Starting phenix.real_space_refine on Sun Aug 24 18:59:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bq2_16170/08_2025/8bq2_16170.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bq2_16170/08_2025/8bq2_16170.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bq2_16170/08_2025/8bq2_16170.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bq2_16170/08_2025/8bq2_16170.map" model { file = "/net/cci-nas-00/data/ceres_data/8bq2_16170/08_2025/8bq2_16170.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bq2_16170/08_2025/8bq2_16170.cif" } resolution = 3.8 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= -0.000 sd= 0.024 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 Ca 18 9.91 5 P 57 5.49 5 S 117 5.16 5 C 13791 2.51 5 N 3975 2.21 5 O 4373 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22331 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2376 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "B" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2376 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "C" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2376 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "D" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2376 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "E" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2376 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "F" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2376 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "G" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2376 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "H" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2376 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "I" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2376 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "W" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 650 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CA': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.70, per 1000 atoms: 0.26 Number of scatterers: 22331 At special positions: 0 Unit cell: (114.4, 117.26, 217.36, 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) Ca 18 19.99 S 117 16.00 P 57 15.00 O 4373 8.00 N 3975 7.00 C 13791 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 934.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5094 Finding SS restraints... Secondary structure from input PDB file: 153 helices and 18 sheets defined 54.2% alpha, 16.4% beta 0 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 2.72 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 removed outlier: 3.511A pdb=" N GLY A 32 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 44 removed outlier: 3.782A pdb=" N VAL A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A 39 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 44 " --> pdb=" O LYS A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 54 Processing helix chain 'A' and resid 56 through 63 removed outlier: 3.921A pdb=" N LEU A 60 " --> pdb=" O PRO A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 82 removed outlier: 3.731A pdb=" N LYS A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 97 Processing helix chain 'A' and resid 106 through 113 Processing helix chain 'A' and resid 132 through 144 removed outlier: 3.600A pdb=" N ILE A 136 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N CYS A 137 " --> pdb=" O LYS A 133 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 146 No H-bonds generated for 'chain 'A' and resid 145 through 146' Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 167 through 179 removed outlier: 3.895A pdb=" N LEU A 171 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 186 Processing helix chain 'A' and resid 196 through 214 removed outlier: 4.008A pdb=" N LEU A 204 " --> pdb=" O GLN A 200 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR A 205 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN A 206 " --> pdb=" O GLN A 202 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A 214 " --> pdb=" O MET A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 232 removed outlier: 3.961A pdb=" N TYR A 232 " --> pdb=" O TYR A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 237 through 260 removed outlier: 3.664A pdb=" N MET A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS A 244 " --> pdb=" O ALA A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 296 removed outlier: 4.177A pdb=" N ILE A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 32 removed outlier: 3.512A pdb=" N GLY B 32 " --> pdb=" O GLU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 44 removed outlier: 3.782A pdb=" N VAL B 38 " --> pdb=" O ASN B 34 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B 39 " --> pdb=" O ALA B 35 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B 44 " --> pdb=" O LYS B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 54 Processing helix chain 'B' and resid 56 through 63 removed outlier: 3.921A pdb=" N LEU B 60 " --> pdb=" O PRO B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 82 removed outlier: 3.731A pdb=" N LYS B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 97 Processing helix chain 'B' and resid 106 through 113 Processing helix chain 'B' and resid 132 through 144 removed outlier: 3.600A pdb=" N ILE B 136 " --> pdb=" O GLY B 132 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N CYS B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL B 142 " --> pdb=" O HIS B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 146 No H-bonds generated for 'chain 'B' and resid 145 through 146' Processing helix chain 'B' and resid 147 through 151 Processing helix chain 'B' and resid 167 through 179 removed outlier: 3.895A pdb=" N LEU B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR B 178 " --> pdb=" O VAL B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 186 Processing helix chain 'B' and resid 196 through 214 removed outlier: 4.008A pdb=" N LEU B 204 " --> pdb=" O GLN B 200 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TYR B 205 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN B 206 " --> pdb=" O GLN B 202 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 214 " --> pdb=" O MET B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.961A pdb=" N TYR B 232 " --> pdb=" O TYR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 237 through 260 removed outlier: 3.663A pdb=" N MET B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS B 244 " --> pdb=" O ALA B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 296 removed outlier: 4.178A pdb=" N ILE B 292 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA B 293 " --> pdb=" O GLY B 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 32 removed outlier: 3.512A pdb=" N GLY C 32 " --> pdb=" O GLU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 44 removed outlier: 3.782A pdb=" N VAL C 38 " --> pdb=" O ASN C 34 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS C 39 " --> pdb=" O ALA C 35 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA C 44 " --> pdb=" O LYS C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 54 Processing helix chain 'C' and resid 56 through 63 removed outlier: 3.920A pdb=" N LEU C 60 " --> pdb=" O PRO C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 82 removed outlier: 3.731A pdb=" N LYS C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU C 81 " --> pdb=" O GLU C 77 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 97 Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 132 through 144 removed outlier: 3.599A pdb=" N ILE C 136 " --> pdb=" O GLY C 132 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N CYS C 137 " --> pdb=" O LYS C 133 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL C 142 " --> pdb=" O HIS C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 146 No H-bonds generated for 'chain 'C' and resid 145 through 146' Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 167 through 179 removed outlier: 3.895A pdb=" N LEU C 171 " --> pdb=" O ARG C 167 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG C 177 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR C 178 " --> pdb=" O VAL C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 186 Processing helix