Starting phenix.real_space_refine on Sat Jul 4 04:46:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ufi_26476/07_2026/7ufi_26476.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ufi_26476/07_2026/7ufi_26476.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ufi_26476/07_2026/7ufi_26476.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ufi_26476/07_2026/7ufi_26476.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ufi_26476/07_2026/7ufi_26476.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ufi_26476/07_2026/7ufi_26476.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ufi_26476/07_2026/7ufi_26476.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ufi_26476/07_2026/7ufi_26476.cif" } resolution = 3.4 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= 0.001 sd= 0.023 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: 5 Type Number sf(0) Gaussians P 63 5.49 5 S 77 5.16 5 C 11446 2.51 5 N 3177 2.21 5 O 3556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18319 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 430 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "B" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 431 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "1" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "2" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "3" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "4" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "5" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "6" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "7" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "1" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.21, per 1000 atoms: 0.23 Number of scatterers: 18319 At special positions: 0 Unit cell: (99.594, 144.864, 150.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 77 16.00 P 63 15.00 O 3556 8.00 N 3177 7.00 C 11446 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 777.1 milliseconds 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4102 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 7 sheets defined 56.3% alpha, 3.3% beta 21 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain '1' and resid 5 through 14 Processing helix chain '1' and resid 19 through 36 removed outlier: 3.878A pdb=" N SER 1 36 " --> pdb=" O CYS 1 32 " (cutoff:3.500A) Processing helix chain '1' and resid 54 through 74 removed outlier: 6.885A pdb=" N ALA 1 69 " --> pdb=" O GLN 1 65 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ALA 1 70 " --> pdb=" O ALA 1 66 " (cutoff:3.500A) Processing helix chain '1' and resid 89 through 101 Processing helix chain '1' and resid 113 through 127 Proline residue: 1 124 - end of helix Processing helix chain '1' and resid 136 through 140 removed outlier: 3.550A pdb=" N LEU 1 139 " --> pdb=" O PHE 1 136 " (cutoff:3.500A) Processing helix chain '1' and resid 149 through 162 Processing helix chain '1' and resid 171 through 173 No H-bonds generated for 'chain '1' and resid 171 through 173' Processing helix chain '1' and resid 174 through 181 removed outlier: 3.577A pdb=" N LEU 1 178 " --> pdb=" O SER 1 174 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN 1 181 " --> pdb=" O VAL 1 177 " (cutoff:3.500A) Processing helix chain '1' and resid 181 through 188 Processing helix chain '1' and resid 204 through 217 removed outlier: 3.713A pdb=" N THR 1 208 " --> pdb=" O GLY 1 204 " (cutoff:3.500A) Processing helix chain '1' and resid 227 through 238 removed outlier: 3.720A pdb=" N LYS 1 232 " --> pdb=" O GLU 1 228 " (cutoff:3.500A) Processing helix chain '1' and resid 241 through 259 removed outlier: 3.606A pdb=" N ASN 1 259 " --> pdb=" O GLU 1 255 " (cutoff:3.500A) Processing helix chain '1' and resid 268 through 276 Processing helix chain '1' and resid 308 through 313 Processing helix chain '2' and resid 5 through 14 Processing helix chain '2' and resid 19 through 36 removed outlier: 3.900A pdb=" N SER 2 36 " --> pdb=" O CYS 2 32 " (cutoff:3.500A) Processing helix chain '2' and resid 54 through 74 removed outlier: 6.860A pdb=" N ALA 2 69 " --> pdb=" O GLN 2 65 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ALA 2 70 " --> pdb=" O ALA 2 66 " (cutoff:3.500A) Processing helix chain '2' and resid 89 through 101 Processing helix chain '2' and resid 113 through 127 Proline residue: 2 124 - end of helix Processing helix chain '2' and resid 136 through 140 removed outlier: 3.830A pdb=" N LEU 2 139 " --> pdb=" O PHE 2 136 " (cutoff:3.500A) Processing helix chain '2' and resid 149 through 162 Processing helix chain '2' and resid 171 through 173 No H-bonds generated for 'chain '2' and resid 171 through 173' Processing helix chain '2' and resid 174 through 181 removed outlier: 3.568A pdb=" N LEU 2 178 " --> pdb=" O SER 2 174 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN 2 181 " --> pdb=" O VAL 2 177 " (cutoff:3.500A) Processing helix chain '2' and resid 181 through 188 Processing helix chain '2' and resid 204 through 217 removed outlier: 3.750A pdb=" N THR 2 208 " --> pdb=" O GLY 2 204 " (cutoff:3.500A) Processing helix chain '2' and resid 227 through 238 removed outlier: 3.735A pdb=" N LYS 2 232 " --> pdb=" O GLU 2 228 " (cutoff:3.500A) Processing helix chain '2' and resid 241 through 259 removed outlier: 3.536A pdb=" N ASN 2 259 " --> pdb=" O GLU 2 255 " (cutoff:3.500A) Processing helix chain '2' and resid 268 through 276 Processing helix chain '2' and resid 308 through 313 Processing helix chain '3' and resid 5 through 14 Processing helix chain '3' and resid 19 through 36 removed outlier: 3.887A pdb=" N SER 3 36 " --> pdb=" O CYS 3 32 " (cutoff:3.500A) Processing helix chain '3' and resid 54 through 74 removed outlier: 6.706A pdb=" N ALA 3 69 " --> pdb=" O GLN 3 65 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ALA 3 70 " --> pdb=" O ALA 3 66 " (cutoff:3.500A) Processing helix chain '3' and resid 89 through 101 Processing helix chain '3' and resid 113 through 127 Proline residue: 3 124 - end of helix Processing helix chain '3' and resid 136 through 140 removed outlier: 3.917A pdb=" N LEU 3 139 " --> pdb=" O PHE 3 136 " (cutoff:3.500A) Processing helix chain '3' and resid 149 through 162 Processing helix chain '3' and resid 171 through 173 No H-bonds generated for 'chain '3' and resid 171 through 173' Processing helix chain '3' and resid 174 through 181 removed outlier: 3.559A pdb=" N LEU 3 178 " --> pdb=" O SER 3 174 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN 3 181 " --> pdb=" O VAL 3 177 " (cutoff:3.500A) Processing helix chain '3' and resid 181 through 188 Processing helix chain '3' and resid 204 through 217 removed outlier: 3.759A pdb=" N THR 3 208 " --> pdb=" O GLY 3 204 " (cutoff:3.500A) Processing helix chain '3' and resid 227 through 238 removed outlier: 3.723A pdb=" N LYS 3 232 " --> pdb=" O GLU 3 228 " (cutoff:3.500A) Processing helix chain '3' and resid 241 through 259 removed outlier: 3.515A pdb=" N ASN 3 259 " --> pdb=" O GLU 3 255 " (cutoff:3.500A) Processing helix chain '3' and resid 268 through 276 Processing helix chain '3' and resid 308 through 313 Processing helix chain '4' and resid 5 through 14 Processing helix chain '4' and resid 19 through 36 removed outlier: 3.988A pdb=" N SER 4 36 " --> pdb=" O CYS 4 32 " (cutoff:3.500A) Processing helix chain '4' and resid 54 through 74 removed outlier: 6.768A pdb=" N ALA 4 69 " --> pdb=" O GLN 4 65 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ALA 4 70 " --> pdb=" O ALA 4 66 " (cutoff:3.500A) Processing helix chain '4' and resid 89 through 101 Processing helix chain '4' and resid 113 through 127 Proline residue: 4 124 - end of helix Processing helix chain '4' and resid 136 through 140 removed outlier: 3.726A pdb=" N LEU 4 139 " --> pdb=" O PHE 4 136 " (cutoff:3.500A) Processing helix chain '4' and resid 149 through 162 Processing helix chain '4' and resid 171 through 173 No H-bonds generated for 'chain '4' and resid 171 through 173' Processing helix chain '4' and resid 174 through 181 removed outlier: 3.554A pdb=" N LEU 4 178 " --> pdb=" O SER 4 174 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN 4 181 " --> pdb=" O VAL 4 177 " (cutoff:3.500A) Processing helix chain '4' and resid 181 through 188 Processing helix chain '4' and resid 204 through 217 removed outlier: 3.710A pdb=" N THR 4 208 " --> pdb=" O GLY 4 204 " (cutoff:3.500A) Processing helix chain '4' and resid 227 through 238 removed outlier: 3.741A pdb=" N LYS 4 232 " --> pdb=" O GLU 4 228 " (cutoff:3.500A) Processing helix chain '4' and resid 241 through 259 removed outlier: 3.539A pdb=" N ASN 4 259 " --> pdb=" O GLU 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 268 through 276 Processing helix chain '4' and resid 308 through 313 Processing helix chain '5' and resid 5 through 14 Processing helix chain '5' and resid 19 through 36 removed outlier: 3.900A pdb=" N SER 5 36 " --> pdb=" O CYS 5 32 " (cutoff:3.500A) Processing helix chain '5' and resid 54 through 74 removed outlier: 6.929A pdb=" N ALA 5 69 " --> pdb=" O GLN 5 65 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ALA 5 70 " --> pdb=" O ALA 5 66 " (cutoff:3.500A) Processing helix chain '5' and resid 89 through 101 Processing helix chain '5' and resid 113 through 127 Proline residue: 5 124 - end of helix Processing helix chain '5' and resid 136 through 140 removed outlier: 3.941A pdb=" N LEU 5 139 " --> pdb=" O PHE 5 136 " (cutoff:3.500A) Processing helix chain '5' and resid 149 through 162 Processing helix chain '5' and resid 171 through 173 No H-bonds generated for 'chain '5' and resid 171 through 173' Processing helix chain '5' and resid 174 through 181 removed outlier: 3.594A pdb=" N LEU 5 178 " --> pdb=" O SER 5 174 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN 5 181 " --> pdb=" O VAL 5 177 " (cutoff:3.500A) Processing helix chain '5' and resid 181 through 188 Processing helix chain '5' and resid 204 through 217 removed outlier: 3.727A pdb=" N THR 5 208 " --> pdb=" O GLY 5 204 " (cutoff:3.500A) Processing helix chain '5' and resid 227 through 238 removed outlier: 3.768A pdb=" N LYS 5 232 " --> pdb=" O GLU 5 228 " (cutoff:3.500A) Processing helix chain '5' and resid 241 through 259 removed outlier: 3.540A pdb=" N ASN 5 259 " --> pdb=" O GLU 5 255 " (cutoff:3.500A) Processing helix chain '5' and resid 268 through 276 Processing helix chain '5' and resid 308 through 313 Processing helix chain '6' and resid 5 through 14 Processing helix chain '6' and resid 19 through 36 removed outlier: 3.805A pdb=" N SER 6 36 " --> pdb=" O CYS 6 32 " (cutoff:3.500A) Processing helix chain '6' and resid 54 through 74 removed outlier: 6.810A pdb=" N ALA 6 69 " --> pdb=" O GLN 6 65 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ALA 6 70 " --> pdb=" O ALA 6 66 " (cutoff:3.500A) Processing helix chain '6' and resid 89 through 101 Processing helix chain '6' and resid 113 through 127 Proline residue: 6 124 - end of helix Processing helix chain '6' and resid 136 through 140 removed outlier: 3.882A pdb=" N LEU 6 139 " --> pdb=" O PHE 6 136 " (cutoff:3.500A) Processing helix chain '6' and resid 149 through 162 Processing helix chain '6' and resid 171 through 173 No H-bonds generated for 'chain '6' and resid 171 through 173' Processing helix chain '6' and resid 174 through 181 removed outlier: 3.572A pdb=" N LEU 6 178 " --> pdb=" O SER 6 174 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN 6 181 " --> pdb=" O VAL 6 177 " (cutoff:3.500A) Processing helix chain '6' and resid 181 through 188 Processing helix chain '6' and resid 204 through 217 removed outlier: 3.729A pdb=" N THR 6 208 " --> pdb=" O GLY 6 204 " (cutoff:3.500A) Processing helix chain '6' and resid 227 through 238 removed outlier: 3.695A pdb=" N LYS 6 232 " --> pdb=" O GLU 6 228 " (cutoff:3.500A) Processing helix chain '6' and resid 241 through 259 Processing helix chain '6' and resid 268 through 276 Processing helix chain '6' and resid 308 through 313 Processing helix chain '7' and resid 5 through 14 Processing helix chain '7' and resid 19 through 36 removed outlier: 3.935A pdb=" N SER 7 36 " --> pdb=" O CYS 7 32 " (cutoff:3.500A) Processing helix chain '7' and resid 54 through 74 removed outlier: 6.785A pdb=" N ALA 7 69 " --> pdb=" O GLN 7 65 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ALA 7 70 " --> pdb=" O ALA 7 66 " (cutoff:3.500A) Processing helix chain '7' and resid 89 through 101 Processing helix chain '7' and resid 113 through 127 Proline residue: 7 124 - end of helix Processing helix chain '7' and resid 136 through 140 removed outlier: 3.605A pdb=" N LEU 7 139 " --> pdb=" O PHE 7 136 " (cutoff:3.500A) Processing helix chain '7' and resid 149 through 162 Processing helix chain '7' and resid 171 through 173 No H-bonds generated for 'chain '7' and resid 171 through 173' Processing helix chain '7' and resid 174 through 181 removed outlier: 3.563A pdb=" N LEU 7 178 " --> pdb=" O SER 7 174 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN 7 181 " --> pdb=" O VAL 7 177 " (cutoff:3.500A) Processing helix chain '7' and resid 181 through 188 Processing helix chain '7' and resid 204 through 217 removed outlier: 3.758A pdb=" N THR 7 208 " --> pdb=" O GLY 7 204 " (cutoff:3.500A) Processing helix chain '7' and resid 227 through 238 removed outlier: 3.695A pdb=" N LYS 7 232 " --> pdb=" O GLU 7 228 " (cutoff:3.500A) Processing helix chain '7' and resid 241 through 259 removed outlier: 3.522A pdb=" N ASN 7 259 " --> pdb=" O GLU 7 255 " (cutoff:3.500A) Processing helix chain '7' and resid 268 through 276 Processing helix chain '7' and resid 308 through 313 Processing sheet with id=AA1, first strand: chain '1' and resid 131 through 133 removed outlier: 6.838A pdb=" N ILE 1 131 " --> pdb=" O VAL 1 167 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N PHE 1 169 " --> pdb=" O ILE 1 131 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE 1 133 " --> pdb=" O PHE 1 169 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET 1 45 " --> pdb=" O ILE 1 166 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE 1 168 " --> pdb=" O MET 1 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 131 through 133 removed outlier: 6.822A pdb=" N ILE 2 131 " --> pdb=" O VAL 2 167 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N PHE 2 169 " --> pdb=" O ILE 2 131 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE 2 133 " --> pdb=" O PHE 2 169 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET 2 45 " --> pdb=" O ILE 2 166 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE 2 168 " --> pdb=" O MET 2 45 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '3' and resid 131 through 133 removed outlier: 6.859A pdb=" N ILE 3 131 " --> pdb=" O VAL 3 167 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N PHE 3 169 " --> pdb=" O ILE 3 131 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE 3 133 " --> pdb=" O PHE 3 169 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET 3 45 " --> pdb=" O ILE 3 166 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE 3 168 " --> pdb=" O MET 3 45 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '4' and resid 131 through 133 removed outlier: 6.821A pdb=" N ILE 4 131 " --> pdb=" O VAL 4 167 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N PHE 4 169 " --> pdb=" O ILE 4 131 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE 4 133 " --> pdb=" O PHE 4 169 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '5' and resid 131 through 133 removed outlier: 6.806A pdb=" N ILE 5 131 " --> pdb=" O VAL 5 167 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N PHE 5 169 " --> pdb=" O ILE 5 131 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE 5 133 " --> pdb=" O PHE 5 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '6' and resid 131 through 133 removed outlier: 6.829A pdb=" N ILE 6 131 " --> pdb=" O VAL 6 167 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N PHE 6 169 " --> pdb=" O ILE 6 131 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE 6 133 " --> pdb=" O PHE 6 169 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET 6 45 " --> pdb=" O ILE 6 166 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE 6 168 " --> pdb=" O MET 6 45 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '7' and resid 131 through 133 removed outlier: 6.840A pdb=" N ILE 7 131 " --> pdb=" O VAL 7 167 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N PHE 7 169 " --> pdb=" O ILE 7 131 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE 7 133 " --> pdb=" O PHE 7 169 " (cutoff:3.500A) 761 hydrogen bonds defined for protein. 2262 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 55 hydrogen bonds 110 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 2.64 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3581 1.33 - 1.46: 4386 1.46 - 1.58: 10556 1.58 - 1.70: 116 1.70 - 1.82: 133 Bond restraints: 18772 Sorted by residual: bond pdb=" N ILE 5 76 " pdb=" CA ILE 5 76 " ideal model delta sigma weight residual 1.458 1.497 -0.039 9.00e-03 1.23e+04 1.86e+01 bond pdb=" N ILE 4 76 " pdb=" CA ILE 4 76 " ideal model delta sigma weight residual 1.458 1.496 -0.038 9.00e-03 1.23e+04 1.81e+01 bond pdb=" N ILE 2 76 " pdb=" CA ILE 2 76 " ideal model delta sigma weight residual 1.458 1.496 -0.038 9.00e-03 1.23e+04 1.77e+01 bond pdb=" N ILE 6 76 " pdb=" CA ILE 6 76 " ideal model delta sigma weight residual 1.458 1.496 -0.038 9.00e-03 1.23e+04 1.76e+01 bond pdb=" N ILE 3 76 " pdb=" CA ILE 3 76 " ideal model delta sigma weight residual 1.458 1.496 -0.038 9.00e-03 1.23e+04 1.76e+01 ... (remaining 18767 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.88: 24666 3.88 - 7.76: 924 7.76 - 11.64: 3 11.64 - 15.52: 11 15.52 - 19.40: 8 Bond angle restraints: 25612 Sorted by residual: angle pdb=" PB ATP 2 401 " pdb=" O3B ATP 2 401 " pdb=" PG ATP 2 401 " ideal model delta sigma weight residual 139.87 120.47 19.40 1.00e+00 1.00e+00 3.77e+02 angle pdb=" PB ATP 1 401 " pdb=" O3B ATP 1 401 " pdb=" PG ATP 1 401 " ideal model delta sigma weight residual 139.87 120.58 19.29 1.00e+00 1.00e+00 3.72e+02 angle pdb=" PB ATP 7 401 " pdb=" O3B ATP 7 401 " pdb=" PG ATP 7 401 " ideal model delta sigma weight residual 139.87 120.77 19.10 1.00e+00 1.00e+00 3.65e+02 angle pdb=" PB ATP 3 401 " pdb=" O3B ATP 3 401 " pdb=" PG ATP 3 401 " ideal model delta sigma weight residual 139.87 120.91 18.96 1.00e+00 1.00e+00 3.59e+02 angle pdb=" PB ATP 6 401 " pdb=" O3B ATP 6 401 " pdb=" PG ATP 6 401 " ideal model delta sigma weight residual 139.87 122.05 17.82 1.00e+00 1.00e+00 3.17e+02 ... (remaining 25607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 9230 16.69 - 33.38: 1174 33.38 - 50.07: 678 50.07 - 66.76: 151 66.76 - 83.45: 35 Dihedral angle restraints: 11268 sinusoidal: 4926 harmonic: 6342 Sorted by residual: dihedral pdb=" CA PHE 2 288 " pdb=" C PHE 2 288 " pdb=" N GLU 2 289 " pdb=" CA GLU 2 289 " ideal model delta harmonic sigma weight residual -180.00 -153.78 -26.22 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA PHE 4 288 " pdb=" C PHE 4 288 " pdb=" N GLU 4 289 " pdb=" CA GLU 4 289 " ideal model delta harmonic sigma weight residual -180.00 -154.89 -25.11 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA PHE 5 288 " pdb=" C PHE 5 288 " pdb=" N GLU 5 289 " pdb=" CA GLU 5 289 " ideal model delta harmonic sigma weight residual -180.00 -154.97 -25.03 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 11265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1108 0.045 - 0.089: 938 0.089 - 0.134: 555 0.134 - 0.178: 218 0.178 - 0.223: 44 Chirality restraints: 2863 Sorted by residual: chirality pdb=" CA VAL 1 17 " pdb=" N VAL 1 17 " pdb=" C VAL 1 17 " pdb=" CB VAL 1 17 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA VAL 3 17 " pdb=" N VAL 3 17 " pdb=" C VAL 3 17 " pdb=" CB VAL 3 17 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C3' DT B 39 " pdb=" C4' DT B 39 " pdb=" O3' DT B 39 " pdb=" C2' DT B 39 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 2860 not shown) Planarity restraints: 3122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ATP 7 401 " -0.020 2.00e-02 2.50e+03 8.57e-03 2.02e+00 pdb=" C2 ATP 7 401 " -0.002 2.00e-02 2.50e+03 pdb=" C4 ATP 7 401 " 0.008 2.00e-02 2.50e+03 pdb=" C5 ATP 7 401 " 0.005 2.00e-02 2.50e+03 pdb=" C6 ATP 7 401 " 0.002 