start: 0.8391 (mmt) cc_final: 0.8154 (mmm) REVERT: H 356 ASN cc_start: 0.8339 (t0) cc_final: 0.7744 (m-40) REVERT: H 420 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.5337 (tp30) REVERT: H 429 GLU cc_start: 0.6866 (mt-10) cc_final: 0.6196 (pp20) REVERT: I 81 PHE cc_start: 0.4930 (OUTLIER) cc_final: 0.2703 (t80) REVERT: I 84 LEU cc_start: 0.8062 (tp) cc_final: 0.7834 (mt) REVERT: I 127 CYS cc_start: 0.6736 (p) cc_final: 0.6529 (p) REVERT: I 130 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8302 (tm) REVERT: I 136 THR cc_start: 0.8991 (m) cc_final: 0.8727 (p) REVERT: I 167 PHE cc_start: 0.8207 (m-80) cc_final: 0.7945 (m-10) REVERT: I 222 TYR cc_start: 0.8219 (OUTLIER) cc_final: 0.7854 (m-80) REVERT: I 233 MET cc_start: 0.7594 (mtp) cc_final: 0.7068 (mtp) REVERT: I 355 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7354 (t0) REVERT: I 383 GLU cc_start: 0.7475 (tt0) cc_final: 0.7226 (tm-30) REVERT: I 425 TYR cc_start: 0.6226 (m-10) cc_final: 0.6024 (m-10) REVERT: E 24 TYR cc_start: 0.8018 (m-10) cc_final: 0.7639 (m-80) REVERT: E 36 MET cc_start: 0.7991 (tmm) cc_final: 0.7688 (tmm) REVERT: E 83 TYR cc_start: 0.7159 (m-80) cc_final: 0.6180 (m-10) REVERT: E 88 HIS cc_start: 0.8167 (p90) cc_final: 0.7910 (p90) REVERT: E 103 TYR cc_start: 0.8299 (t80) cc_final: 0.7785 (t80) REVERT: E 167 LEU cc_start: 0.8428 (mp) cc_final: 0.8164 (mp) REVERT: E 177 VAL cc_start: 0.8526 (t) cc_final: 0.8240 (m) REVERT: E 356 ASN cc_start: 0.7730 (t0) cc_final: 0.7414 (m-40) REVERT: J 50 TYR cc_start: 0.7606 (m-80) cc_final: 0.7058 (m-10) REVERT: J 51 TYR cc_start: 0.7932 (m-80) cc_final: 0.7721 (m-10) REVERT: J 136 THR cc_start: 0.8880 (m) cc_final: 0.8452 (p) REVERT: J 200 TYR cc_start: 0.8279 (m-80) cc_final: 0.7898 (m-80) REVERT: J 222 TYR cc_start: 0.8265 (OUTLIER) cc_final: 0.7898 (m-80) REVERT: J 383 GLU cc_start: 0.7800 (tt0) cc_final: 0.7152 (tm-30) REVERT: J 403 MET cc_start: 0.8390 (mmm) cc_final: 0.8122 (mmm) REVERT: J 406 MET cc_start: 0.7130 (ptm) cc_final: 0.5362 (tpt) REVERT: C 81 PHE cc_start: 0.4905 (OUTLIER) cc_final: 0.2801 (t80) REVERT: C 84 LEU cc_start: 0.8392 (tp) cc_final: 0.8145 (mt) REVERT: C 130 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8593 (tm) REVERT: C 136 THR cc_start: 0.9074 (m) cc_final: 0.8747 (p) REVERT: C 167 PHE cc_start: 0.8327 (m-80) cc_final: 0.7437 (m-80) REVERT: C 222 TYR cc_start: 0.8200 (OUTLIER) cc_final: 0.6121 (m-80) REVERT: C 247 ASN cc_start: 0.7581 (m-40) cc_final: 0.7227 (p0) REVERT: C 257 MET cc_start: 0.7847 (mmm) cc_final: 0.7229 (mmm) REVERT: C 304 ASP cc_start: 0.5762 (p0) cc_final: 0.5440 (p0) REVERT: C 312 THR cc_start: 0.8931 (p) cc_final: 0.8543 (t) REVERT: C 330 MET cc_start: 0.7637 (mmt) cc_final: 0.7399 (mmt) REVERT: C 333 ILE cc_start: 0.9074 (tp) cc_final: 0.8601 (mm) REVERT: C 383 GLU cc_start: 0.7672 (tt0) cc_final: 0.7375 (tm-30) REVERT: C 406 MET cc_start: 0.7363 (ptm) cc_final: 0.6245 (tpt) REVERT: D 50 TYR cc_start: 0.7752 (m-80) cc_final: 0.6951 (m-80) REVERT: D 99 ASN cc_start: 0.7798 (m-40) cc_final: 0.7366 (m-40) REVERT: D 130 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8177 (tm) REVERT: D 133 PHE cc_start: 0.8720 (m-80) cc_final: 0.8395 (m-80) REVERT: D 222 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.7601 (m-10) REVERT: D 391 ARG cc_start: 0.7090 (mmm-85) cc_final: 0.6768 (mmm-85) REVERT: D 406 MET cc_start: 0.7371 (ptm) cc_final: 0.5824 (mmm) REVERT: F 47 ASP cc_start: 0.4278 (OUTLIER) cc_final: 0.3457 (m-30) REVERT: F 157 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8362 (mp) REVERT: F 191 THR cc_start: 0.8415 (p) cc_final: 0.8117 (t) REVERT: F 210 TYR cc_start: 0.7190 (m-10) cc_final: 0.6504 (m-10) REVERT: F 356 ASN cc_start: 0.7894 (t0) cc_final: 0.7675 (m-40) REVERT: F 425 MET cc_start: 0.7755 (mmp) cc_final: 0.7175 (mmp) REVERT: A 24 TYR cc_start: 0.8058 (m-10) cc_final: 0.7555 (m-80) REVERT: A 83 TYR cc_start: 0.7207 (m-80) cc_final: 0.6070 (m-10) REVERT: A 215 ARG cc_start: 0.6841 (OUTLIER) cc_final: 0.6608 (mtm110) REVERT: A 262 TYR cc_start: 0.7054 (m-10) cc_final: 0.6844 (m-10) REVERT: A 356 ASN cc_start: 0.8107 (t0) cc_final: 0.7876 (m-40) REVERT: A 382 THR cc_start: 0.6428 (p) cc_final: 0.6200 (p) REVERT: B 108 TYR cc_start: 0.5825 (m-80) cc_final: 0.5340 (m-80) REVERT: B 167 LEU cc_start: 0.8633 (mp) cc_final: 0.8400 (mp) REVERT: B 202 PHE cc_start: 0.8163 (m-80) cc_final: 0.7716 (m-10) REVERT: B 224 TYR cc_start: 0.7484 (OUTLIER) cc_final: 0.7239 (m-10) REVERT: B 269 LEU cc_start: 0.8533 (mp) cc_final: 0.8245 (mt) REVERT: B 290 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7201 (tm-30) REVERT: B 302 MET cc_start: 0.8375 (mmt) cc_final: 0.8127 (mmm) REVERT: B 356 ASN cc_start: 0.8040 (t0) cc_final: 0.7581 (m-40) REVERT: B 413 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.6265 (mmp) REVERT: B 415 GLU cc_start: 0.7725 (tt0) cc_final: 0.7080 (tm-30) REVERT: L 133 PHE cc_start: 0.8493 (m-80) cc_final: 0.8256 (m-10) REVERT: L 167 PHE cc_start: 0.8108 (m-80) cc_final: 0.7621 (m-10) REVERT: L 222 TYR cc_start: 0.8044 (OUTLIER) cc_final: 0.7278 (m-80) REVERT: L 225 LEU cc_start: 0.8328 (mp) cc_final: 0.7858 (tt) REVERT: L 257 MET cc_start: 0.7278 (mmm) cc_final: 0.6851 (mmm) REVERT: L 327 ASP cc_start: 0.6700 (t0) cc_final: 0.6453 (t0) REVERT: G 108 TYR cc_start: 0.5642 (m-80) cc_final: 0.5311 (m-80) REVERT: G 138 PHE cc_start: 0.9122 (m-10) cc_final: 0.8793 (m-10) REVERT: G 210 TYR cc_start: 0.7063 (m-10) cc_final: 0.6268 (m-80) REVERT: G 254 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7769 (mt-10) REVERT: G 351 PHE cc_start: 0.6993 (m-80) cc_final: 0.6687 (m-80) REVERT: G 356 ASN cc_start: 0.8027 (t0) cc_final: 0.7622 (m-40) REVERT: G 431 ASP cc_start: 0.6896 (m-30) cc_final: 0.6690 (m-30) outliers start: 232 outliers final: 144 residues processed: 1238 average time/residue: 0.2656 time to fit residues: 527.4573 Evaluate side-chains 1145 residues out of total 4368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 978 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 GLN Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 158 GLU Chi-restraints excluded: chain K residue 163 ILE Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 222 TYR Chi-restraints excluded: chain K residue 293 MET Chi-restraints excluded: chain K residue 313 VAL Chi-restraints excluded: chain K residue 338 SER Chi-restraints excluded: chain K residue 355 ASP Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 190 THR Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 287 SER Chi-restraints excluded: chain H residue 328 VAL Chi-restraints excluded: chain H residue 353 VAL Chi-restraints excluded: chain H residue 377 MET Chi-restraints excluded: chain H residue 420 GLU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 81 PHE Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 222 TYR Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 347 ASN Chi-restraints excluded: chain I residue 355 ASP Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 222 TYR Chi-restraints excluded: chain J residue 263 LEU Chi-restraints excluded: chain J residue 371 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 81 PHE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 222 TYR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 393 HIS Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 215 ARG Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain L residue 11 GLN Chi-restraints excluded: chain L residue 57 HIS Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 172 SER Chi-restraints excluded: chain L residue 222 TYR Chi-restraints excluded: chain L residue 347 ASN Chi-restraints excluded: chain L residue 355 ASP Chi-restraints excluded: chain L residue 371 SER Chi-restraints excluded: chain L residue 388 MET Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 88 HIS Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 224 TYR Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 269 LEU Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 328 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 248 optimal weight: 8.9990 chunk 333 optimal weight: 10.0000 chunk 216 optimal weight: 7.9990 chunk 419 optimal weight: 5.9990 chunk 459 optimal weight: 9.9990 chunk 423 optimal weight: 20.0000 chunk 278 optimal weight: 10.0000 chunk 141 optimal weight: 0.3980 chunk 70 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 452 optimal weight: 6.9990 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 99 ASN K 298 ASN H 285 GLN H 301 GLN ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 307 HIS I 423 GLN E 128 GLN J 298 ASN C 190 HIS C 423 GLN D 57 HIS D 279 GLN F 31 GLN F 393 HIS L 191 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.129390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.119146 restraints weight = 74522.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.122198 restraints weight = 39529.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.124195 restraints weight = 23442.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.125515 restraints weight = 14983.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.126420 restraints weight = 10158.279| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 41436 Z= 0.174 Angle : 0.696 18.135 56298 Z= 0.348 Chirality : 0.046 0.276 6162 Planarity : 0.005 0.084 7308 Dihedral : 9.961 161.325 5695 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 5.84 % Allowed : 22.07 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.64 (0.12), residues: 5088 helix: 1.70 (0.11), residues: 2358 sheet: 0.45 (0.19), residues: 786 loop : -1.21 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 402 TYR 0.023 0.002 TYR E 103 PHE 0.028 0.002 PHE J 294 TRP 0.018 0.002 TRP G 346 HIS 0.017 0.001 HIS L 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (41436) covalent geometry : angle 0.69625 / 0.35 (56298) hydrogen bonds : bond 0.04810 / 3.34 ( 1959) hydrogen bonds : angle 4.72047 / 3.40 ( 5607) *********************** 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 1329 residues out of total 4368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 253 poor density : 1076 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 50 TYR cc_start: 0.7546 (m-80) cc_final: 0.6970 (m-10) REVERT: K 81 PHE cc_start: 0.5551 (OUTLIER) cc_final: 0.5153 (t80) REVERT: K 130 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8087 (tm) REVERT: K 213 ARG cc_start: 0.7275 (ttp80) cc_final: 0.6856 (ttp80) REVERT: K 222 TYR cc_start: 0.8335 (OUTLIER) cc_final: 0.7425 (m-10) REVERT: K 247 ASN cc_start: 0.7498 (m-40) cc_final: 0.7279 (p0) REVERT: K 257 MET cc_start: 0.7337 (mmm) cc_final: 0.6834 (mmm) REVERT: K 312 THR cc_start: 0.8632 (p) cc_final: 0.8423 (p) REVERT: K 323 MET cc_start: 0.8599 (ttt) cc_final: 0.7834 (ttt) REVERT: K 363 MET cc_start: 0.7803 (mmt) cc_final: 0.7576 (mmt) REVERT: H 93 ILE cc_start: 0.8643 (mp) cc_final: 0.8360 (mt) REVERT: H 356 ASN cc_start: 0.8426 (t0) cc_final: 0.7714 (m-40) REVERT: H 415 GLU cc_start: 0.7444 (tt0) cc_final: 0.6864 (tm-30) REVERT: H 420 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.5526 (tp30) REVERT: I 127 CYS cc_start: 0.6647 (p) cc_final: 0.6402 (p) REVERT: I 130 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8303 (tm) REVERT: I 136 THR cc_start: 0.9025 (m) cc_final: 0.8812 (p) REVERT: I 167 PHE cc_start: 0.8231 (m-80) cc_final: 0.7986 (m-10) REVERT: I 233 MET cc_start: 0.7551 (mtp) cc_final: 0.7056 (mtp) REVERT: I 323 MET cc_start: 0.8059 (ttt) cc_final: 0.7810 (ttt) REVERT: I 355 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7316 (t0) REVERT: E 24 TYR cc_start: 0.7978 (m-10) cc_final: 0.7569 (m-80) REVERT: E 36 MET cc_start: 0.7871 (tmm) cc_final: 0.7497 (tmm) REVERT: E 83 TYR cc_start: 0.7192 (m-80) cc_final: 0.6125 (m-10) REVERT: E 88 HIS cc_start: 0.7780 (p90) cc_final: 0.7028 (p90) REVERT: E 103 TYR cc_start: 0.8317 (t80) cc_final: 0.7909 (t80) REVERT: E 167 LEU cc_start: 0.8450 (mp) cc_final: 0.8211 (mp) REVERT: E 302 MET cc_start: 0.7689 (mmm) cc_final: 0.7457 (mtp) REVERT: E 356 ASN cc_start: 0.7942 (t0) cc_final: 0.7643 (m-40) REVERT: J 50 TYR cc_start: 0.7623 (m-80) cc_final: 0.7002 (m-10) REVERT: J 99 ASN cc_start: 0.7963 (m-40) cc_final: 0.7514 (m-40) REVERT: J 133 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.8225 (m-10) REVERT: J 136 THR cc_start: 0.8827 (m) cc_final: 0.8427 (p) REVERT: J 159 TYR cc_start: 0.7724 (OUTLIER) cc_final: 0.6720 (m-80) REVERT: J 200 TYR cc_start: 0.8229 (m-80) cc_final: 0.7910 (m-80) REVERT: J 217 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7165 (mt) REVERT: J 247 ASN cc_start: 0.7415 (m-40) cc_final: 0.6917 (p0) REVERT: J 307 HIS cc_start: 0.6543 (m170) cc_final: 0.6256 (m170) REVERT: J 323 MET cc_start: 0.7597 (ttp) cc_final: 0.7053 (ttt) REVERT: J 344 TRP cc_start: 0.5935 (p90) cc_final: 0.5176 (p-90) REVERT: J 406 MET cc_start: 0.7076 (ptm) cc_final: 0.5468 (tpt) REVERT: C 81 PHE cc_start: 0.5419 (OUTLIER) cc_final: 0.3171 (t80) REVERT: C 84 LEU cc_start: 0.8420 (tp) cc_final: 0.8102 (mt) REVERT: C 136 THR cc_start: 0.8954 (m) cc_final: 0.8649 (p) REVERT: C 164 MET cc_start: 0.7276 (mmt) cc_final: 0.6973 (mmt) REVERT: C 222 TYR cc_start: 0.8111 (OUTLIER) cc_final: 0.6164 (m-80) REVERT: C 247 ASN cc_start: 0.7535 (m-40) cc_final: 0.7129 (p0) REVERT: C 257 MET cc_start: 0.7823 (mmm) cc_final: 0.7093 (mmm) REVERT: C 312 THR cc_start: 0.8854 (p) cc_final: 0.8560 (p) REVERT: C 333 ILE cc_start: 0.9009 (tp) cc_final: 0.8567 (mm) REVERT: C 397 TRP cc_start: 0.7713 (m100) cc_final: 0.6808 (m100) REVERT: C 406 MET cc_start: 0.7264 (ptm) cc_final: 0.6258 (tpt) REVERT: D 50 TYR cc_start: 0.7767 (m-80) cc_final: 0.6950 (m-80) REVERT: D 99 ASN cc_start: 0.7768 (m-40) cc_final: 0.7318 (m-40) REVERT: D 130 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8160 (tm) REVERT: D 222 TYR cc_start: 0.8369 (OUTLIER) cc_final: 0.7646 (m-10) REVERT: D 391 ARG cc_start: 0.7092 (mmm-85) cc_final: 0.6749 (mmm-85) REVERT: D 406 MET cc_start: 0.7204 (ptm) cc_final: 0.5640 (mmm) REVERT: F 157 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8339 (mp) REVERT: F 191 THR cc_start: 0.8369 (p) cc_final: 0.8092 (t) REVERT: F 420 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.5758 (tp30) REVERT: A 24 TYR cc_start: 0.7979 (m-10) cc_final: 0.7536 (m-80) REVERT: A 83 TYR cc_start: 0.7157 (m-80) cc_final: 0.6036 (m-10) REVERT: A 163 LYS cc_start: 0.7429 (pttm) cc_final: 0.7110 (pttm) REVERT: A 262 TYR cc_start: 0.7079 (m-10) cc_final: 0.6755 (m-10) REVERT: A 282 TYR cc_start: 0.7022 (m-80) cc_final: 0.6639 (m-80) REVERT: A 356 ASN cc_start: 0.8110 (t0) cc_final: 0.7886 (m-40) REVERT: B 108 TYR cc_start: 0.5602 (m-80) cc_final: 0.5337 (m-80) REVERT: B 154 MET cc_start: 0.6846 (tpt) cc_final: 0.6599 (tpp) REVERT: B 167 LEU cc_start: 0.8516 (mp) cc_final: 0.8301 (mp) REVERT: B 202 PHE cc_start: 0.8095 (m-80) cc_final: 0.7654 (m-10) REVERT: B 269 LEU cc_start: 0.8452 (mp) cc_final: 0.8086 (mt) REVERT: B 290 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7105 (tm-30) REVERT: B 302 MET cc_start: 0.8297 (mmt) cc_final: 0.7997 (mmm) REVERT: B 356 ASN cc_start: 0.7987 (t0) cc_final: 0.7562 (m-40) REVERT: B 413 MET cc_start: 0.7544 (mmp) cc_final: 0.6387 (mmp) REVERT: B 415 GLU cc_start: 0.7658 (tt0) cc_final: 0.7084 (tm-30) REVERT: L 45 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7760 (tp30) REVERT: L 158 GLU cc_start: 0.7826 (tp30) cc_final: 0.7371 (tp30) REVERT: L 167 PHE cc_start: 0.8175 (m-80) cc_final: 0.7404 (m-10) REVERT: L 200 TYR cc_start: 0.8286 (m-80) cc_final: 0.7234 (m-80) REVERT: L 222 TYR cc_start: 0.7834 (OUTLIER) cc_final: 0.7340 (m-80) REVERT: L 225 LEU cc_start: 0.8263 (mp) cc_final: 0.7714 (tt) REVERT: L 247 ASN cc_start: 0.7512 (m-40) cc_final: 0.6959 (p0) REVERT: L 257 MET cc_start: 0.7370 (mmm) cc_final: 0.6766 (mmt) REVERT: L 312 THR cc_start: 0.8248 (p) cc_final: 0.7805 (t) REVERT: G 47 ASP cc_start: 0.5054 (OUTLIER) cc_final: 0.3991 (m-30) REVERT: G 138 PHE cc_start: 0.9044 (m-10) cc_final: 0.8655 (m-10) REVERT: G 224 TYR cc_start: 0.7482 (OUTLIER) cc_final: 0.6304 (m-10) REVERT: G 251 ASP cc_start: 0.6542 (m-30) cc_final: 0.5769 (m-30) REVERT: G 267 PHE cc_start: 0.8206 (m-80) cc_final: 0.7989 (m-80) REVERT: G 319 TYR cc_start: 0.8344 (m-80) cc_final: 0.8040 (m-80) REVERT: G 356 ASN cc_start: 0.8054 (t0) cc_final: 0.7669 (m-40) REVERT: G 397 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7216 (mp) REVERT: G 420 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6208 (tp30) outliers start: 253 outliers final: 149 residues processed: 1238 average time/residue: 0.2487 time to fit residues: 499.4874 Evaluate side-chains 1161 residues out of total 4368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 991 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 GLN Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 81 PHE Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 163 ILE Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 222 TYR Chi-restraints excluded: chain K residue 293 MET Chi-restraints excluded: chain K residue 313 VAL Chi-restraints excluded: chain K residue 338 SER Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 172 TYR Chi-restraints excluded: chain H residue 190 THR Chi-restraints excluded: chain H residue 205 ASP Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 256 GLN Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 328 VAL Chi-restraints excluded: chain H residue 377 MET Chi-restraints excluded: chain H residue 420 GLU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 159 TYR Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 347 ASN Chi-restraints excluded: chain I residue 355 ASP Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 81 PHE Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 133 PHE Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 159 TYR Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 172 SER Chi-restraints excluded: chain J residue 178 THR Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 312 THR Chi-restraints excluded: chain J residue 371 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 81 PHE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 222 TYR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 420 GLU Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain L residue 11 GLN Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 152 ILE Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 172 SER Chi-restraints excluded: chain L residue 222 TYR Chi-restraints excluded: chain L residue 347 ASN Chi-restraints excluded: chain L residue 371 SER Chi-restraints excluded: chain L residue 388 MET Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 88 HIS Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 224 TYR Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 287 SER Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 328 VAL Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 379 SER Chi-restraints excluded: chain G residue 397 LEU Chi-restraints excluded: chain G residue 420 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 154 optimal weight: 10.0000 chunk 172 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 116 optimal weight: 20.0000 chunk 496 optimal weight: 6.9990 chunk 233 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 411 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 327 optimal weight: 0.0670 chunk 163 optimal weight: 9.9990 overall best weight: 3.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 14 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 GLN H 285 GLN ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 190 HIS E 101 ASN E 128 GLN E 139 HIS J 134 GLN F 393 HIS B 101 ASN L 191 GLN G 285 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.130908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.120533 restraints weight = 74559.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.123655 restraints weight = 39750.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.125691 restraints weight = 23553.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.127022 restraints weight = 15061.