chain 'C' and resid 196 through 214 removed outlier: 4.008A pdb=" N LEU C 204 " --> pdb=" O GLN C 200 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR C 205 " --> pdb=" O THR C 201 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN C 206 " --> pdb=" O GLN C 202 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER C 214 " --> pdb=" O MET C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 232 removed outlier: 3.961A pdb=" N TYR C 232 " --> pdb=" O TYR C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 237 through 260 removed outlier: 3.663A pdb=" N MET C 243 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS C 244 " --> pdb=" O ALA C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 296 removed outlier: 4.178A pdb=" N ILE C 292 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA C 293 " --> pdb=" O GLY C 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 32 removed outlier: 3.512A pdb=" N GLY D 32 " --> pdb=" O GLU D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 44 removed outlier: 3.782A pdb=" N VAL D 38 " --> pdb=" O ASN D 34 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 54 Processing helix chain 'D' and resid 56 through 63 removed outlier: 3.920A pdb=" N LEU D 60 " --> pdb=" O PRO D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 removed outlier: 3.731A pdb=" N LYS D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 97 Processing helix chain 'D' and resid 106 through 113 Processing helix chain 'D' and resid 132 through 144 removed outlier: 3.599A pdb=" N ILE D 136 " --> pdb=" O GLY D 132 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N CYS D 137 " --> pdb=" O LYS D 133 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL D 142 " --> pdb=" O HIS D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 146 No H-bonds generated for 'chain 'D' and resid 145 through 146' Processing helix chain 'D' and resid 147 through 151 Processing helix chain 'D' and resid 167 through 179 removed outlier: 3.895A pdb=" N LEU D 171 " --> pdb=" O ARG D 167 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG D 177 " --> pdb=" O ALA D 173 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR D 178 " --> pdb=" O VAL D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 186 Processing helix chain 'D' and resid 196 through 214 removed outlier: 4.008A pdb=" N LEU D 204 " --> pdb=" O GLN D 200 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR D 205 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN D 206 " --> pdb=" O GLN D 202 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU D 213 " --> pdb=" O ALA D 209 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER D 214 " --> pdb=" O MET D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 232 removed outlier: 3.961A pdb=" N TYR D 232 " --> pdb=" O TYR D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 237 through 260 removed outlier: 3.663A pdb=" N MET D 243 " --> pdb=" O SER D 239 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N HIS D 244 " --> pdb=" O ALA D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 296 removed outlier: 4.178A pdb=" N ILE D 292 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA D 293 " --> pdb=" O GLY D 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 32 removed outlier: 3.512A pdb=" N GLY E 32 " --> pdb=" O GLU E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 44 removed outlier: 3.782A pdb=" N VAL E 38 " --> pdb=" O ASN E 34 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS E 39 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA E 44 " --> pdb=" O LYS E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 54 Processing helix chain 'E' and resid 56 through 63 removed outlier: 3.921A pdb=" N LEU E 60 " --> pdb=" O PRO E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 82 removed outlier: 3.731A pdb=" N LYS E 80 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU E 81 " --> pdb=" O GLU E 77 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 97 Processing helix chain 'E' and resid 106 through 113 Processing helix chain 'E' and resid 132 through 144 removed outlier: 3.599A pdb=" N ILE E 136 " --> pdb=" O GLY E 132 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N CYS E 137 " --> pdb=" O LYS E 133 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL E 142 " --> pdb=" O HIS E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 146 No H-bonds generated for 'chain 'E' and resid 145 through 146' Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 167 through 179 removed outlier: 3.895A pdb=" N LEU E 171 " --> pdb=" O ARG E 167 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR E 178 " --> pdb=" O VAL E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 186 Processing helix chain 'E' and resid 196 through 214 removed outlier: 4.008A pdb=" N LEU E 204 " --> pdb=" O GLN E 200 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR E 205 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN E 206 " --> pdb=" O GLN E 202 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER E 214 " --> pdb=" O MET E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 232 removed outlier: 3.961A pdb=" N TYR E 232 " --> pdb=" O TYR E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 236 No H-bonds generated for 'chain 'E' and resid 234 through 236' Processing helix chain 'E' and resid 237 through 260 removed outlier: 3.663A pdb=" N MET E 243 " --> pdb=" O SER E 239 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS E 244 " --> pdb=" O ALA E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 296 removed outlier: 4.177A pdb=" N ILE E 292 " --> pdb=" O GLY E 288 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA E 293 " --> pdb=" O GLY E 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 32 removed outlier: 3.512A pdb=" N GLY F 32 " --> pdb=" O GLU F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 44 removed outlier: 3.782A pdb=" N VAL F 38 " --> pdb=" O ASN F 34 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS F 39 " --> pdb=" O ALA F 35 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA F 44 " --> pdb=" O LYS F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 54 Processing helix chain 'F' and resid 56 through 63 removed outlier: 3.921A pdb=" N LEU F 60 " --> pdb=" O PRO F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 82 removed outlier: 3.730A pdb=" N LYS F 80 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU F 81 " --> pdb=" O GLU F 77 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL F 82 " --> pdb=" O ALA F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 97 Processing helix chain 'F' and resid 106 through 113 Processing helix chain 'F' and resid 132 through 144 removed outlier: 3.599A pdb=" N ILE F 136 " --> pdb=" O GLY F 132 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N CYS F 137 " --> pdb=" O LYS F 133 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL F 142 " --> pdb=" O HIS F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 146 No H-bonds generated for 'chain 'F' and resid 145 through 146' Processing helix chain 'F' and resid 147 through 151 Processing helix chain 'F' and resid 167 through 179 removed outlier: 3.896A pdb=" N LEU F 171 " --> pdb=" O ARG F 167 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG F 177 " --> pdb=" O ALA F 173 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR F 178 " --> pdb=" O VAL F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 186 Processing helix chain 'F' and resid 196 through 214 removed outlier: 4.009A pdb=" N LEU F 204 " --> pdb=" O GLN F 200 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR F 205 " --> pdb=" O THR F 201 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN F 206 " --> pdb=" O GLN F 202 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU F 213 " --> pdb=" O ALA F 209 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER F 214 " --> pdb=" O MET F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 232 removed outlier: 3.961A pdb=" N TYR F 232 " --> pdb=" O TYR F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 236 No H-bonds generated for 'chain 'F' and resid 234 through 236' Processing helix chain 'F' and resid 237 through 260 removed outlier: 3.664A pdb=" N MET F 243 " --> pdb=" O SER F 239 