2.00e-02 2.50e+03 pdb=" C8 ATP 7 401 " 0.002 2.00e-02 2.50e+03 pdb=" N1 ATP 7 401 " -0.003 2.00e-02 2.50e+03 pdb=" N3 ATP 7 401 " 0.007 2.00e-02 2.50e+03 pdb=" N6 ATP 7 401 " -0.011 2.00e-02 2.50e+03 pdb=" N7 ATP 7 401 " 0.001 2.00e-02 2.50e+03 pdb=" N9 ATP 7 401 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE 7 168 " 0.006 2.00e-02 2.50e+03 1.28e-02 1.64e+00 pdb=" C ILE 7 168 " -0.022 2.00e-02 2.50e+03 pdb=" O ILE 7 168 " 0.008 2.00e-02 2.50e+03 pdb=" N PHE 7 169 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 2 199 " -0.015 2.00e-02 2.50e+03 9.04e-03 1.63e+00 pdb=" CG TYR 2 199 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR 2 199 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR 2 199 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR 2 199 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR 2 199 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR 2 199 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR 2 199 " -0.005 2.00e-02 2.50e+03 ... (remaining 3119 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 14 2.30 - 2.95: 6840 2.95 - 3.60: 26620 3.60 - 4.25: 40909 4.25 - 4.90: 69158 Nonbonded interactions: 143541 Sorted by model distance: nonbonded pdb=" OE1 GLN 5 200 " pdb=" CG LEU 5 299 " model vdw 1.645 3.470 nonbonded pdb=" OE1 GLN 5 200 " pdb=" CB LEU 5 299 " model vdw 1.709 3.440 nonbonded pdb=" NE2 GLN 5 200 " pdb=" CD2 LEU 5 299 " model vdw 1.874 3.540 nonbonded pdb=" OE1 GLN 5 200 " pdb=" CD1 LEU 5 299 " model vdw 1.929 3.460 nonbonded pdb=" OE1 GLN 5 200 " pdb=" CD2 LEU 5 299 " model vdw 1.953 3.460 ... (remaining 143536 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 '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.840 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.020 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 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 : 0.013 0.146 18773 Z= 1.015 Angle : 1.832 19.404 25612 Z= 1.363 Chirality : 0.080 0.223 2863 Planarity : 0.003 0.015 3122 Dihedral : 19.526 83.452 7166 Min Nonbonded Distance : 1.645 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.51 % Allowed : 9.11 % Favored : 90.38 % Rotamer: Outliers : 11.94 % Allowed : 14.23 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.89 (0.15), residues: 2163 helix: -1.98 (0.12), residues: 1127 sheet: -3.45 (0.31), residues: 224 loop : -2.99 (0.18), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 6 195 TYR 0.020 0.003 TYR 2 199 PHE 0.017 0.003 PHE 7 209 TRP 0.021 0.003 TRP 4 154 HIS 0.006 0.001 HIS 2 138 Details of bonding type rmsd/Z covalent geometry : bond 0.01315 / 1.01 (18772) covalent geometry : angle 1.83236 / 1.36 (25612) hydrogen bonds : bond 0.17555 / 19.20 ( 816) hydrogen bonds : angle 7.32010 / 8.41 ( 2372) Misc. bond : bond 0.14647 / 7.32 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 956 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 732 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 19 THR cc_start: 0.7610 (OUTLIER) cc_final: 0.6935 (t) REVERT: 1 22 VAL cc_start: 0.6374 (t) cc_final: 0.6116 (p) REVERT: 1 23 ARG cc_start: 0.8149 (mtm180) cc_final: 0.7830 (mtm110) REVERT: 1 26 LEU cc_start: 0.7049 (mt) cc_final: 0.6679 (mt) REVERT: 1 30 ASP cc_start: 0.7085 (m-30) cc_final: 0.6724 (m-30) REVERT: 1 37 ASP cc_start: 0.7944 (p0) cc_final: 0.6600 (p0) REVERT: 1 38 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.6946 (mp) REVERT: 1 39 GLU cc_start: 0.6615 (mp0) cc_final: 0.5311 (mp0) REVERT: 1 46 MET cc_start: 0.8275 (tpt) cc_final: 0.7632 (tpp) REVERT: 1 60 LYS cc_start: 0.7904 (mmmt) cc_final: 0.7608 (mmmm) REVERT: 1 64 ASN cc_start: 0.7741 (m-40) cc_final: 0.7505 (m110) REVERT: 1 83 GLU cc_start: 0.7792 (tt0) cc_final: 0.7116 (mt-10) REVERT: 1 86 ASP cc_start: 0.7946 (t70) cc_final: 0.7570 (t70) REVERT: 1 92 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7456 (t0) REVERT: 1 109 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.5961 (tt0) REVERT: 1 110 THR cc_start: 0.7681 (OUTLIER) cc_final: 0.6607 (p) REVERT: 1 114 ARG cc_start: 0.6952 (ptp90) cc_final: 0.6619 (mtm-85) REVERT: 1 118 ARG cc_start: 0.7915 (ttm170) cc_final: 0.7704 (ttm-80) REVERT: 1 129 LYS cc_start: 0.8184 (mtpt) cc_final: 0.7954 (mtpt) REVERT: 1 150 GLN cc_start: 0.8078 (mt0) cc_final: 0.7763 (mt0) REVERT: 1 168 ILE cc_start: 0.8087 (pt) cc_final: 0.7574 (pt) REVERT: 1 175 LYS cc_start: 0.7602 (ttmt) cc_final: 0.7172 (tttm) REVERT: 1 179 GLN cc_start: 0.7236 (mt0) cc_final: 0.6837 (mt0) REVERT: 1 187 ARG cc_start: 0.7630 (mtt90) cc_final: 0.7400 (mtt-85) REVERT: 1 192 VAL cc_start: 0.8237 (OUTLIER) cc_final: 0.8031 (m) REVERT: 1 193 GLU cc_start: 0.8014 (tp30) cc_final: 0.7385 (tp30) REVERT: 1 197 PHE cc_start: 0.8456 (m-80) cc_final: 0.8211 (m-10) REVERT: 1 215 LYS cc_start: 0.7779 (mmtt) cc_final: 0.7563 (mmtt) REVERT: 1 259 ASN cc_start: 0.7072 (p0) cc_final: 0.6839 (p0) REVERT: 1 261 HIS cc_start: 0.6245 (m170) cc_final: 0.5829 (m90) REVERT: 1 274 LYS cc_start: 0.8035 (mttt) cc_final: 0.7806 (mtmm) REVERT: 1 285 LYS cc_start: 0.7301 (tppt) cc_final: 0.6783 (tppt) REVERT: 1 300 ARG cc_start: 0.7695 (mtm-85) cc_final: 0.7379 (mtm-85) REVERT: 1 310 ASP cc_start: 0.7342 (m-30) cc_final: 0.7013 (m-30) REVERT: 1 311 TYR cc_start: 0.7894 (t80) cc_final: 0.7546 (t80) REVERT: 2 8 ARG cc_start: 0.7355 (ttm170) cc_final: 0.7105 (ttp-170) REVERT: 2 14 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.7005 (mtm-85) REVERT: 2 24 LYS cc_start: 0.7295 (tttt) cc_final: 0.7037 (ttmm) REVERT: 2 33 ARG cc_start: 0.7829 (ttp80) cc_final: 0.7356 (ttp-170) REVERT: 2 39 GLU cc_start: 0.6237 (mp0) cc_final: 0.5705 (mp0) REVERT: 2 40 SER cc_start: 0.7082 (m) cc_final: 0.6715 (t) REVERT: 2 89 LYS cc_start: 0.7551 (mmmt) cc_final: 0.7119 (mmmt) REVERT: 2 96 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7346 (tm-30) REVERT: 2 100 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7807 (tm-30) REVERT: 2 122 LEU cc_start: 0.7672 (tp) cc_final: 0.7380 (tp) REVERT: 2 141 GLU cc_start: 0.7481 (tt0) cc_final: 0.6901 (tt0) REVERT: 2 150 GLN cc_start: 0.7622 (mt0) cc_final: 0.6909 (mm-40) REVERT: 2 162 THR cc_start: 0.8349 (t) cc_final: 0.7967 (p) REVERT: 2 163 LYS cc_start: 0.8062 (mppt) cc_final: 0.7541 (mmtp) REVERT: 2 164 CYS cc_start: 0.8115 (t) cc_final: 0.7459 (p) REVERT: 2 171 MET cc_start: 0.8519 (mtp) cc_final: 0.8264 (mtp) REVERT: 2 179 GLN cc_start: 0.7721 (mt0) cc_final: 0.7512 (mt0) REVERT: 2 193 GLU cc_start: 0.7542 (tp30) cc_final: 0.7098 (tp30) REVERT: 2 200 GLN cc_start: 0.3923 (OUTLIER) cc_final: 0.3654 (tm-30) REVERT: 2 214 ASP cc_start: 0.7526 (t70) cc_final: 0.7178 (t0) REVERT: 2 235 TYR cc_start: 0.7771 (t80) cc_final: 0.7135 (t80) REVERT: 2 242 MET cc_start: 0.7350 (tpp) cc_final: 0.7052 (tmm) REVERT: 2 255 GLU cc_start: 0.8038 (tp30) cc_final: 0.7205 (mm-30) REVERT: 2 259 ASN cc_start: 0.7530 (p0) cc_final: 0.7318 (p0) REVERT: 2 262 GLU cc_start: 0.6711 (mp0) cc_final: 0.6282 (mp0) REVERT: 2 268 ASP cc_start: 0.6802 (p0) cc_final: 0.6465 (p0) REVERT: 2 286 ASN cc_start: 0.8600 (t0) cc_final: 0.8166 (t0) REVERT: 2 310 ASP cc_start: 0.7014 (m-30) cc_final: 0.6550 (m-30) REVERT: 3 30 ASP cc_start: 0.7717 (m-30) cc_final: 0.6917 (m-30) REVERT: 3 33 ARG cc_start: 0.7943 (ttp80) cc_final: 0.7628 (ttp-110) REVERT: 3 34 ASP cc_start: 0.7513 (m-30) cc_final: 0.6468 (m-30) REVERT: 3 39 GLU cc_start: 0.7284 (mp0) cc_final: 0.6853 (mp0) REVERT: 3 46 MET cc_start: 0.8169 (tpt) cc_final: 0.7540 (tpp) REVERT: 3 48 TYR cc_start: 0.7704 (m-80) cc_final: 0.7472 (m-80) REVERT: 3 61 LYS cc_start: 0.8198 (tptp) cc_final: 0.7846 (tptp) REVERT: 3 81 HIS cc_start: 0.8467 (t70) cc_final: 0.8044 (t-90) REVERT: 3 89 LYS cc_start: 0.8071 (mmmt) cc_final: 0.7790 (mmmt) REVERT: 3 118 ARG cc_start: 0.7660 (ttm170) cc_final: 0.7349 (ttt90) REVERT: 3 126 VAL cc_start: 0.8197 (m) cc_final: 0.7929 (p) REVERT: 3 143 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.7367 (ppt170) REVERT: 3 157 MET cc_start: 0.7671 (ttm) cc_final: 0.7080 (tpp) REVERT: 3 173 TYR cc_start: 0.8455 (p90) cc_final: 0.7759 (p90) REVERT: 3 175 LYS cc_start: 0.7820 (ttmt) cc_final: 0.7351 (ttmm) REVERT: 3 179 GLN cc_start: 0.7736 (mt0) cc_final: 0.7475 (mt0) REVERT: 3 207 LYS cc_start: 0.8144 (tttt) cc_final: 0.7562 (ttmt) REVERT: 3 214 ASP cc_start: 0.7636 (t70) cc_final: 0.7303 (t0) REVERT: 3 220 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.6353 (pm20) REVERT: 3 225 LEU cc_start: 0.7561 (mp) cc_final: 0.7358 (mt) REVERT: 3 233 LYS cc_start: 0.7176 (mtpt) cc_final: 0.6827 (mtmm) REVERT: 3 247 ASN cc_start: 0.8171 (m-40) cc_final: 0.7876 (m-40) REVERT: 3 250 TYR cc_start: 0.7707 (t80) cc_final: 0.7175 (t80) REVERT: 3 268 ASP cc_start: 0.7042 (p0) cc_final: 0.6676 (p0) REVERT: 3 282 ASN cc_start: 0.8012 (t0) cc_final: 0.7732 (t0) REVERT: 3 289 GLU cc_start: 0.5929 (OUTLIER) cc_final: 0.5705 (pt0) REVERT: 3 300 ARG cc_start: 0.8250 (mtm-85) cc_final: 0.7630 (mtt90) REVERT: 4 16 PHE cc_start: 0.7528 (t80) cc_final: 0.7235 (t80) REVERT: 4 18 SER cc_start: 0.7927 (p) cc_final: 0.7408 (p) REVERT: 4 19 THR cc_start: 0.7697 (OUTLIER) cc_final: 0.7075 (p) REVERT: 4 23 ARG cc_start: 0.6925 (mtm180) cc_final: 0.6382 (mtm-85) REVERT: 4 46 MET cc_start: 0.7926 (tpt) cc_final: 0.7615 (tpt) REVERT: 4 53 VAL cc_start: 0.7746 (OUTLIER) cc_final: 0.7512 (m) REVERT: 4 55 LYS cc_start: 0.7047 (mtmt) cc_final: 0.6804 (mtmm) REVERT: 4 62 TYR cc_start: 0.7875 (t80) cc_final: 0.7609 (t80) REVERT: 4 64 ASN cc_start: 0.7528 (m-40) cc_final: 0.7247 (m-40) REVERT: 4 83 GLU cc_start: 0.7323 (tt0) cc_final: 0.6251 (tt0) REVERT: 4 98 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7862 (mm) REVERT: 4 109 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6997 (pp20) REVERT: 4 133 ILE cc_start: 0.6833 (mt) cc_final: 0.6631 (mm) REVERT: 4 149 THR cc_start: 0.5316 (OUTLIER) cc_final: 0.4877 (t) REVERT: 4 154 TRP cc_start: 0.7475 (t60) cc_final: 0.7075 (t60) REVERT: 4 155 LEU cc_start: 0.8123 (mt) cc_final: 0.7865 (mm) REVERT: 4 192 VAL cc_start: 0.7641 (OUTLIER) cc_final: 0.7423 (p) REVERT: 4 220 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7748 (pm20) REVERT: 4 227 ASN cc_start: 0.6222 (m-40) cc_final: 0.6015 (p0) REVERT: 4 238 SER cc_start: 0.7646 (p) cc_final: 0.7398 (p) REVERT: 4 239 GLN cc_start: 0.6386 (mp10) cc_final: 0.6182 (mp10) REVERT: 4 247 ASN cc_start: 0.7610 (m-40) cc_final: 0.7311 (t0) REVERT: 4 253 SER cc_start: 0.7753 (p) cc_final: 0.7420 (p) REVERT: 4 271 PHE cc_start: 0.7634 (t80) cc_final: 0.7377 (t80) REVERT: 4 274 LYS cc_start: 0.7871 (mttt) cc_final: 0.7387 (mttt) REVERT: 4 279 ASP cc_start: 0.7728 (p0) cc_final: 0.7462 (t70) REVERT: 4 295 THR cc_start: 0.7989 (p) cc_final: 0.7539 (p) REVERT: 4 298 MET cc_start: 0.6436 (mtt) cc_final: 0.5909 (mtt) REVERT: 5 60 LYS cc_start: 0.6944 (mmmt) cc_final: 0.6684 (mmtt) REVERT: 5 105 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6508 (mm) REVERT: 5 109 GLU cc_start: 0.3836 (OUTLIER) cc_final: 0.3278 (tt0) REVERT: 5 142 GLU cc_start: 0.4856 (OUTLIER) cc_final: 0.4551 (mm-30) REVERT: 5 171 MET cc_start: 0.7619 (mtp) cc_final: 0.6815 (mtp) REVERT: 5 215 LYS cc_start: 0.7401 (mmtt) cc_final: 0.6911 (tmtt) REVERT: 6 19 THR cc_start: 0.7528 (OUTLIER) cc_final: 0.7228 (p) REVERT: 6 30 ASP cc_start: 0.6853 (m-30) cc_final: 0.6504 (m-30) REVERT: 6 33 ARG cc_start: 0.7847 (ttp80) cc_final: 0.7638 (ttp-110) REVERT: 6 53 VAL cc_start: 0.7553 (OUTLIER) cc_final: 0.7180 (m) REVERT: 6 62 TYR cc_start: 0.7767 (t80) cc_final: 0.7352 (t80) REVERT: 6 64 ASN cc_start: 0.6537 (m-40) cc_final: 0.6292 (m110) REVERT: 6 76 ILE cc_start: 0.6439 (OUTLIER) cc_final: 0.6194 (mm) REVERT: 6 83 GLU cc_start: 0.7076 (tt0) cc_final: 0.6842 (tt0) REVERT: 6 96 GLU cc_start: 0.7501 (tm-30) cc_final: 0.6973 (mt-10) REVERT: 6 105 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7235 (pt) REVERT: 6 111 ASP cc_start: 0.7032 (t70) cc_final: 0.6707 (t0) REVERT: 6 134 ASP cc_start: 0.6673 (t0) cc_final: 0.6095 (t0) REVERT: 6 137 GLN cc_start: 0.7960 (pm20) cc_final: 0.6832 (pm20) REVERT: 6 141 GLU cc_start: 0.7220 (tt0) cc_final: 0.6465 (tt0) REVERT: 6 149 THR cc_start: 0.7696 (OUTLIER) cc_final: 0.7302 (p) REVERT: 6 150 GLN cc_start: 0.7514 (mt0) cc_final: 0.7227 (mt0) REVERT: 6 156 LYS cc_start: 0.7574 (ttpt) cc_final: 0.7302 (ttpp) REVERT: 6 158 ILE cc_start: 0.7359 (tp) cc_final: 0.7098 (mm) REVERT: 6 164 CYS cc_start: 0.7742 (t) cc_final: 0.7164 (p) REVERT: 6 171 MET cc_start: 0.8255 (mtp) cc_final: 0.7950 (mmm) REVERT: 6 175 LYS cc_start: 0.7640 (ttmt) cc_final: 0.7423 (ttmm) REVERT: 6 181 ASN cc_start: 0.7956 (t0) cc_final: 0.7738 (t0) REVERT: 6 187 ARG cc_start: 0.7891 (mtt90) cc_final: 0.7258 (tpp80) REVERT: 6 189 SER cc_start: 0.8548 (p) cc_final: 0.8161 (m) REVERT: 6 191 GLN cc_start: 0.7940 (mt0) cc_final: 0.7715 (mt0) REVERT: 6 192 VAL cc_start: 0.8458 (OUTLIER) cc_final: 0.8182 (t) REVERT: 6 198 SER cc_start: 0.7506 (p) cc_final: 0.6928 (t) REVERT: 6 231 GLN cc_start: 0.8344 (tt0) cc_final: 0.8016 (tt0) REVERT: 6 233 LYS cc_start: 0.7799 (mtpt) cc_final: 0.7501 (mmtm) REVERT: 6 234 LEU cc_start: 0.8154 (mt) cc_final: 0.7933 (mt) REVERT: 6 255 GLU cc_start: 0.7122 (tp30) cc_final: 0.6648 (tt0) REVERT: 6 268 ASP cc_start: 0.8177 (p0) cc_final: 0.7148 (p0) REVERT: 6 274 LYS cc_start: 0.7962 (mttt) cc_final: 0.7717 (mmtt) REVERT: 6 283 SER cc_start: 0.8121 (p) cc_final: 0.7791 (t) REVERT: 7 24 LYS cc_start: 0.7684 (tttt) cc_final: 0.7272 (ttpp) REVERT: 7 28 TYR cc_start: 0.8021 (m-10) cc_final: 0.7769 (m-10) REVERT: 7 33 ARG cc_start: 0.7486 (ttp80) cc_final: 0.6938 (ttm170) REVERT: 7 38 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6967 (mt) REVERT: 7 39 GLU cc_start: 0.7686 (mp0) cc_final: 0.6861 (mp0) REVERT: 7 41 GLU cc_start: 0.7547 (tt0) cc_final: 0.7244 (tt0) REVERT: 7 43 THR cc_start: 0.7429 (OUTLIER) cc_final: 0.7165 (m) REVERT: 7 44 CYS cc_start: 0.7985 (m) cc_final: 0.7598 (m) REVERT: 7 83 GLU cc_start: 0.7206 (tt0) cc_final: 0.6898 (mt-10) REVERT: 7 86 ASP cc_start: 0.8378 (t70) cc_final: 0.8053 (t0) REVERT: 7 98 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6390 (mm) REVERT: 7 111 ASP cc_start: 0.6858 (t70) cc_final: 0.6523 (t70) REVERT: 7 115 LEU cc_start: 0.6541 (pp) cc_final: 0.6335 (pp) REVERT: 7 119 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7477 (pt) REVERT: 7 146 ARG cc_start: 0.7566 (ptm160) cc_final: 0.7225 (ptm160) REVERT: 7 147 VAL cc_start: 0.7468 (m) cc_final: 0.7218 (p) REVERT: 7 156 LYS cc_start: 0.7552 (ttpt) cc_final: 0.7089 (tttm) REVERT: 7 157 MET cc_start: 0.7693 (ttm) cc_final: 0.7164 (ttm) REVERT: 7 160 ASN cc_start: 0.7611 (m-40) cc_final: 0.7263 (p0) REVERT: 7 166 ILE cc_start: 0.8259 (mt) cc_final: 0.7921 (tp) REVERT: 7 175 LYS cc_start: 0.7369 (ttmt) cc_final: 0.7080 (ttmt) REVERT: 7 181 ASN cc_start: 0.7465 (t0) cc_final: 0.6991 (t0) REVERT: 7 192 VAL cc_start: 0.8572 (OUTLIER) cc_final: 0.8318 (t) REVERT: 7 214 ASP cc_start: 0.7416 (t70) cc_final: 0.7009 (t0) REVERT: 7 225 LEU cc_start: 0.7094 (mp) cc_final: 0.6576 (mt) REVERT: 7 232 LYS cc_start: 0.7702 (ttmm) cc_final: 0.7099 (ttpp) REVERT: 7 241 ASN cc_start: 0.7234 (t0) cc_final: 0.6996 (t0) REVERT: 7 246 ARG cc_start: 0.7664 (mmm-85) cc_final: 0.7332 (mmm160) REVERT: 7 250 TYR cc_start: 0.7774 (t80) cc_final: 0.7238 (t80) REVERT: 7 279 ASP cc_start: 0.7862 (p0) cc_final: 0.7532 (p0) REVERT: 7 309 GLU cc_start: 0.6685 (mt-10) cc_final: 0.6460 (mt-10) REVERT: 7 313 ARG cc_start: 0.6960 (ttp-170) cc_final: 0.6450 (ttp-170) outliers start: 224 outliers final: 72 residues processed: 883 average time/residue: 0.1612 time to fit residues: 201.8775 Evaluate side-chains 749 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 645 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 14 ARG Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 38 LEU Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 1 residue 92 ASP Chi-restraints excluded: chain 1 residue 109 GLU Chi-restraints excluded: chain 1 residue 110 THR Chi-restraints excluded: chain 1 residue 119 LEU Chi-restraints excluded: chain 1 residue 142 GLU Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 1 residue 149 THR Chi-restraints excluded: chain 1 residue 192 VAL Chi-restraints excluded: chain 1 residue 211 GLU Chi-restraints excluded: chain 1 residue 289 GLU Chi-restraints excluded: chain 1 residue 294 VAL Chi-restraints excluded: chain 2 residue 14 ARG Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 105 LEU Chi-restraints excluded: chain 2 residue 119 LEU Chi-restraints excluded: chain 2 residue 120 THR Chi-restraints excluded: chain 2 residue 149 THR Chi-restraints excluded: chain 2 residue 192 VAL Chi-restraints excluded: chain 2 residue 200 GLN Chi-restraints excluded: chain 2 residue 208 THR Chi-restraints excluded: chain 2 residue 211 GLU Chi-restraints excluded: chain 2 residue 263 THR Chi-restraints excluded: chain 3 residue 19 THR Chi-restraints excluded: chain 3 residue 32 CYS Chi-restraints excluded: chain 3 residue 110 THR Chi-restraints excluded: chain 3 residue 119 LEU Chi-restraints excluded: chain 3 residue 142 GLU Chi-restraints excluded: chain 3 residue 143 ARG Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 149 THR Chi-restraints excluded: chain 3 residue 211 GLU Chi-restraints excluded: chain 3 residue 220 GLU Chi-restraints excluded: chain 3 residue 263 THR Chi-restraints excluded: chain 3 residue 270 VAL Chi-restraints excluded: chain 3 residue 289 GLU Chi-restraints excluded: chain 4 residue 14 ARG Chi-restraints excluded: chain 4 residue 19 THR Chi-restraints excluded: chain 4 residue 29 MET Chi-restraints excluded: chain 4 residue 53 VAL Chi-restraints excluded: chain 4 residue 98 LEU Chi-restraints excluded: chain 4 residue 109 GLU Chi-restraints excluded: chain 4 residue 110 THR Chi-restraints excluded: chain 4 residue 119 LEU Chi-restraints excluded: chain 4 residue 142 GLU Chi-restraints excluded: chain 4 residue 148 LEU Chi-restraints excluded: chain 4 residue 149 THR Chi-restraints excluded: chain 4 residue 192 VAL Chi-restraints excluded: chain 4 residue 211 GLU Chi-restraints excluded: chain 4 residue 220 GLU Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 289 GLU Chi-restraints excluded: chain 4 residue 294 VAL Chi-restraints excluded: chain 5 residue 14 ARG Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 29 MET Chi-restraints excluded: chain 5 residue 32 CYS Chi-restraints excluded: chain 5 residue 76 ILE Chi-restraints excluded: chain 5 residue 77 ILE Chi-restraints excluded: chain 5 residue 105 LEU Chi-restraints excluded: chain 5 residue 109 GLU Chi-restraints excluded: chain 5 residue 110 THR Chi-restraints excluded: chain 5 residue 119 LEU Chi-restraints excluded: chain 5 residue 120 THR Chi-restraints excluded: chain 5 residue 142 GLU Chi-restraints excluded: chain 5 residue 211 GLU Chi-restraints excluded: chain 5 residue 220 GLU Chi-restraints excluded: chain 5 residue 263 THR Chi-restraints excluded: chain 5 residue 289 GLU Chi-restraints excluded: chain 5 residue 293 GLU Chi-restraints excluded: chain 6 residue 6 GLU Chi-restraints excluded: chain 6 residue 14 ARG Chi-restraints excluded: chain 6 residue 19 THR Chi-restraints excluded: chain 6 residue 32 CYS Chi-restraints excluded: chain 6 residue 53 VAL Chi-restraints excluded: chain 6 residue 76 ILE Chi-restraints excluded: chain 6 residue 105 LEU Chi-restraints excluded: chain 6 residue 119 LEU Chi-restraints excluded: chain 6 residue 120 THR Chi-restraints excluded: chain 6 residue 123 ILE Chi-restraints excluded: chain 6 residue 142 GLU Chi-restraints excluded: chain 6 residue 143 ARG Chi-restraints excluded: chain 6 residue 148 LEU Chi-restraints excluded: chain 6 residue 149 THR Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 6 residue 211 GLU Chi-restraints excluded: chain 6 residue 263 THR Chi-restraints excluded: chain 6 residue 289 GLU Chi-restraints excluded: chain 6 residue 293 GLU Chi-restraints excluded: chain 6 residue 294 VAL Chi-restraints excluded: chain 7 residue 14 ARG Chi-restraints excluded: chain 7 residue 19 THR Chi-restraints excluded: chain 7 residue 38 LEU Chi-restraints excluded: chain 7 residue 43 THR Chi-restraints excluded: chain 7 residue 98 LEU Chi-restraints excluded: chain 7 residue 119 LEU Chi-restraints excluded: chain 