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.127929 restraints weight = 10192.194| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 41436 Z= 0.143 Angle : 0.666 18.230 56298 Z= 0.331 Chirality : 0.045 0.216 6162 Planarity : 0.005 0.086 7308 Dihedral : 9.610 156.943 5692 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 5.10 % Allowed : 23.04 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.12), residues: 5088 helix: 1.74 (0.11), residues: 2358 sheet: 0.49 (0.19), residues: 774 loop : -1.24 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 215 TYR 0.019 0.001 TYR A 319 PHE 0.031 0.002 PHE B 149 TRP 0.020 0.002 TRP G 346 HIS 0.017 0.001 HIS D 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (41436) covalent geometry : angle 0.66639 / 0.33 (56298) hydrogen bonds : bond 0.04432 / 3.08 ( 1959) hydrogen bonds : angle 4.63332 / 3.33 ( 5607) *********************** 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 1315 residues out of total 4368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 221 poor density : 1094 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: K 50 TYR cc_start: 0.7675 (m-80) cc_final: 0.7027 (m-10) REVERT: K 81 PHE cc_start: 0.5582 (OUTLIER) cc_final: 0.5164 (t80) REVERT: K 130 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8168 (tm) REVERT: K 158 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6421 (mt-10) REVERT: K 213 ARG cc_start: 0.7336 (ttp80) cc_final: 0.6950 (ttp80) REVERT: K 222 TYR cc_start: 0.8198 (OUTLIER) cc_final: 0.7588 (m-80) REVERT: K 247 ASN cc_start: 0.7608 (m-40) cc_final: 0.7363 (p0) REVERT: K 257 MET cc_start: 0.7418 (mmm) cc_final: 0.7207 (mmp) REVERT: K 282 ARG cc_start: 0.7803 (tpp80) cc_final: 0.7419 (tpp80) REVERT: K 300 MET cc_start: 0.7903 (mtt) cc_final: 0.7626 (mtm) REVERT: K 355 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7638 (m-30) REVERT: K 363 MET cc_start: 0.7845 (mmt) cc_final: 0.7608 (mmt) REVERT: H 93 ILE cc_start: 0.8552 (mp) cc_final: 0.8304 (mt) REVERT: H 163 LYS cc_start: 0.8488 (ttpp) cc_final: 0.8254 (ptmm) REVERT: H 251 ASP cc_start: 0.6631 (m-30) cc_final: 0.6365 (m-30) REVERT: H 356 ASN cc_start: 0.8424 (t0) cc_final: 0.7711 (m-40) REVERT: H 415 GLU cc_start: 0.7256 (tt0) cc_final: 0.6655 (tm-30) REVERT: H 420 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.5213 (tp30) REVERT: I 127 CYS cc_start: 0.6969 (p) cc_final: 0.6733 (p) REVERT: I 130 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8458 (tm) REVERT: I 136 THR cc_start: 0.9023 (m) cc_final: 0.8799 (p) REVERT: I 167 PHE cc_start: 0.8315 (m-80) cc_final: 0.7799 (m-10) REVERT: I 198 GLU cc_start: 0.8095 (pp20) cc_final: 0.7701 (pp20) REVERT: I 200 TYR cc_start: 0.8303 (m-80) cc_final: 0.6872 (m-80) REVERT: I 233 MET cc_start: 0.7554 (mtp) cc_final: 0.6923 (mtp) REVERT: I 247 ASN cc_start: 0.7536 (m-40) cc_final: 0.7152 (p0) REVERT: I 355 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7347 (t0) REVERT: E 24 TYR cc_start: 0.7937 (m-10) cc_final: 0.7618 (m-80) REVERT: E 36 MET cc_start: 0.7827 (tmm) cc_final: 0.7416 (tmm) REVERT: E 83 TYR cc_start: 0.7095 (m-80) cc_final: 0.5883 (m-10) REVERT: E 97 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6718 (tm-30) REVERT: E 103 TYR cc_start: 0.8171 (t80) cc_final: 0.7918 (t80) REVERT: E 167 LEU cc_start: 0.8385 (mp) cc_final: 0.8169 (mp) REVERT: E 302 MET cc_start: 0.7716 (mmm) cc_final: 0.7512 (mtp) REVERT: E 319 TYR cc_start: 0.8498 (m-80) cc_final: 0.7987 (m-80) REVERT: E 356 ASN cc_start: 0.7949 (t0) cc_final: 0.7747 (m-40) REVERT: E 429 GLU cc_start: 0.5852 (tm-30) cc_final: 0.5602 (tm-30) REVERT: J 50 TYR cc_start: 0.7645 (m-80) cc_final: 0.7044 (m-80) REVERT: J 99 ASN cc_start: 0.7889 (m-40) cc_final: 0.7538 (m-40) REVERT: J 136 THR cc_start: 0.8760 (m) cc_final: 0.8545 (p) REVERT: J 159 TYR cc_start: 0.7747 (OUTLIER) cc_final: 0.6673 (m-80) REVERT: J 200 TYR cc_start: 0.8255 (m-80) cc_final: 0.7969 (m-80) REVERT: J 213 ARG cc_start: 0.7739 (ptm-80) cc_final: 0.7349 (ptt90) REVERT: J 217 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7206 (mt) REVERT: J 247 ASN cc_start: 0.7556 (m-40) cc_final: 0.6997 (p0) REVERT: J 306 ARG cc_start: 0.6949 (mmt90) cc_final: 0.6386 (mtt-85) REVERT: J 307 HIS cc_start: 0.6484 (m170) cc_final: 0.6263 (m170) REVERT: J 344 TRP cc_start: 0.5808 (p90) cc_final: 0.5067 (p-90) REVERT: J 403 MET cc_start: 0.8348 (mmm) cc_final: 0.7977 (tpt) REVERT: J 406 MET cc_start: 0.7131 (ptm) cc_final: 0.5439 (tpt) REVERT: C 81 PHE cc_start: 0.5390 (OUTLIER) cc_final: 0.3719 (t80) REVERT: C 136 THR cc_start: 0.8903 (m) cc_final: 0.8627 (p) REVERT: C 164 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.6985 (mmt) REVERT: C 167 PHE cc_start: 0.8208 (m-80) cc_final: 0.7512 (m-80) REVERT: C 168 SER cc_start: 0.8215 (m) cc_final: 0.7758 (p) REVERT: C 222 TYR cc_start: 0.8069 (OUTLIER) cc_final: 0.6073 (m-80) REVERT: C 247 ASN cc_start: 0.7484 (m-40) cc_final: 0.7119 (p0) REVERT: C 257 MET cc_start: 0.7823 (mmm) cc_final: 0.6977 (mmm) REVERT: C 333 ILE cc_start: 0.8866 (tp) cc_final: 0.8466 (mm) REVERT: C 406 MET cc_start: 0.7168 (ptm) cc_final: 0.6094 (tpt) REVERT: D 11 GLN cc_start: 0.7204 (pt0) cc_final: 0.6999 (pm20) REVERT: D 50 TYR cc_start: 0.7814 (m-80) cc_final: 0.6965 (m-80) REVERT: D 99 ASN cc_start: 0.7731 (m-40) cc_final: 0.7314 (m-40) REVERT: D 130 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8193 (tm) REVERT: D 200 TYR cc_start: 0.8189 (m-80) cc_final: 0.7466 (m-80) REVERT: D 251 ARG cc_start: 0.8708 (mtp-110) cc_final: 0.8109 (ttm-80) REVERT: D 306 ARG cc_start: 0.6513 (mmt90) cc_final: 0.6216 (mtt-85) REVERT: D 379 LYS cc_start: 0.8041 (mtpp) cc_final: 0.7656 (ttmm) REVERT: D 391 ARG cc_start: 0.7064 (mmm-85) cc_final: 0.6645 (mmm-85) REVERT: D 406 MET cc_start: 0.7100 (ptm) cc_final: 0.5612 (mmm) REVERT: F 47 ASP cc_start: 0.4093 (OUTLIER) cc_final: 0.3159 (m-30) REVERT: F 121 ARG cc_start: 0.7949 (tpp-160) cc_final: 0.7505 (mpt180) REVERT: F 157 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8288 (mp) REVERT: F 177 VAL cc_start: 0.8103 (OUTLIER) cc_final: 0.7215 (t) REVERT: F 191 THR cc_start: 0.8241 (p) cc_final: 0.7937 (t) REVERT: F 420 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.5623 (tp30) REVERT: A 24 TYR cc_start: 0.7939 (m-10) cc_final: 0.7485 (m-80) REVERT: A 83 TYR cc_start: 0.6892 (m-80) cc_final: 0.6369 (m-10) REVERT: A 163 LYS cc_start: 0.7640 (pttm) cc_final: 0.7353 (pttm) REVERT: A 282 TYR cc_start: 0.7059 (m-80) cc_final: 0.6667 (m-80) REVERT: B 163 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.6885 (pttm) REVERT: B 167 LEU cc_start: 0.8495 (mp) cc_final: 0.8243 (mp) REVERT: B 177 VAL cc_start: 0.8318 (m) cc_final: 0.7887 (t) REVERT: B 202 PHE cc_start: 0.8065 (m-80) cc_final: 0.7619 (m-10) REVERT: B 290 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7117 (tm-30) REVERT: B 302 MET cc_start: 0.8336 (mmt) cc_final: 0.8072 (mmm) REVERT: B 316 CYS cc_start: 0.7774 (m) cc_final: 0.7492 (m) REVERT: B 356 ASN cc_start: 0.8068 (t0) cc_final: 0.7736 (m-40) REVERT: B 413 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.6595 (mmp) REVERT: B 415 GLU cc_start: 0.7615 (tt0) cc_final: 0.7026 (tm-30) REVERT: L 45 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7725 (tp30) REVERT: L 158 GLU cc_start: 0.7584 (tp30) cc_final: 0.7351 (tp30) REVERT: L 167 PHE cc_start: 0.8161 (m-80) cc_final: 0.7395 (m-10) REVERT: L 200 TYR cc_start: 0.8266 (m-80) cc_final: 0.7256 (m-80) REVERT: L 225 LEU cc_start: 0.8243 (mp) cc_final: 0.7636 (tt) REVERT: L 247 ASN cc_start: 0.7519 (m-40) cc_final: 0.7187 (p0) REVERT: L 257 MET cc_start: 0.7245 (mmm) cc_final: 0.6993 (mmt) REVERT: L 377 LEU cc_start: 0.7766 (mp) cc_final: 0.7227 (mt) REVERT: G 47 ASP cc_start: 0.5045 (OUTLIER) cc_final: 0.4558 (t70) REVERT: G 138 PHE cc_start: 0.9054 (m-10) cc_final: 0.8797 (m-10) REVERT: G 316 CYS cc_start: 0.8421 (m) cc_final: 0.8190 (m) REVERT: G 319 TYR cc_start: 0.8373 (m-80) cc_final: 0.8049 (m-80) REVERT: G 356 ASN cc_start: 0.8120 (t0) cc_final: 0.7685 (m-40) REVERT: G 420 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6286 (tp30) REVERT: G 429 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6692 (pp20) outliers start: 221 outliers final: 143 residues processed: 1239 average time/residue: 0.2477 time to fit residues: 494.7043 Evaluate side-chains 1173 residues out of total 4368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 1006 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 GLN Chi-restraints excluded: chain K residue 81 PHE Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 158 GLU Chi-restraints excluded: chain K residue 163 ILE Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 222 TYR Chi-restraints excluded: chain K residue 293 MET Chi-restraints excluded: chain K residue 313 VAL Chi-restraints excluded: chain K residue 338 SER Chi-restraints excluded: chain K residue 355 ASP Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 205 ASP Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 287 SER Chi-restraints excluded: chain H residue 328 VAL Chi-restraints excluded: chain H residue 353 VAL Chi-restraints excluded: chain H residue 377 MET Chi-restraints excluded: chain H residue 420 GLU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 194 GLU Chi-restraints excluded: chain I residue 347 ASN Chi-restraints excluded: chain I residue 355 ASP Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 81 PHE Chi-restraints excluded: chain J residue 159 TYR Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 172 SER Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 312 THR Chi-restraints excluded: chain J residue 371 SER Chi-restraints excluded: chain J residue 381 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 81 PHE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 222 TYR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 420 GLU Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 11 GLN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 81 PHE Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 172 SER Chi-restraints excluded: chain L residue 388 MET Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 224 TYR Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 287 SER Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 328 VAL Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 420 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 377 optimal weight: 20.0000 chunk 181 optimal weight: 9.9990 chunk 490 optimal weight: 1.9990 chunk 196 optimal weight: 6.9990 chunk 453 optimal weight: 2.9990 chunk 313 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 502 optimal weight: 0.0770 chunk 3 optimal weight: 10.0000 chunk 416 optimal weight: 4.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 423 GLN C 14 ASN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 GLN D 57 HIS ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN F 101 ASN F 356 ASN A 101 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.131305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.120965 restraints weight = 74687.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.124056 restraints weight = 39727.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.126077 restraints weight = 23512.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.127393 restraints weight = 15018.