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS F 244 " --> pdb=" O ALA F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 296 removed outlier: 4.177A pdb=" N ILE F 292 " --> pdb=" O GLY F 288 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA F 293 " --> pdb=" O GLY F 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 32 removed outlier: 3.512A pdb=" N GLY G 32 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 44 removed outlier: 3.781A pdb=" N VAL G 38 " --> pdb=" O ASN G 34 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS G 39 " --> pdb=" O ALA G 35 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA G 44 " --> pdb=" O LYS G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 54 Processing helix chain 'G' and resid 56 through 63 removed outlier: 3.920A pdb=" N LEU G 60 " --> pdb=" O PRO G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 82 removed outlier: 3.731A pdb=" N LYS G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU G 81 " --> pdb=" O GLU G 77 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL G 82 " --> pdb=" O ALA G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 97 Processing helix chain 'G' and resid 106 through 113 Processing helix chain 'G' and resid 132 through 144 removed outlier: 3.599A pdb=" N ILE G 136 " --> pdb=" O GLY G 132 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N CYS G 137 " --> pdb=" O LYS G 133 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL G 142 " --> pdb=" O HIS G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 146 No H-bonds generated for 'chain 'G' and resid 145 through 146' Processing helix chain 'G' and resid 147 through 151 Processing helix chain 'G' and resid 167 through 179 removed outlier: 3.895A pdb=" N LEU G 171 " --> pdb=" O ARG G 167 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG G 177 " --> pdb=" O ALA G 173 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR G 178 " --> pdb=" O VAL G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 186 Processing helix chain 'G' and resid 196 through 214 removed outlier: 4.009A pdb=" N LEU G 204 " --> pdb=" O GLN G 200 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR G 205 " --> pdb=" O THR G 201 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN G 206 " --> pdb=" O GLN G 202 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU G 213 " --> pdb=" O ALA G 209 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER G 214 " --> pdb=" O MET G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 232 removed outlier: 3.961A pdb=" N TYR G 232 " --> pdb=" O TYR G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 236 No H-bonds generated for 'chain 'G' and resid 234 through 236' Processing helix chain 'G' and resid 237 through 260 removed outlier: 3.662A pdb=" N MET G 243 " --> pdb=" O SER G 239 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS G 244 " --> pdb=" O ALA G 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 296 removed outlier: 4.177A pdb=" N ILE G 292 " --> pdb=" O GLY G 288 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA G 293 " --> pdb=" O GLY G 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 32 removed outlier: 3.512A pdb=" N GLY H 32 " --> pdb=" O GLU H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 44 removed outlier: 3.782A pdb=" N VAL H 38 " --> pdb=" O ASN H 34 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 54 Processing helix chain 'H' and resid 56 through 63 removed outlier: 3.921A pdb=" N LEU H 60 " --> pdb=" O PRO H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 82 removed outlier: 3.731A pdb=" N LYS H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU H 81 " --> pdb=" O GLU H 77 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL H 82 " --> pdb=" O ALA H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 97 Processing helix chain 'H' and resid 106 through 113 Processing helix chain 'H' and resid 132 through 144 removed outlier: 3.600A pdb=" N ILE H 136 " --> pdb=" O GLY H 132 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N CYS H 137 " --> pdb=" O LYS H 133 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL H 142 " --> pdb=" O HIS H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 146 No H-bonds generated for 'chain 'H' and resid 145 through 146' Processing helix chain 'H' and resid 147 through 151 Processing helix chain 'H' and resid 167 through 179 removed outlier: 3.895A pdb=" N LEU H 171 " --> pdb=" O ARG H 167 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG H 177 " --> pdb=" O ALA H 173 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR H 178 " --> pdb=" O VAL H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 186 Processing helix chain 'H' and resid 196 through 214 removed outlier: 4.008A pdb=" N LEU H 204 " --> pdb=" O GLN H 200 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR H 205 " --> pdb=" O THR H 201 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN H 206 " --> pdb=" O GLN H 202 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL H 212 " --> pdb=" O SER H 208 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU H 213 " --> pdb=" O ALA H 209 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER H 214 " --> pdb=" O MET H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 232 removed outlier: 3.961A pdb=" N TYR H 232 " --> pdb=" O TYR H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 234 through 236 No H-bonds generated for 'chain 'H' and resid 234 through 236' Processing helix chain 'H' and resid 237 through 260 removed outlier: 3.663A pdb=" N MET H 243 " --> pdb=" O SER H 239 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N HIS H 244 " --> pdb=" O ALA H 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 288 through 296 removed outlier: 4.177A pdb=" N ILE H 292 " --> pdb=" O GLY H 288 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA H 293 " --> pdb=" O GLY H 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 32 removed outlier: 3.513A pdb=" N GLY I 32 " --> pdb=" O GLU I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 44 removed outlier: 3.782A pdb=" N VAL I 38 " --> pdb=" O ASN I 34 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS I 39 " --> pdb=" O ALA I 35 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA I 44 " --> pdb=" O LYS I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 54 Processing helix chain 'I' and resid 56 through 63 removed outlier: 3.920A pdb=" N LEU I 60 " --> pdb=" O PRO I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 82 removed outlier: 3.731A pdb=" N LYS I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU I 81 " --> pdb=" O GLU I 77 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL I 82 " --> pdb=" O ALA I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 97 Processing helix chain 'I' and resid 106 through 113 Processing helix chain 'I' and resid 132 through 144 removed outlier: 3.600A pdb=" N ILE I 136 " --> pdb=" O GLY I 132 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N CYS I 137 " --> pdb=" O LYS I 133 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL I 142 " --> pdb=" O HIS I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 146 No H-bonds generated for 'chain 'I' and resid 145 through 146' Processing helix chain 'I' and resid 147 through 151 Processing helix chain 'I' and resid 167 through 179 removed outlier: 3.895A pdb=" N LEU I 171 " --> pdb=" O ARG I 167 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG I 177 " --> pdb=" O ALA I 173 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR I 178 " --> pdb=" O VAL I 174 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 186 Processing helix chain 'I' and resid 196 through 214 removed outlier: 4.008A pdb=" N LEU I 204 " --> pdb=" O GLN I 200 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR I 205 " --> pdb=" O THR I 201 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN I 206 " --> pdb=" O GLN I 202 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL I 212 " --> pdb=" O SER I 208 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU I 213 " --> pdb=" O ALA I 209 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER I 214 " --> pdb=" O MET I 210 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 232 removed outlier: 3.961A pdb=" N TYR I 232 " --> pdb=" O