7 residue 123 ILE Chi-restraints excluded: chain 7 residue 142 GLU Chi-restraints excluded: chain 7 residue 149 THR Chi-restraints excluded: chain 7 residue 192 VAL Chi-restraints excluded: chain 7 residue 270 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 0.8980 chunk 212 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 282 ASN 2 138 HIS 2 231 GLN 2 261 HIS 3 138 HIS 4 138 HIS 4 259 ASN 5 138 HIS 6 138 HIS 6 183 GLN 6 200 GLN 6 314 HIS 7 138 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.170299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.136697 restraints weight = 26366.725| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.28 r_work: 0.3563 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 18773 Z= 0.196 Angle : 0.761 12.796 25612 Z= 0.385 Chirality : 0.045 0.205 2863 Planarity : 0.006 0.098 3122 Dihedral : 17.363 90.473 3050 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 6.82 % Allowed : 23.29 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.17), residues: 2163 helix: -0.44 (0.14), residues: 1183 sheet: -3.16 (0.32), residues: 238 loop : -2.65 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 1 33 TYR 0.023 0.002 TYR 6 199 PHE 0.022 0.002 PHE 2 271 TRP 0.017 0.002 TRP 6 154 HIS 0.006 0.001 HIS 4 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 (18772) covalent geometry : angle 0.76110 / 0.38 (25612) hydrogen bonds : bond 0.04453 / 4.90 ( 816) hydrogen bonds : angle 4.38242 / 5.04 ( 2372) Misc. bond : bond 0.00073 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 655 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 14 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.7007 (mtm-85) REVERT: 1 19 THR cc_start: 0.8851 (OUTLIER) cc_final: 0.8187 (t) REVERT: 1 26 LEU cc_start: 0.8466 (mt) cc_final: 0.8015 (mt) REVERT: 1 30 ASP cc_start: 0.7781 (m-30) cc_final: 0.7487 (m-30) REVERT: 1 37 ASP cc_start: 0.8190 (p0) cc_final: 0.7013 (p0) REVERT: 1 38 LEU cc_start: 0.7910 (mp) cc_final: 0.7315 (mt) REVERT: 1 39 GLU cc_start: 0.7153 (mp0) cc_final: 0.5922 (mp0) REVERT: 1 45 MET cc_start: 0.8672 (ttm) cc_final: 0.8364 (ttp) REVERT: 1 46 MET cc_start: 0.8109 (tpt) cc_final: 0.7806 (tpp) REVERT: 1 60 LYS cc_start: 0.8610 (mmmt) cc_final: 0.8264 (mmtp) REVERT: 1 83 GLU cc_start: 0.7140 (tt0) cc_final: 0.6839 (mt-10) REVERT: 1 100 GLU cc_start: 0.7490 (tm-30) cc_final: 0.7135 (tm-30) REVERT: 1 101 MET cc_start: 0.7754 (ttp) cc_final: 0.7352 (ttp) REVERT: 1 109 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.6351 (tt0) REVERT: 1 114 ARG cc_start: 0.7766 (ptp90) cc_final: 0.7436 (mtm-85) REVERT: 1 129 LYS cc_start: 0.8541 (mtpt) cc_final: 0.8256 (mtpt) REVERT: 1 134 ASP cc_start: 0.7128 (t0) cc_final: 0.6837 (t0) REVERT: 1 149 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8318 (p) REVERT: 1 150 GLN cc_start: 0.8311 (mt0) cc_final: 0.8099 (mt0) REVERT: 1 163 LYS cc_start: 0.8283 (mptt) cc_final: 0.8021 (mmtm) REVERT: 1 261 HIS cc_start: 0.6263 (m170) cc_final: 0.6028 (m90) REVERT: 1 271 PHE cc_start: 0.7961 (t80) cc_final: 0.7374 (t80) REVERT: 1 274 LYS cc_start: 0.8607 (mttt) cc_final: 0.8390 (mtpp) REVERT: 1 285 LYS cc_start: 0.7515 (tppt) cc_final: 0.7178 (tppt) REVERT: 2 33 ARG cc_start: 0.8267 (ttp80) cc_final: 0.7934 (ttp-170) REVERT: 2 39 GLU cc_start: 0.6889 (mp0) cc_final: 0.6423 (mp0) REVERT: 2 89 LYS cc_start: 0.8308 (mmmt) cc_final: 0.7927 (mmmt) REVERT: 2 96 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7481 (tm-30) REVERT: 2 122 LEU cc_start: 0.8465 (tp) cc_final: 0.8215 (tp) REVERT: 2 129 LYS cc_start: 0.8433 (mmpt) cc_final: 0.8171 (mmpt) REVERT: 2 150 GLN cc_start: 0.8150 (mt0) cc_final: 0.7567 (mm-40) REVERT: 2 163 LYS cc_start: 0.8398 (mppt) cc_final: 0.8097 (mmtm) REVERT: 2 164 CYS cc_start: 0.8099 (t) cc_final: 0.7746 (m) REVERT: 2 181 ASN cc_start: 0.7908 (t0) cc_final: 0.7521 (t0) REVERT: 2 200 GLN cc_start: 0.5840 (OUTLIER) cc_final: 0.5380 (tm-30) REVERT: 2 232 LYS cc_start: 0.8202 (ttmm) cc_final: 0.7890 (ttmm) REVERT: 2 259 ASN cc_start: 0.8347 (OUTLIER) cc_final: 0.8117 (p0) REVERT: 2 286 ASN cc_start: 0.8876 (t0) cc_final: 0.8646 (t0) REVERT: 2 310 ASP cc_start: 0.7627 (m-30) cc_final: 0.7320 (m-30) REVERT: 3 34 ASP cc_start: 0.8186 (m-30) cc_final: 0.7756 (m-30) REVERT: 3 38 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7426 (mm) REVERT: 3 39 GLU cc_start: 0.7514 (mp0) cc_final: 0.7148 (mp0) REVERT: 3 46 MET cc_start: 0.7925 (tpt) cc_final: 0.7583 (tpp) REVERT: 3 61 LYS cc_start: 0.8633 (tptp) cc_final: 0.8432 (tptp) REVERT: 3 96 GLU cc_start: 0.7346 (tm-30) cc_final: 0.7101 (tm-30) REVERT: 3 175 LYS cc_start: 0.8434 (ttmt) cc_final: 0.8196 (ttmm) REVERT: 3 181 ASN cc_start: 0.7638 (t0) cc_final: 0.7397 (t0) REVERT: 3 207 LYS cc_start: 0.8632 (tttt) cc_final: 0.8228 (ttmt) REVERT: 3 215 LYS cc_start: 0.8549 (mmtt) cc_final: 0.8184 (mtmt) REVERT: 3 220 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6253 (pm20) REVERT: 3 232 LYS cc_start: 0.7898 (ttmm) cc_final: 0.7596 (ttmm) REVERT: 3 233 LYS cc_start: 0.7787 (mtpt) cc_final: 0.7511 (mtmm) REVERT: 3 241 ASN cc_start: 0.7459 (m-40) cc_final: 0.7239 (t0) REVERT: 3 247 ASN cc_start: 0.8794 (m-40) cc_final: 0.8362 (m-40) REVERT: 3 255 GLU cc_start: 0.7973 (tp30) cc_final: 0.7629 (tp30) REVERT: 3 259 ASN cc_start: 0.7844 (OUTLIER) cc_final: 0.7200 (p0) REVERT: 3 268 ASP cc_start: 0.7350 (p0) cc_final: 0.6933 (p0) REVERT: 3 279 ASP cc_start: 0.6678 (p0) cc_final: 0.6448 (p0) REVERT: 3 282 ASN cc_start: 0.8058 (t0) cc_final: 0.7725 (t0) REVERT: 4 19 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.8081 (p) REVERT: 4 23 ARG cc_start: 0.6892 (mtm180) cc_final: 0.6658 (mtm110) REVERT: 4 29 MET cc_start: 0.7936 (mtt) cc_final: 0.7567 (mmp) REVERT: 4 46 MET cc_start: 0.7831 (tpt) cc_final: 0.7389 (tpt) REVERT: 4 62 TYR cc_start: 0.8197 (t80) cc_final: 0.7926 (t80) REVERT: 4 83 GLU cc_start: 0.6983 (tt0) cc_final: 0.6169 (tt0) REVERT: 4 133 ILE cc_start: 0.7776 (mt) cc_final: 0.7543 (mm) REVERT: 4 149 THR cc_start: 0.5102 (OUTLIER) cc_final: 0.4552 (t) REVERT: 4 155 LEU cc_start: 0.8345 (mt) cc_final: 0.8004 (mm) REVERT: 4 253 SER cc_start: 0.8299 (p) cc_final: 0.8006 (p) REVERT: 4 295 THR cc_start: 0.8747 (p) cc_final: 0.8106 (t) REVERT: 4 298 MET cc_start: 0.6878 (mtt) cc_final: 0.6650 (mtt) REVERT: 4 304 LYS cc_start: 0.7095 (tppt) cc_final: 0.6836 (tppt) REVERT: 4 311 TYR cc_start: 0.6543 (t80) cc_final: 0.6291 (t80) REVERT: 5 55 LYS cc_start: 0.7352 (mtmm) cc_final: 0.6726 (mtmm) REVERT: 5 60 LYS cc_start: 0.7095 (mmmt) cc_final: 0.6745 (mmtt) REVERT: 5 84 LEU cc_start: 0.6997 (mp) cc_final: 0.6780 (mt) REVERT: 5 171 MET cc_start: 0.7730 (mtp) cc_final: 0.6929 (mtp) REVERT: 6 30 ASP cc_start: 0.7446 (m-30) cc_final: 0.7201 (m-30) REVERT: 6 64 ASN cc_start: 0.7130 (m-40) cc_final: 0.6872 (m110) REVERT: 6 111 ASP cc_start: 0.7272 (t70) cc_final: 0.6983 (t0) REVERT: 6 119 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8026 (tp) REVERT: 6 134 ASP cc_start: 0.7350 (t0) cc_final: 0.6943 (t0) REVERT: 6 135 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6825 (mm-30) REVERT: 6 141 GLU cc_start: 0.6380 (tt0) cc_final: 0.5858 (tt0) REVERT: 6 143 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7450 (ppt170) REVERT: 6 144 SER cc_start: 0.6933 (p) cc_final: 0.5228 (p) REVERT: 6 149 THR cc_start: 0.8232 (OUTLIER) cc_final: 0.7823 (p) REVERT: 6 150 GLN cc_start: 0.8265 (mt0) cc_final: 0.8044 (mt0) REVERT: 6 153 ASN cc_start: 0.8062 (m-40) cc_final: 0.7809 (m-40) REVERT: 6 158 ILE cc_start: 0.8467 (tp) cc_final: 0.7867 (mm) REVERT: 6 175 LYS cc_start: 0.8402 (ttmt) cc_final: 0.8065 (ttmm) REVERT: 6 189 SER cc_start: 0.8708 (p) cc_final: 0.8431 (t) REVERT: 6 198 SER cc_start: 0.7911 (p) cc_final: 0.7676 (p) REVERT: 6 255 GLU cc_start: 0.7560 (tp30) cc_final: 0.7323 (tt0) REVERT: 6 268 ASP cc_start: 0.7904 (p0) cc_final: 0.7337 (p0) REVERT: 6 283 SER cc_start: 0.8293 (p) cc_final: 0.8005 (t) REVERT: 7 39 GLU cc_start: 0.7764 (mp0) cc_final: 0.7152 (mp0) REVERT: 7 43 THR cc_start: 0.8129 (OUTLIER) cc_final: 0.7843 (m) REVERT: 7 60 LYS cc_start: 0.8530 (mtpp) cc_final: 0.8269 (mttp) REVERT: 7 86 ASP cc_start: 0.8375 (t70) cc_final: 0.8169 (t0) REVERT: 7 129 LYS cc_start: 0.8338 (mmmm) cc_final: 0.7799 (mttp) REVERT: 7 156 LYS cc_start: 0.8681 (ttpt) cc_final: 0.8337 (tttp) REVERT: 7 214 ASP cc_start: 0.7574 (t70) cc_final: 0.7334 (t0) REVERT: 7 225 LEU cc_start: 0.8530 (mp) cc_final: 0.8189 (mt) REVERT: 7 232 LYS cc_start: 0.8552 (ttmm) cc_final: 0.7877 (ttpp) REVERT: 7 276 THR cc_start: 0.8793 (t) cc_final: 0.8554 (m) REVERT: 7 286 ASN cc_start: 0.8562 (t0) cc_final: 0.8327 (t0) REVERT: 7 313 ARG cc_start: 0.7054 (ttp-170) cc_final: 0.6767 (ttp-170) outliers start: 128 outliers final: 67 residues processed: 721 average time/residue: 0.1666 time to fit residues: 169.5240 Evaluate side-chains 698 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 616 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 14 ARG Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 1 residue 53 VAL Chi-restraints excluded: chain 1 residue 109 GLU Chi-restraints excluded: chain 1 residue 110 THR Chi-restraints excluded: chain 1 residue 117 LYS Chi-restraints excluded: chain 1 residue 119 LEU Chi-restraints excluded: chain 1 residue 142 GLU Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 1 residue 149 THR Chi-restraints excluded: chain 1 residue 176 VAL Chi-restraints excluded: chain 1 residue 295 THR Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 22 VAL Chi-restraints excluded: chain 2 residue 46 MET Chi-restraints excluded: chain 2 residue 149 THR Chi-restraints excluded: chain 2 residue 200 GLN Chi-restraints excluded: chain 2 residue 259 ASN Chi-restraints excluded: chain 2 residue 261 HIS Chi-restraints excluded: chain 2 residue 294 VAL Chi-restraints excluded: chain 2 residue 314 HIS Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 19 THR Chi-restraints excluded: chain 3 residue 38 LEU Chi-restraints excluded: chain 3 residue 110 THR Chi-restraints excluded: chain 3 residue 142 GLU Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 149 THR Chi-restraints excluded: chain 3 residue 220 GLU Chi-restraints excluded: chain 3 residue 259 ASN Chi-restraints excluded: chain 3 residue 270 VAL Chi-restraints excluded: chain 3 residue 273 SER Chi-restraints excluded: chain 4 residue 10 SER Chi-restraints excluded: chain 4 residue 14 ARG Chi-restraints excluded: chain 4 residue 19 THR Chi-restraints excluded: chain 4 residue 27 SER Chi-restraints excluded: chain 4 residue 47 VAL Chi-restraints excluded: chain 4 residue 60 LYS Chi-restraints excluded: chain 4 residue 110 THR Chi-restraints excluded: chain 4 residue 119 LEU Chi-restraints excluded: chain 4 residue 142 GLU Chi-restraints excluded: chain 4 residue 148 LEU Chi-restraints excluded: chain 4 residue 149 THR Chi-restraints excluded: chain 4 residue 211 GLU Chi-restraints excluded: chain 4 residue 230 LEU Chi-restraints excluded: chain 4 residue 231 GLN Chi-restraints excluded: chain 4 residue 269 PHE Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 38 LEU Chi-restraints excluded: chain 5 residue 76 ILE Chi-restraints excluded: chain 5 residue 97 LEU Chi-restraints excluded: chain 5 residue 99 VAL Chi-restraints excluded: chain 5 residue 110 THR Chi-restraints excluded: chain 5 residue 142 GLU Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 211 GLU Chi-restraints excluded: chain 5 residue 259 ASN Chi-restraints excluded: chain 6 residue 6 GLU Chi-restraints excluded: chain 6 residue 14 ARG Chi-restraints excluded: chain 6 residue 99 VAL Chi-restraints excluded: chain 6 residue 118 ARG Chi-restraints excluded: chain 6 residue 119 LEU Chi-restraints excluded: chain 6 residue 142 GLU Chi-restraints excluded: chain 6 residue 143 ARG Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 148 LEU Chi-restraints excluded: chain 6 residue 149 THR Chi-restraints excluded: chain 6 residue 259 ASN Chi-restraints excluded: chain 6 residue 263 THR Chi-restraints excluded: chain 7 residue 19 THR Chi-restraints excluded: chain 7 residue 43 THR Chi-restraints excluded: chain 7 residue 53 VAL Chi-restraints excluded: chain 7 residue 63 LEU Chi-restraints excluded: chain 7 residue 77 ILE Chi-restraints excluded: chain 7 residue 117 LYS Chi-restraints excluded: chain 7 residue 119 LEU Chi-restraints excluded: chain 7 residue 120 THR Chi-restraints excluded: chain 7 residue 142 GLU Chi-restraints excluded: chain 7 residue 148 LEU Chi-restraints excluded: chain 7 residue 149 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 174 optimal weight: 0.5980 chunk 220 optimal weight: 0.6980 chunk 206 optimal weight: 1.9990 chunk 177 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 64 ASN 1 87 ASN 1 231 GLN 2 179 GLN 2 231 GLN 2 261 HIS 3 259 ASN 4 259 ASN 6 160 ASN 6 183 GLN ** 6 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 227 ASN 7 87 ASN 7 247 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.169716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.134275 restraints weight = 26549.445| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.28 r_work: 0.3554 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18773 Z= 0.152 Angle : 0.680 11.909 25612 Z= 0.343 Chirality : 0.043 0.215 2863 Planarity : 0.005 0.079 3122 Dihedral : 16.060 90.124 2931 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 6.34 % Allowed : 25.43 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.18), residues: 2163 helix: 0.25 (0.15), residues: 1183 sheet: -2.87 (0.33), residues: 238 loop : -2.47 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 1 33 TYR 0.025 0.002 TYR 3 199 PHE 0.022 0.002 PHE 1 269 TRP 0.017 0.002 TRP 6 154 HIS 0.013 0.001 HIS 2 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (18772) covalent geometry : angle 0.67956 / 0.34 (25612) hydrogen bonds : bond 0.03869 / 4.26 ( 816) hydrogen bonds : angle 3.99703 / 4.61 ( 2372) Misc. bond : bond 0.00646 / 0.32 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 627 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 19 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8361 (t) REVERT: 1 23 ARG cc_start: 0.8425 (mtm110) cc_final: 0.8162 (mtm110) REVERT: 1 29 MET cc_start: 0.8627 (mmm) cc_final: 0.8265 (mtm) REVERT: 1 30 ASP cc_start: 0.7840 (m-30) cc_final: 0.7511 (m-30) REVERT: 1 37 ASP cc_start: 0.8044 (p0) cc_final: 0.7420 (p0) REVERT: 1 38 LEU cc_start: 0.8142 (mp) cc_final: 0.7917 (mt) REVERT: 1 39 GLU cc_start: 0.7160 (mp0) cc_final: 0.6108 (mp0) REVERT: 1 45 MET cc_start: 0.8654 (ttm) cc_final: 0.8347 (ttp) REVERT: 1 60 LYS cc_start: 0.8568 (mmmt) cc_final: 0.8250 (mmtp) REVERT: 1 83 GLU cc_start: 0.7201 (tt0) cc_final: 0.6923 (mt-10) REVERT: 1 100 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7056 (tm-30) REVERT: 1 101 MET cc_start: 0.7731 (ttp) cc_final: 0.7361 (ttp) REVERT: 1 105 LEU cc_start: 0.7778 (pp) cc_final: 0.7531 (mp) REVERT: 1 109 GLU cc_start: 0.6603 (OUTLIER) cc_final: 0.6285 (tt0) REVERT: 1 114 ARG cc_start: 0.7780 (ptp90) cc_final: 0.7528 (mtm-85) REVERT: 1 129 LYS cc_start: 0.8549 (mtpt) cc_final: 0.8228 (mtpt) REVERT: 1 134 ASP cc_start: 0.7103 (t0) cc_final: 0.6822 (t0) REVERT: 1 149 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8361 (p) REVERT: 1 163 LYS cc_start: 0.8221 (mptt) cc_final: 0.7969 (mmtm) REVERT: 1 255 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6880 (tp30) REVERT: 1 269 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7579 (m-80) REVERT: 1 274 LYS cc_start: 0.8607 (mttt) cc_final: 0.8355 (mtpp) REVERT: 1 279 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.8090 (p0) REVERT: 1 285 LYS cc_start: 0.7544 (tppt) cc_final: 0.7161 (tppt) REVERT: 1 310 ASP cc_start: 0.7864 (m-30) cc_final: 0.7530 (t0) REVERT: 2 6 GLU cc_start: 0.7422 (pm20) cc_final: 0.7006 (tm-30) REVERT: 2 24 LYS cc_start: 0.8255 (ttpp) cc_final: 0.7974 (ttmm) REVERT: 2 89 LYS cc_start: 0.8292 (mmmt) cc_final: 0.7889 (mmmt) REVERT: 2 96 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7462 (tp30) REVERT: 2 116 THR cc_start: 0.8077 (m) cc_final: 0.7621 (p) REVERT: 2 122 LEU cc_start: 0.8495 (tp) cc_final: 0.8189 (tp) REVERT: 2 129 LYS cc_start: 0.8414 (mmpt) cc_final: 0.8176 (mmpt) REVERT: 2 163 LYS cc_start: 0.8396 (mppt) cc_final: 0.7899 (mmtm) REVERT: 2 181 ASN cc_start: 0.7983 (t0) cc_final: 0.7582 (t0) REVERT: 2 193 GLU cc_start: 0.7551 (tp30) cc_final: 0.7187 (tp30) REVERT: 2 200 GLN cc_start: 0.6123 (OUTLIER) cc_final: 0.5766 (tm-30) REVERT: 2 211 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7262 (mm-30) REVERT: 2 232 LYS cc_start: 0.8245 (ttmm) cc_final: 0.7863 (ttmm) REVERT: 3 30 ASP cc_start: 0.8054 (m-30) cc_final: 0.7742 (m-30) REVERT: 3 34 ASP cc_start: 0.8203 (m-30) cc_final: 0.7718 (m-30) REVERT: 3 38 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7392 (mm) REVERT: 3 39 GLU cc_start: 0.7510 (mp0) cc_final: 0.7082 (mp0) REVERT: 3 61 LYS cc_start: 0.8597 (tptp) cc_final: 0.8342 (tptp) REVERT: 3 87 ASN cc_start: 0.7975 (t0) cc_final: 0.7563 (t0) REVERT: 3 92 ASP cc_start: 0.7766 (t0) cc_final: 0.7506 (t0) REVERT: 3 96 GLU cc_start: 0.7403 (tm-30) cc_final: 0.7113 (tm-30) REVERT: 3 175 LYS cc_start: 0.8316 (ttmt) cc_final: 0.8102 (ttmm) REVERT: 3 181 ASN cc_start: 0.7680 (t0) cc_final: 0.7377 (t0) REVERT: 3 207 LYS cc_start: 0.8647 (tttt) cc_final: 0.8026 (ttmm) REVERT: 3 232 LYS cc_start: 0.8119 (ttmm) cc_final: 0.7791 (ttmm) REVERT: 3 233 LYS cc_start: 0.7808 (mtpt) cc_final: 0.7508 (mtmm) REVERT: 3 247 ASN cc_start: 0.8779 (m-40) cc_final: 0.8372 (m-40) REVERT: 3 255 GLU cc_start: 0.8025 (tp30) cc_final: 0.7611 (tp30) REVERT: 3 259 ASN cc_start: 0.7773 (OUTLIER) cc_final: 0.7153 (p0) REVERT: 3 268 ASP cc_start: 0.7472 (p0) cc_final: 0.7091 (p0) REVERT: 3 269 PHE cc_start: 0.7219 (OUTLIER) cc_final: 0.5550 (t80) REVERT: 3 282 ASN cc_start: 0.8019 (t0) cc_final: 0.7708 (t0) REVERT: 4 19 THR cc_start: 0.8416 (OUTLIER) cc_final: 0.8006 (p) REVERT: 4 23 ARG cc_start: 0.6604 (mtm180) cc_final: 0.6338 (mtm110) REVERT: 4 29 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7670 (mmp) REVERT: 4 33 ARG cc_start: 0.8087 (ttp80) cc_final: 0.7832 (ttp80) REVERT: 4 45 MET cc_start: 0.7647 (ttp) cc_final: 0.6663 (ttp) REVERT: 4 46 MET cc_start: 0.8278 (tpt) cc_final: 0.7360 (tpt) REVERT: 4 62 TYR cc_start: 0.8073 (t80) cc_final: 0.7651 (t80) REVERT: 4 83 GLU cc_start: 0.6784 (tt0) cc_final: 0.6114 (tt0) REVERT: 4 133 ILE cc_start: 0.7804 (mt) cc_final: 0.7583 (mm) REVERT: 4 137 GLN cc_start: 0.7043 (pt0) cc_final: 0.6233 (pt0) REVERT: 4 149 THR cc_start: 0.5169 (OUTLIER) cc_final: 0.4650 (t) REVERT: 4 154 TRP cc_start: 0.8007 (t60) cc_final: 0.7641 (t60) REVERT: 4 155 LEU cc_start: 0.8336 (mt) cc_final: 0.8038 (mm) REVERT: 4 171 MET cc_start: 0.8522 (mtp) cc_final: 0.8003 (mtp) REVERT: 4 178 LEU cc_start: 0.7325 (tp) cc_final: 0.7021 (pp) REVERT: 4 190 ILE cc_start: 0.8393 (mt) cc_final: 0.8083 (pt) REVERT: 4 227 ASN cc_start: 0.7439 (p0) cc_final: 0.7120 (p0) REVERT: 4 228 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7415 (tm-30) REVERT: 4 253 SER cc_start: 0.8281 (p) cc_final: 0.8061 (p) REVERT: 4 274 LYS cc_start: 0.8161 (mttt) cc_final: 0.7827 (mtmt) REVERT: 4 285 LYS cc_start: 0.6949 (OUTLIER) cc_final: 0.6616 (ptpp) REVERT: 4 304 LYS cc_start: 0.7249 (tppt) cc_final: 0.6954 (tppt) REVERT: 5 60 LYS cc_start: 0.7356 (mmmt) cc_final: 0.6994 (mmtt) REVERT: 5 171 MET cc_start: 0.7801 (mtp) cc_final: 0.7057 (mtp) REVERT: 6 5 ARG cc_start: 0.6645 (tpp80) cc_final: 0.6297 (tpp-160) REVERT: 6 24 LYS cc_start: 0.8574 (ttpp) cc_final: 0.8323 (ttmm) REVERT: 6 30 ASP cc_start: 0.7340 (m-30) cc_final: 0.7093 (m-30) REVERT: 6 64 ASN cc_start: 0.6982 (m-40) cc_final: 0.6738 (m110) REVERT: 6 95 ARG cc_start: 0.8042 (ttm170) cc_final: 0.7817 (ttp80) REVERT: 6 96 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7584 (tm-30) REVERT: 6 115 LEU cc_start: 0.7060 (pp) cc_final: 0.6634 (tp) REVERT: 6 119 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8039 (tp) REVERT: 6 134 ASP cc_start: 0.7303 (t0) cc_final: 0.7031 (t0) REVERT: 6 149 THR cc_start: 0.8149 (OUTLIER) cc_final: 0.7743 (p) REVERT: 6 150 GLN cc_start: 0.8307 (mt0) cc_final: 0.7970 (mt0) REVERT: 6 153 ASN cc_start: 0.8056 (m-40) cc_final: 0.7708 (m-40) REVERT: 