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.128307 restraints weight = 10182.136| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 41436 Z= 0.142 Angle : 0.667 19.853 56298 Z= 0.330 Chirality : 0.044 0.213 6162 Planarity : 0.005 0.077 7308 Dihedral : 9.389 154.043 5692 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 5.29 % Allowed : 23.08 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.12), residues: 5088 helix: 1.80 (0.11), residues: 2310 sheet: 0.43 (0.19), residues: 786 loop : -1.20 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 380 TYR 0.025 0.001 TYR A 224 PHE 0.032 0.002 PHE B 49 TRP 0.026 0.002 TRP D 344 HIS 0.014 0.001 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (41436) covalent geometry : angle 0.66738 / 0.33 (56298) hydrogen bonds : bond 0.04262 / 2.95 ( 1959) hydrogen bonds : angle 4.61429 / 3.31 ( 5607) *********************** 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 1336 residues out of total 4368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 229 poor density : 1107 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 50 TYR cc_start: 0.7711 (m-80) cc_final: 0.7049 (m-10) REVERT: K 81 PHE cc_start: 0.5631 (OUTLIER) cc_final: 0.5389 (t80) REVERT: K 130 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8109 (tm) REVERT: K 213 ARG cc_start: 0.7152 (ttp80) cc_final: 0.6734 (ttp80) REVERT: K 247 ASN cc_start: 0.7584 (m-40) cc_final: 0.7366 (p0) REVERT: K 355 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7555 (m-30) REVERT: K 363 MET cc_start: 0.7849 (mmt) cc_final: 0.7623 (mmt) REVERT: K 401 GLU cc_start: 0.5348 (mp0) cc_final: 0.5117 (mt-10) REVERT: H 93 ILE cc_start: 0.8407 (mp) cc_final: 0.8186 (mt) REVERT: H 163 LYS cc_start: 0.8572 (ttpp) cc_final: 0.8311 (ptmm) REVERT: H 224 TYR cc_start: 0.6993 (OUTLIER) cc_final: 0.6448 (m-10) REVERT: H 346 TRP cc_start: 0.8139 (p-90) cc_final: 0.7485 (p90) REVERT: H 356 ASN cc_start: 0.8417 (t0) cc_final: 0.7725 (m-40) REVERT: H 407 TRP cc_start: 0.8427 (m100) cc_final: 0.8114 (m100) REVERT: H 413 MET cc_start: 0.7693 (mmp) cc_final: 0.7476 (mmp) REVERT: H 415 GLU cc_start: 0.7235 (tt0) cc_final: 0.6626 (tm-30) REVERT: H 420 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.5263 (tp30) REVERT: I 130 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8431 (tm) REVERT: I 167 PHE cc_start: 0.8329 (m-80) cc_final: 0.7831 (m-10) REVERT: I 198 GLU cc_start: 0.8186 (pp20) cc_final: 0.7943 (pp20) REVERT: I 200 TYR cc_start: 0.8328 (m-80) cc_final: 0.6987 (m-80) REVERT: I 233 MET cc_start: 0.7541 (mtp) cc_final: 0.7061 (mtp) REVERT: I 247 ASN cc_start: 0.7442 (m-40) cc_final: 0.7103 (p0) REVERT: I 355 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7321 (t0) REVERT: E 24 TYR cc_start: 0.7914 (m-10) cc_final: 0.7588 (m-80) REVERT: E 36 MET cc_start: 0.7832 (tmm) cc_final: 0.7464 (tmm) REVERT: E 83 TYR cc_start: 0.7071 (m-80) cc_final: 0.5845 (m-10) REVERT: E 97 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6735 (tm-30) REVERT: E 103 TYR cc_start: 0.8139 (t80) cc_final: 0.7863 (t80) REVERT: E 167 LEU cc_start: 0.8327 (mp) cc_final: 0.8049 (mp) REVERT: E 282 TYR cc_start: 0.7480 (m-80) cc_final: 0.7032 (m-80) REVERT: E 319 TYR cc_start: 0.8493 (m-80) cc_final: 0.8032 (m-80) REVERT: E 356 ASN cc_start: 0.8061 (t0) cc_final: 0.7860 (m-40) REVERT: J 99 ASN cc_start: 0.7885 (m-40) cc_final: 0.7559 (m-40) REVERT: J 136 THR cc_start: 0.8853 (m) cc_final: 0.8546 (p) REVERT: J 159 TYR cc_start: 0.7779 (OUTLIER) cc_final: 0.6595 (m-80) REVERT: J 200 TYR cc_start: 0.8315 (m-80) cc_final: 0.7917 (m-80) REVERT: J 213 ARG cc_start: 0.7711 (ptm-80) cc_final: 0.7307 (ptt90) REVERT: J 217 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7478 (mt) REVERT: J 247 ASN cc_start: 0.7386 (m-40) cc_final: 0.7010 (p0) REVERT: J 307 HIS cc_start: 0.6473 (m170) cc_final: 0.6230 (m170) REVERT: J 344 TRP cc_start: 0.5750 (p90) cc_final: 0.5016 (p-90) REVERT: J 403 MET cc_start: 0.8416 (mmm) cc_final: 0.8115 (tpt) REVERT: J 406 MET cc_start: 0.7088 (ptm) cc_final: 0.5392 (tpt) REVERT: C 81 PHE cc_start: 0.5517 (OUTLIER) cc_final: 0.3871 (t80) REVERT: C 117 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.8023 (mm) REVERT: C 136 THR cc_start: 0.8857 (m) cc_final: 0.8649 (p) REVERT: C 164 MET cc_start: 0.7324 (OUTLIER) cc_final: 0.6832 (mmt) REVERT: C 247 ASN cc_start: 0.7579 (m-40) cc_final: 0.7219 (p0) REVERT: C 257 MET cc_start: 0.7597 (mmm) cc_final: 0.6942 (mmm) REVERT: C 330 MET cc_start: 0.7481 (mmt) cc_final: 0.7196 (mmt) REVERT: C 333 ILE cc_start: 0.8883 (tp) cc_final: 0.8348 (mm) REVERT: C 406 MET cc_start: 0.7068 (ptm) cc_final: 0.5972 (tpt) REVERT: D 50 TYR cc_start: 0.7841 (m-80) cc_final: 0.7005 (m-80) REVERT: D 73 MET cc_start: 0.8278 (mmm) cc_final: 0.7981 (mmm) REVERT: D 167 PHE cc_start: 0.8378 (m-80) cc_final: 0.8145 (m-80) REVERT: D 200 TYR cc_start: 0.8215 (m-80) cc_final: 0.7442 (m-80) REVERT: D 222 TYR cc_start: 0.8353 (OUTLIER) cc_final: 0.7841 (m-80) REVERT: D 306 ARG cc_start: 0.6531 (mmt90) cc_final: 0.6255 (mtt-85) REVERT: D 379 LYS cc_start: 0.8011 (mtpp) cc_final: 0.7633 (ttmm) REVERT: D 406 MET cc_start: 0.7128 (ptm) cc_final: 0.5640 (mmm) REVERT: F 47 ASP cc_start: 0.4155 (OUTLIER) cc_final: 0.3924 (t70) REVERT: F 157 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8281 (mp) REVERT: F 191 THR cc_start: 0.8073 (p) cc_final: 0.7870 (t) REVERT: F 248 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7425 (tt) REVERT: F 420 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.5656 (tp30) REVERT: A 24 TYR cc_start: 0.7929 (m-10) cc_final: 0.7462 (m-80) REVERT: A 83 TYR cc_start: 0.6885 (m-80) cc_final: 0.6419 (m-10) REVERT: A 163 LYS cc_start: 0.7647 (pttm) cc_final: 0.7370 (pttm) REVERT: B 102 ASN cc_start: 0.8469 (t0) cc_final: 0.7884 (t0) REVERT: B 163 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.6795 (pttm) REVERT: B 167 LEU cc_start: 0.8448 (mp) cc_final: 0.7965 (mp) REVERT: B 316 CYS cc_start: 0.7952 (m) cc_final: 0.7616 (m) REVERT: B 356 ASN cc_start: 0.7983 (t0) cc_final: 0.7727 (t0) REVERT: B 378 LEU cc_start: 0.7820 (mp) cc_final: 0.7535 (mp) REVERT: B 415 GLU cc_start: 0.7639 (tt0) cc_final: 0.6911 (tm-30) REVERT: L 117 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7760 (mm) REVERT: L 121 ARG cc_start: 0.6759 (mmm-85) cc_final: 0.6523 (mmm-85) REVERT: L 167 PHE cc_start: 0.8194 (m-80) cc_final: 0.7457 (m-10) REVERT: L 194 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.6183 (pm20) REVERT: L 200 TYR cc_start: 0.8226 (m-80) cc_final: 0.7184 (m-80) REVERT: L 225 LEU cc_start: 0.8262 (mp) cc_final: 0.7724 (tt) REVERT: L 247 ASN cc_start: 0.7622 (m-40) cc_final: 0.7268 (p0) REVERT: L 257 MET cc_start: 0.7121 (mmm) cc_final: 0.6517 (mmt) REVERT: L 312 THR cc_start: 0.8161 (p) cc_final: 0.7699 (t) REVERT: L 383 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7353 (tm-30) REVERT: L 390 ARG cc_start: 0.6675 (mtm110) cc_final: 0.6151 (ptt90) REVERT: G 47 ASP cc_start: 0.5030 (OUTLIER) cc_final: 0.4804 (t70) REVERT: G 138 PHE cc_start: 0.8997 (m-10) cc_final: 0.8788 (m-10) REVERT: G 316 CYS cc_start: 0.8450 (m) cc_final: 0.8216 (m) REVERT: G 319 TYR cc_start: 0.8413 (m-80) cc_final: 0.7903 (m-80) REVERT: G 356 ASN cc_start: 0.8139 (t0) cc_final: 0.7768 (m-40) REVERT: G 420 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6324 (tp30) REVERT: G 429 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6730 (pp20) outliers start: 229 outliers final: 152 residues processed: 1259 average time/residue: 0.2516 time to fit residues: 512.4001 Evaluate side-chains 1179 residues out of total 4368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 1003 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 GLN Chi-restraints excluded: chain K residue 81 PHE Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 163 ILE Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 293 MET Chi-restraints excluded: chain K residue 313 VAL Chi-restraints excluded: chain K residue 338 SER Chi-restraints excluded: chain K residue 355 ASP Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 205 ASP Chi-restraints excluded: chain H residue 224 TYR Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 287 SER Chi-restraints excluded: chain H residue 328 VAL Chi-restraints excluded: chain H residue 353 VAL Chi-restraints excluded: chain H residue 377 MET Chi-restraints excluded: chain H residue 420 GLU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 194 GLU Chi-restraints excluded: chain I residue 264 HIS Chi-restraints excluded: chain I residue 355 ASP Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 81 PHE Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 159 TYR Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 172 SER Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 312 THR Chi-restraints excluded: chain J residue 371 SER Chi-restraints excluded: chain J residue 381 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 81 PHE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 420 GLU Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 11 GLN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 152 ILE Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 172 SER Chi-restraints excluded: chain L residue 194 GLU Chi-restraints excluded: chain L residue 347 ASN Chi-restraints excluded: chain L residue 383 GLU Chi-restraints excluded: chain L residue 388 MET Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 76 ASP Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 88 HIS Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 224 TYR Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 287 SER Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 328 VAL Chi-restraints excluded: chain G residue 379 SER Chi-restraints excluded: chain G residue 420 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 118 optimal weight: 0.9990 chunk 418 optimal weight: 7.9990 chunk 312 optimal weight: 7.9990 chunk 222 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 480 optimal weight: 7.9990 chunk 347 optimal weight: 1.9990 chunk 490 optimal weight: 4.9990 chunk 242 optimal weight: 6.9990 chunk 500 optimal weight: 9.9990 chunk 408 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 279 GLN H 50 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 HIS J 131 GLN C 423 GLN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN F 393 HIS ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 126 ASN L 384 GLN G 101 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.129902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.119629 restraints weight = 74758.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.122684 restraints weight = 39765.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.124687 restraints weight = 23565.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.125987 restraints weight = 15060.