TYR I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 234 through 236 No H-bonds generated for 'chain 'I' and resid 234 through 236' Processing helix chain 'I' and resid 237 through 260 removed outlier: 3.663A pdb=" N MET I 243 " --> pdb=" O SER I 239 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N HIS I 244 " --> pdb=" O ALA I 240 " (cutoff:3.500A) Processing helix chain 'I' and resid 288 through 296 removed outlier: 4.178A pdb=" N ILE I 292 " --> pdb=" O GLY I 288 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA I 293 " --> pdb=" O GLY I 289 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88 removed outlier: 5.574A pdb=" N LYS B 156 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU B 218 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B 262 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR B 123 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ASN B 267 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET B 125 " --> pdb=" O ASN B 267 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE B 122 " --> pdb=" O THR B 298 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N LEU B 300 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLU B 124 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU B 302 " --> pdb=" O GLU B 124 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE B 126 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N LYS B 304 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG B 299 " --> pdb=" O TYR B 315 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 189 through 193 removed outlier: 5.574A pdb=" N LYS A 156 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 218 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA A 262 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR A 123 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ASN A 267 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET A 125 " --> pdb=" O ASN A 267 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE A 122 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N LEU A 300 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLU A 124 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU A 302 " --> pdb=" O GLU A 124 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE A 126 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N LYS A 304 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG A 299 " --> pdb=" O TYR A 315 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 271 Processing sheet with id=AA4, first strand: chain 'B' and resid 87 through 88 removed outlier: 5.573A pdb=" N LYS C 156 " --> pdb=" O TYR C 216 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU C 218 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA C 262 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR C 123 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ASN C 267 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET C 125 " --> pdb=" O ASN C 267 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE C 122 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N LEU C 300 " --> pdb=" O ILE C 122 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLU C 124 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU C 302 " --> pdb=" O GLU C 124 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE C 126 " --> pdb=" O LEU C 302 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N LYS C 304 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG C 299 " --> pdb=" O TYR C 315 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 269 through 271 Processing sheet with id=AA6, first strand: chain 'C' and resid 87 through 88 removed outlier: 5.574A pdb=" N LYS D 156 " --> pdb=" O TYR D 216 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU D 218 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA D 262 " --> pdb=" O ALA D 217 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N THR D 123 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ASN D 267 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET D 125 " --> pdb=" O ASN D 267 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE D 122 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N LEU D 300 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLU D 124 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU D 302 " --> pdb=" O GLU D 124 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE D 126 " --> pdb=" O LEU D 302 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N LYS D 304 " --> pdb=" O PHE D 126 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG D 299 " --> pdb=" O TYR D 315 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 269 through 271 Processing sheet with id=AA8, first strand: chain 'D' and resid 87 through 88 removed outlier: 5.573A pdb=" N LYS E 156 " --> pdb=" O TYR E 216 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU E 218 " --> pdb=" O LYS E 156 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA E 262 " --> pdb=" O ALA E 217 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N THR E 123 " --> pdb=" O ILE E 265 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ASN E 267 " --> pdb=" O THR E 123 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET E 125 " --> pdb=" O ASN E 267 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE E 122 " --> pdb=" O THR E 298 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N LEU E 300 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLU E 124 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU E 302 " --> pdb=" O GLU E 124 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE E 126 " --> pdb=" O LEU E 302 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N LYS E 304 " --> pdb=" O PHE E 126 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ARG E 299 " --> pdb=" O TYR E 315 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 269 through 271 Processing sheet with id=AB1, first strand: chain 'E' and resid 87 through 88 removed outlier: 5.573A pdb=" N LYS F 156 " --> pdb=" O TYR F 216 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU F 218 " --> pdb=" O LYS F 156 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA F 262 " --> pdb=" O ALA F 217 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR F 123 " --> pdb=" O ILE F 265 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ASN F 267 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET F 125 " --> pdb=" O ASN F 267 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE F 122 " --> pdb=" O THR F 298 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N LEU F 300 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLU F 124 " --> pdb=" O LEU F 300 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU F 302 " --> pdb=" O GLU F 124 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE F 126 " --> pdb=" O LEU F 302 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N LYS F 304 " --> pdb=" O PHE F 126 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ARG F 299 " --> pdb=" O TYR F 315 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 269 through 271 Processing sheet with id=AB3, first strand: chain 'F' and resid 87 through 88 removed outlier: 5.573A pdb=" N LYS G 156 " --> pdb=" O TYR G 216 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU G 218 " --> pdb=" O LYS G 156 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA G 262 " --> pdb=" O ALA G 217 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR G 123 " --> pdb=" O ILE G 265 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ASN G 267 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N MET G 125 " --> pdb=" O ASN G 267 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE G 122 " --> pdb=" O THR G 298 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N LEU G 300 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLU G 124 " --> pdb=" O LEU G 300 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU G 302 " --> pdb=" O GLU G 124 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE G 126 " --> pdb=" O LEU G 302 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N LYS G 304 " --> pdb=" O PHE G 126 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG G 299 " --> pdb=" O TYR G 315 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 269 through 271 Processing