Starting phenix.real_space_refine on Sat Sep 28 06:29:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ufi_26476/09_2024/7ufi_26476.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ufi_26476/09_2024/7ufi_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ufi_26476/09_2024/7ufi_26476.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ufi_26476/09_2024/7ufi_26476.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ufi_26476/09_2024/7ufi_26476.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ufi_26476/09_2024/7ufi_26476.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 11.41, per 1000 atoms: 0.62 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: 4.68 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 6.04 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: 5.61 Time building geometry restraints manager: 5.07 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: 24694 3.88 - 7.76: 897 7.76 - 11.64: 2 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 - 17.38: 9413 17.38 - 34.76: 1222 34.76 - 52.14: 671 52.14 - 69.52: 146 69.52 - 86.90: 33 Dihedral angle restraints: 11485 sinusoidal: 5143 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 11482 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1151 0.045 - 0.089: 933 0.089 - 0.134: 528 0.134 - 0.178: 209 0.178 - 0.223: 42 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=" CA VAL 7 17 " pdb=" N VAL 7 17 " pdb=" C VAL 7 17 " pdb=" CB VAL 7 17 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.12e+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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.750 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 44.870 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 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 0.046 18772 Z= 0.855 Angle : 1.831 19.404 25612 Z= 1.363 Chirality : 0.079 0.223 2863 Planarity : 0.003 0.015 3122 Dihedral : 20.086 86.898 7383 Min Nonbonded Distance : 1.645 Molprobity Statistics. All-atom Clashscore : 3.99 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.021 0.003 TRP 4 154 HIS 0.006 0.001 HIS 2 138 PHE 0.017 0.003 PHE 7 209 TYR 0.020 0.003 TYR 2 199 ARG 0.004 0.001 ARG 6 195 *********************** 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 fitting. rotamer outliers: 224 poor density : 732 time to evaluate : 1.974 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: 0.6934 (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: 0.6725 (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: 0.8086 (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: 0.5828 (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: 0.7694 (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: 0.3924 (OUTLIER) cc_final: 0.3654 (tm-30) REVERT: 2 214 ASP cc_start: 0.7525 (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: 0.7319 (p0) REVERT: 2 262 GLU cc_start: 0.6711 (mp0) cc_final: 0.6281 (mp0) REVERT: 2 268 ASP cc_start: 0.6802 (p0) cc_final: 0.6464 (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: 0.6469 (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: 0.7789 (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: 0.7930 (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: 0.7302 (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: 0.7174 (t80) REVERT: 3 268 ASP cc_start: 0.7042 (p0) cc_final: 0.6677 (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: 0.5706 (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: 0.7232 (t80) REVERT: 4 18 SER cc_start: 0.7927 (p) cc_final: 0.7410 (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: 0.6383 (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: 0.6803 (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: 0.6252 (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: 0.6630 (mm) REVERT: 4 149 THR cc_start: 0.5316 (OUTLIER) cc_final: 0.4878 (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: 4 242 MET cc_start: 0.7918 (tpp) cc_final: 0.7676 (tpt) REVERT: 4 247 ASN cc_start: 0.7610 (m-40) cc_final: 0.7310 (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: 0.7729 (p0) cc_final: 0.7462 (t70) REVERT: 4 295 THR cc_start: 0.7989 (p) cc_final: 0.7538 (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: 0.3279 (tt0) REVERT: 5 142 GLU cc_start: 0.4856 (OUTLIER) cc_final: 0.4552 (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: 0.7181 (m) REVERT: 6 62 TYR cc_start: 0.7766 (t80) cc_final: 0.7352 (t80) REVERT: 6 64 ASN cc_start: 0.6537 (m-40) cc_final: 0.6290 (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: 0.6094 (t0) REVERT: 6 137 GLN cc_start: 0.7960 (pm20) cc_final: 0.6833 (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: 0.7951 (mmm) REVERT: 