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.126899 restraints weight = 10232.399| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.5446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 41436 Z= 0.170 Angle : 0.701 19.099 56298 Z= 0.345 Chirality : 0.045 0.227 6162 Planarity : 0.005 0.060 7308 Dihedral : 9.399 156.004 5692 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 5.24 % Allowed : 24.05 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.56 (0.12), residues: 5088 helix: 1.67 (0.11), residues: 2298 sheet: 0.32 (0.19), residues: 786 loop : -1.16 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 402 TYR 0.029 0.002 TYR A 103 PHE 0.032 0.002 PHE J 389 TRP 0.024 0.002 TRP G 346 HIS 0.028 0.001 HIS D 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (41436) covalent geometry : angle 0.70107 / 0.35 (56298) hydrogen bonds : bond 0.04382 / 3.05 ( 1959) hydrogen bonds : angle 4.66458 / 3.34 ( 5607) *********************** 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 1277 residues out of total 4368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 227 poor density : 1050 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 50 TYR cc_start: 0.7596 (m-80) cc_final: 0.7106 (m-10) REVERT: K 81 PHE cc_start: 0.5794 (OUTLIER) cc_final: 0.5490 (t80) REVERT: K 257 MET cc_start: 0.7786 (mmm) cc_final: 0.7585 (mmm) REVERT: K 355 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7622 (m-30) REVERT: K 363 MET cc_start: 0.7819 (mmt) cc_final: 0.7593 (mmt) REVERT: K 401 GLU cc_start: 0.5661 (mp0) cc_final: 0.5339 (mt-10) REVERT: H 163 LYS cc_start: 0.8492 (ttpp) cc_final: 0.8284 (ptmm) REVERT: H 224 TYR cc_start: 0.6975 (OUTLIER) cc_final: 0.6466 (m-80) REVERT: H 356 ASN cc_start: 0.8465 (t0) cc_final: 0.7776 (m-40) REVERT: H 407 TRP cc_start: 0.8512 (m100) cc_final: 0.8191 (m100) REVERT: H 415 GLU cc_start: 0.7286 (tt0) cc_final: 0.6704 (tm-30) REVERT: H 420 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.5302 (tp30) REVERT: I 130 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8496 (tm) REVERT: I 167 PHE cc_start: 0.8417 (m-80) cc_final: 0.7838 (m-10) REVERT: I 198 GLU cc_start: 0.8290 (pp20) cc_final: 0.7925 (pp20) REVERT: I 200 TYR cc_start: 0.8319 (m-80) cc_final: 0.6948 (m-80) REVERT: I 233 MET cc_start: 0.7547 (mtp) cc_final: 0.6979 (mtp) REVERT: I 247 ASN cc_start: 0.7466 (m-40) cc_final: 0.7125 (p0) REVERT: I 290 THR cc_start: 0.8643 (p) cc_final: 0.8421 (p) REVERT: I 312 THR cc_start: 0.8405 (m) cc_final: 0.8196 (m) REVERT: E 24 TYR cc_start: 0.7980 (m-10) cc_final: 0.7645 (m-80) REVERT: E 36 MET cc_start: 0.7876 (tmm) cc_final: 0.7492 (tmm) REVERT: E 83 TYR cc_start: 0.7232 (m-80) cc_final: 0.5841 (m-10) REVERT: E 97 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6762 (tm-30) REVERT: E 103 TYR cc_start: 0.8220 (t80) cc_final: 0.7978 (t80) REVERT: E 167 LEU cc_start: 0.8255 (mp) cc_final: 0.8047 (mp) REVERT: E 251 ASP cc_start: 0.6824 (m-30) cc_final: 0.6537 (m-30) REVERT: E 319 TYR cc_start: 0.8502 (m-80) cc_final: 0.8028 (m-80) REVERT: E 356 ASN cc_start: 0.8093 (t0) cc_final: 0.7882 (m-40) REVERT: J 99 ASN cc_start: 0.7934 (m-40) cc_final: 0.7604 (m-40) REVERT: J 136 THR cc_start: 0.8875 (m) cc_final: 0.8550 (p) REVERT: J 200 TYR cc_start: 0.8339 (m-80) cc_final: 0.7910 (m-80) REVERT: J 217 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7605 (mt) REVERT: J 247 ASN cc_start: 0.7494 (m-40) cc_final: 0.7113 (p0) REVERT: J 344 TRP cc_start: 0.5759 (p90) cc_final: 0.4971 (p-90) REVERT: J 406 MET cc_start: 0.7021 (ptm) cc_final: 0.5274 (tpt) REVERT: C 81 PHE cc_start: 0.5786 (OUTLIER) cc_final: 0.3862 (t80) REVERT: C 136 THR cc_start: 0.8988 (m) cc_final: 0.8719 (p) REVERT: C 164 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.6967 (mmt) REVERT: C 247 ASN cc_start: 0.7594 (m-40) cc_final: 0.7280 (p0) REVERT: C 299 MET cc_start: 0.7986 (mmm) cc_final: 0.7541 (mmt) REVERT: C 323 MET cc_start: 0.8272 (ttt) cc_final: 0.8019 (ttt) REVERT: C 333 ILE cc_start: 0.8863 (tp) cc_final: 0.8423 (mm) REVERT: C 406 MET cc_start: 0.7188 (ptm) cc_final: 0.6094 (tpt) REVERT: D 50 TYR cc_start: 0.7801 (m-80) cc_final: 0.7063 (m-80) REVERT: D 194 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6847 (pt0) REVERT: D 200 TYR cc_start: 0.8223 (m-80) cc_final: 0.7514 (m-80) REVERT: D 213 ARG cc_start: 0.7011 (ptm-80) cc_final: 0.6747 (ptt90) REVERT: D 222 TYR cc_start: 0.8404 (OUTLIER) cc_final: 0.7964 (m-80) REVERT: D 251 ARG cc_start: 0.8835 (mtp85) cc_final: 0.8374 (ttm-80) REVERT: D 306 ARG cc_start: 0.6537 (mmt90) cc_final: 0.6271 (mtt-85) REVERT: D 379 LYS cc_start: 0.8050 (mtpp) cc_final: 0.7682 (ttmm) REVERT: D 391 ARG cc_start: 0.7043 (mmm-85) cc_final: 0.6818 (mmm-85) REVERT: D 406 MET cc_start: 0.7091 (ptm) cc_final: 0.5562 (mmm) REVERT: F 47 ASP cc_start: 0.4179 (OUTLIER) cc_final: 0.3695 (t70) REVERT: F 156 ARG cc_start: 0.7527 (mmp-170) cc_final: 0.7312 (mmp-170) REVERT: F 157 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8238 (mp) REVERT: F 191 THR cc_start: 0.8177 (p) cc_final: 0.7897 (t) REVERT: F 224 TYR cc_start: 0.7661 (OUTLIER) cc_final: 0.6247 (m-10) REVERT: F 248 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7457 (tt) REVERT: F 420 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.5712 (tp30) REVERT: F 430 LYS cc_start: 0.8304 (ttpp) cc_final: 0.8030 (ttpp) REVERT: F 432 TYR cc_start: 0.7401 (OUTLIER) cc_final: 0.6605 (t80) REVERT: A 24 TYR cc_start: 0.7985 (m-10) cc_final: 0.7485 (m-80) REVERT: A 83 TYR cc_start: 0.7003 (m-80) cc_final: 0.6614 (m-10) REVERT: A 96 LYS cc_start: 0.6737 (tppt) cc_final: 0.6391 (mppt) REVERT: A 163 LYS cc_start: 0.7718 (pttm) cc_final: 0.7420 (pttm) REVERT: B 102 ASN cc_start: 0.8488 (t0) cc_final: 0.7882 (t0) REVERT: B 121 ARG cc_start: 0.7895 (tpp-160) cc_final: 0.7610 (mmt-90) REVERT: B 163 LYS cc_start: 0.7345 (OUTLIER) cc_final: 0.6708 (pttm) REVERT: B 290 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7019 (tm-30) REVERT: B 316 CYS cc_start: 0.7761 (m) cc_final: 0.7508 (m) REVERT: B 319 TYR cc_start: 0.8371 (m-80) cc_final: 0.7898 (m-80) REVERT: B 378 LEU cc_start: 0.7878 (mp) cc_final: 0.7575 (mp) REVERT: B 413 MET cc_start: 0.7848 (mmp) cc_final: 0.7413 (mmp) REVERT: B 415 GLU cc_start: 0.7593 (tt0) cc_final: 0.6742 (tm-30) REVERT: L 77 ARG cc_start: 0.6120 (tpm170) cc_final: 0.5026 (tpp-160) REVERT: L 117 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7724 (mm) REVERT: L 167 PHE cc_start: 0.8240 (m-80) cc_final: 0.7450 (m-10) REVERT: L 194 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6317 (pm20) REVERT: L 200 TYR cc_start: 0.8211 (m-80) cc_final: 0.7157 (m-80) REVERT: L 247 ASN cc_start: 0.7649 (m-40) cc_final: 0.7282 (p0) REVERT: L 257 MET cc_start: 0.7220 (mmm) cc_final: 0.6577 (mmt) REVERT: L 312 THR cc_start: 0.8151 (p) cc_final: 0.7651 (t) REVERT: L 383 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7422 (tm-30) REVERT: G 47 ASP cc_start: 0.4695 (OUTLIER) cc_final: 0.4198 (t70) REVERT: G 112 LYS cc_start: 0.5354 (mmmt) cc_final: 0.5112 (mmtt) REVERT: G 138 PHE cc_start: 0.8997 (m-10) cc_final: 0.8787 (m-10) REVERT: G 316 CYS cc_start: 0.8447 (m) cc_final: 0.8192 (m) REVERT: G 356 ASN cc_start: 0.8143 (t0) cc_final: 0.7771 (m-40) REVERT: G 420 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6347 (tp30) REVERT: G 429 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6868 (mt-10) outliers start: 227 outliers final: 164 residues processed: 1203 average time/residue: 0.2545 time to fit residues: 495.6423 Evaluate side-chains 1171 residues out of total 4368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 983 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 GLN Chi-restraints excluded: chain K residue 81 PHE Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 158 GLU Chi-restraints excluded: chain K residue 163 ILE Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 293 MET Chi-restraints excluded: chain K residue 313 VAL Chi-restraints excluded: chain K residue 338 SER Chi-restraints excluded: chain K residue 355 ASP Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 205 ASP Chi-restraints excluded: chain H residue 224 TYR Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 287 SER Chi-restraints excluded: chain H residue 328 VAL Chi-restraints excluded: chain H residue 345 ASP Chi-restraints excluded: chain H residue 353 VAL Chi-restraints excluded: chain H residue 377 MET Chi-restraints excluded: chain H residue 420 GLU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 194 GLU Chi-restraints excluded: chain I residue 303 CYS Chi-restraints excluded: chain I residue 355 ASP Chi-restraints excluded: chain I residue 363 MET Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 81 PHE Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 172 SER Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 222 TYR Chi-restraints excluded: chain J residue 312 THR Chi-restraints excluded: chain J residue 321 MET Chi-restraints excluded: chain J residue 371 SER Chi-restraints excluded: chain J residue 381 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 81 PHE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 85 GLN Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 420 GLU Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 432 TYR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 11 GLN Chi-restraints excluded: chain L residue 81 PHE Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 152 ILE Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 172 SER Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 194 GLU Chi-restraints excluded: chain L residue 347 ASN Chi-restraints excluded: chain L residue 383 GLU Chi-restraints excluded: chain L residue 388 MET Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 88 HIS Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 224 TYR Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 287 SER Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 328 VAL Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 420 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 179 optimal weight: 5.9990 chunk 276 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 chunk 337 optimal weight: 20.0000 chunk 157 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 chunk 336 optimal weight: 20.0000 chunk 490 optimal weight: 7.9990 chunk 335 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 129 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 14 ASN K 279 GLN H 50 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 134 GLN C 191 GLN D 279 GLN D 423 GLN F 31 GLN F 101 ASN F 393 HIS A 356 ASN B 406 HIS L 99 ASN L 134 GLN L 256 ASN G 301 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.127142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.117131 restraints weight = 75261.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.120086 restraints weight = 40249.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.122057 restraints weight = 24021.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.123302 restraints weight = 15368.