sheet with id=AB5, first strand: chain 'G' and resid 87 through 88 removed outlier: 5.573A pdb=" N LYS H 156 " --> pdb=" O TYR H 216 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU H 218 " --> pdb=" O LYS H 156 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA H 262 " --> pdb=" O ALA H 217 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR H 123 " --> pdb=" O ILE H 265 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ASN H 267 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET H 125 " --> pdb=" O ASN H 267 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE H 122 " --> pdb=" O THR H 298 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N LEU H 300 " --> pdb=" O ILE H 122 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLU H 124 " --> pdb=" O LEU H 300 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU H 302 " --> pdb=" O GLU H 124 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE H 126 " --> pdb=" O LEU H 302 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N LYS H 304 " --> pdb=" O PHE H 126 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG H 299 " --> pdb=" O TYR H 315 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 269 through 271 Processing sheet with id=AB7, first strand: chain 'H' and resid 87 through 88 removed outlier: 5.574A pdb=" N LYS I 156 " --> pdb=" O TYR I 216 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU I 218 " --> pdb=" O LYS I 156 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA I 262 " --> pdb=" O ALA I 217 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR I 123 " --> pdb=" O ILE I 265 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ASN I 267 " --> pdb=" O THR I 123 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET I 125 " --> pdb=" O ASN I 267 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE I 122 " --> pdb=" O THR I 298 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N LEU I 300 " --> pdb=" O ILE I 122 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLU I 124 " --> pdb=" O LEU I 300 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU I 302 " --> pdb=" O GLU I 124 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE I 126 " --> pdb=" O LEU I 302 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N LYS I 304 " --> pdb=" O PHE I 126 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG I 299 " --> pdb=" O TYR I 315 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 269 through 271 Processing sheet with id=AB9, first strand: chain 'I' and resid 269 through 271 980 hydrogen bonds defined for protein. 2700 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 4.34 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7448 1.34 - 1.46: 4142 1.46 - 1.57: 10843 1.57 - 1.69: 104 1.69 - 1.81: 189 Bond restraints: 22726 Sorted by residual: bond pdb=" O4' DG W 14 " pdb=" C1' DG W 14 " ideal model delta sigma weight residual 1.414 1.449 -0.035 2.00e-02 2.50e+03 3.04e+00 bond pdb=" O5' DG W 29 " pdb=" C5' DG W 29 " ideal model delta sigma weight residual 1.423 1.473 -0.050 3.00e-02 1.11e+03 2.76e+00 bond pdb=" C5' DG W 29 " pdb=" C4' DG W 29 " ideal model delta sigma weight residual 1.518 1.551 -0.033 2.00e-02 2.50e+03 2.64e+00 bond pdb=" CB ARG G 235 " pdb=" CG ARG G 235 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.69e+00 bond pdb=" CB ARG B 235 " pdb=" CG ARG B 235 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.67e+00 ... (remaining 22721 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 30303 1.69 - 3.37: 452 3.37 - 5.06: 79 5.06 - 6.74: 20 6.74 - 8.43: 1 Bond angle restraints: 30855 Sorted by residual: angle pdb=" O4' DG W 20 " pdb=" C1' DG W 20 " pdb=" N9 DG W 20 " ideal model delta sigma weight residual 108.40 99.97 8.43 1.50e+00 4.44e-01 3.16e+01 angle pdb=" O3' DG W 29 " pdb=" C3' DG W 29 " pdb=" C2' DG W 29 " ideal model delta sigma weight residual 111.50 105.18 6.32 1.50e+00 4.44e-01 1.77e+01 angle pdb=" CA ARG G 27 " pdb=" CB ARG G 27 " pdb=" CG ARG G 27 " ideal model delta sigma weight residual 114.10 120.50 -6.40 2.00e+00 2.50e-01 1.03e+01 angle pdb=" CA ARG B 27 " pdb=" CB ARG B 27 " pdb=" CG ARG B 27 " ideal model delta sigma weight residual 114.10 120.50 -6.40 2.00e+00 2.50e-01 1.02e+01 angle pdb=" CA ARG H 27 " pdb=" CB ARG H 27 " pdb=" CG ARG H 27 " ideal model delta sigma weight residual 114.10 120.48 -6.38 2.00e+00 2.50e-01 1.02e+01 ... (remaining 30850 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 12434 16.69 - 33.37: 977 33.37 - 50.06: 283 50.06 - 66.74: 136 66.74 - 83.43: 52 Dihedral angle restraints: 13882 sinusoidal: 5926 harmonic: 7956 Sorted by residual: dihedral pdb=" CA ARG G 95 " pdb=" CB ARG G 95 " pdb=" CG ARG G 95 " pdb=" CD ARG G 95 " ideal model delta sinusoidal sigma weight residual -60.00 -119.32 59.32 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG B 95 " pdb=" CB ARG B 95 " pdb=" CG ARG B 95 " pdb=" CD ARG B 95 " ideal model delta sinusoidal sigma weight residual -60.00 -119.31 59.31 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG E 95 " pdb=" CB ARG E 95 " pdb=" CG ARG E 95 " pdb=" CD ARG E 95 " ideal model delta sinusoidal sigma weight residual -60.00 -119.30 59.30 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 13879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2950 0.053 - 0.106: 474 0.106 - 0.158: 79 0.158 - 0.211: 0 0.211 - 0.264: 1 Chirality restraints: 3504 Sorted by residual: chirality pdb=" P DA W 6 " pdb=" OP1 DA W 6 " pdb=" OP2 DA W 6 " pdb=" O5' DA W 6 " both_signs ideal model delta sigma weight residual True 2.35 -2.08 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" C1' DG W 20 " pdb=" O4' DG W 20 " pdb=" C2' DG W 20 " pdb=" N9 DG W 20 " both_signs ideal model delta sigma weight residual False 2.42 2.56 -0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA ILE G 160 " pdb=" N ILE G 160 " pdb=" C ILE G 160 " pdb=" CB ILE G 160 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 ... (remaining 3501 not shown) Planarity restraints: 3846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG W 20 " -0.046 2.00e-02 2.50e+03 4.33e-02 5.63e+01 pdb=" N9 DG W 20 " 0.034 2.00e-02 2.50e+03 pdb=" C8 DG W 20 " -0.062 2.00e-02 2.50e+03 pdb=" N7 DG W 20 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DG W 20 " 0.015 2.00e-02 2.50e+03 pdb=" C6 DG W 20 " -0.008 2.00e-02 2.50e+03 pdb=" O6 DG W 20 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG W 20 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG W 20 " 0.003 2.00e-02 2.50e+03 pdb=" N2 DG W 20 " -0.064 2.00e-02 2.50e+03 pdb=" N3 DG W 20 " 0.058 2.00e-02 2.50e+03 pdb=" C4 DG W 20 " 0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG W 17 " -0.042 2.00e-02 2.50e+03 4.30e-02 5.54e+01 pdb=" N9 DG W 17 " -0.015 2.00e-02 2.50e+03 pdb=" C8 DG W 17 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG W 17 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG W 17 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DG W 17 " -0.002 2.00e-02 2.50e+03 pdb=" O6 DG W 17 " -0.004 2.00e-02 2.50e+03 pdb=" N1 DG W 17 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG W 17 " -0.030 2.00e-02 2.50e+03 pdb=" N2 DG W 17 " -0.045 2.00e-02 2.50e+03 pdb=" N3 DG W 17 " 0.131 2.00e-02 2.50e+03 pdb=" C4 DG W 17 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG W 4 " 0.020 2.00e-02 2.50e+03 4.02e-02 4.85e+01 pdb=" N9 DG W 4 " -0.004 2.00e-02 2.50e+03 pdb=" C8 DG W 4 " 0.000 2.00e-02 2.50e+03 pdb=" N7 DG W 4 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DG W 4 " -0.045 2.00e-02 2.50e+03 pdb=" C6 DG W 4 " 0.064 2.00e-02 2.50e+03 pdb=" O6 DG W 4 " -0.003 2.00e-02 2.50e+03 pdb=" N1 DG W 4 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DG W 4 " -0.005 2.00e-02 2.50e+03 pdb=" N2 DG W 4 " -0.027 2.00e-02 2.50e+03 pdb=" N3 DG W 4 " 0.075 2.00e-02 2.50e+03 pdb=" C4 DG W 4 " -0.079 2.00e-02 2.50e+03 ... (remaining 3843 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3155 2.76 - 3.29: 20542 3.29 - 3.83: 35205 3.83 - 4.36: 42507 4.36 - 4.90: 73823 Nonbonded interactions: 175232 Sorted by model distance: nonbonded pdb=" OG1 THR B 103 " pdb=" OD2 ASP B 110 " model vdw 2.219 3.040 nonbonded pdb=" OG1 THR D 103 " pdb=" OD2 ASP D 110 " model vdw 2.220 3.040 nonbonded pdb=" OG1 THR E 103 " pdb=" OD2 ASP E 110 " model vdw 2.220 3.040 nonbonded