6 164 CYS cc_start: 0.7976 (t) cc_final: 0.7590 (p) REVERT: 6 168 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7756 (mm) REVERT: 6 175 LYS cc_start: 0.8337 (ttmt) cc_final: 0.7977 (ttmm) REVERT: 6 181 ASN cc_start: 0.8422 (t0) cc_final: 0.8197 (t0) REVERT: 6 189 SER cc_start: 0.8669 (p) cc_final: 0.8353 (t) REVERT: 6 192 VAL cc_start: 0.8950 (OUTLIER) cc_final: 0.8699 (t) REVERT: 6 198 SER cc_start: 0.7955 (p) cc_final: 0.7723 (p) REVERT: 6 230 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7879 (tp) REVERT: 6 247 ASN cc_start: 0.8368 (m-40) cc_final: 0.7612 (m-40) REVERT: 6 255 GLU cc_start: 0.7344 (tp30) cc_final: 0.6659 (mm-30) REVERT: 6 271 PHE cc_start: 0.7093 (t80) cc_final: 0.6567 (t80) REVERT: 7 39 GLU cc_start: 0.7709 (mp0) cc_final: 0.7042 (mp0) REVERT: 7 43 THR cc_start: 0.7893 (OUTLIER) cc_final: 0.7679 (m) REVERT: 7 61 LYS cc_start: 0.8330 (tptp) cc_final: 0.8111 (ttmm) REVERT: 7 86 ASP cc_start: 0.8290 (t70) cc_final: 0.8051 (t0) REVERT: 7 129 LYS cc_start: 0.8391 (mmmm) cc_final: 0.7964 (mttp) REVERT: 7 156 LYS cc_start: 0.8701 (ttpt) cc_final: 0.8372 (tttp) REVERT: 7 162 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8364 (p) REVERT: 7 166 ILE cc_start: 0.8501 (tp) cc_final: 0.8231 (tp) REVERT: 7 232 LYS cc_start: 0.8558 (ttmm) cc_final: 0.7844 (ttpp) REVERT: 7 286 ASN cc_start: 0.8566 (t0) cc_final: 0.8347 (t0) outliers start: 119 outliers final: 66 residues processed: 687 average time/residue: 0.1530 time to fit residues: 148.8630 Evaluate side-chains 692 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 606 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 1 residue 53 VAL Chi-restraints excluded: chain 1 residue 109 GLU Chi-restraints excluded: chain 1 residue 110 THR Chi-restraints excluded: chain 1 residue 117 LYS Chi-restraints excluded: chain 1 residue 119 LEU Chi-restraints excluded: chain 1 residue 142 GLU Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 1 residue 149 THR Chi-restraints excluded: chain 1 residue 176 VAL Chi-restraints excluded: chain 1 residue 217 LEU Chi-restraints excluded: chain 1 residue 269 PHE Chi-restraints excluded: chain 1 residue 279 ASP Chi-restraints excluded: chain 1 residue 295 THR Chi-restraints excluded: chain 1 residue 309 GLU Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 22 VAL Chi-restraints excluded: chain 2 residue 45 MET Chi-restraints excluded: chain 2 residue 149 THR Chi-restraints excluded: chain 2 residue 200 GLN Chi-restraints excluded: chain 2 residue 213 LEU Chi-restraints excluded: chain 2 residue 261 HIS Chi-restraints excluded: chain 2 residue 262 GLU Chi-restraints excluded: chain 2 residue 294 VAL Chi-restraints excluded: chain 2 residue 314 HIS Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 19 THR Chi-restraints excluded: chain 3 residue 35 LEU Chi-restraints excluded: chain 3 residue 38 LEU Chi-restraints excluded: chain 3 residue 41 GLU Chi-restraints excluded: chain 3 residue 63 LEU Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 110 THR Chi-restraints excluded: chain 3 residue 142 GLU Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 149 THR Chi-restraints excluded: chain 3 residue 259 ASN Chi-restraints excluded: chain 3 residue 269 PHE Chi-restraints excluded: chain 3 residue 270 VAL Chi-restraints excluded: chain 4 residue 10 SER Chi-restraints excluded: chain 4 residue 19 THR Chi-restraints excluded: chain 4 residue 29 MET Chi-restraints excluded: chain 4 residue 60 LYS Chi-restraints excluded: chain 4 residue 110 THR Chi-restraints excluded: chain 4 residue 119 LEU Chi-restraints excluded: chain 4 residue 130 LEU Chi-restraints excluded: chain 4 residue 131 ILE Chi-restraints excluded: chain 4 residue 142 GLU Chi-restraints excluded: chain 4 residue 148 LEU Chi-restraints excluded: chain 4 residue 149 THR Chi-restraints excluded: chain 4 residue 198 SER Chi-restraints excluded: chain 4 residue 211 GLU Chi-restraints excluded: chain 4 residue 231 GLN Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 285 LYS Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 29 MET Chi-restraints excluded: chain 5 residue 46 MET Chi-restraints excluded: chain 5 residue 92 ASP Chi-restraints excluded: chain 5 residue 97 LEU Chi-restraints excluded: chain 5 residue 110 THR Chi-restraints excluded: chain 5 residue 142 GLU Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 211 GLU Chi-restraints excluded: chain 6 residue 6 GLU Chi-restraints excluded: chain 6 residue 63 LEU Chi-restraints excluded: chain 6 residue 99 VAL Chi-restraints excluded: chain 6 residue 119 LEU Chi-restraints excluded: chain 6 residue 142 GLU Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 148 LEU Chi-restraints excluded: chain 6 residue 149 THR Chi-restraints excluded: chain 6 residue 168 ILE Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 6 residue 230 LEU Chi-restraints excluded: chain 7 residue 19 THR Chi-restraints excluded: chain 7 residue 43 THR Chi-restraints excluded: chain 7 residue 53 VAL Chi-restraints excluded: chain 7 residue 117 LYS Chi-restraints excluded: chain 7 residue 119 LEU Chi-restraints excluded: chain 7 residue 142 GLU Chi-restraints excluded: chain 7 residue 148 LEU Chi-restraints excluded: chain 7 residue 149 THR Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 309 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 67 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 3 optimal weight: 50.0000 chunk 14 optimal weight: 0.9990 chunk 78 optimal weight: 0.0270 chunk 1 optimal weight: 50.0000 chunk 99 optimal weight: 0.8980 chunk 129 optimal weight: 0.0670 chunk 193 optimal weight: 0.0870 chunk 121 optimal weight: 1.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 64 ASN 1 138 HIS ** 1 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 259 ASN 1 282 ASN 2 183 GLN 2 261 HIS 3 183 GLN 3 241 ASN 4 231 GLN ** 6 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 227 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.170124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.135013 restraints weight = 26561.100| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.25 r_work: 0.3565 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18773 Z= 0.132 Angle : 0.647 12.226 25612 Z= 0.327 Chirality : 0.041 0.164 2863 Planarity : 0.004 0.056 3122 Dihedral : 15.747 88.052 2909 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 6.29 % Allowed : 26.33 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.18), residues: 2163 helix: 0.63 (0.15), residues: 1183 sheet: -2.67 (0.35), residues: 238 loop : -2.35 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 3 313 TYR 0.022 0.002 TYR 6 199 PHE 0.016 0.001 PHE 1 237 TRP 0.016 0.001 TRP 6 154 HIS 0.004 0.001 HIS 2 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (18772) covalent geometry : angle 0.64725 / 0.33 (25612) hydrogen bonds : bond 0.03419 / 3.77 ( 816) hydrogen bonds : angle 3.81096 / 4.45 ( 2372) Misc. bond : bond 0.00181 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 627 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 19 THR cc_start: 0.8879 (OUTLIER) cc_final: 0.8451 (t) REVERT: 1 29 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8262 (mtm) REVERT: 1 30 ASP cc_start: 0.7800 (m-30) cc_final: 0.7489 (m-30) REVERT: 1 37 ASP cc_start: 0.7964 (p0) cc_final: 0.7113 (p0) REVERT: 1 38 LEU cc_start: 0.8154 (mp) cc_final: 0.7826 (mt) REVERT: 1 39 GLU cc_start: 0.7105 (mp0) cc_final: 0.6035 (mp0) REVERT: 1 45 MET cc_start: 0.8627 (ttm) cc_final: 0.8403 (ttp) REVERT: 1 60 LYS cc_start: 0.8540 (mmmt) cc_final: 0.8220 (mmtp) REVERT: 1 83 GLU cc_start: 0.7164 (tt0) cc_final: 0.6874 (mt-10) REVERT: 1 95 ARG cc_start: 0.8015 (ptp-170) cc_final: 0.7789 (ptp-170) REVERT: 1 100 GLU cc_start: 0.7432 (tm-30) cc_final: 0.7063 (tm-30) REVERT: 1 101 MET cc_start: 0.7773 (ttp) cc_final: 0.7426 (ttp) REVERT: 1 105 LEU cc_start: 0.7735 (pp) cc_final: 0.7452 (mp) REVERT: 1 109 GLU cc_start: 0.6721 (OUTLIER) cc_final: 0.6494 (tt0) REVERT: 1 129 LYS cc_start: 0.8579 (mtpt) cc_final: 0.8218 (mtpt) REVERT: 1 134 ASP cc_start: 0.7146 (t0) cc_final: 0.6847 (t0) REVERT: 1 149 THR cc_start: 0.8580 (OUTLIER) cc_final: 0.8281 (p) REVERT: 1 162 THR cc_start: 0.8258 (OUTLIER) cc_final: 0.8028 (t) REVERT: 1 163 LYS cc_start: 0.8204 (mptt) cc_final: 0.7965 (mmtm) REVERT: 1 171 MET cc_start: 0.8443 (mtp) cc_final: 0.8219 (mmm) REVERT: 1 269 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7707 (m-80) REVERT: 1 274 LYS cc_start: 0.8587 (mttt) cc_final: 0.8334 (mtpp) REVERT: 1 279 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.8092 (p0) REVERT: 1 285 LYS cc_start: 0.7587 (tppt) cc_final: 0.7241 (tppt) REVERT: 1 297 ASP cc_start: 0.8016 (t0) cc_final: 0.7718 (t0) REVERT: 1 310 ASP cc_start: 0.7903 (m-30) cc_final: 0.7525 (t0) REVERT: 2 6 GLU cc_start: 0.7436 (pm20) cc_final: 0.7050 (tm-30) REVERT: 2 24 LYS cc_start: 0.8396 (ttpp) cc_final: 0.8116 (ttmm) REVERT: 2 46 MET cc_start: 0.8122 (ttt) cc_final: 0.7903 (ttt) REVERT: 2 89 LYS cc_start: 0.8233 (mmmt) cc_final: 0.7867 (mmmt) REVERT: 2 116 THR cc_start: 0.7868 (m) cc_final: 0.7500 (p) REVERT: 2 122 LEU cc_start: 0.8471 (tp) cc_final: 0.8178 (tp) REVERT: 2 135 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7032 (mm-30) REVERT: 2 146 ARG cc_start: 0.7128 (ptm-80) cc_final: 0.6658 (ptm-80) REVERT: 2 150 GLN cc_start: 0.8063 (mt0) cc_final: 0.7699 (mt0) REVERT: 2 163 LYS cc_start: 0.8286 (mppt) cc_final: 0.7864 (mmtm) REVERT: 2 181 ASN cc_start: 0.7892 (t0) cc_final: 0.7666 (t0) REVERT: 2 183 GLN cc_start: 0.7876 (mm110) cc_final: 0.7608 (mm-40) REVERT: 2 211 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7167 (mp0) REVERT: 2 228 GLU cc_start: 0.7763 (tp30) cc_final: 0.7535 (tp30) REVERT: 2 235 TYR cc_start: 0.8207 (t80) cc_final: 0.7855 (t80) REVERT: 2 261 HIS cc_start: 0.7485 (OUTLIER) cc_final: 0.7076 (t70) REVERT: 3 27 SER cc_start: 0.8919 (m) cc_final: 0.8528 (p) REVERT: 3 30 ASP cc_start: 0.8010 (m-30) cc_final: 0.7738 (m-30) REVERT: 3 34 ASP cc_start: 0.8254 (m-30) cc_final: 0.7764 (m-30) REVERT: 3 38 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7400 (mm) REVERT: 3 39 GLU cc_start: 0.7528 (mp0) cc_final: 0.7066 (mp0) REVERT: 3 46 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7619 (tpt) REVERT: 3 61 LYS cc_start: 0.8469 (tptp) cc_final: 0.7985 (tptp) REVERT: 3 87 ASN cc_start: 0.7890 (t0) cc_final: 0.7623 (t0) REVERT: 3 92 ASP cc_start: 0.7753 (t0) cc_final: 0.7522 (t0) REVERT: 3 96 GLU cc_start: 0.7407 (tm-30) cc_final: 0.7138 (tm-30) REVERT: 3 181 ASN cc_start: 0.7671 (t0) cc_final: 0.7414 (t0) REVERT: 3 207 LYS cc_start: 0.8647 (tttt) cc_final: 0.8022 (ttmm) REVERT: 3 220 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.6366 (pm20) REVERT: 3 232 LYS cc_start: 0.8098 (ttmm) cc_final: 0.7836 (ttmm) REVERT: 3 233 LYS cc_start: 0.7750 (mtpt) cc_final: 0.7485 (mtmm) REVERT: 3 247 ASN cc_start: 0.8681 (m-40) cc_final: 0.8358 (m-40) REVERT: 3 250 TYR cc_start: 0.8545 (t80) cc_final: 0.7964 (t80) REVERT: 3 259 ASN cc_start: 0.7975 (OUTLIER) cc_final: 0.7554 (p0) REVERT: 3 268 ASP cc_start: 0.7426 (p0) cc_final: 0.7076 (p0) REVERT: 3 269 PHE cc_start: 0.7189 (OUTLIER) cc_final: 0.5555 (t80) REVERT: 3 282 ASN cc_start: 0.8040 (t0) cc_final: 0.7782 (t0) REVERT: 3 300 ARG cc_start: 0.8349 (ptp90) cc_final: 0.8139 (ptp90) REVERT: 4 19 THR cc_start: 0.8433 (OUTLIER) cc_final: 0.8048 (p) REVERT: 4 23 ARG cc_start: 0.6717 (mtm180) cc_final: 0.6401 (mtm110) REVERT: 4 29 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7598 (mmp) REVERT: 4 45 MET cc_start: 0.7528 (ttp) cc_final: 0.6512 (ttp) REVERT: 4 46 MET cc_start: 0.8288 (tpt) cc_final: 0.7521 (tpt) REVERT: 4 58 VAL cc_start: 0.8141 (OUTLIER) cc_final: 0.7931 (t) REVERT: 4 62 TYR cc_start: 0.8072 (t80) cc_final: 0.7595 (t80) REVERT: 4 63 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7333 (tp) REVERT: 4 83 GLU cc_start: 0.6732 (tt0) cc_final: 0.6021 (tt0) REVERT: 4 118 ARG cc_start: 0.6879 (mtp180) cc_final: 0.6607 (mtp180) REVERT: 4 133 ILE cc_start: 0.7799 (mt) cc_final: 0.7576 (mm) REVERT: 4 137 GLN cc_start: 0.7148 (OUTLIER) cc_final: 0.6369 (pt0) REVERT: 4 149 THR cc_start: 0.5229 (OUTLIER) cc_final: 0.4678 (t) REVERT: 4 154 TRP cc_start: 0.8005 (t60) cc_final: 0.7647 (t60) REVERT: 4 155 LEU cc_start: 0.8348 (mt) cc_final: 0.8054 (mm) REVERT: 4 171 MET cc_start: 0.8622 (mtp) cc_final: 0.8113 (mtp) REVERT: 4 178 LEU cc_start: 0.7367 (tp) cc_final: 0.7079 (pp) REVERT: 4 228 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7451 (tm-30) REVERT: 4 253 SER cc_start: 0.8291 (p) cc_final: 0.8071 (p) REVERT: 4 263 THR cc_start: 0.7913 (t) cc_final: 0.7601 (m) REVERT: 4 274 LYS cc_start: 0.8024 (mttt) cc_final: 0.7783 (mtmt) REVERT: 4 304 LYS cc_start: 0.7261 (tppt) cc_final: 0.6976 (tppt) REVERT: 5 60 LYS cc_start: 0.7301 (mmmt) cc_final: 0.6982 (mmtt) REVERT: 5 157 MET cc_start: 0.6795 (tmm) cc_final: 0.6542 (ppp) REVERT: 5 171 MET cc_start: 0.7694 (mtp) cc_final: 0.7104 (mtp) REVERT: 6 24 LYS cc_start: 0.8582 (ttpp) cc_final: 0.8364 (ttmm) REVERT: 6 30 ASP cc_start: 0.7293 (m-30) cc_final: 0.7072 (m-30) REVERT: 6 64 ASN cc_start: 0.7003 (m-40) cc_final: 0.6778 (m-40) REVERT: 6 96 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7625 (tm-30) REVERT: 6 115 LEU cc_start: 0.7133 (pp) cc_final: 0.6641 (tp) REVERT: 6 119 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8073 (tp) REVERT: 6 149 THR cc_start: 0.8203 (p) cc_final: 0.7836 (p) REVERT: 6 150 GLN cc_start: 0.8314 (mt0) cc_final: 0.7951 (mt0) REVERT: 6 153 ASN cc_start: 0.8121 (m-40) cc_final: 0.7745 (m-40) REVERT: 6 162 THR cc_start: 0.8616 (OUTLIER) cc_final: 0.8235 (p) REVERT: 6 164 CYS cc_start: 0.8019 (t) cc_final: 0.7629 (p) REVERT: 6 175 LYS cc_start: 0.8325 (ttmt) cc_final: 0.8053 (ttmm) REVERT: 6 181 ASN cc_start: 0.8450 (t0) cc_final: 0.8231 (t0) REVERT: 6 189 SER cc_start: 0.8653 (p) cc_final: 0.8344 (t) REVERT: 6 192 VAL cc_start: 0.8933 (OUTLIER) cc_final: 0.8708 (t) REVERT: 6 198 SER cc_start: 0.7905 (p) cc_final: 0.7677 (p) REVERT: 6 219 PHE cc_start: 0.6266 (m-80) cc_final: 0.6062 (m-80) REVERT: 6 230 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7853 (tp) REVERT: 6 237 PHE cc_start: 0.8052 (t80) cc_final: 0.7677 (t80) REVERT: 6 242 MET cc_start: 0.8612 (tpp) cc_final: 0.8303 (mmm) REVERT: 6 255 GLU cc_start: 0.7368 (tp30) cc_final: 0.6432 (mm-30) REVERT: 6 259 ASN cc_start: 0.7213 (OUTLIER) cc_final: 0.6428 (p0) REVERT: 6 275 LEU cc_start: 0.6696 (tp) cc_final: 0.6344 (mp) REVERT: 7 8 ARG cc_start: 0.8678 (mtm180) cc_final: 0.8465 (mtm-85) REVERT: 7 14 ARG cc_start: 0.8200 (mtm-85) cc_final: 0.7961 (mtt90) REVERT: 7 39 GLU cc_start: 0.7664 (mp0) cc_final: 0.7029 (mp0) REVERT: 7 95 ARG cc_start: 0.8324 (ptp90) cc_final: 0.8121 (ptm160) REVERT: 7 119 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7909 (tt) REVERT: 7 129 LYS cc_start: 0.8358 (mmmm) cc_final: 0.8002 (mmmm) REVERT: 7 156 LYS cc_start: 0.8727 (ttpt) cc_final: 0.8396 (tttp) REVERT: 7 232 LYS cc_start: 0.8494 (ttmm) cc_final: 0.7838 (ttpp) REVERT: 7 286 ASN cc_start: 0.8560 (t0) cc_final: 0.8319 (t0) REVERT: 7 309 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7300 (mt-10) outliers start: 118 outliers final: 71 residues processed: 682 average time/residue: 0.1543 time to fit residues: 148.7372 Evaluate side-chains 687 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 590 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 29 MET Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 1 residue 53 VAL Chi-restraints excluded: chain 1 residue 109 GLU Chi-restraints excluded: chain 1 residue 110 THR Chi-restraints excluded: chain 1 residue 117 LYS Chi-restraints excluded: chain 1 residue 119 LEU Chi-restraints excluded: chain 1 residue 142 GLU Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 1 residue 149 THR Chi-restraints excluded: chain 1 residue 162 THR Chi-restraints excluded: chain 1 residue 176 VAL Chi-restraints excluded: chain 1 residue 217 LEU Chi-restraints excluded: chain 1 residue 261 HIS Chi-restraints excluded: chain 1 residue 269 PHE Chi-restraints excluded: chain 1 residue 279 ASP Chi-restraints excluded: chain 1 residue 295 THR Chi-restraints excluded: chain 1 residue 309 GLU Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 22 VAL Chi-restraints excluded: chain 2 residue 45 MET Chi-restraints excluded: chain 2 residue 213 LEU Chi-restraints excluded: chain 2 residue 261 HIS Chi-restraints excluded: chain 2 residue 294 VAL Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 19 THR Chi-restraints excluded: chain 3 residue 35 LEU Chi-restraints excluded: chain 3 residue 38 LEU Chi-restraints excluded: chain 3 residue 41 GLU Chi-restraints excluded: chain 3 residue 45 MET Chi-restraints excluded: chain 3 residue 46 MET Chi-restraints excluded: chain 3 residue 63 LEU Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 142 GLU Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 149 THR Chi-restraints excluded: chain 3 residue 220 GLU Chi-restraints excluded: chain 3 residue 259 ASN Chi-restraints excluded: chain 3 residue 269 PHE Chi-restraints excluded: chain 3 residue 270 VAL Chi-restraints excluded: chain 3 residue 285 LYS Chi-restraints excluded: chain 3 residue 312 LEU Chi-restraints excluded: chain 4 residue 10 SER Chi-restraints excluded: chain 4 residue 19 THR Chi-restraints excluded: chain 4 residue 29 MET Chi-restraints excluded: chain 4 residue 58 VAL Chi-restraints excluded: chain 4 residue 60 LYS Chi-restraints excluded: chain 4 residue 63 LEU Chi-restraints excluded: chain 4 residue 110 THR Chi-restraints excluded: chain 4 residue 119 LEU Chi-restraints excluded: chain 4 residue 130 LEU Chi-restraints excluded: chain 4 residue 131 ILE Chi-restraints excluded: chain 4 residue 137 GLN Chi-restraints excluded: chain 4 residue 142 GLU Chi-restraints excluded: chain 4 residue 148 LEU Chi-restraints excluded: chain 4 residue 149 THR Chi-restraints excluded: chain 4 residue 211 GLU Chi-restraints excluded: chain 4 residue 230 LEU Chi-restraints excluded: chain 4 residue 269 PHE Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 279 ASP Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 29 MET Chi-restraints excluded: chain 5 residue 38 LEU Chi-restraints excluded: chain 5 residue 46 MET Chi-restraints excluded: chain 5 residue 97 LEU Chi-restraints excluded: chain 5 residue 99 VAL Chi-restraints excluded: chain 5 residue 142 GLU Chi-restraints excluded: chain 5 residue 147 VAL Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 158 ILE Chi-restraints excluded: chain 5 residue 211 GLU Chi-restraints excluded: chain 5 residue 259 ASN Chi-restraints excluded: chain 5 residue 299 LEU Chi-restraints excluded: chain 6 residue 6 GLU Chi-restraints excluded: chain 6 residue 63 LEU Chi-restraints excluded: chain 6 residue 99 VAL Chi-restraints excluded: chain 6 residue 119 LEU Chi-restraints excluded: chain 6 residue 142 GLU Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 148 LEU Chi-restraints excluded: chain 6 residue 162 THR Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 6 residue 230 LEU Chi-restraints excluded: chain 6 residue 259 ASN Chi-restraints excluded: chain 6 residue 304 LYS Chi-restraints excluded: chain 7 residue 19 THR Chi-restraints excluded: chain 7 residue 53 VAL Chi-restraints excluded: chain 7 residue 117 LYS Chi-restraints excluded: chain 7 residue 119 LEU Chi-restraints excluded: chain 7 residue 142 GLU Chi-restraints excluded: chain 7 residue 146 ARG Chi-restraints excluded: chain 7 residue 148 LEU Chi-restraints excluded: chain 7 residue 149 THR Chi-restraints excluded: chain 7 residue 214 ASP Chi-restraints excluded: chain 7 residue 309 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 139 optimal weight: 2.9990 chunk 7 optimal weight: 0.0870 chunk 183 optimal weight: 0.6980 chunk 132 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 64 ASN ** 1 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 259 ASN 1 282 ASN ** 3 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 239 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.168610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.133212 restraints weight = 26401.574| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.27 