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.124206 restraints weight = 10520.636| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.5655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 41436 Z= 0.230 Angle : 0.764 22.121 56298 Z= 0.378 Chirality : 0.048 0.381 6162 Planarity : 0.005 0.071 7308 Dihedral : 9.607 158.678 5692 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 5.52 % Allowed : 24.45 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.19 (0.12), residues: 5088 helix: 1.29 (0.11), residues: 2310 sheet: 0.14 (0.18), residues: 816 loop : -1.27 (0.14), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 79 TYR 0.035 0.002 TYR A 103 PHE 0.047 0.002 PHE B 149 TRP 0.024 0.002 TRP D 344 HIS 0.013 0.002 HIS B 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.23 (41436) covalent geometry : angle 0.76354 / 0.38 (56298) hydrogen bonds : bond 0.04755 / 3.31 ( 1959) hydrogen bonds : angle 4.84900 / 3.47 ( 5607) *********************** 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 1255 residues out of total 4368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 239 poor density : 1016 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 50 TYR cc_start: 0.7544 (m-80) cc_final: 0.6983 (m-10) REVERT: K 257 MET cc_start: 0.7663 (mmm) cc_final: 0.7409 (mmm) REVERT: K 355 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7626 (m-30) REVERT: K 363 MET cc_start: 0.7882 (mmt) cc_final: 0.7663 (mmt) REVERT: K 385 PHE cc_start: 0.8015 (t80) cc_final: 0.7807 (t80) REVERT: H 102 ASN cc_start: 0.8781 (t0) cc_final: 0.8176 (t0) REVERT: H 224 TYR cc_start: 0.7069 (OUTLIER) cc_final: 0.6490 (m-10) REVERT: H 356 ASN cc_start: 0.8461 (t0) cc_final: 0.7796 (m-40) REVERT: H 407 TRP cc_start: 0.8521 (m100) cc_final: 0.8218 (m100) REVERT: H 415 GLU cc_start: 0.7319 (tt0) cc_final: 0.6712 (tm-30) REVERT: H 420 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.5564 (tp30) REVERT: I 77 ARG cc_start: 0.5002 (tpm170) cc_final: 0.4659 (tpp-160) REVERT: I 130 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8573 (tm) REVERT: I 167 PHE cc_start: 0.8368 (m-80) cc_final: 0.7943 (m-10) REVERT: I 233 MET cc_start: 0.7563 (mtp) cc_final: 0.7010 (mtp) REVERT: I 247 ASN cc_start: 0.7666 (m-40) cc_final: 0.7171 (p0) REVERT: I 257 MET cc_start: 0.8322 (mmm) cc_final: 0.7969 (mmp) REVERT: I 290 THR cc_start: 0.8722 (p) cc_final: 0.8519 (p) REVERT: E 36 MET cc_start: 0.7808 (tmm) cc_final: 0.7547 (tmm) REVERT: E 319 TYR cc_start: 0.8614 (m-80) cc_final: 0.8172 (m-80) REVERT: J 99 ASN cc_start: 0.7797 (m-40) cc_final: 0.7429 (m-40) REVERT: J 136 THR cc_start: 0.8933 (m) cc_final: 0.8585 (p) REVERT: J 159 TYR cc_start: 0.7790 (OUTLIER) cc_final: 0.6571 (m-80) REVERT: J 200 TYR cc_start: 0.8351 (m-80) cc_final: 0.7896 (m-80) REVERT: J 217 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7716 (mt) REVERT: J 247 ASN cc_start: 0.7522 (m-40) cc_final: 0.7165 (p0) REVERT: J 344 TRP cc_start: 0.5889 (p90) cc_final: 0.5079 (p-90) REVERT: J 406 MET cc_start: 0.7031 (ptm) cc_final: 0.5273 (tpt) REVERT: C 81 PHE cc_start: 0.5756 (OUTLIER) cc_final: 0.4056 (t80) REVERT: C 133 PHE cc_start: 0.8364 (m-80) cc_final: 0.7982 (m-80) REVERT: C 136 THR cc_start: 0.9113 (m) cc_final: 0.8791 (p) REVERT: C 164 MET cc_start: 0.7267 (OUTLIER) cc_final: 0.6904 (mmt) REVERT: C 333 ILE cc_start: 0.8785 (tp) cc_final: 0.8416 (mm) REVERT: C 406 MET cc_start: 0.7253 (ptm) cc_final: 0.6284 (tpt) REVERT: D 50 TYR cc_start: 0.7853 (m-80) cc_final: 0.7156 (m-80) REVERT: D 73 MET cc_start: 0.8403 (mmm) cc_final: 0.8165 (mmm) REVERT: D 86 ARG cc_start: 0.7776 (tpp80) cc_final: 0.7513 (tpp80) REVERT: D 194 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6855 (pt0) REVERT: D 200 TYR cc_start: 0.8254 (m-80) cc_final: 0.7495 (m-80) REVERT: D 213 ARG cc_start: 0.7062 (ptm-80) cc_final: 0.6832 (ptt90) REVERT: D 222 TYR cc_start: 0.8474 (OUTLIER) cc_final: 0.8046 (m-80) REVERT: D 257 MET cc_start: 0.7728 (mmm) cc_final: 0.7487 (mmp) REVERT: D 306 ARG cc_start: 0.6538 (mmt90) cc_final: 0.6334 (mtt-85) REVERT: D 379 LYS cc_start: 0.8035 (mtpp) cc_final: 0.7798 (tptp) REVERT: D 391 ARG cc_start: 0.6886 (mmm-85) cc_final: 0.6596 (mmm-85) REVERT: D 406 MET cc_start: 0.7220 (ptm) cc_final: 0.5680 (mmm) REVERT: F 47 ASP cc_start: 0.4362 (OUTLIER) cc_final: 0.4115 (t70) REVERT: F 156 ARG cc_start: 0.7719 (mmp-170) cc_final: 0.7511 (mmp-170) REVERT: F 157 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8302 (mp) REVERT: F 191 THR cc_start: 0.8267 (p) cc_final: 0.7969 (t) REVERT: F 248 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7582 (tt) REVERT: F 420 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.5630 (tp30) REVERT: F 432 TYR cc_start: 0.7482 (OUTLIER) cc_final: 0.6727 (t80) REVERT: A 24 TYR cc_start: 0.8081 (m-10) cc_final: 0.7569 (m-80) REVERT: A 83 TYR cc_start: 0.7120 (m-80) cc_final: 0.6725 (m-10) REVERT: A 96 LYS cc_start: 0.7168 (tppt) cc_final: 0.6835 (mppt) REVERT: A 163 LYS cc_start: 0.7583 (pttm) cc_final: 0.7228 (pttm) REVERT: B 102 ASN cc_start: 0.8527 (t0) cc_final: 0.7915 (t0) REVERT: B 121 ARG cc_start: 0.7919 (tpp-160) cc_final: 0.7648 (mmt-90) REVERT: B 163 LYS cc_start: 0.7371 (OUTLIER) cc_final: 0.6765 (pttm) REVERT: B 290 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7270 (tm-30) REVERT: B 316 CYS cc_start: 0.7759 (m) cc_final: 0.7490 (m) REVERT: B 319 TYR cc_start: 0.8355 (m-80) cc_final: 0.8050 (m-80) REVERT: B 378 LEU cc_start: 0.7953 (mp) cc_final: 0.7686 (mp) REVERT: B 415 GLU cc_start: 0.7416 (tt0) cc_final: 0.6923 (tm-30) REVERT: L 73 MET cc_start: 0.7832 (mmm) cc_final: 0.7629 (mmm) REVERT: L 77 ARG cc_start: 0.5685 (tpm170) cc_final: 0.4618 (tpp-160) REVERT: L 167 PHE cc_start: 0.8213 (m-80) cc_final: 0.7739 (m-10) REVERT: L 247 ASN cc_start: 0.7596 (m-40) cc_final: 0.7213 (p0) REVERT: L 257 MET cc_start: 0.7103 (mmm) cc_final: 0.6547 (mmt) REVERT: L 383 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7469 (tm-30) REVERT: L 410 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7856 (mt-10) REVERT: G 356 ASN cc_start: 0.8110 (t0) cc_final: 0.7762 (m-40) REVERT: G 420 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6388 (tp30) REVERT: G 429 GLU cc_start: 0.7161 (mt-10) cc_final: 0.6896 (mt-10) outliers start: 239 outliers final: 188 residues processed: 1180 average time/residue: 0.2515 time to fit residues: 481.7316 Evaluate side-chains 1170 residues out of total 4368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 963 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 GLN Chi-restraints excluded: chain K residue 14 ASN Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 81 PHE Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 163 ILE Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 293 MET Chi-restraints excluded: chain K residue 313 VAL Chi-restraints excluded: chain K residue 338 SER Chi-restraints excluded: chain K residue 355 ASP Chi-restraints excluded: chain K residue 371 SER Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 224 TYR Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 287 SER Chi-restraints excluded: chain H residue 328 VAL Chi-restraints excluded: chain H residue 345 ASP Chi-restraints excluded: chain H residue 353 VAL Chi-restraints excluded: chain H residue 377 MET Chi-restraints excluded: chain H residue 420 GLU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 159 TYR Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 194 GLU Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 303 CYS Chi-restraints excluded: chain I residue 355 ASP Chi-restraints excluded: chain I residue 363 MET Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 81 PHE Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 159 TYR Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 172 SER Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 222 TYR Chi-restraints excluded: chain J residue 230 SER Chi-restraints excluded: chain J residue 321 MET Chi-restraints excluded: chain J residue 371 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 81 PHE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 85 GLN Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 420 GLU Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 432 TYR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain L residue 11 GLN Chi-restraints excluded: chain L residue 81 PHE Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 152 ILE Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 172 SER Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 215 LEU Chi-restraints excluded: chain L residue 347 ASN Chi-restraints excluded: chain L residue 372 THR Chi-restraints excluded: chain L residue 383 GLU Chi-restraints excluded: chain L residue 388 MET Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 88 HIS Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 224 TYR Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 287 SER Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 328 VAL Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 379 SER Chi-restraints excluded: chain G residue 420 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 56 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 360 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 247 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 chunk 350 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 448 optimal weight: 0.0470 chunk 130 optimal weight: 6.9990 overall best weight: 4.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 279 GLN H 50 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 GLN ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 GLN ** J 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN D 57 HIS ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN F 101 ASN A 15 GLN L 256 ASN G 301 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.129043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.118940 restraints weight = 74860.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.122001 restraints weight = 39621.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.123987 restraints weight = 23335.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.125283 restraints weight = 14828.