pdb=" OG1 THR A 103 " pdb=" OD2 ASP A 110 " model vdw 2.220 3.040 nonbonded pdb=" OG1 THR C 103 " pdb=" OD2 ASP C 110 " model vdw 2.220 3.040 ... (remaining 175227 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 21 through 402) selection = (chain 'B' and resid 21 through 401) selection = (chain 'C' and resid 21 through 401) selection = (chain 'D' and resid 21 through 401) selection = (chain 'E' and resid 21 through 401) selection = (chain 'F' and resid 21 through 401) selection = (chain 'G' and resid 21 through 401) selection = (chain 'H' and resid 21 through 401) selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.650 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 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 : 0.003 0.050 22726 Z= 0.117 Angle : 0.543 8.428 30855 Z= 0.315 Chirality : 0.039 0.264 3504 Planarity : 0.006 0.061 3846 Dihedral : 15.173 83.429 8788 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.15), residues: 2754 helix: -0.20 (0.14), residues: 1260 sheet: 2.47 (0.24), residues: 468 loop : -1.59 (0.16), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG G 229 TYR 0.018 0.002 TYR F 228 PHE 0.015 0.002 PHE F 195 HIS 0.014 0.003 HIS F 47 Details of bonding type rmsd covalent geometry : bond 0.00252 (22726) covalent geometry : angle 0.54348 (30855) hydrogen bonds : bond 0.18017 ( 980) hydrogen bonds : angle 7.27245 ( 2700) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8045 (mmm) cc_final: 0.7702 (mtt) REVERT: A 253 LEU cc_start: 0.9290 (tp) cc_final: 0.8933 (tt) REVERT: B 36 ASN cc_start: 0.7169 (t0) cc_final: 0.6969 (t0) REVERT: C 36 ASN cc_start: 0.8119 (t0) cc_final: 0.7907 (t0) REVERT: C 251 MET cc_start: 0.8038 (tpp) cc_final: 0.7765 (tpt) REVERT: E 36 ASN cc_start: 0.7981 (t0) cc_final: 0.7718 (t0) REVERT: E 222 ASP cc_start: 0.8265 (t0) cc_final: 0.7924 (t70) REVERT: E 326 MET cc_start: 0.8111 (ttm) cc_final: 0.7896 (ttt) REVERT: I 34 ASN cc_start: 0.8241 (p0) cc_final: 0.7993 (p0) REVERT: I 62 ASN cc_start: 0.8303 (m-40) cc_final: 0.7775 (m110) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.2004 time to fit residues: 58.8751 Evaluate side-chains 114 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 50.0000 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 244 HIS E 244 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.070117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.052421 restraints weight = 65413.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.053945 restraints weight = 37886.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.054962 restraints weight = 26893.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.055612 restraints weight = 21658.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.055932 restraints weight = 18965.781| |-----------------------------------------------------------------------------| r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 22726 Z= 0.144 Angle : 0.502 5.992 30855 Z= 0.270 Chirality : 0.040 0.137 3504 Planarity : 0.003 0.031 3846 Dihedral : 13.544 82.522 3694 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.76 % Allowed : 7.97 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.15), residues: 2754 helix: 0.12 (0.14), residues: 1278 sheet: 3.51 (0.23), residues: 396 loop : -1.62 (0.15), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 306 TYR 0.015 0.001 TYR C 315 PHE 0.018 0.001 PHE C 259 HIS 0.003 0.001 HIS F 244 Details of bonding type rmsd covalent geometry : bond 0.00326 (22726) covalent geometry : angle 0.50170 (30855) hydrogen bonds : bond 0.03416 ( 980) hydrogen bonds : angle 4.95039 ( 2700) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8558 (mmm) cc_final: 0.8258 (mtt) REVERT: B 84 MET cc_start: 0.8454 (mmm) cc_final: 0.8067 (mtt) REVERT: C 70 LYS cc_start: 0.8801 (mttt) cc_final: 0.8467 (mmmt) REVERT: C 84 MET cc_start: 0.8697 (mmm) cc_final: 0.8373 (mtt) REVERT: C 251 MET cc_start: 0.8149 (tpp) cc_final: 0.7937 (tpp) REVERT: E 36 ASN cc_start: 0.8156 (t0) cc_final: 0.7765 (t0) REVERT: E 222 ASP cc_start: 0.8196 (t0) cc_final: 0.7779 (t70) REVERT: E 326 MET cc_start: 0.8137 (ttm) cc_final: 0.7912 (ttt) REVERT: F 158 MET cc_start: 0.8480 (ttm) cc_final: 0.8223 (ttm) outliers start: 17 outliers final: 12 residues processed: 138 average time/residue: 0.1712 time to fit residues: 37.7696 Evaluate side-chains 118 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 38 optimal weight: 10.0000 chunk 178 optimal weight: 4.9990 chunk 252 optimal weight: 0.9990 chunk 243 optimal weight: 0.0060 chunk 153 optimal weight: 0.0070 chunk 232 optimal weight: 10.0000 chunk 140 optimal weight: 7.9990 chunk 277 optimal weight: 20.0000 chunk 101 optimal weight: 0.7980 chunk 262 optimal weight: 10.0000 chunk 257 optimal weight: 0.4980 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN H 244 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.072820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.055617 restraints weight = 63747.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.057258 restraints weight = 36065.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.058347 restraints weight = 25171.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.059062 restraints weight = 20064.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.059404 restraints weight = 17397.454| |-----------------------------------------------------------------------------| r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22726 Z= 0.083 Angle : 0.413 5.051 30855 Z= 0.222 Chirality : 0.038 0.139 3504 Planarity : 0.003 0.033 3846 Dihedral : 13.133 88.560 3694 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 0.49 % Allowed : 8.83 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.16), residues: 2754 helix: 0.59 (0.15), residues: 1215 sheet: 3.43 (0.24), residues: 396 loop : -1.08 (0.16), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 306 TYR 0.007 0.001 TYR H 54 PHE 0.008 0.001 PHE I 327 HIS 0.001 0.000 HIS F 244 Details of bonding type rmsd covalent geometry : bond 0.00166 (22726) covalent geometry : angle 0.41254 (30855) hydrogen bonds : bond 0.02454 ( 980) hydrogen bonds : angle 4.21660 ( 2700) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8539 (mmm) cc_final: 0.8117 (mtt) REVERT: A 158 MET cc_start: 0.8264 (ttm) cc_final: 0.7817 (mtp) REVERT: B 84 MET cc_start: 0.8469 (mmm) cc_final: 0.8257 (mtt) REVERT: C 70 LYS cc_start: 0.8717 (mttt) cc_final: 0.8471 (mmmt) REVERT: C 84 MET cc_start: 0.8639 (mmm) cc_final: 0.8325 (mtt) REVERT: E 36 ASN cc_start: 0.7934 (t0) cc_final: 0.7644 (t0) REVERT: E 222 ASP cc_start: 0.8036 (t0) cc_final: 0.7665 (t70) REVERT: E 326 MET cc_start: 0.8007 (ttm) cc_final: 0.7536 (mtp) outliers start: 11 outliers final: 7 residues processed: 132 average time/residue: 0.1804 time to fit residues: 36.6513 Evaluate side-chains 118 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 254 optimal weight: 9.9990 chunk 213 optimal weight: 10.0000 chunk 228 optimal weight: 5.9990 chunk 178 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 177 optimal weight: 0.8980 chunk 114 optimal weight: 9.9990 chunk 233 optimal weight: 4.9990 chunk 144 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.066968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.049166 restraints weight = 66678.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.050616 restraints weight = 39218.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.051576 restraints weight = 28163.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.052176 restraints weight = 22907.