r_work: 0.3546 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18773 Z= 0.141 Angle : 0.648 10.976 25612 Z= 0.325 Chirality : 0.041 0.186 2863 Planarity : 0.004 0.039 3122 Dihedral : 15.456 87.130 2901 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 6.56 % Allowed : 26.28 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.18), residues: 2163 helix: 0.78 (0.15), residues: 1190 sheet: -2.54 (0.35), residues: 238 loop : -2.25 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 4 14 TYR 0.024 0.002 TYR 6 199 PHE 0.014 0.002 PHE 1 237 TRP 0.018 0.002 TRP 6 154 HIS 0.003 0.001 HIS 3 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (18772) covalent geometry : angle 0.64771 / 0.32 (25612) hydrogen bonds : bond 0.03347 / 3.71 ( 816) hydrogen bonds : angle 3.78406 / 4.43 ( 2372) Misc. bond : bond 0.00173 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 603 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 11 ARG cc_start: 0.8132 (mtp180) cc_final: 0.7837 (ttp-170) REVERT: 1 19 THR cc_start: 0.8849 (OUTLIER) cc_final: 0.8404 (t) REVERT: 1 23 ARG cc_start: 0.8406 (mtm110) cc_final: 0.8185 (mtm110) REVERT: 1 29 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8265 (mtm) REVERT: 1 30 ASP cc_start: 0.7872 (m-30) cc_final: 0.7570 (m-30) REVERT: 1 37 ASP cc_start: 0.8002 (p0) cc_final: 0.7605 (p0) REVERT: 1 38 LEU cc_start: 0.8029 (mp) cc_final: 0.7760 (mt) REVERT: 1 39 GLU cc_start: 0.7110 (mp0) cc_final: 0.6616 (mp0) REVERT: 1 60 LYS cc_start: 0.8550 (mmmt) cc_final: 0.8232 (mmtp) REVERT: 1 83 GLU cc_start: 0.7213 (tt0) cc_final: 0.6913 (mt-10) REVERT: 1 100 GLU cc_start: 0.7442 (tm-30) cc_final: 0.7077 (tm-30) REVERT: 1 101 MET cc_start: 0.7800 (ttp) cc_final: 0.7430 (ttp) REVERT: 1 105 LEU cc_start: 0.7719 (pp) cc_final: 0.7456 (mp) REVERT: 1 129 LYS cc_start: 0.8584 (mtpt) cc_final: 0.8220 (mtpt) REVERT: 1 134 ASP cc_start: 0.7247 (t0) cc_final: 0.6944 (t0) REVERT: 1 149 THR cc_start: 0.8586 (p) cc_final: 0.8299 (p) REVERT: 1 162 THR cc_start: 0.8280 (OUTLIER) cc_final: 0.8035 (t) REVERT: 1 163 LYS cc_start: 0.8255 (mptt) cc_final: 0.8010 (mmtm) REVERT: 1 269 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7833 (m-80) REVERT: 1 274 LYS cc_start: 0.8627 (mttt) cc_final: 0.8358 (mtpp) REVERT: 1 279 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8106 (p0) REVERT: 1 285 LYS cc_start: 0.7585 (tppt) cc_final: 0.7282 (tppt) REVERT: 2 6 GLU cc_start: 0.7442 (pm20) cc_final: 0.7083 (tm-30) REVERT: 2 33 ARG cc_start: 0.8257 (ttp80) cc_final: 0.8055 (ttp-170) REVERT: 2 46 MET cc_start: 0.8019 (ttt) cc_final: 0.7777 (ttt) REVERT: 2 96 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7417 (tp30) REVERT: 2 116 THR cc_start: 0.7897 (m) cc_final: 0.7522 (p) REVERT: 2 122 LEU cc_start: 0.8500 (tp) cc_final: 0.8212 (tp) REVERT: 2 135 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7091 (mm-30) REVERT: 2 150 GLN cc_start: 0.8099 (mt0) cc_final: 0.7728 (mt0) REVERT: 2 163 LYS cc_start: 0.8271 (mppt) cc_final: 0.7842 (mmtm) REVERT: 2 175 LYS cc_start: 0.8863 (ttmt) cc_final: 0.8574 (ttmm) REVERT: 2 211 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7197 (mp0) REVERT: 2 228 GLU cc_start: 0.7689 (tp30) cc_final: 0.7359 (tp30) REVERT: 2 235 TYR cc_start: 0.8226 (t80) cc_final: 0.7755 (t80) REVERT: 2 296 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7547 (tm-30) REVERT: 3 24 LYS cc_start: 0.8690 (tttt) cc_final: 0.8346 (ttpp) REVERT: 3 27 SER cc_start: 0.8924 (m) cc_final: 0.8542 (p) REVERT: 3 30 ASP cc_start: 0.8092 (m-30) cc_final: 0.7800 (m-30) REVERT: 3 34 ASP cc_start: 0.8223 (m-30) cc_final: 0.7769 (m-30) REVERT: 3 39 GLU cc_start: 0.7485 (mp0) cc_final: 0.7049 (mp0) REVERT: 3 46 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7568 (tpp) REVERT: 3 61 LYS cc_start: 0.8529 (tptp) cc_final: 0.8043 (tptp) REVERT: 3 87 ASN cc_start: 0.7972 (t0) cc_final: 0.7604 (t0) REVERT: 3 92 ASP cc_start: 0.7804 (t0) cc_final: 0.7529 (t0) REVERT: 3 96 GLU cc_start: 0.7416 (tm-30) cc_final: 0.7172 (tm-30) REVERT: 3 181 ASN cc_start: 0.7650 (t0) cc_final: 0.7356 (t0) REVERT: 3 207 LYS cc_start: 0.8761 (tttt) cc_final: 0.8046 (ttmm) REVERT: 3 230 LEU cc_start: 0.7558 (tp) cc_final: 0.7053 (tp) REVERT: 3 232 LYS cc_start: 0.8066 (ttmm) cc_final: 0.7808 (ttmm) REVERT: 3 233 LYS cc_start: 0.7631 (mtpt) cc_final: 0.7412 (mtmm) REVERT: 3 247 ASN cc_start: 0.8650 (m-40) cc_final: 0.8360 (m-40) REVERT: 3 250 TYR cc_start: 0.8553 (t80) cc_final: 0.7939 (t80) REVERT: 3 255 GLU cc_start: 0.8049 (tp30) cc_final: 0.7542 (tp30) REVERT: 3 259 ASN cc_start: 0.7975 (OUTLIER) cc_final: 0.7459 (p0) REVERT: 3 268 ASP cc_start: 0.7501 (p0) cc_final: 0.7104 (p0) REVERT: 3 269 PHE cc_start: 0.7211 (OUTLIER) cc_final: 0.5554 (t80) REVERT: 3 282 ASN cc_start: 0.8071 (t0) cc_final: 0.7808 (t0) REVERT: 4 19 THR cc_start: 0.8421 (p) cc_final: 0.8096 (p) REVERT: 4 23 ARG cc_start: 0.6830 (mtm180) cc_final: 0.6461 (mtm110) REVERT: 4 29 MET cc_start: 0.8141 (mtt) cc_final: 0.7685 (mmp) REVERT: 4 45 MET cc_start: 0.7513 (ttp) cc_final: 0.6558 (ttp) REVERT: 4 46 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7504 (tpt) REVERT: 4 62 TYR cc_start: 0.8086 (t80) cc_final: 0.7609 (t80) REVERT: 4 63 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7345 (tp) REVERT: 4 83 GLU cc_start: 0.6770 (tt0) cc_final: 0.6052 (tt0) REVERT: 4 114 ARG cc_start: 0.7789 (ttp80) cc_final: 0.7491 (ptt90) REVERT: 4 133 ILE cc_start: 0.7815 (mt) cc_final: 0.7594 (mm) REVERT: 4 137 GLN cc_start: 0.7145 (OUTLIER) cc_final: 0.6544 (pm20) REVERT: 4 149 THR cc_start: 0.5214 (OUTLIER) cc_final: 0.4683 (t) REVERT: 4 154 TRP cc_start: 0.8052 (t60) cc_final: 0.7694 (t60) REVERT: 4 155 LEU cc_start: 0.8389 (mt) cc_final: 0.8082 (mm) REVERT: 4 171 MET cc_start: 0.8635 (mtp) cc_final: 0.8220 (mtp) REVERT: 4 178 LEU cc_start: 0.7386 (tp) cc_final: 0.7105 (pp) REVERT: 4 190 ILE cc_start: 0.8347 (mt) cc_final: 0.8081 (pt) REVERT: 4 228 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7498 (tm-30) REVERT: 4 253 SER cc_start: 0.8266 (p) cc_final: 0.8058 (p) REVERT: 4 263 THR cc_start: 0.7882 (t) cc_final: 0.7601 (m) REVERT: 4 274 LYS cc_start: 0.8034 (mttt) cc_final: 0.7764 (mtmt) REVERT: 5 60 LYS cc_start: 0.7295 (mmmt) cc_final: 0.7034 (mmtt) REVERT: 5 63 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7383 (tt) REVERT: 5 157 MET cc_start: 0.6915 (tmm) cc_final: 0.6649 (ppp) REVERT: 5 171 MET cc_start: 0.7634 (mtp) cc_final: 0.7060 (mtp) REVERT: 6 24 LYS cc_start: 0.8605 (ttpp) cc_final: 0.8379 (ttmm) REVERT: 6 30 ASP cc_start: 0.7322 (m-30) cc_final: 0.7078 (m-30) REVERT: 6 64 ASN cc_start: 0.6926 (m-40) cc_final: 0.6698 (m-40) REVERT: 6 80 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.7026 (mt) REVERT: 6 96 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7616 (tm-30) REVERT: 6 115 LEU cc_start: 0.7148 (pp) cc_final: 0.6651 (tp) REVERT: 6 135 GLU cc_start: 0.6544 (mm-30) cc_final: 0.6141 (mm-30) REVERT: 6 149 THR cc_start: 0.8289 (p) cc_final: 0.7882 (p) REVERT: 6 150 GLN cc_start: 0.8356 (mt0) cc_final: 0.7978 (mt0) REVERT: 6 153 ASN cc_start: 0.7975 (m-40) cc_final: 0.7667 (m-40) REVERT: 6 162 THR cc_start: 0.8509 (OUTLIER) cc_final: 0.8144 (p) REVERT: 6 164 CYS cc_start: 0.7979 (t) cc_final: 0.7550 (p) REVERT: 6 175 LYS cc_start: 0.8360 (ttmt) cc_final: 0.7983 (ttmm) REVERT: 6 181 ASN cc_start: 0.8379 (t0) cc_final: 0.8131 (t0) REVERT: 6 189 SER cc_start: 0.8618 (p) cc_final: 0.8311 (t) REVERT: 6 192 VAL cc_start: 0.8944 (OUTLIER) cc_final: 0.8700 (t) REVERT: 6 237 PHE cc_start: 0.8011 (t80) cc_final: 0.7568 (t80) REVERT: 6 255 GLU cc_start: 0.7322 (tp30) cc_final: 0.6729 (mm-30) REVERT: 6 259 ASN cc_start: 0.7092 (OUTLIER) cc_final: 0.6376 (p0) REVERT: 6 262 GLU cc_start: 0.6494 (mp0) cc_final: 0.6045 (mp0) REVERT: 6 270 VAL cc_start: 0.8167 (p) cc_final: 0.7955 (m) REVERT: 7 39 GLU cc_start: 0.7674 (mp0) cc_final: 0.7136 (mp0) REVERT: 7 46 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7387 (tpp) REVERT: 7 61 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8014 (ttmm) REVERT: 7 119 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7887 (tt) REVERT: 7 129 LYS cc_start: 0.8384 (mmmm) cc_final: 0.7982 (mttp) REVERT: 7 156 LYS cc_start: 0.8753 (ttpt) cc_final: 0.8394 (tttp) REVERT: 7 162 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8297 (p) REVERT: 7 232 LYS cc_start: 0.8489 (ttmm) cc_final: 0.7833 (ttpp) REVERT: 7 286 ASN cc_start: 0.8571 (t0) cc_final: 0.8320 (t0) REVERT: 7 293 GLU cc_start: 0.6924 (tm-30) cc_final: 0.6669 (tm-30) outliers start: 123 outliers final: 73 residues processed: 667 average time/residue: 0.1664 time to fit residues: 158.8598 Evaluate side-chains 691 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 596 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 29 MET Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 1 residue 107 LEU Chi-restraints excluded: chain 1 residue 110 THR Chi-restraints excluded: chain 1 residue 117 LYS Chi-restraints excluded: chain 1 residue 119 LEU Chi-restraints excluded: chain 1 residue 142 GLU Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 1 residue 162 THR Chi-restraints excluded: chain 1 residue 176 VAL Chi-restraints excluded: chain 1 residue 215 LYS Chi-restraints excluded: chain 1 residue 217 LEU Chi-restraints excluded: chain 1 residue 269 PHE Chi-restraints excluded: chain 1 residue 279 ASP Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 22 VAL Chi-restraints excluded: chain 2 residue 45 MET Chi-restraints excluded: chain 2 residue 96 GLU Chi-restraints excluded: chain 2 residue 117 LYS Chi-restraints excluded: chain 2 residue 192 VAL Chi-restraints excluded: chain 2 residue 213 LEU Chi-restraints excluded: chain 2 residue 294 VAL Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 35 LEU Chi-restraints excluded: chain 3 residue 45 MET Chi-restraints excluded: chain 3 residue 46 MET Chi-restraints excluded: chain 3 residue 63 LEU Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 99 VAL Chi-restraints excluded: chain 3 residue 142 GLU Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 193 GLU Chi-restraints excluded: chain 3 residue 259 ASN Chi-restraints excluded: chain 3 residue 269 PHE Chi-restraints excluded: chain 3 residue 270 VAL Chi-restraints excluded: chain 3 residue 312 LEU Chi-restraints excluded: chain 4 residue 25 ILE Chi-restraints excluded: chain 4 residue 27 SER Chi-restraints excluded: chain 4 residue 30 ASP Chi-restraints excluded: chain 4 residue 46 MET Chi-restraints excluded: chain 4 residue 60 LYS Chi-restraints excluded: chain 4 residue 63 LEU Chi-restraints excluded: chain 4 residue 110 THR Chi-restraints excluded: chain 4 residue 119 LEU Chi-restraints excluded: chain 4 residue 130 LEU Chi-restraints excluded: chain 4 residue 131 ILE Chi-restraints excluded: chain 4 residue 137 GLN Chi-restraints excluded: chain 4 residue 142 GLU Chi-restraints excluded: chain 4 residue 148 LEU Chi-restraints excluded: chain 4 residue 149 THR Chi-restraints excluded: chain 4 residue 162 THR Chi-restraints excluded: chain 4 residue 211 GLU Chi-restraints excluded: chain 4 residue 230 LEU Chi-restraints excluded: chain 4 residue 269 PHE Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 279 ASP Chi-restraints excluded: chain 4 residue 298 MET Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 29 MET Chi-restraints excluded: chain 5 residue 38 LEU Chi-restraints excluded: chain 5 residue 46 MET Chi-restraints excluded: chain 5 residue 63 LEU Chi-restraints excluded: chain 5 residue 97 LEU Chi-restraints excluded: chain 5 residue 142 GLU Chi-restraints excluded: chain 5 residue 147 VAL Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 158 ILE Chi-restraints excluded: chain 5 residue 211 GLU Chi-restraints excluded: chain 5 residue 299 LEU Chi-restraints excluded: chain 6 residue 63 LEU Chi-restraints excluded: chain 6 residue 80 LEU Chi-restraints excluded: chain 6 residue 118 ARG Chi-restraints excluded: chain 6 residue 142 GLU Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 148 LEU Chi-restraints excluded: chain 6 residue 162 THR Chi-restraints excluded: chain 6 residue 179 GLN Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 6 residue 259 ASN Chi-restraints excluded: chain 6 residue 269 PHE Chi-restraints excluded: chain 6 residue 304 LYS Chi-restraints excluded: chain 7 residue 19 THR Chi-restraints excluded: chain 7 residue 46 MET Chi-restraints excluded: chain 7 residue 53 VAL Chi-restraints excluded: chain 7 residue 61 LYS Chi-restraints excluded: chain 7 residue 117 LYS Chi-restraints excluded: chain 7 residue 119 LEU Chi-restraints excluded: chain 7 residue 142 GLU Chi-restraints excluded: chain 7 residue 146 ARG Chi-restraints excluded: chain 7 residue 148 LEU Chi-restraints excluded: chain 7 residue 149 THR Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 214 ASP Chi-restraints excluded: chain 7 residue 309 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 63 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 140 optimal weight: 0.6980 chunk 150 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 64 ASN 1 87 ASN ** 1 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 282 ASN 2 183 GLN 3 259 ASN 4 183 GLN 4 247 ASN 7 247 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.168829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.135228 restraints weight = 26106.647| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.27 r_work: 0.3548 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18773 Z= 0.145 Angle : 0.645 11.188 25612 Z= 0.323 Chirality : 0.042 0.185 2863 Planarity : 0.004 0.046 3122 Dihedral : 15.098 86.783 2889 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 6.13 % Allowed : 26.71 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.19), residues: 2163 helix: 0.87 (0.15), residues: 1190 sheet: -2.12 (0.38), residues: 224 loop : -2.21 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 5 114 TYR 0.026 0.002 TYR 6 199 PHE 0.019 0.002 PHE 6 206 TRP 0.021 0.002 TRP 6 154 HIS 0.006 0.001 HIS 4 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (18772) covalent geometry : angle 0.64479 / 0.32 (25612) hydrogen bonds : bond 0.03281 / 3.62 ( 816) hydrogen bonds : angle 3.74039 / 4.40 ( 2372) Misc. bond : bond 0.00212 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 594 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 11 ARG cc_start: 0.8156 (mtp180) cc_final: 0.7858 (ttp-170) REVERT: 1 22 VAL cc_start: 0.8094 (t) cc_final: 0.7859 (p) REVERT: 1 29 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8217 (mtm) REVERT: 1 30 ASP cc_start: 0.8069 (m-30) cc_final: 0.7811 (m-30) REVERT: 1 31 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7327 (ttt90) REVERT: 1 37 ASP cc_start: 0.7959 (p0) cc_final: 0.7658 (p0) REVERT: 1 38 LEU cc_start: 0.8059 (mp) cc_final: 0.7798 (mt) REVERT: 1 39 GLU cc_start: 0.7161 (mp0) cc_final: 0.6696 (mp0) REVERT: 1 48 TYR cc_start: 0.8646 (m-80) cc_final: 0.8103 (m-80) REVERT: 1 60 LYS cc_start: 0.8529 (mmmt) cc_final: 0.8247 (mmtp) REVERT: 1 83 GLU cc_start: 0.7182 (tt0) cc_final: 0.6917 (mt-10) REVERT: 1 100 GLU cc_start: 0.7430 (tm-30) cc_final: 0.7057 (tm-30) REVERT: 1 101 MET cc_start: 0.7829 (ttp) cc_final: 0.7490 (ttp) REVERT: 1 105 LEU cc_start: 0.7636 (pp) cc_final: 0.7395 (mp) REVERT: 1 129 LYS cc_start: 0.8535 (mtpt) cc_final: 0.8177 (mtpt) REVERT: 1 147 VAL cc_start: 0.8267 (OUTLIER) cc_final: 0.8061 (p) REVERT: 1 149 THR cc_start: 0.8608 (p) cc_final: 0.8281 (p) REVERT: 1 162 THR cc_start: 0.8232 (OUTLIER) cc_final: 0.7990 (t) REVERT: 1 163 LYS cc_start: 0.8223 (mptt) cc_final: 0.7996 (mmtt) REVERT: 1 228 GLU cc_start: 0.7381 (tm-30) cc_final: 0.7157 (tm-30) REVERT: 1 269 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.7724 (m-80) REVERT: 1 274 LYS cc_start: 0.8645 (mttt) cc_final: 0.8360 (mtpp) REVERT: 1 279 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8087 (p0) REVERT: 1 285 LYS cc_start: 0.7588 (tppt) cc_final: 0.7317 (tppt) REVERT: 2 33 ARG cc_start: 0.8287 (ttp80) cc_final: 0.8031 (ttp-170) REVERT: 2 65 GLN cc_start: 0.7816 (pp30) cc_final: 0.7483 (pt0) REVERT: 2 116 THR cc_start: 0.8016 (m) cc_final: 0.7643 (p) REVERT: 2 122 LEU cc_start: 0.8546 (tp) cc_final: 0.8213 (tp) REVERT: 2 135 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7110 (mm-30) REVERT: 2 141 GLU cc_start: 0.6337 (tm-30) cc_final: 0.5890 (tm-30) REVERT: 2 146 ARG cc_start: 0.7187 (ptm-80) cc_final: 0.6579 (ptm-80) REVERT: 2 150 GLN cc_start: 0.8008 (mt0) cc_final: 0.7693 (mt0) REVERT: 2 163 LYS cc_start: 0.8237 (mppt) cc_final: 0.7802 (mmtm) REVERT: 2 175 LYS cc_start: 0.8882 (ttmt) cc_final: 0.8608 (ttmm) REVERT: 2 211 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7380 (mp0) REVERT: 2 228 GLU cc_start: 0.7653 (tp30) cc_final: 0.7326 (tp30) REVERT: 2 242 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.7819 (tmm) REVERT: 2 309 GLU cc_start: 0.6929 (pm20) cc_final: 0.6555 (mp0) REVERT: 3 24 LYS cc_start: 0.8679 (tttt) cc_final: 0.8214 (ttpp) REVERT: 3 27 SER cc_start: 0.8884 (m) cc_final: 0.8437 (p) REVERT: 3 39 GLU cc_start: 0.7457 (mp0) cc_final: 0.6989 (mp0) REVERT: 3 46 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7674 (tpp) REVERT: 3 92 ASP cc_start: 0.7783 (t0) cc_final: 0.7496 (t0) REVERT: 3 96 GLU cc_start: 0.7390 (tm-30) cc_final: 0.7156 (tm-30) REVERT: 3 175 LYS cc_start: 0.8129 (ttmm) cc_final: 0.7703 (mtpp) REVERT: 3 181 ASN cc_start: 0.7678 (t0) cc_final: 0.7362 (t0) REVERT: 3 207 LYS cc_start: 0.8761 (tttt) cc_final: 0.8033 (ttmm) REVERT: 3 230 LEU cc_start: 0.7588 (tp) cc_final: 0.7060 (tp) REVERT: 3 232 LYS cc_start: 0.8096 (ttmm) cc_final: 0.7875 (ttmm) REVERT: 3 233 LYS cc_start: 0.7667 (mtpt) cc_final: 0.7434 (mtmm) REVERT: 3 247 ASN cc_start: 0.8644 (m-40) cc_final: 0.8383 (m-40) REVERT: 3 250 TYR cc_start: 0.8490 (t80) cc_final: 0.7906 (t80) REVERT: 3 255 GLU cc_start: 0.7962 (tp30) cc_final: 0.7514 (tp30) REVERT: 3 259 ASN cc_start: 0.7900 (OUTLIER) cc_final: 0.7336 (p0) REVERT: 3 268 ASP cc_start: 0.7499 (p0) cc_final: 0.7092 (p0) REVERT: 3 269 PHE cc_start: 0.7192 (OUTLIER) cc_final: 0.5518 (t80) REVERT: 3 282 ASN cc_start: 0.8043 (t0) cc_final: 0.7742 (t0) REVERT: 3 300 ARG cc_start: 0.8342 (ptp90) cc_final: 0.7997 (ptp90) REVERT: 4 19 THR cc_start: 0.8504 (p) cc_final: 0.8150 (p) REVERT: 4 23 ARG cc_start: 0.6977 (mtm180) cc_final: 0.6576 (mtm110) REVERT: 4 29 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7833 (mmp) REVERT: 4 46 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7399 (tpt) REVERT: 4 62 TYR cc_start: 0.8092 (t80) cc_final: 0.7682 (t80) REVERT: 4 63 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7318 (tp) REVERT: 4 83 GLU cc_start: 0.6764 (tt0) cc_final: 0.5938 (tt0) REVERT: 4 114 ARG cc_start: 0.7818 (ttp80) cc_final: 0.7381 (ptt90) REVERT: 4 118 ARG cc_start: 0.6845 (mtp180) cc_final: 0.6641 (mtp180) REVERT: 4 131 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.7892 (tp) REVERT: 4 133 ILE cc_start: 0.7840 (mt) cc_final: 0.7618 (mm) REVERT: 4 146 ARG cc_start: 0.6707 (ptm160) cc_final: 0.6314 (ptm160) REVERT: 4 154 TRP cc_start: 0.8012 (t60) cc_final: 0.7683 (t60) REVERT: 4 155 LEU cc_start: 0.8390 (mt) cc_final: 0.8097 (mm) REVERT: 4 171 MET cc_start: 0.8626 (mtp) cc_final: 0.8287 (mtp) REVERT: 4 187 ARG cc_start: 0.7713 (mtm-85) cc_final: 0.7387 (mtm-85) REVERT: 4 254 ILE cc_start: 0.7711 (pt) cc_final: 0.7219 (mm) REVERT: 4 255 GLU cc_start: 0.7278 (tp30) cc_final: 0.6933 (tt0) REVERT: 4 274 LYS cc_start: 0.7996 (mttt) cc_final: 0.7705 (mtmt) REVERT: 4 298 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.6866 (mpp) REVERT: 4 300 ARG cc_start: 0.7777 (mtm-85) cc_final: 0.7506 (mtm-85) REVERT: 5 55 LYS cc_start: 0.7017 (mtmm) cc_final: 0.6182 (mtmm) REVERT: 5 60 LYS cc_start: 0.7296 (mmmt) cc_final: 0.6924 (tppt) REVERT: 5 157 MET cc_start: 0.6941 (tmm) cc_final: 0.6646 (ppp) REVERT: 5 171 MET cc_start: 0.7650 (mtp) cc_final: 0.7070 (mtp) REVERT: 6 24 LYS cc_start: 0.8556 (ttpp) cc_final: 0.8255 (ttmm) REVERT: 6 30 ASP cc_start: 0.7374 (m-30) cc_final: 0.7134 (m-30) REVERT: 6 64 ASN cc_start: 0.7184 (m-40) cc_final: 0.6911 (m-40) REVERT: 6 80 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6997 (mt) REVERT: 6 96 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7584 (tm-30) REVERT: 6 107 LEU cc_start: 0.8348 (pt) cc_final: 0.7978 (tp) REVERT: 6 135 GLU cc_start: 0.6464 (mm-30) cc_final: 0.6023 (mm-30) REVERT: 6 149 THR cc_start: 0.8336 (p) cc_final: 0.7953 (p) REVERT: 6 150 GLN cc_start: 0.8378 (mt0) cc_final: 0.7951 (mt0) REVERT: 6 153 ASN cc_start: 0.7935 (m-40) cc_final: 0.7679 (m-40) REVERT: 6 162 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8054 (p) REVERT: 6 164 CYS cc_start: 0.7905 (t) cc_final: 0.7505 (p) REVERT: 6 175 LYS cc_start: 0.8366 (ttmt) cc_final: 0.7967 (ttmm) REVERT: 6 181 ASN cc_start: 0.8445 (t0) cc_final: 0.8208 (t0) REVERT: 6 189 SER cc_start: 0.8621 (p) cc_final: 0.8307 (t) REVERT: 6 192 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8688 (t) REVERT: 6 237 PHE cc_start: 0.8074 (t80) cc_final: 0.7693 (t80) REVERT: 6 243 ARG cc_start: 0.8197 (ttm-80) cc_final: 0.7707 (ttm-80) REVERT: 6 255 GLU cc_start: 0.7297 (tp30) cc_final: 0.6349 (mm-30) REVERT: 6 259 ASN cc_start: 0.7335 (OUTLIER) cc_final: 0.6707 (p0) REVERT: 6 262 GLU cc_start: 0.6409 (mp0) cc_final: 0.6100 (mp0) REVERT: 6 270 VAL cc_start: 0.8114 (p) cc_final: 0.7903 (m) REVERT: 7 39 GLU cc_start: 0.7687 (mp0) cc_final: 0.7155 (mp0) REVERT: 7 46 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7296 (tpp) REVERT: 7 61 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8037 (ttmm) REVERT: 7 99 VAL cc_start: 0.8884 (p) cc_final: 0.8571 (t) REVERT: 7 119 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7880 (tt) REVERT: 7 129 LYS cc_start: 0.8366 (mmmm) cc_final: 0.8001 (mttp) REVERT: 7 156 LYS cc_start: 0.8760 (ttpt) cc_final: 0.8403 (tttp) REVERT: 7 162 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8321 (p) REVERT: 7 228 GLU cc_start: 0.7029 (tm-30) cc_final: 0.6419 (tm-30) REVERT: 7 232 LYS cc_start: 0.8481 (ttmm) cc_final: 0.7805 (ttpp) REVERT: 7 286 ASN cc_start: 0.8572 (t0) cc_final: 0.8320 (t0) outliers start: 115 outliers final: 66 residues processed: 656 average time/residue: 0.1585 time to fit residues: 147.5018 Evaluate side-chains 669 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 580 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 1 residue 29 MET Chi-restraints excluded: chain 1 residue 31 ARG Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 1 residue 82 ILE Chi-restraints excluded: chain 1 residue 107 LEU Chi-restraints excluded: chain 1 residue 110 THR Chi-restraints excluded: chain 1 residue 117 LYS Chi-restraints excluded: chain 1 residue 119 LEU Chi-restraints excluded: chain 1 residue 142 GLU Chi-restraints excluded: chain 1 residue 147 VAL Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 1 residue 162 THR Chi-restraints excluded: chain 1 residue 176 VAL Chi-restraints excluded: chain 1 residue 215 LYS Chi-restraints excluded: chain 1 residue 217 LEU Chi-restraints excluded: chain 1 residue 269 PHE Chi-restraints excluded: chain 1 residue 279 ASP Chi-restraints excluded: chain 1 residue 309 GLU Chi-restraints excluded: chain 2 residue 22 VAL Chi-restraints excluded: chain 2 residue 45 MET Chi-restraints excluded: chain 2 residue 192 VAL Chi-restraints excluded: chain 2 residue 208 THR Chi-restraints excluded: chain 2 residue 213 LEU Chi-restraints excluded: chain 2 residue 242 MET Chi-restraints excluded: chain 2 residue 294 VAL Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 35 LEU Chi-restraints excluded: chain 3 residue 45 MET Chi-restraints excluded: chain 3 residue 46 MET Chi-restraints excluded: chain 3 residue 63 LEU Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 99 VAL Chi-restraints excluded: chain 3 residue 142 GLU Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 193 GLU Chi-restraints excluded: chain 3 residue 259 ASN Chi-restraints excluded: chain 3 residue 269 PHE Chi-restraints excluded: chain 3 residue 270 VAL Chi-restraints excluded: chain 3 residue 312 LEU Chi-restraints excluded: chain 4 residue 27 SER Chi-restraints excluded: chain 4 residue 29 MET Chi-restraints excluded: chain 4 residue 30 ASP Chi-restraints excluded: chain 4 residue 46 MET Chi-restraints excluded: chain 4 residue 60 LYS Chi-restraints excluded: chain 4 residue 63 LEU Chi-restraints excluded: chain 4 residue 110 THR Chi-restraints excluded: chain 4 residue 119 LEU Chi-restraints excluded: chain 4 residue 130 LEU Chi-restraints excluded: chain 4 residue 131 ILE Chi-restraints excluded: chain 4 residue 142 GLU Chi-restraints excluded: chain 4 residue 162 THR Chi-restraints excluded: chain 4 residue 211 GLU Chi-restraints excluded: chain 4 residue 269 PHE Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 279 ASP Chi-restraints excluded: chain 4 residue 298 MET Chi-restraints excluded: chain 5 residue 29 MET Chi-restraints excluded: chain 5 residue 46 MET Chi-restraints excluded: chain 5 residue 97 LEU Chi-restraints excluded: chain 5 residue 142 GLU Chi-restraints excluded: chain 5 residue 147 VAL Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 158 ILE Chi-restraints excluded: chain 5 residue 211 GLU Chi-restraints excluded: chain 5 residue 259 ASN Chi-restraints excluded: chain 5 residue 299 LEU Chi-restraints excluded: chain 6 residue 63 LEU Chi-restraints excluded: chain 6 residue 80 LEU Chi-restraints excluded: chain 6 residue 99 VAL Chi-restraints excluded: chain 6 residue 142 GLU Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 148 LEU Chi-restraints excluded: chain 6 residue 162 THR Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 6 residue 259 ASN Chi-restraints excluded: chain 6 residue 269 PHE Chi-restraints excluded: chain 6 residue 304 LYS Chi-restraints excluded: chain 7 residue 46 MET Chi-restraints excluded: chain 7 residue 53 VAL Chi-restraints excluded: chain 7 residue 61 LYS Chi-restraints excluded: chain 7 residue 117 LYS Chi-restraints excluded: chain 7 residue 119 LEU Chi-restraints excluded: chain 7 residue 142 GLU Chi-restraints excluded: chain 7 residue 146 ARG Chi-restraints excluded: chain 7 residue 148 LEU Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 214 ASP Chi-restraints excluded: chain 7 residue 309 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 94 optimal weight: 0.7980 chunk 154 optimal weight: 0.3980 chunk 32 optimal weight: 0.8980 chunk 220 optimal weight: 0.6980 chunk 209 optimal weight: 0.5980 chunk 197 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 chunk 198 optimal weight: 0.4980 chunk 72 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 64 ASN 1 87 ASN ** 1 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 282 ASN 4 247 ASN 7 247 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.168854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.134007 restraints weight = 26388.289| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.24 r_work: 0.3555 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18773 Z= 0.142 Angle : 0.668 13.938 25612 Z= 0.331 Chirality : 0.042 0.208 2863 Planarity : 0.004 0.044 3122 Dihedral : 14.930 86.935 2881 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 6.61 % Allowed : 26.76 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.19), residues: 2163 helix: 0.94 (0.15), residues: 1190 sheet: -2.00 (0.39), residues: 224 loop : -2.16 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 1 23 TYR 0.023 0.002 TYR 6 199 PHE 0.012 0.001 PHE 6 206 TRP 0.024 0.002 TRP 6 154 HIS 0.004 0.001 HIS 4 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (18772) covalent geometry : angle 0.66819 / 0.33 (25612) hydrogen bonds : bond 0.03181 / 3.52 ( 816) hydrogen bonds : angle 3.68747 / 4.32 ( 2372) Misc. bond : bond 0.00219 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 582 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 11 ARG cc_start: 0.8161 (mtp180) cc_final: 0.7784 (mtp85) REVERT: 1 22 VAL cc_start: 0.8031 (t) cc_final: 0.7827 (p) REVERT: 1 23 ARG cc_start: 0.8351 (mtm110) cc_final: 0.7830 (mtm-85) REVERT: 1 29 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8338 (mtm) REVERT: 1 31 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7507 (ttt90) REVERT: 1 37 ASP cc_start: 0.7993 (p0) cc_final: 0.7666 (p0) REVERT: 1 38 LEU cc_start: 0.8016 (mp) cc_final: 0.7741 (mt) REVERT: 1 39 GLU cc_start: 0.7188 (mp0) cc_final: 0.6692 (mp0) REVERT: 1 48 TYR cc_start: 0.8687 (m-80) cc_final: 0.8159 (m-80) REVERT: 1 60 LYS cc_start: 0.8481 (mmmt) cc_final: 0.8200 (mmtp) REVERT: 1 83 GLU cc_start: 0.7205 (tt0) cc_final: 0.6925 (mt-10) REVERT: 1 100 GLU cc_start: 0.7476 (tm-30) cc_final: 0.7089 (tm-30) REVERT: 1 101 MET cc_start: 0.7795 (ttp) cc_final: 0.7463 (ttp) REVERT: 1 129 LYS cc_start: 0.8458 (mtpt) cc_final: 0.8074 (mtpt) REVERT: 1 147 VAL cc_start: 0.8295 (OUTLIER) cc_final: 0.7995 (m) REVERT: 1 149 THR cc_start: 0.8584 (p) cc_final: 0.8256 (p) REVERT: 1 162 THR cc_start: 0.8253 (OUTLIER) cc_final: 0.8005 (t) REVERT: 1 163 LYS cc_start: 0.8226 (mptt) cc_final: 0.7986 (mmtt) REVERT: 1 228 GLU cc_start: 0.7625 (tm-30) cc_final: 0.7384 (tm-30) REVERT: 1 269 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7771 (m-80) REVERT: 1 274 LYS cc_start: 0.8661 (mttt) cc_final: 0.8374 (mtpp) REVERT: 1 279 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8138 (p0) REVERT: 1 285 LYS cc_start: 0.7622 (tppt) cc_final: 0.7337 (tppt) REVERT: 2 33 ARG cc_start: 0.8252 (ttp80) cc_final: 0.8022 (ttp-170) REVERT: 2 65 GLN cc_start: 0.7714 (pp30) cc_final: 0.7363 (pt0) REVERT: 2 116 THR cc_start: 0.7879 (m) cc_final: 0.7534 (p) REVERT: 2 122 LEU cc_start: 0.8553 (tp) cc_final: 0.8162 (tp) REVERT: 2 135 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7135 (mm-30) REVERT: 2 141 GLU cc_start: 0.6427 (tm-30) cc_final: 0.5902 (tm-30) REVERT: 2 146 ARG cc_start: 0.7190 (ptm-80) cc_final: 0.6529 (ptm-80) REVERT: 2 150 GLN cc_start: 0.7996 (mt0) cc_final: 0.7583 (mt0) REVERT: 2 163 LYS cc_start: 0.8205 (mppt) cc_final: 0.7826 (mmtm) REVERT: 2 175 LYS cc_start: 0.8896 (ttmt) cc_final: 0.8606 (ttmm) REVERT: 2 211 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7366 (mp0) REVERT: 2 228 GLU cc_start: 0.7624 (tp30) cc_final: 0.7307 (tp30) REVERT: 2 230 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7532 (tp) REVERT: 2 235 TYR cc_start: 0.8079 (t80) cc_final: 0.7353 (t80) REVERT: 2 242 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.7861 (tmm) REVERT: 2 300 ARG cc_start: 0.7820 (mtm-85) cc_final: 0.7558 (mtm-85) REVERT: 3 24 LYS cc_start: 0.8695 (tttt) cc_final: 0.8224 (ttpp) REVERT: 3 27 SER cc_start: 0.8821 (m) cc_final: 0.8358 (p) REVERT: 3 39 GLU cc_start: 0.7457 (mp0) cc_final: 0.6985 (mp0) REVERT: 3 46 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7760 (tpt) REVERT: 3 61 LYS cc_start: 0.8361 (tptt) cc_final: 0.8153 (tptp) REVERT: 3 92 ASP cc_start: 0.7783 (t0) cc_final: 0.7500 (t0) REVERT: 3 96 GLU cc_start: 0.7476 (tm-30) cc_final: 0.7200 (tm-30) REVERT: 3 175 LYS cc_start: 0.8210 (ttmm) cc_final: 0.7714 (mtpp) REVERT: 3 181 ASN cc_start: 0.7697 (t0) cc_final: 0.7386 (t0) REVERT: 3 207 LYS cc_start: 0.8813 (tttt) cc_final: 0.8089 (ttmm) REVERT: 3 232 LYS cc_start: 0.8134 (ttmm) cc_final: 0.7890 (ttmm) REVERT: 3 242 MET cc_start: 0.8267 (tpp) cc_final: 0.8004 (mmm) REVERT: 3 250 TYR cc_start: 0.8491 (t80) cc_final: 0.7955 (t80) REVERT: 3 255 GLU cc_start: 0.7933 (tp30) cc_final: 0.7649 (tp30) REVERT: 3 259 ASN cc_start: 0.8190 (OUTLIER) cc_final: 0.7485 (p0) REVERT: 3 268 ASP cc_start: 0.7553 (p0) cc_final: 0.7189 (p0) REVERT: 3 269 PHE cc_start: 0.7231 (OUTLIER) cc_final: 0.5521 (t80) REVERT: 3 282 ASN cc_start: 0.8072 (t0) cc_final: 0.7763 (t0) REVERT: 3 300 ARG cc_start: 0.8339 (ptp90) cc_final: 0.7861 (mtt-85) REVERT: 4 19 THR cc_start: 0.8491 (p) cc_final: 0.8132 (p) REVERT: 4 23 ARG cc_start: 0.7038 (mtm180) cc_final: 0.6685 (mtm110) REVERT: 4 29 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7777 (mmp) REVERT: 4 46 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.7411 (tpt) REVERT: 4 62 TYR cc_start: 0.8102 (t80) cc_final: 0.7702 (t80) REVERT: 4 63 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7331 (tp) REVERT: 4 83 GLU cc_start: 0.6770 (tt0) cc_final: 0.5950 (tt0) REVERT: 4 118 ARG cc_start: 0.6832 (mtp180) cc_final: 0.6626 (mtp180) REVERT: 4 131 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.7925 (tp) REVERT: 4 133 ILE cc_start: 0.7855 (mt) cc_final: 0.7618 (mm) REVERT: 4 154 TRP cc_start: 0.8027 (t60) cc_final: 0.7652 (t60) REVERT: 4 155 LEU cc_start: 0.8333 (mt) cc_final: 0.8069 (mm) REVERT: 4 178 LEU cc_start: 0.7160 (pp) cc_final: 0.6924 (tt) REVERT: 4 187 ARG cc_start: 0.7598 (mtm-85) cc_final: 0.7003 (mmm-85) REVERT: 4 254 ILE cc_start: 0.7702 (pt) cc_final: 0.7244 (mm) REVERT: 4 274 LYS cc_start: 0.8064 (mttt) cc_final: 0.7772 (mtmt) REVERT: 4 298 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6914 (mpp) REVERT: 4 300 ARG cc_start: 0.7889 (mtm-85) cc_final: 0.7667 (mtm-85) REVERT: 5 55 LYS cc_start: 0.7038 (mtmm) cc_final: 0.6198 (mtmm) REVERT: 5 60 LYS cc_start: 0.7072 (mmmt) cc_final: 0.6719 (tppt) REVERT: 5 137 GLN cc_start: 0.7992 (pm20) cc_final: 0.7158 (pm20) REVERT: 5 157 MET cc_start: 0.6954 (tmm) cc_final: 0.6680 (ppp) REVERT: 5 171 MET cc_start: 0.7759 (mtp) cc_final: 0.7180 (mtp) REVERT: 6 5 ARG cc_start: 0.6945 (tpp-160) cc_final: 0.6572 (tpm170) REVERT: 6 24 LYS cc_start: 0.8556 (ttpp) cc_final: 0.8248 (ttmm) REVERT: 6 30 ASP cc_start: 0.7405 (m-30) cc_final: 0.7156 (m-30) REVERT: 6 80 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6961 (mt) REVERT: 6 107 LEU cc_start: 0.8364 (pt) cc_final: 0.7836 (tp) REVERT: 6 135 GLU cc_start: 0.6428 (mm-30) cc_final: 0.5582 (mm-30) REVERT: 6 137 GLN cc_start: 0.7890 (pm20) cc_final: 0.7291 (pm20) REVERT: 6 149 THR cc_start: 0.8336 (p) cc_final: 0.7963 (p) REVERT: 6 150 GLN cc_start: 0.8380 (mt0) cc_final: 0.8022 (mt0) REVERT: 6 153 ASN cc_start: 0.7962 (m110) cc_final: 0.7725 (m-40) REVERT: 6 162 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.8178 (p) REVERT: 6 164 CYS cc_start: 0.7953 (t) cc_final: 0.7748 (m) REVERT: 6 175 LYS cc_start: 0.8396 (ttmt) cc_final: 0.8008 (ttmm) REVERT: 6 181 ASN cc_start: 0.8514 (t0) cc_final: 0.8280 (t0) REVERT: 6 189 SER cc_start: 0.8561 (p) cc_final: 0.8282 (m) REVERT: 6 192 VAL cc_start: 0.8981 (OUTLIER) cc_final: 0.8740 (t) REVERT: 6 237 PHE cc_start: 0.8179 (t80) cc_final: 0.7799 (t80) REVERT: 6 243 ARG cc_start: 0.8229 (ttm-80) cc_final: 0.7757 (ttm-80) REVERT: 6 255 GLU cc_start: 0.7312 (tp30) cc_final: 0.6697 (mm-30) REVERT: 6 259 ASN cc_start: 0.7311 (OUTLIER) cc_final: 0.6647 (p0) REVERT: 6 262 GLU cc_start: 0.6477 (mp0) cc_final: 0.6087 (mp0) REVERT: 6 266 GLU cc_start: 0.7005 (tp30) cc_final: 0.6248 (tp30) REVERT: 7 39 GLU cc_start: 0.7736 (mp0) cc_final: 0.7220 (mp0) REVERT: 7 46 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7454 (tpp) REVERT: 7 61 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7989 (ttmm) REVERT: 7 99 VAL cc_start: 0.8916 (p) cc_final: 0.8609 (t) REVERT: 7 119 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7902 (tt) REVERT: 7 129 LYS cc_start: 0.8339 (mmmm) cc_final: 0.7978 (mttm) REVERT: 7 156 LYS cc_start: 0.8784 (ttpt) cc_final: 0.8437 (tttp) REVERT: 7 162 THR cc_start: 0.8690 (OUTLIER) cc_final: 0.8310 (p) REVERT: 7 228 GLU cc_start: 0.7098 (tm-30) cc_final: 0.6500 (tm-30) REVERT: 7 232 LYS cc_start: 0.8493 (ttmm) cc_final: 0.7817 (ttpp) REVERT: 7 286 ASN cc_start: 0.8585 (t0) cc_final: 0.8344 (t0) outliers start: 124 outliers final: 72 residues processed: 649 average time/residue: 0.1699 time to fit residues: 157.1403 Evaluate side-chains 672 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 576 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 29 MET Chi-restraints excluded: chain 1 residue 31 ARG Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 82 ILE Chi-restraints excluded: chain 1 residue 107 LEU Chi-restraints excluded: chain 1 residue 110 THR Chi-restraints excluded: chain 1 residue 117 LYS Chi-restraints excluded: chain 1 residue 119 LEU Chi-restraints excluded: chain 1 residue 142 GLU Chi-restraints excluded: chain 1 residue 147 VAL Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 1 residue 162 THR Chi-restraints excluded: chain 1 residue 176 VAL Chi-restraints excluded: chain 1 residue 215 LYS Chi-restraints excluded: chain 1 residue 217 LEU Chi-restraints excluded: chain 1 residue 269 PHE Chi-restraints excluded: chain 1 residue 279 ASP Chi-restraints excluded: chain 1 residue 309 GLU Chi-restraints excluded: chain 2 residue 22 VAL Chi-restraints excluded: chain 2 residue 45 MET Chi-restraints excluded: chain 2 residue 101 MET Chi-restraints excluded: chain 2 residue 192 VAL Chi-restraints excluded: chain 2 residue 213 LEU Chi-restraints excluded: chain 2 residue 230 LEU Chi-restraints excluded: chain 2 residue 242 MET Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 35 LEU Chi-restraints excluded: chain 3 residue 45 MET Chi-restraints excluded: chain 3 residue 46 MET Chi-restraints excluded: chain 3 residue 63 LEU Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 99 VAL Chi-restraints excluded: chain 3 residue 115 LEU Chi-restraints excluded: chain 3 residue 142 GLU Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 193 GLU Chi-restraints excluded: chain 3 residue 259 ASN Chi-restraints excluded: chain 3 residue 269 PHE Chi-restraints excluded: chain 3 residue 270 VAL Chi-restraints excluded: chain 3 residue 312 LEU Chi-restraints excluded: chain 4 residue 27 SER Chi-restraints excluded: chain 4 residue 29 MET Chi-restraints excluded: chain 4 residue 30 ASP Chi-restraints excluded: chain 4 residue 46 MET Chi-restraints excluded: chain 4 residue 60 LYS Chi-restraints excluded: chain 4 residue 63 LEU Chi-restraints excluded: chain 4 residue 110 THR Chi-restraints excluded: chain 4 residue 119 LEU Chi-restraints excluded: chain 4 residue 130 LEU Chi-restraints excluded: chain 4 residue 131 ILE Chi-restraints excluded: chain 4 residue 142 GLU Chi-restraints excluded: chain 4 residue 162 THR Chi-restraints excluded: chain 4 residue 211 GLU Chi-restraints excluded: chain 4 residue 230 LEU Chi-restraints excluded: chain 4 residue 231 GLN Chi-restraints excluded: chain 4 residue 264 ILE Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 279 ASP Chi-restraints excluded: chain 4 residue 298 MET Chi-restraints excluded: chain 5 residue 29 MET Chi-restraints excluded: chain 5 residue 38 LEU Chi-restraints excluded: chain 5 residue 46 MET Chi-restraints excluded: chain 5 residue 97 LEU Chi-restraints excluded: chain 5 residue 142 GLU Chi-restraints excluded: chain 5 residue 147 VAL Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 211 GLU Chi-restraints excluded: chain 5 residue 299 LEU Chi-restraints excluded: chain 6 residue 63 LEU Chi-restraints excluded: chain 6 residue 80 LEU Chi-restraints excluded: chain 6 residue 115 LEU Chi-restraints excluded: chain 6 residue 118 ARG Chi-restraints excluded: chain 6 residue 142 GLU Chi-restraints excluded: chain 6 residue 143 ARG Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 148 LEU Chi-restraints excluded: chain 6 residue 162 THR Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 6 residue 259 ASN Chi-restraints excluded: chain 6 residue 269 PHE Chi-restraints excluded: chain 7 residue 46 MET Chi-restraints excluded: chain 7 residue 53 VAL Chi-restraints excluded: chain 7 residue 61 LYS Chi-restraints excluded: chain 7 residue 107 LEU Chi-restraints excluded: chain 7 residue 117 LYS Chi-restraints excluded: chain 7 residue 119 LEU Chi-restraints excluded: chain 7 residue 142 GLU Chi-restraints excluded: chain 7 residue 146 ARG Chi-restraints excluded: chain 7 residue 148 LEU Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 195 ARG Chi-restraints excluded: chain 7 residue 214 ASP Chi-restraints excluded: chain 7 residue 269 PHE Chi-restraints excluded: chain 7 residue 305 ASP Chi-restraints excluded: chain 7 residue 309 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 64 optimal weight: 0.0370 chunk 169 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 177 optimal weight: 1.9990 chunk 204 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 64 ASN 1 87 ASN ** 1 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 282 ASN 3 183 GLN 3 259 ASN 4 247 ASN 6 183 GLN 7 247 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.168520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.133416 restraints weight = 26357.719| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.26 r_work: 0.3547 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 18773 Z= 0.146 Angle : 0.685 13.727 25612 Z= 0.337 Chirality : 0.042 0.201 2863 Planarity : 0.004 0.045 3122 Dihedral : 14.855 87.169 2881 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 5.92 % Allowed : 28.04 % Favored : 66.