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.126175 restraints weight = 9990.884| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.5806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 41436 Z= 0.168 Angle : 0.731 22.046 56298 Z= 0.359 Chirality : 0.046 0.369 6162 Planarity : 0.005 0.067 7308 Dihedral : 9.453 157.976 5692 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 5.19 % Allowed : 25.62 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.25 (0.12), residues: 5088 helix: 1.35 (0.11), residues: 2298 sheet: 0.13 (0.19), residues: 804 loop : -1.21 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 79 TYR 0.030 0.002 TYR A 103 PHE 0.039 0.002 PHE K 294 TRP 0.026 0.002 TRP G 346 HIS 0.010 0.001 HIS B 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (41436) covalent geometry : angle 0.73138 / 0.36 (56298) hydrogen bonds : bond 0.04496 / 3.13 ( 1959) hydrogen bonds : angle 4.76149 / 3.40 ( 5607) *********************** 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 1245 residues out of total 4368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 1020 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 50 TYR cc_start: 0.7600 (m-80) cc_final: 0.7131 (m-10) REVERT: K 222 TYR cc_start: 0.8316 (m-80) cc_final: 0.8099 (m-80) REVERT: K 355 ASP cc_start: 0.7937 (OUTLIER) cc_final: 0.7622 (m-30) REVERT: K 363 MET cc_start: 0.7862 (mmt) cc_final: 0.7592 (mmt) REVERT: H 102 ASN cc_start: 0.8721 (t0) cc_final: 0.8092 (t0) REVERT: H 155 GLU cc_start: 0.7403 (tp30) cc_final: 0.7168 (tp30) REVERT: H 224 TYR cc_start: 0.6980 (OUTLIER) cc_final: 0.6394 (m-10) REVERT: H 297 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6836 (mm-30) REVERT: H 356 ASN cc_start: 0.8428 (t0) cc_final: 0.7799 (m-40) REVERT: H 407 TRP cc_start: 0.8491 (m100) cc_final: 0.8173 (m100) REVERT: H 415 GLU cc_start: 0.7182 (tt0) cc_final: 0.6640 (tm-30) REVERT: H 420 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.5245 (tp30) REVERT: I 130 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8621 (tm) REVERT: I 167 PHE cc_start: 0.8389 (m-80) cc_final: 0.7869 (m-10) REVERT: I 200 TYR cc_start: 0.8263 (m-80) cc_final: 0.6948 (m-80) REVERT: I 233 MET cc_start: 0.7541 (mtp) cc_final: 0.6996 (mtp) REVERT: I 247 ASN cc_start: 0.7556 (m-40) cc_final: 0.7131 (p0) REVERT: I 335 SER cc_start: 0.8120 (p) cc_final: 0.7824 (t) REVERT: E 36 MET cc_start: 0.7756 (tmm) cc_final: 0.7458 (tmm) REVERT: E 97 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6814 (tm-30) REVERT: E 319 TYR cc_start: 0.8560 (m-80) cc_final: 0.8075 (m-80) REVERT: J 50 TYR cc_start: 0.7666 (m-80) cc_final: 0.7108 (m-80) REVERT: J 99 ASN cc_start: 0.7759 (m-40) cc_final: 0.7414 (m-40) REVERT: J 136 THR cc_start: 0.8884 (m) cc_final: 0.8546 (p) REVERT: J 200 TYR cc_start: 0.8293 (m-80) cc_final: 0.7883 (m-80) REVERT: J 217 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7865 (mt) REVERT: J 247 ASN cc_start: 0.7535 (m-40) cc_final: 0.7294 (p0) REVERT: J 300 MET cc_start: 0.7147 (mpp) cc_final: 0.6683 (ptt) REVERT: J 401 GLU cc_start: 0.5803 (mp0) cc_final: 0.5444 (mt-10) REVERT: J 406 MET cc_start: 0.6897 (ptm) cc_final: 0.5180 (tpt) REVERT: C 81 PHE cc_start: 0.5702 (OUTLIER) cc_final: 0.3922 (t80) REVERT: C 136 THR cc_start: 0.9043 (m) cc_final: 0.8719 (p) REVERT: C 164 MET cc_start: 0.7215 (OUTLIER) cc_final: 0.6882 (mmt) REVERT: C 257 MET cc_start: 0.7031 (mmm) cc_final: 0.6580 (mmm) REVERT: C 333 ILE cc_start: 0.8800 (tp) cc_final: 0.8322 (mm) REVERT: C 406 MET cc_start: 0.7174 (ptm) cc_final: 0.6273 (tpt) REVERT: D 50 TYR cc_start: 0.7830 (m-80) cc_final: 0.7084 (m-80) REVERT: D 73 MET cc_start: 0.8370 (mmm) cc_final: 0.8164 (mmm) REVERT: D 200 TYR cc_start: 0.8242 (m-80) cc_final: 0.7414 (m-80) REVERT: D 213 ARG cc_start: 0.7003 (ptm-80) cc_final: 0.6749 (ptt90) REVERT: D 222 TYR cc_start: 0.8420 (OUTLIER) cc_final: 0.7999 (m-80) REVERT: D 306 ARG cc_start: 0.6526 (mmt90) cc_final: 0.6294 (mtt-85) REVERT: D 379 LYS cc_start: 0.7995 (mtpp) cc_final: 0.7621 (ttmm) REVERT: D 391 ARG cc_start: 0.6719 (mmm-85) cc_final: 0.6447 (mmm-85) REVERT: D 406 MET cc_start: 0.7185 (ptm) cc_final: 0.5657 (mmm) REVERT: F 47 ASP cc_start: 0.4340 (OUTLIER) cc_final: 0.4103 (t70) REVERT: F 157 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8269 (mp) REVERT: F 191 THR cc_start: 0.8206 (p) cc_final: 0.7944 (t) REVERT: F 248 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7557 (tt) REVERT: F 338 LYS cc_start: 0.8395 (mmmm) cc_final: 0.7747 (tmtt) REVERT: F 420 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.5537 (tp30) REVERT: F 432 TYR cc_start: 0.7434 (OUTLIER) cc_final: 0.6695 (t80) REVERT: A 24 TYR cc_start: 0.8038 (m-10) cc_final: 0.7525 (m-80) REVERT: A 83 TYR cc_start: 0.7077 (m-80) cc_final: 0.6678 (m-10) REVERT: A 96 LYS cc_start: 0.6862 (tppt) cc_final: 0.6577 (mppt) REVERT: A 163 LYS cc_start: 0.7731 (pttm) cc_final: 0.7405 (pttm) REVERT: A 202 PHE cc_start: 0.7902 (m-10) cc_final: 0.7553 (m-10) REVERT: A 413 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7436 (tpp) REVERT: B 102 ASN cc_start: 0.8458 (t0) cc_final: 0.7846 (t0) REVERT: B 121 ARG cc_start: 0.7883 (tpp-160) cc_final: 0.7651 (mmt-90) REVERT: B 163 LYS cc_start: 0.7409 (OUTLIER) cc_final: 0.6591 (pttm) REVERT: B 177 VAL cc_start: 0.8391 (m) cc_final: 0.8054 (t) REVERT: B 221 ARG cc_start: 0.7146 (mtp180) cc_final: 0.6889 (ttt180) REVERT: B 290 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7210 (tm-30) REVERT: B 316 CYS cc_start: 0.7721 (m) cc_final: 0.7481 (m) REVERT: B 319 TYR cc_start: 0.8348 (m-80) cc_final: 0.8002 (m-80) REVERT: B 378 LEU cc_start: 0.7955 (mp) cc_final: 0.7661 (mp) REVERT: B 415 GLU cc_start: 0.7366 (tt0) cc_final: 0.6754 (tm-30) REVERT: L 117 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7746 (mm) REVERT: L 167 PHE cc_start: 0.8204 (m-80) cc_final: 0.7423 (m-10) REVERT: L 194 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6347 (pm20) REVERT: L 200 TYR cc_start: 0.8223 (m-80) cc_final: 0.7410 (m-80) REVERT: L 247 ASN cc_start: 0.7650 (m-40) cc_final: 0.7296 (p0) REVERT: L 257 MET cc_start: 0.7218 (mmm) cc_final: 0.6768 (mmm) REVERT: L 383 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7454 (tm-30) REVERT: L 410 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7533 (mm-30) REVERT: G 112 LYS cc_start: 0.5453 (mmmt) cc_final: 0.5181 (mmtt) REVERT: G 356 ASN cc_start: 0.8069 (t0) cc_final: 0.7738 (m-40) REVERT: G 415 GLU cc_start: 0.7352 (tt0) cc_final: 0.6372 (tm-30) REVERT: G 420 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6225 (tp30) outliers start: 225 outliers final: 181 residues processed: 1176 average time/residue: 0.2469 time to fit residues: 469.8892 Evaluate side-chains 1167 residues out of total 4368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 965 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 GLN Chi-restraints excluded: chain K residue 14 ASN Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 81 PHE Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 163 ILE Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 293 MET Chi-restraints excluded: chain K residue 313 VAL Chi-restraints excluded: chain K residue 338 SER Chi-restraints excluded: chain K residue 355 ASP Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 224 TYR Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 287 SER Chi-restraints excluded: chain H residue 328 VAL Chi-restraints excluded: chain H residue 345 ASP Chi-restraints excluded: chain H residue 353 VAL Chi-restraints excluded: chain H residue 377 MET Chi-restraints excluded: chain H residue 420 GLU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 194 GLU Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 303 CYS Chi-restraints excluded: chain I residue 348 ASN Chi-restraints excluded: chain I residue 355 ASP Chi-restraints excluded: chain I residue 363 MET Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 81 PHE Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 172 SER Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 222 TYR Chi-restraints excluded: chain J residue 230 SER Chi-restraints excluded: chain J residue 276 ARG Chi-restraints excluded: chain J residue 321 MET Chi-restraints excluded: chain J residue 371 SER Chi-restraints excluded: chain J residue 372 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 81 PHE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 85 GLN Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 420 GLU Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 432 TYR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain L residue 11 GLN Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 152 ILE Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 172 SER Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 194 GLU Chi-restraints excluded: chain L residue 215 LEU Chi-restraints excluded: chain L residue 347 ASN Chi-restraints excluded: chain L residue 368 ILE Chi-restraints excluded: chain L residue 372 THR Chi-restraints excluded: chain L residue 383 GLU Chi-restraints excluded: chain L residue 388 MET Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 121 ARG Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 224 TYR Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 287 SER Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 328 VAL Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 379 SER Chi-restraints excluded: chain G residue 420 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 136 optimal weight: 0.8980 chunk 275 optimal weight: 30.0000 chunk 250 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 218 optimal weight: 7.9990 chunk 198 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 269 optimal weight: 8.9990 chunk 230 optimal weight: 5.9990 chunk 133 optimal weight: 8.9990 chunk 500 optimal weight: 4.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 14 ASN K 43 GLN ** K 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 279 GLN H 50 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 HIS ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 307 HIS C 191 GLN D 14 ASN D 57 HIS ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 393 HIS L 43 GLN L 256 ASN G 301 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.128423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.118112 restraints weight = 75101.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.121178 restraints weight = 40018.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.123212 restraints weight = 23807.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.124565 restraints weight = 15263.