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.052511 restraints weight = 20202.955| |-----------------------------------------------------------------------------| r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 22726 Z= 0.263 Angle : 0.583 8.076 30855 Z= 0.307 Chirality : 0.043 0.165 3504 Planarity : 0.004 0.042 3846 Dihedral : 13.521 89.230 3694 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.34 % Allowed : 9.05 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.16), residues: 2754 helix: 0.49 (0.15), residues: 1287 sheet: 2.55 (0.26), residues: 423 loop : -1.46 (0.17), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 306 TYR 0.028 0.002 TYR C 315 PHE 0.019 0.002 PHE G 248 HIS 0.006 0.001 HIS F 244 Details of bonding type rmsd covalent geometry : bond 0.00606 (22726) covalent geometry : angle 0.58273 (30855) hydrogen bonds : bond 0.04244 ( 980) hydrogen bonds : angle 4.74505 ( 2700) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.8601 (mmm) cc_final: 0.8323 (mtt) REVERT: A 158 MET cc_start: 0.8254 (ttp) cc_final: 0.7879 (mtp) REVERT: C 84 MET cc_start: 0.8592 (mmm) cc_final: 0.8387 (mtt) REVERT: D 235 ARG cc_start: 0.7590 (tpt90) cc_final: 0.7228 (tpt-90) REVERT: F 72 ASP cc_start: 0.7519 (m-30) cc_final: 0.7254 (m-30) REVERT: G 27 ARG cc_start: 0.7712 (tpp-160) cc_final: 0.7435 (tpm170) REVERT: H 211 MET cc_start: 0.8523 (ttm) cc_final: 0.8299 (ttm) outliers start: 30 outliers final: 17 residues processed: 133 average time/residue: 0.1697 time to fit residues: 35.4527 Evaluate side-chains 124 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 184 optimal weight: 9.9990 chunk 218 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 243 optimal weight: 7.9990 chunk 237 optimal weight: 2.9990 chunk 239 optimal weight: 0.9990 chunk 274 optimal weight: 9.9990 chunk 134 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS B 244 HIS C 244 HIS F 244 HIS G 244 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.070060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.052732 restraints weight = 63839.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.054300 restraints weight = 36589.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.055342 restraints weight = 25806.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.056003 restraints weight = 20734.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.056378 restraints weight = 18118.147| |-----------------------------------------------------------------------------| r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 22726 Z= 0.106 Angle : 0.427 6.652 30855 Z= 0.230 Chirality : 0.039 0.130 3504 Planarity : 0.003 0.046 3846 Dihedral : 13.065 82.442 3694 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.90 % Allowed : 9.59 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.16), residues: 2754 helix: 0.97 (0.15), residues: 1215 sheet: 2.67 (0.26), residues: 414 loop : -1.02 (0.17), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 306 TYR 0.009 0.001 TYR C 315 PHE 0.010 0.001 PHE A 327 HIS 0.003 0.000 HIS F 244 Details of bonding type rmsd covalent geometry : bond 0.00233 (22726) covalent geometry : angle 0.42749 (30855) hydrogen bonds : bond 0.02724 ( 980) hydrogen bonds : angle 4.15372 ( 2700) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.8645 (mmm) cc_final: 0.8287 (mtt) REVERT: A 158 MET cc_start: 0.8235 (ttp) cc_final: 0.7958 (mtp) REVERT: E 222 ASP cc_start: 0.8156 (t0) cc_final: 0.7748 (t70) REVERT: E 326 MET cc_start: 0.7869 (ttt) cc_final: 0.7634 (mtp) REVERT: G 84 MET cc_start: 0.8503 (mmm) cc_final: 0.8224 (mmm) REVERT: G 326 MET cc_start: 0.8415 (tpt) cc_final: 0.8171 (tpp) outliers start: 20 outliers final: 15 residues processed: 132 average time/residue: 0.1637 time to fit residues: 34.4130 Evaluate side-chains 122 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 83 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 281 optimal weight: 8.9990 chunk 173 optimal weight: 0.5980 chunk 201 optimal weight: 6.9990 chunk 219 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 248 optimal weight: 30.0000 chunk 270 optimal weight: 3.9990 chunk 220 optimal weight: 0.9980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.070407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.053076 restraints weight = 64178.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.054649 restraints weight = 36682.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.055711 restraints weight = 25880.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.056311 restraints weight = 20712.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.056760 restraints weight = 18144.150| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22726 Z= 0.101 Angle : 0.418 7.911 30855 Z= 0.224 Chirality : 0.038 0.133 3504 Planarity : 0.003 0.042 3846 Dihedral : 12.861 84.114 3694 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.99 % Allowed : 9.72 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.16), residues: 2754 helix: 1.15 (0.15), residues: 1224 sheet: 2.65 (0.26), residues: 414 loop : -0.98 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 306 TYR 0.010 0.001 TYR C 315 PHE 0.014 0.001 PHE B 46 HIS 0.002 0.000 HIS F 244 Details of bonding type rmsd covalent geometry : bond 0.00222 (22726) covalent geometry : angle 0.41761 (30855) hydrogen bonds : bond 0.02570 ( 980) hydrogen bonds : angle 3.91709 ( 2700) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.8626 (mmm) cc_final: 0.8265 (mtt) REVERT: A 158 MET cc_start: 0.8168 (ttm) cc_final: 0.7945 (mtp) REVERT: C 70 LYS cc_start: 0.8884 (mttt) cc_final: 0.8648 (mtpp) REVERT: E 222 ASP cc_start: 0.8105 (t0) cc_final: 0.7679 (t70) REVERT: E 326 MET cc_start: 0.7680 (ttt) cc_final: 0.7451 (mtp) REVERT: H 211 MET cc_start: 0.8268 (ttm) cc_final: 0.7722 (ttm) outliers start: 22 outliers final: 16 residues processed: 126 average time/residue: 0.1545 time to fit residues: 32.0879 Evaluate side-chains 123 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 211 MET Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 63 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 262 optimal weight: 9.9990 chunk 195 optimal weight: 0.6980 chunk 162 optimal weight: 0.7980 chunk 119 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 149 optimal weight: 4.9990 chunk 267 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 overall best weight: 4.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.068116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.050651 restraints weight = 64614.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.052183 restraints weight = 37330.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.053183 restraints weight = 26531.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.053751 restraints weight = 21456.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.054227 restraints weight = 18940.425| |-----------------------------------------------------------------------------| r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 22726 Z= 0.211 Angle : 0.518 7.907 30855 Z= 0.273 Chirality : 0.041 0.135 3504 Planarity : 0.003 0.051 3846 Dihedral : 13.176 86.048 3694 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.85 % Allowed : 10.08 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.16), residues: 2754 helix: 1.07 (0.15), residues: 1224 sheet: 2.30 (0.26), residues: 423 loop : -1.03 (0.17), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 306 TYR 0.018 0.002 TYR D 315 PHE 0.017 0.002 PHE G 248 HIS 0.004 0.001 HIS E 244 Details of bonding type rmsd covalent geometry : bond 0.00488 (22726) covalent geometry : angle 0.51765 (30855) hydrogen bonds : bond 0.03689 ( 980) hydrogen bonds : angle 4.33722 ( 2700) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.795 Fit side-chains REVERT: A 62 ASN cc_start: 0.8417 (t0) cc_final: 0.8210 (t0) REVERT: A 84 MET cc_start: 0.8683 (mmm) cc_final: 0.8350 (mtt) REVERT: A 158 MET cc_start: 0.8286 (ttp) cc_final: 0.7991 (mtp) REVERT: E 84 MET cc_start: 0.8705 (mmm) cc_final: 0.8485 (mtt) REVERT: E 326 MET cc_start: 0.7806 (ttt) cc_final: 0.7571 (mtp) REVERT: H 211 MET cc_start: 0.8444 (ttm) cc_final: 0.7976 (ttm) outliers start: 19 outliers final: 16 residues processed: 123 average time/residue: 0.1537 time to fit residues: 30.3339 Evaluate side-chains 119 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 57 optimal weight: 4.9990 chunk 245 optimal weight: 9.9990 chunk 281 optimal weight: 8.9990 chunk 64 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.069611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.052199 restraints weight = 64202.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.053761 restraints weight = 36914.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.054798 restraints weight = 26120.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.055404 restraints weight = 21017.