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.19), residues: 2163 helix: 0.88 (0.15), residues: 1204 sheet: -1.93 (0.39), residues: 224 loop : -2.01 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 7 33 TYR 0.023 0.002 TYR 6 199 PHE 0.012 0.001 PHE 6 206 TRP 0.039 0.002 TRP 6 154 HIS 0.003 0.001 HIS 3 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (18772) covalent geometry : angle 0.68497 / 0.34 (25612) hydrogen bonds : bond 0.03186 / 3.53 ( 816) hydrogen bonds : angle 3.69396 / 4.32 ( 2372) Misc. bond : bond 0.00222 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 589 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 11 ARG cc_start: 0.8193 (mtp180) cc_final: 0.7813 (mtp85) REVERT: 1 22 VAL cc_start: 0.8082 (t) cc_final: 0.7839 (p) REVERT: 1 23 ARG cc_start: 0.8393 (mtm110) cc_final: 0.8141 (mtm110) REVERT: 1 29 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8280 (mtm) REVERT: 1 37 ASP cc_start: 0.8008 (p0) cc_final: 0.7698 (p0) REVERT: 1 38 LEU cc_start: 0.7988 (mp) cc_final: 0.7708 (mt) REVERT: 1 39 GLU cc_start: 0.7171 (mp0) cc_final: 0.6697 (mp0) REVERT: 1 48 TYR cc_start: 0.8694 (m-80) cc_final: 0.8132 (m-80) REVERT: 1 57 THR cc_start: 0.8343 (t) cc_final: 0.8002 (t) REVERT: 1 60 LYS cc_start: 0.8509 (mmmt) cc_final: 0.8192 (mttp) REVERT: 1 81 HIS cc_start: 0.8005 (t70) cc_final: 0.7802 (t70) REVERT: 1 83 GLU cc_start: 0.7266 (tt0) cc_final: 0.6988 (mt-10) REVERT: 1 100 GLU cc_start: 0.7454 (tm-30) cc_final: 0.7079 (tm-30) REVERT: 1 101 MET cc_start: 0.7779 (ttp) cc_final: 0.7460 (ttp) REVERT: 1 105 LEU cc_start: 0.7589 (pp) cc_final: 0.7313 (mp) REVERT: 1 129 LYS cc_start: 0.8463 (mtpt) cc_final: 0.8099 (mtpt) REVERT: 1 147 VAL cc_start: 0.8286 (OUTLIER) cc_final: 0.7986 (m) REVERT: 1 149 THR cc_start: 0.8594 (p) cc_final: 0.8273 (p) REVERT: 1 162 THR cc_start: 0.8231 (OUTLIER) cc_final: 0.7979 (t) REVERT: 1 163 LYS cc_start: 0.8217 (mptt) cc_final: 0.7971 (mmtt) REVERT: 1 228 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7400 (tm-30) REVERT: 1 269 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7764 (m-80) REVERT: 1 274 LYS cc_start: 0.8654 (mttt) cc_final: 0.8320 (mtpp) REVERT: 1 285 LYS cc_start: 0.7679 (tppt) cc_final: 0.7369 (tppt) REVERT: 2 33 ARG cc_start: 0.8265 (ttp80) cc_final: 0.8048 (ttp-170) REVERT: 2 40 SER cc_start: 0.8096 (m) cc_final: 0.7861 (t) REVERT: 2 65 GLN cc_start: 0.7693 (pp30) cc_final: 0.7359 (pt0) REVERT: 2 116 THR cc_start: 0.8073 (m) cc_final: 0.7677 (p) REVERT: 2 122 LEU cc_start: 0.8582 (tp) cc_final: 0.8178 (tp) REVERT: 2 135 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7120 (mm-30) REVERT: 2 141 GLU cc_start: 0.6512 (tm-30) cc_final: 0.6011 (tm-30) REVERT: 2 146 ARG cc_start: 0.7232 (ptm-80) cc_final: 0.6509 (ptm-80) REVERT: 2 150 GLN cc_start: 0.8049 (mt0) cc_final: 0.7617 (mt0) REVERT: 2 163 LYS cc_start: 0.8211 (mppt) cc_final: 0.7845 (mmtm) REVERT: 2 175 LYS cc_start: 0.8901 (ttmt) cc_final: 0.8604 (ttmm) REVERT: 2 211 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7373 (mp0) REVERT: 2 228 GLU cc_start: 0.7592 (tp30) cc_final: 0.7280 (tp30) REVERT: 2 230 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7518 (tp) REVERT: 2 235 TYR cc_start: 0.8129 (t80) cc_final: 0.7409 (t80) REVERT: 2 242 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.7798 (tmm) REVERT: 2 300 ARG cc_start: 0.7888 (mtm-85) cc_final: 0.7561 (mtm-85) REVERT: 2 312 LEU cc_start: 0.8123 (mt) cc_final: 0.7866 (mm) REVERT: 3 24 LYS cc_start: 0.8729 (tttt) cc_final: 0.8224 (ttpp) REVERT: 3 27 SER cc_start: 0.8801 (m) cc_final: 0.8346 (p) REVERT: 3 39 GLU cc_start: 0.7409 (mp0) cc_final: 0.6944 (mp0) REVERT: 3 46 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7846 (tpt) REVERT: 3 92 ASP cc_start: 0.7815 (t0) cc_final: 0.7487 (t0) REVERT: 3 96 GLU cc_start: 0.7473 (tm-30) cc_final: 0.7205 (tm-30) REVERT: 3 175 LYS cc_start: 0.8176 (ttmm) cc_final: 0.7707 (mtpp) REVERT: 3 181 ASN cc_start: 0.7710 (t0) cc_final: 0.7405 (t0) REVERT: 3 207 LYS cc_start: 0.8807 (tttt) cc_final: 0.8108 (ttmm) REVERT: 3 232 LYS cc_start: 0.8200 (ttmm) cc_final: 0.7945 (ttmm) REVERT: 3 250 TYR cc_start: 0.8487 (t80) cc_final: 0.7946 (t80) REVERT: 3 255 GLU cc_start: 0.7923 (tp30) cc_final: 0.7541 (tp30) REVERT: 3 259 ASN cc_start: 0.7943 (OUTLIER) cc_final: 0.7519 (p0) REVERT: 3 268 ASP cc_start: 0.7578 (p0) cc_final: 0.7177 (p0) REVERT: 3 269 PHE cc_start: 0.7263 (OUTLIER) cc_final: 0.5558 (t80) REVERT: 3 282 ASN cc_start: 0.8030 (t0) cc_final: 0.7750 (t0) REVERT: 4 19 THR cc_start: 0.8543 (p) cc_final: 0.8182 (p) REVERT: 4 23 ARG cc_start: 0.7031 (mtm180) cc_final: 0.6691 (mtm110) REVERT: 4 29 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7829 (mmp) REVERT: 4 46 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7402 (tpt) REVERT: 4 62 TYR cc_start: 0.8092 (t80) cc_final: 0.7706 (t80) REVERT: 4 63 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7342 (tp) REVERT: 4 83 GLU cc_start: 0.6755 (tt0) cc_final: 0.5934 (tt0) REVERT: 4 96 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6685 (tp30) REVERT: 4 118 ARG cc_start: 0.7021 (mtp180) cc_final: 0.6808 (mtp180) REVERT: 4 131 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.7937 (tp) REVERT: 4 133 ILE cc_start: 0.7850 (mt) cc_final: 0.7588 (mm) REVERT: 4 146 ARG cc_start: 0.6656 (ptm160) cc_final: 0.6101 (ptm160) REVERT: 4 154 TRP cc_start: 0.8027 (t60) cc_final: 0.7698 (t60) REVERT: 4 155 LEU cc_start: 0.8352 (mt) cc_final: 0.8096 (mm) REVERT: 4 178 LEU cc_start: 0.7152 (pp) cc_final: 0.6937 (tt) REVERT: 4 187 ARG cc_start: 0.7540 (mtm-85) cc_final: 0.7018 (mmm-85) REVERT: 4 254 ILE cc_start: 0.7698 (pt) cc_final: 0.7229 (mm) REVERT: 4 255 GLU cc_start: 0.7348 (tp30) cc_final: 0.7045 (tt0) REVERT: 4 298 MET cc_start: 0.7417 (OUTLIER) cc_final: 0.6978 (mpp) REVERT: 5 55 LYS cc_start: 0.6989 (mtmm) cc_final: 0.6180 (mtmm) REVERT: 5 60 LYS cc_start: 0.7261 (mmmt) cc_final: 0.6646 (tppt) REVERT: 5 81 HIS cc_start: 0.5778 (t70) cc_final: 0.5571 (t-170) REVERT: 5 82 ILE cc_start: 0.5839 (mp) cc_final: 0.5531 (mp) REVERT: 5 137 GLN cc_start: 0.8007 (pm20) cc_final: 0.7201 (pm20) REVERT: 5 171 MET cc_start: 0.7760 (mtp) cc_final: 0.7198 (mtp) REVERT: 5 241 ASN cc_start: 0.7255 (t0) cc_final: 0.6668 (t0) REVERT: 6 5 ARG cc_start: 0.6982 (tpp-160) cc_final: 0.6646 (tpm170) REVERT: 6 24 LYS cc_start: 0.8580 (ttpp) cc_final: 0.8272 (ttmm) REVERT: 6 30 ASP cc_start: 0.7423 (m-30) cc_final: 0.7174 (m-30) REVERT: 6 107 LEU cc_start: 0.8399 (pt) cc_final: 0.7906 (tp) REVERT: 6 135 GLU cc_start: 0.6506 (mm-30) cc_final: 0.5787 (mm-30) REVERT: 6 137 GLN cc_start: 0.7914 (pm20) cc_final: 0.7406 (pm20) REVERT: 6 149 THR cc_start: 0.8360 (p) cc_final: 0.8010 (p) REVERT: 6 150 GLN cc_start: 0.8409 (mt0) cc_final: 0.8065 (mt0) REVERT: 6 153 ASN cc_start: 0.7937 (m110) cc_final: 0.7709 (m-40) REVERT: 6 162 THR cc_start: 0.8404 (OUTLIER) cc_final: 0.8133 (p) REVERT: 6 175 LYS cc_start: 0.8360 (ttmt) cc_final: 0.8026 (ttmm) REVERT: 6 181 ASN cc_start: 0.8534 (t0) cc_final: 0.8296 (t0) REVERT: 6 185 HIS cc_start: 0.8154 (t70) cc_final: 0.7835 (t70) REVERT: 6 189 SER cc_start: 0.8543 (p) cc_final: 0.8277 (m) REVERT: 6 192 VAL cc_start: 0.8984 (OUTLIER) cc_final: 0.8761 (t) REVERT: 6 237 PHE cc_start: 0.8169 (t80) cc_final: 0.7784 (t80) REVERT: 6 243 ARG cc_start: 0.8198 (ttm-80) cc_final: 0.7732 (ttm-80) REVERT: 6 255 GLU cc_start: 0.7305 (tp30) cc_final: 0.6661 (mm-30) REVERT: 6 259 ASN cc_start: 0.7302 (OUTLIER) cc_final: 0.6660 (p0) REVERT: 6 262 GLU cc_start: 0.6390 (mp0) cc_final: 0.6152 (mp0) REVERT: 6 266 GLU cc_start: 0.7056 (tp30) cc_final: 0.6370 (tp30) REVERT: 7 37 ASP cc_start: 0.7597 (p0) cc_final: 0.6009 (p0) REVERT: 7 39 GLU cc_start: 0.7755 (mp0) cc_final: 0.6897 (mp0) REVERT: 7 46 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7392 (tpp) REVERT: 7 61 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7964 (ttmm) REVERT: 7 99 VAL cc_start: 0.8940 (p) cc_final: 0.8635 (t) REVERT: 7 119 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7889 (tt) REVERT: 7 129 LYS cc_start: 0.8340 (mmmm) cc_final: 0.7971 (mttm) REVERT: 7 156 LYS cc_start: 0.8776 (ttpt) cc_final: 0.8440 (tttp) REVERT: 7 162 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8443 (p) REVERT: 7 228 GLU cc_start: 0.7143 (tm-30) cc_final: 0.6546 (tm-30) REVERT: 7 232 LYS cc_start: 0.8460 (ttmm) cc_final: 0.7792 (ttpp) REVERT: 7 286 ASN cc_start: 0.8554 (t0) cc_final: 0.8316 (t0) outliers start: 111 outliers final: 74 residues processed: 642 average time/residue: 0.1614 time to fit residues: 148.0050 Evaluate side-chains 679 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 583 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 1 residue 29 MET Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 82 ILE Chi-restraints excluded: chain 1 residue 107 LEU Chi-restraints excluded: chain 1 residue 110 THR Chi-restraints excluded: chain 1 residue 117 LYS Chi-restraints excluded: chain 1 residue 119 LEU Chi-restraints excluded: chain 1 residue 142 GLU Chi-restraints excluded: chain 1 residue 147 VAL Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 1 residue 162 THR Chi-restraints excluded: chain 1 residue 176 VAL Chi-restraints excluded: chain 1 residue 215 LYS Chi-restraints excluded: chain 1 residue 217 LEU Chi-restraints excluded: chain 1 residue 269 PHE Chi-restraints excluded: chain 1 residue 279 ASP Chi-restraints excluded: chain 1 residue 309 GLU Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 22 VAL Chi-restraints excluded: chain 2 residue 45 MET Chi-restraints excluded: chain 2 residue 101 MET Chi-restraints excluded: chain 2 residue 192 VAL Chi-restraints excluded: chain 2 residue 208 THR Chi-restraints excluded: chain 2 residue 213 LEU Chi-restraints excluded: chain 2 residue 230 LEU Chi-restraints excluded: chain 2 residue 242 MET Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 19 THR Chi-restraints excluded: chain 3 residue 35 LEU Chi-restraints excluded: chain 3 residue 46 MET Chi-restraints excluded: chain 3 residue 63 LEU Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 115 LEU Chi-restraints excluded: chain 3 residue 142 GLU Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 193 GLU Chi-restraints excluded: chain 3 residue 259 ASN Chi-restraints excluded: chain 3 residue 269 PHE Chi-restraints excluded: chain 3 residue 270 VAL Chi-restraints excluded: chain 4 residue 25 ILE Chi-restraints excluded: chain 4 residue 27 SER Chi-restraints excluded: chain 4 residue 29 MET Chi-restraints excluded: chain 4 residue 30 ASP Chi-restraints excluded: chain 4 residue 46 MET Chi-restraints excluded: chain 4 residue 60 LYS Chi-restraints excluded: chain 4 residue 63 LEU Chi-restraints excluded: chain 4 residue 96 GLU Chi-restraints excluded: chain 4 residue 110 THR Chi-restraints excluded: chain 4 residue 119 LEU Chi-restraints excluded: chain 4 residue 130 LEU Chi-restraints excluded: chain 4 residue 131 ILE Chi-restraints excluded: chain 4 residue 142 GLU Chi-restraints excluded: chain 4 residue 162 THR Chi-restraints excluded: chain 4 residue 230 LEU Chi-restraints excluded: chain 4 residue 231 GLN Chi-restraints excluded: chain 4 residue 264 ILE Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 279 ASP Chi-restraints excluded: chain 4 residue 298 MET Chi-restraints excluded: chain 5 residue 29 MET Chi-restraints excluded: chain 5 residue 38 LEU Chi-restraints excluded: chain 5 residue 46 MET Chi-restraints excluded: chain 5 residue 97 LEU Chi-restraints excluded: chain 5 residue 142 GLU Chi-restraints excluded: chain 5 residue 147 VAL Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 178 LEU Chi-restraints excluded: chain 5 residue 183 GLN Chi-restraints excluded: chain 5 residue 259 ASN Chi-restraints excluded: chain 5 residue 299 LEU Chi-restraints excluded: chain 6 residue 63 LEU Chi-restraints excluded: chain 6 residue 115 LEU Chi-restraints excluded: chain 6 residue 118 ARG Chi-restraints excluded: chain 6 residue 142 GLU Chi-restraints excluded: chain 6 residue 143 ARG Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 148 LEU Chi-restraints excluded: chain 6 residue 162 THR Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 6 residue 259 ASN Chi-restraints excluded: chain 6 residue 269 PHE Chi-restraints excluded: chain 7 residue 46 MET Chi-restraints excluded: chain 7 residue 61 LYS Chi-restraints excluded: chain 7 residue 107 LEU Chi-restraints excluded: chain 7 residue 117 LYS Chi-restraints excluded: chain 7 residue 119 LEU Chi-restraints excluded: chain 7 residue 142 GLU Chi-restraints excluded: chain 7 residue 146 ARG Chi-restraints excluded: chain 7 residue 148 LEU Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 195 ARG Chi-restraints excluded: chain 7 residue 214 ASP Chi-restraints excluded: chain 7 residue 269 PHE Chi-restraints excluded: chain 7 residue 309 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 184 optimal weight: 0.1980 chunk 103 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 206 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 64 ASN 1 87 ASN ** 1 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 282 ASN ** 3 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 247 ASN 7 247 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.167986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.132814 restraints weight = 26247.690| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.25 r_work: 0.3534 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18773 Z= 0.147 Angle : 0.686 13.342 25612 Z= 0.339 Chirality : 0.042 0.196 2863 Planarity : 0.004 0.044 3122 Dihedral : 14.744 86.883 2875 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 5.76 % Allowed : 28.68 % Favored : 65.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.19), residues: 2163 helix: 0.88 (0.15), residues: 1204 sheet: -1.89 (0.39), residues: 224 loop : -1.96 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 7 33 TYR 0.023 0.002 TYR 6 199 PHE 0.017 0.002 PHE 4 206 TRP 0.039 0.002 TRP 6 154 HIS 0.003 0.001 HIS 1 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (18772) covalent geometry : angle 0.68631 / 0.34 (25612) hydrogen bonds : bond 0.03206 / 3.57 ( 816) hydrogen bonds : angle 3.67598 / 4.30 ( 2372) Misc. bond : bond 0.00206 / 0.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 581 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 22 VAL cc_start: 0.8088 (t) cc_final: 0.7828 (p) REVERT: 1 23 ARG cc_start: 0.8406 (mtm110) cc_final: 0.8134 (mtm110) REVERT: 1 37 ASP cc_start: 0.8095 (p0) cc_final: 0.7738 (p0) REVERT: 1 38 LEU cc_start: 0.7955 (mp) cc_final: 0.7686 (mp) REVERT: 1 39 GLU cc_start: 0.7127 (mp0) cc_final: 0.6669 (mp0) REVERT: 1 48 TYR cc_start: 0.8704 (m-80) cc_final: 0.8126 (m-80) REVERT: 1 57 THR cc_start: 0.8259 (t) cc_final: 0.7886 (t) REVERT: 1 60 LYS cc_start: 0.8496 (mmmt) cc_final: 0.8177 (mttp) REVERT: 1 81 HIS cc_start: 0.8025 (t70) cc_final: 0.7815 (t70) REVERT: 1 83 GLU cc_start: 0.7372 (tt0) cc_final: 0.7077 (mt-10) REVERT: 1 100 GLU cc_start: 0.7460 (tm-30) cc_final: 0.7103 (tm-30) REVERT: 1 101 MET cc_start: 0.7771 (ttp) cc_final: 0.7480 (ttp) REVERT: 1 105 LEU cc_start: 0.7622 (pp) cc_final: 0.7312 (mp) REVERT: 1 129 LYS cc_start: 0.8504 (mtpt) cc_final: 0.8137 (mtpt) REVERT: 1 147 VAL cc_start: 0.8230 (OUTLIER) cc_final: 0.7939 (m) REVERT: 1 149 THR cc_start: 0.8585 (p) cc_final: 0.8254 (p) REVERT: 1 162 THR cc_start: 0.8213 (OUTLIER) cc_final: 0.7992 (t) REVERT: 1 228 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7370 (tm-30) REVERT: 1 269 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7776 (m-80) REVERT: 1 274 LYS cc_start: 0.8630 (mttt) cc_final: 0.8318 (mtpp) REVERT: 1 285 LYS cc_start: 0.7697 (tppt) cc_final: 0.7384 (tppt) REVERT: 2 33 ARG cc_start: 0.8271 (ttp80) cc_final: 0.8048 (ttp-170) REVERT: 2 65 GLN cc_start: 0.7666 (pp30) cc_final: 0.7343 (pt0) REVERT: 2 116 THR cc_start: 0.8107 (m) cc_final: 0.7674 (p) REVERT: 2 122 LEU cc_start: 0.8576 (tp) cc_final: 0.8144 (tp) REVERT: 2 135 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7138 (mm-30) REVERT: 2 141 GLU cc_start: 0.6554 (tm-30) cc_final: 0.5977 (tm-30) REVERT: 2 146 ARG cc_start: 0.7260 (ptm-80) cc_final: 0.6525 (ptm-80) REVERT: 2 150 GLN cc_start: 0.8064 (mt0) cc_final: 0.7728 (mt0) REVERT: 2 163 LYS cc_start: 0.8214 (mppt) cc_final: 0.7837 (mmtm) REVERT: 2 175 LYS cc_start: 0.8921 (ttmt) cc_final: 0.8624 (ttmm) REVERT: 2 211 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7359 (mp0) REVERT: 2 230 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7514 (tp) REVERT: 2 235 TYR cc_start: 0.8129 (t80) cc_final: 0.7756 (t80) REVERT: 2 242 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.7781 (tmm) REVERT: 2 300 ARG cc_start: 0.7899 (mtm-85) cc_final: 0.7581 (mtm-85) REVERT: 2 312 LEU cc_start: 0.8137 (mt) cc_final: 0.7866 (mm) REVERT: 3 24 LYS cc_start: 0.8747 (tttt) cc_final: 0.8243 (ttpp) REVERT: 3 27 SER cc_start: 0.8850 (m) cc_final: 0.8413 (p) REVERT: 3 39 GLU cc_start: 0.7381 (mp0) cc_final: 0.6965 (mp0) REVERT: 3 46 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7859 (tpt) REVERT: 3 92 ASP cc_start: 0.7813 (t0) cc_final: 0.7488 (t0) REVERT: 3 96 GLU cc_start: 0.7451 (tm-30) cc_final: 0.7205 (tm-30) REVERT: 3 175 LYS cc_start: 0.8143 (ttmm) cc_final: 0.7672 (mtpp) REVERT: 3 181 ASN cc_start: 0.7706 (t0) cc_final: 0.7386 (t0) REVERT: 3 207 LYS cc_start: 0.8795 (tttt) cc_final: 0.8086 (ttmm) REVERT: 3 232 LYS cc_start: 0.8221 (ttmm) cc_final: 0.7950 (ttmm) REVERT: 3 250 TYR cc_start: 0.8464 (t80) cc_final: 0.7929 (t80) REVERT: 3 255 GLU cc_start: 0.8054 (tp30) cc_final: 0.7706 (tp30) REVERT: 3 268 ASP cc_start: 0.7608 (p0) cc_final: 0.7210 (p0) REVERT: 3 269 PHE cc_start: 0.7250 (OUTLIER) cc_final: 0.5496 (t80) REVERT: 4 19 THR cc_start: 0.8547 (p) cc_final: 0.8269 (p) REVERT: 4 29 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7804 (mmp) REVERT: 4 46 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7305 (tpt) REVERT: 4 62 TYR cc_start: 0.8131 (t80) cc_final: 0.7756 (t80) REVERT: 4 63 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7347 (tp) REVERT: 4 83 GLU cc_start: 0.6767 (tt0) cc_final: 0.5895 (tt0) REVERT: 4 96 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6752 (tp30) REVERT: 4 118 ARG cc_start: 0.6987 (mtp180) cc_final: 0.6754 (mtp180) REVERT: 4 131 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.7943 (tp) REVERT: 4 133 ILE cc_start: 0.7869 (mt) cc_final: 0.7595 (mm) REVERT: 4 146 ARG cc_start: 0.6700 (ptm160) cc_final: 0.6130 (ptm160) REVERT: 4 154 TRP cc_start: 0.8047 (t60) cc_final: 0.7685 (t60) REVERT: 4 155 LEU cc_start: 0.8393 (mt) cc_final: 0.8138 (mm) REVERT: 4 254 ILE cc_start: 0.7711 (pt) cc_final: 0.7236 (mm) REVERT: 4 255 GLU cc_start: 0.7372 (tp30) cc_final: 0.7061 (tt0) REVERT: 4 298 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.7006 (mpp) REVERT: 5 82 ILE cc_start: 0.5961 (mp) cc_final: 0.5684 (mp) REVERT: 5 137 GLN cc_start: 0.7984 (pm20) cc_final: 0.7183 (pm20) REVERT: 5 171 MET cc_start: 0.7773 (mtp) cc_final: 0.7204 (mtp) REVERT: 5 182 SER cc_start: 0.7892 (t) cc_final: 0.7471 (m) REVERT: 5 241 ASN cc_start: 0.7225 (t0) cc_final: 0.6634 (t0) REVERT: 6 5 ARG cc_start: 0.6976 (tpp-160) cc_final: 0.6674 (tpm170) REVERT: 6 24 LYS cc_start: 0.8562 (ttpp) cc_final: 0.8262 (ttmm) REVERT: 6 30 ASP cc_start: 0.7412 (m-30) cc_final: 0.7155 (m-30) REVERT: 6 80 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.7030 (mt) REVERT: 6 107 LEU cc_start: 0.8406 (pt) cc_final: 0.7917 (tp) REVERT: 6 135 GLU cc_start: 0.6511 (mm-30) cc_final: 0.5794 (mm-30) REVERT: 6 137 GLN cc_start: 0.7933 (pm20) cc_final: 0.7398 (pm20) REVERT: 6 149 THR cc_start: 0.8376 (p) cc_final: 0.8031 (p) REVERT: 6 150 GLN cc_start: 0.8413 (mt0) cc_final: 0.8199 (mt0) REVERT: 6 153 ASN