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.125508 restraints weight = 10335.816| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.5924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 41436 Z= 0.180 Angle : 0.754 22.052 56298 Z= 0.369 Chirality : 0.046 0.245 6162 Planarity : 0.005 0.078 7308 Dihedral : 9.472 157.914 5692 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 5.01 % Allowed : 26.29 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 (0.12), residues: 5088 helix: 1.23 (0.11), residues: 2334 sheet: -0.01 (0.18), residues: 816 loop : -1.26 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 390 TYR 0.029 0.002 TYR A 103 PHE 0.040 0.002 PHE K 294 TRP 0.026 0.002 TRP G 346 HIS 0.010 0.001 HIS B 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (41436) covalent geometry : angle 0.75402 / 0.37 (56298) hydrogen bonds : bond 0.04514 / 3.14 ( 1959) hydrogen bonds : angle 4.81103 / 3.43 ( 5607) ********************** 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 1203 residues out of total 4368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 986 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 45 GLU cc_start: 0.7814 (tp30) cc_final: 0.7542 (tp30) REVERT: K 50 TYR cc_start: 0.7606 (m-80) cc_final: 0.7130 (m-80) REVERT: K 81 PHE cc_start: 0.5532 (OUTLIER) cc_final: 0.5312 (t80) REVERT: K 167 PHE cc_start: 0.8003 (m-10) cc_final: 0.7791 (m-10) REVERT: K 222 TYR cc_start: 0.8398 (m-80) cc_final: 0.8194 (m-80) REVERT: K 257 MET cc_start: 0.7724 (mmm) cc_final: 0.7449 (mmt) REVERT: K 355 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7623 (m-30) REVERT: K 363 MET cc_start: 0.7899 (mmt) cc_final: 0.7656 (mmt) REVERT: H 102 ASN cc_start: 0.8726 (t0) cc_final: 0.8065 (t0) REVERT: H 224 TYR cc_start: 0.6847 (OUTLIER) cc_final: 0.6304 (m-10) REVERT: H 225 THR cc_start: 0.6922 (p) cc_final: 0.6231 (t) REVERT: H 282 TYR cc_start: 0.6858 (m-80) cc_final: 0.6626 (m-80) REVERT: H 356 ASN cc_start: 0.8454 (t0) cc_final: 0.7846 (m-40) REVERT: H 407 TRP cc_start: 0.8503 (m100) cc_final: 0.8205 (m100) REVERT: H 415 GLU cc_start: 0.7113 (tt0) cc_final: 0.6643 (tm-30) REVERT: H 420 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.5520 (tp30) REVERT: I 130 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8643 (tm) REVERT: I 167 PHE cc_start: 0.8366 (m-80) cc_final: 0.7820 (m-10) REVERT: I 200 TYR cc_start: 0.8294 (m-80) cc_final: 0.7084 (m-80) REVERT: I 233 MET cc_start: 0.7558 (mtp) cc_final: 0.7001 (mtp) REVERT: I 247 ASN cc_start: 0.7718 (m-40) cc_final: 0.7184 (p0) REVERT: I 335 SER cc_start: 0.8198 (p) cc_final: 0.7884 (t) REVERT: E 36 MET cc_start: 0.7759 (tmm) cc_final: 0.7497 (tmm) REVERT: E 167 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8435 (mm) REVERT: E 319 TYR cc_start: 0.8550 (m-80) cc_final: 0.8100 (m-80) REVERT: J 50 TYR cc_start: 0.7592 (m-80) cc_final: 0.7056 (m-80) REVERT: J 77 ARG cc_start: 0.5041 (tpm170) cc_final: 0.4309 (tpp-160) REVERT: J 99 ASN cc_start: 0.7743 (m-40) cc_final: 0.7379 (m-40) REVERT: J 178 THR cc_start: 0.7678 (OUTLIER) cc_final: 0.7402 (p) REVERT: J 200 TYR cc_start: 0.8308 (m-80) cc_final: 0.7930 (m-80) REVERT: J 247 ASN cc_start: 0.7451 (m-40) cc_final: 0.7184 (p0) REVERT: J 300 MET cc_start: 0.7104 (mpp) cc_final: 0.6650 (ptt) REVERT: J 309 ARG cc_start: 0.6657 (mtt-85) cc_final: 0.5871 (ptp-170) REVERT: J 406 MET cc_start: 0.6860 (ptm) cc_final: 0.5198 (tpt) REVERT: C 133 PHE cc_start: 0.8390 (m-80) cc_final: 0.8015 (m-80) REVERT: C 136 THR cc_start: 0.9049 (m) cc_final: 0.8691 (p) REVERT: C 164 MET cc_start: 0.7198 (OUTLIER) cc_final: 0.6847 (mmt) REVERT: C 257 MET cc_start: 0.7339 (mmm) cc_final: 0.6886 (mmm) REVERT: C 333 ILE cc_start: 0.8771 (tp) cc_final: 0.8324 (mm) REVERT: C 406 MET cc_start: 0.7231 (ptm) cc_final: 0.6328 (tpt) REVERT: D 50 TYR cc_start: 0.7830 (m-80) cc_final: 0.7106 (m-80) REVERT: D 77 ARG cc_start: 0.7013 (tpm170) cc_final: 0.6273 (tpp-160) REVERT: D 200 TYR cc_start: 0.8266 (m-80) cc_final: 0.7583 (m-80) REVERT: D 213 ARG cc_start: 0.6972 (ptm-80) cc_final: 0.6729 (ptt90) REVERT: D 222 TYR cc_start: 0.8444 (OUTLIER) cc_final: 0.8015 (m-80) REVERT: D 306 ARG cc_start: 0.6666 (mmt90) cc_final: 0.6414 (mtt-85) REVERT: D 391 ARG cc_start: 0.6784 (mmm-85) cc_final: 0.6522 (mmm-85) REVERT: D 406 MET cc_start: 0.7209 (ptm) cc_final: 0.5599 (mmm) REVERT: F 47 ASP cc_start: 0.4749 (OUTLIER) cc_final: 0.4375 (t70) REVERT: F 191 THR cc_start: 0.8217 (p) cc_final: 0.7934 (t) REVERT: F 248 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7616 (tt) REVERT: F 338 LYS cc_start: 0.8419 (mmmm) cc_final: 0.7707 (tmtt) REVERT: F 420 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.5508 (tp30) REVERT: F 432 TYR cc_start: 0.7462 (OUTLIER) cc_final: 0.6675 (t80) REVERT: A 24 TYR cc_start: 0.8059 (m-10) cc_final: 0.7544 (m-80) REVERT: A 83 TYR cc_start: 0.7096 (m-80) cc_final: 0.6725 (m-10) REVERT: A 96 LYS cc_start: 0.7226 (tppt) cc_final: 0.6920 (mppt) REVERT: A 163 LYS cc_start: 0.7806 (pttm) cc_final: 0.7498 (pttm) REVERT: A 202 PHE cc_start: 0.7828 (m-10) cc_final: 0.7426 (m-10) REVERT: A 413 MET cc_start: 0.7859 (tpt) cc_final: 0.7205 (mpp) REVERT: B 102 ASN cc_start: 0.8507 (t0) cc_final: 0.7859 (t0) REVERT: B 121 ARG cc_start: 0.7936 (tpp-160) cc_final: 0.7715 (mmt-90) REVERT: B 163 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.6674 (pttm) REVERT: B 290 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7275 (tm-30) REVERT: B 316 CYS cc_start: 0.7731 (m) cc_final: 0.7486 (m) REVERT: B 319 TYR cc_start: 0.8383 (m-80) cc_final: 0.8055 (m-80) REVERT: B 378 LEU cc_start: 0.7996 (mp) cc_final: 0.7717 (mp) REVERT: B 415 GLU cc_start: 0.7120 (tt0) cc_final: 0.6662 (tm-30) REVERT: L 77 ARG cc_start: 0.5710 (tpm170) cc_final: 0.4826 (tpp-160) REVERT: L 117 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7776 (mm) REVERT: L 167 PHE cc_start: 0.8183 (m-80) cc_final: 0.7676 (m-10) REVERT: L 194 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6345 (pm20) REVERT: L 247 ASN cc_start: 0.7644 (m-40) cc_final: 0.7316 (p0) REVERT: L 257 MET cc_start: 0.7204 (mmm) cc_final: 0.6557 (mmm) REVERT: L 312 THR cc_start: 0.8196 (p) cc_final: 0.7606 (t) REVERT: L 383 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7362 (tm-30) REVERT: L 390 ARG cc_start: 0.6581 (mtm110) cc_final: 0.6119 (ptt90) REVERT: G 112 LYS cc_start: 0.5588 (mmmt) cc_final: 0.5298 (mmtt) REVERT: G 224 TYR cc_start: 0.7435 (OUTLIER) cc_final: 0.6097 (m-10) REVERT: G 356 ASN cc_start: 0.8039 (t0) cc_final: 0.7723 (m-40) REVERT: G 415 GLU cc_start: 0.7391 (tt0) cc_final: 0.6411 (tm-30) REVERT: G 420 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.6318 (tp30) outliers start: 217 outliers final: 182 residues processed: 1136 average time/residue: 0.2512 time to fit residues: 460.5009 Evaluate side-chains 1161 residues out of total 4368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 959 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 GLN Chi-restraints excluded: chain K residue 14 ASN Chi-restraints excluded: chain K residue 81 PHE Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 163 ILE Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 293 MET Chi-restraints excluded: chain K residue 313 VAL Chi-restraints excluded: chain K residue 338 SER Chi-restraints excluded: chain K residue 355 ASP Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 224 TYR Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 287 SER Chi-restraints excluded: chain H residue 328 VAL Chi-restraints excluded: chain H residue 345 ASP Chi-restraints excluded: chain H residue 353 VAL Chi-restraints excluded: chain H residue 377 MET Chi-restraints excluded: chain H residue 420 GLU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 194 GLU Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 303 CYS Chi-restraints excluded: chain I residue 348 ASN Chi-restraints excluded: chain I residue 355 ASP Chi-restraints excluded: chain I residue 363 MET Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 172 SER Chi-restraints excluded: chain J residue 178 THR Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 222 TYR Chi-restraints excluded: chain J residue 230 SER Chi-restraints excluded: chain J residue 276 ARG Chi-restraints excluded: chain J residue 321 MET Chi-restraints excluded: chain J residue 371 SER Chi-restraints excluded: chain J residue 372 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain D residue 14 ASN Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 367 PHE Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 420 GLU Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 432 TYR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain L residue 11 GLN Chi-restraints excluded: chain L residue 81 PHE Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 152 ILE Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 172 SER Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 194 GLU Chi-restraints excluded: chain L residue 215 LEU Chi-restraints excluded: chain L residue 224 ASP Chi-restraints excluded: chain L residue 347 ASN Chi-restraints excluded: chain L residue 368 ILE Chi-restraints excluded: chain L residue 372 THR Chi-restraints excluded: chain L residue 383 GLU Chi-restraints excluded: chain L residue 388 MET Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 121 ARG Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 224 TYR Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 287 SER Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 328 VAL Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 379 SER Chi-restraints excluded: chain G residue 420 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 253 optimal weight: 20.0000 chunk 384 optimal weight: 9.9990 chunk 391 optimal weight: 30.0000 chunk 246 optimal weight: 6.9990 chunk 482 optimal weight: 1.9990 chunk 244 optimal weight: 7.9990 chunk 7 optimal weight: 30.0000 chunk 282 optimal weight: 10.0000 chunk 181 optimal weight: 4.9990 chunk 347 optimal weight: 1.9990 chunk 457 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 14 ASN ** K 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 GLN H 50 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 384 GLN ** J 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN D 14 ASN D 57 HIS ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 301 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.128621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.118310 restraints weight = 75661.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.121401 restraints weight = 40232.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.123431 restraints weight = 23877.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.124778 restraints weight = 15263.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.125708 restraints weight = 10320.867| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.6000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 41436 Z= 0.179 Angle : 0.756 22.017 56298 Z= 0.370 Chirality : 0.046 0.271 6162 Planarity : 0.005 0.070 7308 Dihedral : 9.444 158.153 5692 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.82 % Allowed : 26.48 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.11 (0.12), residues: 5088 helix: 1.21 (0.11), residues: 2334 sheet: -0.00 (0.18), residues: 804 loop : -1.28 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 390 TYR 0.033 0.002 TYR B 108 PHE 0.049 0.002 PHE C 167 TRP 0.026 0.002 TRP G 346 HIS 0.011 0.001 HIS B 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (41436) covalent geometry : angle 0.75566 / 0.37 (56298) hydrogen bonds : bond 0.04475 / 3.12 ( 1959) hydrogen bonds : angle 4.81243 / 3.44 ( 5607) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9017.85 seconds wall clock time: 156 minutes 31.67 seconds (9391.67 seconds total)