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.055895 restraints weight = 18423.611| |-----------------------------------------------------------------------------| r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22726 Z= 0.117 Angle : 0.435 6.755 30855 Z= 0.232 Chirality : 0.039 0.143 3504 Planarity : 0.003 0.052 3846 Dihedral : 12.912 87.698 3694 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.90 % Allowed : 10.13 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.16), residues: 2754 helix: 1.11 (0.15), residues: 1233 sheet: 2.07 (0.26), residues: 450 loop : -1.01 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 306 TYR 0.010 0.001 TYR C 315 PHE 0.012 0.001 PHE B 46 HIS 0.002 0.000 HIS E 244 Details of bonding type rmsd covalent geometry : bond 0.00263 (22726) covalent geometry : angle 0.43463 (30855) hydrogen bonds : bond 0.02731 ( 980) hydrogen bonds : angle 3.99740 ( 2700) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.950 Fit side-chains REVERT: A 62 ASN cc_start: 0.8520 (t0) cc_final: 0.8307 (t0) REVERT: A 84 MET cc_start: 0.8662 (mmm) cc_final: 0.8314 (mtt) REVERT: A 158 MET cc_start: 0.8223 (ttp) cc_final: 0.7959 (mtp) REVERT: D 30 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7711 (mp10) REVERT: D 84 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8434 (mtp) REVERT: E 222 ASP cc_start: 0.8167 (t0) cc_final: 0.7734 (t70) REVERT: E 326 MET cc_start: 0.7678 (ttt) cc_final: 0.7448 (mtp) REVERT: H 211 MET cc_start: 0.8450 (ttm) cc_final: 0.8213 (ttm) outliers start: 20 outliers final: 15 residues processed: 123 average time/residue: 0.1545 time to fit residues: 30.9446 Evaluate side-chains 123 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 232 optimal weight: 8.9990 chunk 146 optimal weight: 0.9990 chunk 252 optimal weight: 0.0970 chunk 194 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 2 optimal weight: 0.2980 chunk 207 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 230 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.069981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.052632 restraints weight = 64066.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.054193 restraints weight = 36696.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.055224 restraints weight = 25927.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.055897 restraints weight = 20860.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.056311 restraints weight = 18193.294| |-----------------------------------------------------------------------------| r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 22726 Z= 0.108 Angle : 0.424 6.561 30855 Z= 0.228 Chirality : 0.039 0.139 3504 Planarity : 0.003 0.075 3846 Dihedral : 12.772 88.517 3694 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.90 % Allowed : 10.44 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.16), residues: 2754 helix: 1.20 (0.15), residues: 1233 sheet: 2.26 (0.27), residues: 396 loop : -1.09 (0.17), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 306 TYR 0.010 0.001 TYR C 315 PHE 0.012 0.001 PHE B 46 HIS 0.002 0.000 HIS E 244 Details of bonding type rmsd covalent geometry : bond 0.00241 (22726) covalent geometry : angle 0.42379 (30855) hydrogen bonds : bond 0.02610 ( 980) hydrogen bonds : angle 3.87106 ( 2700) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.869 Fit side-chains REVERT: A 62 ASN cc_start: 0.8557 (t0) cc_final: 0.8344 (t0) REVERT: A 84 MET cc_start: 0.8603 (mmm) cc_final: 0.8283 (mtt) REVERT: A 158 MET cc_start: 0.8177 (ttp) cc_final: 0.7940 (mtp) REVERT: D 30 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7716 (mp10) REVERT: D 84 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8335 (mtp) REVERT: E 222 ASP cc_start: 0.8131 (t0) cc_final: 0.7688 (t70) REVERT: E 326 MET cc_start: 0.7688 (ttt) cc_final: 0.7487 (mtp) REVERT: G 84 MET cc_start: 0.8699 (mmm) cc_final: 0.8456 (mmm) REVERT: H 211 MET cc_start: 0.8459 (ttm) cc_final: 0.8201 (ttm) outliers start: 20 outliers final: 16 residues processed: 121 average time/residue: 0.1446 time to fit residues: 28.0707 Evaluate side-chains 123 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 227 optimal weight: 9.9990 chunk 165 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 264 optimal weight: 8.9990 chunk 42 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 138 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 266 optimal weight: 10.0000 chunk 200 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.069309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.051901 restraints weight = 64565.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.053457 restraints weight = 37068.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.054473 restraints weight = 26220.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.055125 restraints weight = 21128.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.055524 restraints weight = 18494.864| |-----------------------------------------------------------------------------| r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 22726 Z= 0.139 Angle : 0.457 11.439 30855 Z= 0.242 Chirality : 0.039 0.152 3504 Planarity : 0.003 0.029 3846 Dihedral : 12.827 89.915 3694 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.94 % Allowed : 10.48 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.16), residues: 2754 helix: 1.20 (0.15), residues: 1233 sheet: 1.70 (0.26), residues: 468 loop : -0.88 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 235 TYR 0.012 0.001 TYR D 315 PHE 0.012 0.001 PHE B 46 HIS 0.003 0.001 HIS F 244 Details of bonding type rmsd covalent geometry : bond 0.00317 (22726) covalent geometry : angle 0.45699 (30855) hydrogen bonds : bond 0.02962 ( 980) hydrogen bonds : angle 3.98192 ( 2700) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.882 Fit side-chains REVERT: A 62 ASN cc_start: 0.8560 (t0) cc_final: 0.8353 (t0) REVERT: A 84 MET cc_start: 0.8616 (mmm) cc_final: 0.8312 (mtt) REVERT: D 30 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7709 (mp10) REVERT: D 84 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8370 (mtp) REVERT: E 222 ASP cc_start: 0.8171 (t0) cc_final: 0.7713 (t70) REVERT: E 326 MET cc_start: 0.7735 (ttt) cc_final: 0.7531 (mtp) REVERT: G 84 MET cc_start: 0.8682 (mmm) cc_final: 0.8354 (mmm) REVERT: G 326 MET cc_start: 0.8286 (tpp) cc_final: 0.8008 (tpp) REVERT: H 211 MET cc_start: 0.8296 (ttm) cc_final: 0.7648 (ttm) outliers start: 21 outliers final: 17 residues processed: 121 average time/residue: 0.1475 time to fit residues: 28.8610 Evaluate side-chains 125 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 36 ASN Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 181 optimal weight: 6.9990 chunk 176 optimal weight: 0.2980 chunk 231 optimal weight: 0.8980 chunk 125 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 236 optimal weight: 7.9990 chunk 276 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.069372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.051965 restraints weight = 64237.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.053516 restraints weight = 37089.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.054547 restraints weight = 26237.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.055211 restraints weight = 21116.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.055636 restraints weight = 18460.439| |-----------------------------------------------------------------------------| r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 22726 Z= 0.135 Angle : 0.631 59.184 30855 Z= 0.364 Chirality : 0.040 0.479 3504 Planarity : 0.003 0.028 3846 Dihedral : 12.830 89.963 3694 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.76 % Allowed : 10.53 % Favored : 88.71 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.16), residues: 2754 helix: 1.21 (0.15), residues: 1233 sheet: 1.70 (0.26), residues: 468 loop : -0.88 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 306 TYR 0.011 0.001 TYR C 315 PHE 0.011 0.001 PHE B 46 HIS 0.002 0.001 HIS E 244 Details of bonding type rmsd covalent geometry : bond 0.00297 (22726) covalent geometry : angle 0.63094 (30855) hydrogen bonds : bond 0.02928 ( 980) hydrogen bonds : angle 3.98120 ( 2700) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3041.20 seconds wall clock time: 53 minutes 47.83 seconds (3227.83 seconds total)