cc_start: 0.7938 (m110) cc_final: 0.7726 (m-40) REVERT: 6 162 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.8098 (p) REVERT: 6 175 LYS cc_start: 0.8362 (ttmt) cc_final: 0.8033 (ttmm) REVERT: 6 181 ASN cc_start: 0.8558 (t0) cc_final: 0.8320 (t0) REVERT: 6 185 HIS cc_start: 0.8162 (t70) cc_final: 0.7813 (t70) REVERT: 6 192 VAL cc_start: 0.8983 (OUTLIER) cc_final: 0.8782 (t) REVERT: 6 237 PHE cc_start: 0.8188 (t80) cc_final: 0.7805 (t80) REVERT: 6 243 ARG cc_start: 0.8183 (ttm-80) cc_final: 0.7726 (ttm-80) REVERT: 6 255 GLU cc_start: 0.7301 (tp30) cc_final: 0.6327 (mm-30) REVERT: 6 259 ASN cc_start: 0.7199 (OUTLIER) cc_final: 0.6827 (p0) REVERT: 6 262 GLU cc_start: 0.6396 (mp0) cc_final: 0.6160 (mp0) REVERT: 6 266 GLU cc_start: 0.7387 (tp30) cc_final: 0.6912 (tp30) REVERT: 7 39 GLU cc_start: 0.7781 (mp0) cc_final: 0.7265 (mp0) REVERT: 7 46 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7411 (tpp) REVERT: 7 61 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7974 (ttmm) REVERT: 7 99 VAL cc_start: 0.8967 (p) cc_final: 0.8672 (t) REVERT: 7 119 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7890 (tt) REVERT: 7 129 LYS cc_start: 0.8326 (mmmm) cc_final: 0.7974 (mttm) REVERT: 7 156 LYS cc_start: 0.8773 (ttpt) cc_final: 0.8418 (tttp) REVERT: 7 162 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8397 (p) REVERT: 7 228 GLU cc_start: 0.7141 (tm-30) cc_final: 0.6539 (tm-30) REVERT: 7 232 LYS cc_start: 0.8454 (ttmm) cc_final: 0.7775 (ttpp) REVERT: 7 255 GLU cc_start: 0.7534 (tp30) cc_final: 0.7030 (tp30) REVERT: 7 271 PHE cc_start: 0.8252 (t80) cc_final: 0.7980 (t80) REVERT: 7 286 ASN cc_start: 0.8540 (t0) cc_final: 0.8310 (t0) outliers start: 108 outliers final: 73 residues processed: 637 average time/residue: 0.1562 time to fit residues: 141.6872 Evaluate side-chains 672 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 578 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 1 residue 29 MET Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 82 ILE Chi-restraints excluded: chain 1 residue 107 LEU Chi-restraints excluded: chain 1 residue 110 THR Chi-restraints excluded: chain 1 residue 119 LEU Chi-restraints excluded: chain 1 residue 142 GLU Chi-restraints excluded: chain 1 residue 147 VAL Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 1 residue 162 THR Chi-restraints excluded: chain 1 residue 176 VAL Chi-restraints excluded: chain 1 residue 217 LEU Chi-restraints excluded: chain 1 residue 269 PHE Chi-restraints excluded: chain 1 residue 279 ASP Chi-restraints excluded: chain 1 residue 309 GLU Chi-restraints excluded: chain 1 residue 310 ASP Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 22 VAL Chi-restraints excluded: chain 2 residue 45 MET Chi-restraints excluded: chain 2 residue 101 MET Chi-restraints excluded: chain 2 residue 192 VAL Chi-restraints excluded: chain 2 residue 208 THR Chi-restraints excluded: chain 2 residue 213 LEU Chi-restraints excluded: chain 2 residue 230 LEU Chi-restraints excluded: chain 2 residue 242 MET Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 19 THR Chi-restraints excluded: chain 3 residue 35 LEU Chi-restraints excluded: chain 3 residue 46 MET Chi-restraints excluded: chain 3 residue 63 LEU Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 115 LEU Chi-restraints excluded: chain 3 residue 142 GLU Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 193 GLU Chi-restraints excluded: chain 3 residue 269 PHE Chi-restraints excluded: chain 3 residue 270 VAL Chi-restraints excluded: chain 3 residue 312 LEU Chi-restraints excluded: chain 4 residue 27 SER Chi-restraints excluded: chain 4 residue 29 MET Chi-restraints excluded: chain 4 residue 30 ASP Chi-restraints excluded: chain 4 residue 46 MET Chi-restraints excluded: chain 4 residue 60 LYS Chi-restraints excluded: chain 4 residue 63 LEU Chi-restraints excluded: chain 4 residue 96 GLU Chi-restraints excluded: chain 4 residue 110 THR Chi-restraints excluded: chain 4 residue 119 LEU Chi-restraints excluded: chain 4 residue 130 LEU Chi-restraints excluded: chain 4 residue 131 ILE Chi-restraints excluded: chain 4 residue 142 GLU Chi-restraints excluded: chain 4 residue 231 GLN Chi-restraints excluded: chain 4 residue 264 ILE Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 279 ASP Chi-restraints excluded: chain 4 residue 298 MET Chi-restraints excluded: chain 5 residue 29 MET Chi-restraints excluded: chain 5 residue 38 LEU Chi-restraints excluded: chain 5 residue 46 MET Chi-restraints excluded: chain 5 residue 97 LEU Chi-restraints excluded: chain 5 residue 142 GLU Chi-restraints excluded: chain 5 residue 147 VAL Chi-restraints excluded: chain 5 residue 158 ILE Chi-restraints excluded: chain 5 residue 178 LEU Chi-restraints excluded: chain 5 residue 183 GLN Chi-restraints excluded: chain 5 residue 259 ASN Chi-restraints excluded: chain 5 residue 299 LEU Chi-restraints excluded: chain 6 residue 63 LEU Chi-restraints excluded: chain 6 residue 80 LEU Chi-restraints excluded: chain 6 residue 115 LEU Chi-restraints excluded: chain 6 residue 118 ARG Chi-restraints excluded: chain 6 residue 142 GLU Chi-restraints excluded: chain 6 residue 143 ARG Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 148 LEU Chi-restraints excluded: chain 6 residue 162 THR Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 6 residue 259 ASN Chi-restraints excluded: chain 6 residue 269 PHE Chi-restraints excluded: chain 7 residue 46 MET Chi-restraints excluded: chain 7 residue 53 VAL Chi-restraints excluded: chain 7 residue 61 LYS Chi-restraints excluded: chain 7 residue 107 LEU Chi-restraints excluded: chain 7 residue 117 LYS Chi-restraints excluded: chain 7 residue 119 LEU Chi-restraints excluded: chain 7 residue 142 GLU Chi-restraints excluded: chain 7 residue 146 ARG Chi-restraints excluded: chain 7 residue 148 LEU Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 195 ARG Chi-restraints excluded: chain 7 residue 214 ASP Chi-restraints excluded: chain 7 residue 269 PHE Chi-restraints excluded: chain 7 residue 309 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 119 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 129 optimal weight: 7.9990 chunk 56 optimal weight: 0.4980 chunk 128 optimal weight: 0.7980 chunk 147 optimal weight: 0.9980 chunk 162 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 172 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 64 ASN 1 87 ASN ** 1 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 282 ASN ** 3 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 81 HIS 7 247 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.166201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.131470 restraints weight = 26416.004| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.15 r_work: 0.3534 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18773 Z= 0.169 Angle : 0.711 13.613 25612 Z= 0.350 Chirality : 0.043 0.246 2863 Planarity : 0.004 0.047 3122 Dihedral : 14.669 87.903 2875 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 5.01 % Allowed : 29.53 % Favored : 65.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.19), residues: 2163 helix: 0.82 (0.15), residues: 1204 sheet: -1.91 (0.38), residues: 224 loop : -1.95 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 7 33 TYR 0.022 0.002 TYR 6 199 PHE 0.012 0.002 PHE 6 269 TRP 0.041 0.002 TRP 6 154 HIS 0.006 0.001 HIS 1 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (18772) covalent geometry : angle 0.71147 / 0.35 (25612) hydrogen bonds : bond 0.03324 / 3.69 ( 816) hydrogen bonds : angle 3.72526 / 4.37 ( 2372) Misc. bond : bond 0.00227 / 0.11 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 585 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 22 VAL cc_start: 0.8155 (t) cc_final: 0.7932 (p) REVERT: 1 23 ARG cc_start: 0.8314 (mtm110) cc_final: 0.7727 (mtm110) REVERT: 1 37 ASP cc_start: 0.8101 (p0) cc_final: 0.7132 (p0) REVERT: 1 38 LEU cc_start: 0.7970 (mp) cc_final: 0.7602 (mp) REVERT: 1 39 GLU cc_start: 0.7129 (mp0) cc_final: 0.6086 (mp0) REVERT: 1 48 TYR cc_start: 0.8617 (m-80) cc_final: 0.8029 (m-80) REVERT: 1 60 LYS cc_start: 0.8533 (mmmt) cc_final: 0.8316 (mmtp) REVERT: 1 81 HIS cc_start: 0.7997 (t70) cc_final: 0.7769 (t70) REVERT: 1 83 GLU cc_start: 0.7282 (tt0) cc_final: 0.6977 (mt-10) REVERT: 1 100 GLU cc_start: 0.7304 (tm-30) cc_final: 0.6963 (tm-30) REVERT: 1 101 MET cc_start: 0.7679 (ttp) cc_final: 0.7394 (ttp) REVERT: 1 105 LEU cc_start: 0.7694 (pp) cc_final: 0.7382 (mp) REVERT: 1 129 LYS cc_start: 0.8532 (mtpt) cc_final: 0.8146 (mtpt) REVERT: 1 147 VAL cc_start: 0.8314 (OUTLIER) cc_final: 0.8010 (m) REVERT: 1 149 THR cc_start: 0.8628 (p) cc_final: 0.8293 (p) REVERT: 1 162 THR cc_start: 0.8225 (OUTLIER) cc_final: 0.7885 (t) REVERT: 1 166 ILE cc_start: 0.8240 (mt) cc_final: 0.7886 (tt) REVERT: 1 228 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7388 (tm-30) REVERT: 1 269 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7822 (m-80) REVERT: 1 274 LYS cc_start: 0.8622 (mttt) cc_final: 0.8289 (mtpp) REVERT: 1 285 LYS cc_start: 0.7825 (tppt) cc_final: 0.7505 (tppt) REVERT: 2 33 ARG cc_start: 0.8298 (ttp80) cc_final: 0.7956 (ttp-170) REVERT: 2 65 GLN cc_start: 0.7654 (pp30) cc_final: 0.7308 (pt0) REVERT: 2 116 THR cc_start: 0.8036 (m) cc_final: 0.7643 (p) REVERT: 2 135 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7094 (mm-30) REVERT: 2 141 GLU cc_start: 0.6567 (tm-30) cc_final: 0.6028 (tm-30) REVERT: 2 146 ARG cc_start: 0.7396 (ptm-80) cc_final: 0.6688 (ptm-80) REVERT: 2 150 GLN cc_start: 0.8099 (mt0) cc_final: 0.7783 (mt0) REVERT: 2 163 LYS cc_start: 0.8226 (mppt) cc_final: 0.7821 (mmtm) REVERT: 2 175 LYS cc_start: 0.8899 (ttmt) cc_final: 0.8621 (ttmm) REVERT: 2 230 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7520 (tp) REVERT: 2 232 LYS cc_start: 0.8485 (mmmm) cc_final: 0.8090 (ttmm) REVERT: 2 242 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.7784 (tmm) REVERT: 2 300 ARG cc_start: 0.7920 (mtm-85) cc_final: 0.7539 (mtm-85) REVERT: 2 312 LEU cc_start: 0.8217 (mt) cc_final: 0.7977 (mm) REVERT: 3 24 LYS cc_start: 0.8711 (tttt) cc_final: 0.8215 (ttpp) REVERT: 3 27 SER cc_start: 0.8944 (m) cc_final: 0.8528 (p) REVERT: 3 39 GLU cc_start: 0.7458 (mp0) cc_final: 0.7055 (mp0) REVERT: 3 46 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7735 (tpt) REVERT: 3 92 ASP cc_start: 0.7888 (t0) cc_final: 0.7560 (t0) REVERT: 3 96 GLU cc_start: 0.7421 (tm-30) cc_final: 0.7169 (tm-30) REVERT: 3 157 MET cc_start: 0.7822 (tpp) cc_final: 0.6939 (tpp) REVERT: 3 175 LYS cc_start: 0.8175 (ttmm) cc_final: 0.7695 (mtpp) REVERT: 3 181 ASN cc_start: 0.7561 (t0) cc_final: 0.7263 (t0) REVERT: 3 207 LYS cc_start: 0.8751 (tttt) cc_final: 0.8057 (ttmm) REVERT: 3 232 LYS cc_start: 0.8105 (ttmm) cc_final: 0.7882 (ttmm) REVERT: 3 250 TYR cc_start: 0.8498 (t80) cc_final: 0.7938 (t80) REVERT: 3 255 GLU cc_start: 0.7938 (tp30) cc_final: 0.7733 (tp30) REVERT: 3 268 ASP cc_start: 0.7582 (p0) cc_final: 0.7212 (p0) REVERT: 3 269 PHE cc_start: 0.7230 (OUTLIER) cc_final: 0.5564 (t80) REVERT: 4 19 THR cc_start: 0.8615 (p) cc_final: 0.8318 (p) REVERT: 4 23 ARG cc_start: 0.7143 (mtm110) cc_final: 0.6848 (mtm110) REVERT: 4 29 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7878 (mmp) REVERT: 4 46 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.7420 (tpt) REVERT: 4 62 TYR cc_start: 0.8103 (t80) cc_final: 0.7746 (t80) REVERT: 4 63 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7392 (tp) REVERT: 4 83 GLU cc_start: 0.6714 (tt0) cc_final: 0.6041 (tt0) REVERT: 4 96 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6710 (tp30) REVERT: 4 98 LEU cc_start: 0.8597 (mt) cc_final: 0.8241 (mm) REVERT: 4 118 ARG cc_start: 0.7022 (mtp180) cc_final: 0.6777 (mtp180) REVERT: 4 131 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8168 (mm) REVERT: 4 133 ILE cc_start: 0.7846 (mt) cc_final: 0.7588 (mm) REVERT: 4 146 ARG cc_start: 0.6662 (ptm160) cc_final: 0.6139 (ptm160) REVERT: 4 154 TRP cc_start: 0.8135 (t60) cc_final: 0.7799 (t60) REVERT: 4 155 LEU cc_start: 0.8416 (mt) cc_final: 0.8163 (mm) REVERT: 4 254 ILE cc_start: 0.7683 (pt) cc_final: 0.7184 (mm) REVERT: 4 255 GLU cc_start: 0.7390 (tp30) cc_final: 0.7067 (tt0) REVERT: 4 298 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.7226 (mpp) REVERT: 5 171 MET cc_start: 0.7767 (mtp) cc_final: 0.7199 (mtp) REVERT: 5 182 SER cc_start: 0.8008 (t) cc_final: 0.7577 (m) REVERT: 5 241 ASN cc_start: 0.7354 (t0) cc_final: 0.6776 (t0) REVERT: 6 24 LYS cc_start: 0.8574 (ttpp) cc_final: 0.8290 (ttmm) REVERT: 6 30 ASP cc_start: 0.7599 (m-30) cc_final: 0.7380 (m-30) REVERT: 6 80 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6966 (mt) REVERT: 6 107 LEU cc_start: 0.8455 (pt) cc_final: 0.7996 (tp) REVERT: 6 135 GLU cc_start: 0.6572 (mm-30) cc_final: 0.5952 (mm-30) REVERT: 6 137 GLN cc_start: 0.8030 (pm20) cc_final: 0.7525 (pm20) REVERT: 6 149 THR cc_start: 0.8488 (p) cc_final: 0.8134 (p) REVERT: 6 150 GLN cc_start: 0.8440 (mt0) cc_final: 0.8081 (mt0) REVERT: 6 153 ASN cc_start: 0.7890 (m110) cc_final: 0.7677 (m-40) REVERT: 6 162 THR cc_start: 0.8416 (OUTLIER) cc_final: 0.8067 (p) REVERT: 6 175 LYS cc_start: 0.8324 (ttmt) cc_final: 0.8012 (ttmm) REVERT: 6 181 ASN cc_start: 0.8555 (t0) cc_final: 0.8308 (t0) REVERT: 6 237 PHE cc_start: 0.8230 (t80) cc_final: 0.7836 (t80) REVERT: 6 243 ARG cc_start: 0.8183 (ttm-80) cc_final: 0.7717 (ttm-80) REVERT: 6 255 GLU cc_start: 0.7436 (tp30) cc_final: 0.6218 (mm-30) REVERT: 6 259 ASN cc_start: 0.7349 (OUTLIER) cc_final: 0.6951 (p0) REVERT: 6 262 GLU cc_start: 0.6427 (mp0) cc_final: 0.6148 (mp0) REVERT: 6 266 GLU cc_start: 0.7227 (tp30) cc_final: 0.6886 (tp30) REVERT: 6 271 PHE cc_start: 0.7278 (t80) cc_final: 0.6664 (t80) REVERT: 6 275 LEU cc_start: 0.7321 (mm) cc_final: 0.7001 (mp) REVERT: 7 5 ARG cc_start: 0.7626 (tpp80) cc_final: 0.6725 (tpt-90) REVERT: 7 39 GLU cc_start: 0.7700 (mp0) cc_final: 0.7268 (mp0) REVERT: 7 46 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7388 (tpp) REVERT: 7 61 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7938 (ttmm) REVERT: 7 99 VAL cc_start: 0.9029 (p) cc_final: 0.8700 (t) REVERT: 7 119 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7876 (tt) REVERT: 7 129 LYS cc_start: 0.8306 (mmmm) cc_final: 0.7987 (mttm) REVERT: 7 156 LYS cc_start: 0.8752 (ttpt) cc_final: 0.8379 (tttp) REVERT: 7 162 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8451 (p) REVERT: 7 228 GLU cc_start: 0.7116 (tm-30) cc_final: 0.6548 (tm-30) REVERT: 7 232 LYS cc_start: 0.8501 (ttmm) cc_final: 0.7807 (ttpp) REVERT: 7 255 GLU cc_start: 0.7410 (tp30) cc_final: 0.6926 (tp30) outliers start: 94 outliers final: 68 residues processed: 633 average time/residue: 0.1557 time to fit residues: 140.0817 Evaluate side-chains 668 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 580 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 1 residue 29 MET Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 82 ILE Chi-restraints excluded: chain 1 residue 107 LEU Chi-restraints excluded: chain 1 residue 110 THR Chi-restraints excluded: chain 1 residue 119 LEU Chi-restraints excluded: chain 1 residue 147 VAL Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 1 residue 162 THR Chi-restraints excluded: chain 1 residue 176 VAL Chi-restraints excluded: chain 1 residue 217 LEU Chi-restraints excluded: chain 1 residue 269 PHE Chi-restraints excluded: chain 1 residue 279 ASP Chi-restraints excluded: chain 1 residue 309 GLU Chi-restraints excluded: chain 1 residue 310 ASP Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 22 VAL Chi-restraints excluded: chain 2 residue 45 MET Chi-restraints excluded: chain 2 residue 101 MET Chi-restraints excluded: chain 2 residue 192 VAL Chi-restraints excluded: chain 2 residue 200 GLN Chi-restraints excluded: chain 2 residue 208 THR Chi-restraints excluded: chain 2 residue 213 LEU Chi-restraints excluded: chain 2 residue 230 LEU Chi-restraints excluded: chain 2 residue 242 MET Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 35 LEU Chi-restraints excluded: chain 3 residue 45 MET Chi-restraints excluded: chain 3 residue 46 MET Chi-restraints excluded: chain 3 residue 63 LEU Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 142 GLU Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 193 GLU Chi-restraints excluded: chain 3 residue 269 PHE Chi-restraints excluded: chain 3 residue 270 VAL Chi-restraints excluded: chain 3 residue 312 LEU Chi-restraints excluded: chain 4 residue 27 SER Chi-restraints excluded: chain 4 residue 29 MET Chi-restraints excluded: chain 4 residue 30 ASP Chi-restraints excluded: chain 4 residue 46 MET Chi-restraints excluded: chain 4 residue 60 LYS Chi-restraints excluded: chain 4 residue 63 LEU Chi-restraints excluded: chain 4 residue 96 GLU Chi-restraints excluded: chain 4 residue 110 THR Chi-restraints excluded: chain 4 residue 119 LEU Chi-restraints excluded: chain 4 residue 130 LEU Chi-restraints excluded: chain 4 residue 131 ILE Chi-restraints excluded: chain 4 residue 142 GLU Chi-restraints excluded: chain 4 residue 157 MET Chi-restraints excluded: chain 4 residue 231 GLN Chi-restraints excluded: chain 4 residue 264 ILE Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 279 ASP Chi-restraints excluded: chain 4 residue 298 MET Chi-restraints excluded: chain 5 residue 29 MET Chi-restraints excluded: chain 5 residue 38 LEU Chi-restraints excluded: chain 5 residue 46 MET Chi-restraints excluded: chain 5 residue 97 LEU Chi-restraints excluded: chain 5 residue 114 ARG Chi-restraints excluded: chain 5 residue 142 GLU Chi-restraints excluded: chain 5 residue 147 VAL Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 178 LEU Chi-restraints excluded: chain 5 residue 183 GLN Chi-restraints excluded: chain 5 residue 259 ASN Chi-restraints excluded: chain 6 residue 63 LEU Chi-restraints excluded: chain 6 residue 80 LEU Chi-restraints excluded: chain 6 residue 115 LEU Chi-restraints excluded: chain 6 residue 118 ARG Chi-restraints excluded: chain 6 residue 142 GLU Chi-restraints excluded: chain 6 residue 148 LEU Chi-restraints excluded: chain 6 residue 162 THR Chi-restraints excluded: chain 6 residue 259 ASN Chi-restraints excluded: chain 6 residue 269 PHE Chi-restraints excluded: chain 7 residue 46 MET Chi-restraints excluded: chain 7 residue 53 VAL Chi-restraints excluded: chain 7 residue 61 LYS Chi-restraints excluded: chain 7 residue 107 LEU Chi-restraints excluded: chain 7 residue 117 LYS Chi-restraints excluded: chain 7 residue 119 LEU Chi-restraints excluded: chain 7 residue 148 LEU Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 195 ARG Chi-restraints excluded: chain 7 residue 214 ASP Chi-restraints excluded: chain 7 residue 269 PHE Chi-restraints excluded: chain 7 residue 309 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 26 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 144 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 95 optimal weight: 0.0060 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 64 ASN ** 1 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 282 ASN 3 183 GLN 7 247 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.167739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.133153 restraints weight = 26469.923| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.15 r_work: 0.3549 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18773 Z= 0.141 Angle : 0.709 15.072 25612 Z= 0.346 Chirality : 0.042 0.220 2863 Planarity : 0.004 0.046 3122 Dihedral : 14.594 89.549 2868 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 4.80 % Allowed : 30.28 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.19), residues: 2163 helix: 0.89 (0.15), residues: 1204 sheet: -1.88 (0.38), residues: 224 loop : -1.92 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 7 33 TYR 0.023 0.002 TYR 6 199 PHE 0.011 0.002 PHE 4 206 TRP 0.039 0.002 TRP 6 154 HIS 0.007 0.001 HIS 1 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (18772) covalent geometry : angle 0.70850 / 0.35 (25612) hydrogen bonds : bond 0.03154 / 3.50 ( 816) hydrogen bonds : angle 3.68318 / 4.32 ( 2372) Misc. bond : bond 0.00233 / 0.12 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5421.79 seconds wall clock time: 93 minutes 21.78 seconds (5601.78 seconds total)