6 175 LYS cc_start: 0.7640 (ttmt) cc_final: 0.7424 (ttmm) REVERT: 6 181 ASN cc_start: 0.7956 (t0) cc_final: 0.7737 (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: 0.7939 (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: 0.6927 (t) REVERT: 6 231 GLN cc_start: 0.8344 (tt0) cc_final: 0.8017 (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: 6 242 MET cc_start: 0.8142 (tpp) cc_final: 0.7682 (tmm) REVERT: 6 255 GLU cc_start: 0.7122 (tp30) cc_final: 0.6651 (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: 0.6391 (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: 0.6334 (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: 0.7551 (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: 0.6577 (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: 0.7533 (p0) REVERT: 7 309 GLU cc_start: 0.6685 (mt-10) cc_final: 0.6461 (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: 0.3737 time to fit residues: 460.3603 Evaluate side-chains 749 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 645 time to evaluate : 2.770 ------------------------------------------------------------------------------- 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 186 optimal weight: 1.9990 chunk 167 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 173 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 200 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 87 ASN ** 1 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 282 ASN 2 138 HIS 2 231 GLN 2 261 HIS 3 138 HIS 3 259 ASN 4 138 HIS 4 259 ASN 5 138 HIS 6 138 HIS 6 183 GLN ** 6 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 314 HIS 7 138 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18772 Z= 0.257 Angle : 0.720 12.960 25612 Z= 0.366 Chirality : 0.043 0.145 2863 Planarity : 0.006 0.101 3122 Dihedral : 18.521 90.028 3267 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 6.61 % Allowed : 22.76 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.17), residues: 2163 helix: -0.22 (0.14), residues: 1190 sheet: -3.15 (0.32), residues: 238 loop : -2.59 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP 6 154 HIS 0.006 0.001 HIS 4 261 PHE 0.021 0.002 PHE 3 206 TYR 0.020 0.002 TYR 6 199 ARG 0.006 0.001 ARG 1 33 *********************** 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 784 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 660 time to evaluate : 1.922 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: 0.6960 (mtm-85) cc_final: 0.6530 (mtm-85) REVERT: 1 19 THR cc_start: 0.7534 (OUTLIER) cc_final: 0.7032 (t) REVERT: 1 26 LEU cc_start: 0.6950 (mt) cc_final: 0.6630 (mt) REVERT: 1 30 ASP cc_start: 0.7001 (m-30) cc_final: 0.6673 (m-30) REVERT: 1 37 ASP cc_start: 0.7935 (p0) cc_final: 0.6828 (p0) REVERT: 1 38 LEU cc_start: 0.7336 (mp) cc_final: 0.6841 (mt) REVERT: 1 39 GLU cc_start: 0.6412 (mp0) cc_final: 0.5282 (mp0) REVERT: 1 45 MET cc_start: 0.8536 (ttm) cc_final: 0.8259 (ttp) REVERT: 1 46 MET cc_start: 0.8039 (tpt) cc_final: 0.7573 (tpp) REVERT: 1 65 GLN cc_start: 0.7432 (pt0) cc_final: 0.7129 (pp30) REVERT: 1 83 GLU cc_start: 0.7830 (tt0) cc_final: 0.7359 (mt-10) REVERT: 1 86 ASP cc_start: 0.7941 (t70) cc_final: 0.7715 (t70) REVERT: 1 100 GLU cc_start: 0.7591 (tm-30) cc_final: 0.6996 (tm-30) REVERT: 1 101 MET cc_start: 0.8061 (ttp) cc_final: 0.7592 (ttp) REVERT: 1 109 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6513 (tt0) REVERT: 1 114 ARG cc_start: 0.7180 (ptp90) cc_final: 0.6968 (mtm-85) REVERT: 1 129 LYS cc_start: 0.8234 (mtpt) cc_final: 0.7959 (mtpt) REVERT: 1 134 ASP cc_start: 0.7389 (t0) cc_final: 0.6900 (t0) REVERT: 1 150 GLN cc_start: 0.7883 (mt0) cc_final: 0.7599 (mt0) REVERT: 1 175 LYS cc_start: 0.7683 (ttmt) cc_final: 0.7380 (ttpp) REVERT: 1 192 VAL cc_start: 0.8188 (t) cc_final: 0.7785 (m) REVERT: 1 193 GLU cc_start: 0.8019 (tp30) cc_final: 0.7462 (tp30) REVERT: 1 261 HIS cc_start: 0.6298 (m170) cc_final: 0.5956 (m90) REVERT: 1 271 PHE cc_start: 0.7201 (t80) cc_final: 0.6922 (t80) REVERT: 1 274 LYS cc_start: 0.8029 (mttt) cc_final: 0.7751 (mtpp) REVERT: 1 285 LYS cc_start: 0.7297 (tppt) cc_final: 0.6796 (tppt) REVERT: 1 300 ARG cc_start: 0.7902 (mtm-85) cc_final: 0.7418 (ttm-80) REVERT: 1 310 ASP cc_start: 0.7447 (m-30) cc_final: 0.7141 (m-30) REVERT: 2 23 ARG cc_start: 0.7211 (mtm180) cc_final: 0.7000 (mtm-85) REVERT: 2 33 ARG cc_start: 0.7821 (ttp80) cc_final: 0.7363 (ttp-170) REVERT: 2 39 GLU cc_start: 0.6048 (mp0) cc_final: 0.5664 (mp0) REVERT: 2 89 LYS cc_start: 0.7480 (mmmt) cc_final: 0.6991 (mmmt) REVERT: 2 96 GLU cc_start: 0.7515 (tm-30) cc_final: 0.7220 (tp30) REVERT: 2 100 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7303 (tm-30) REVERT: 2 122 LEU cc_start: 0.7512 (tp) cc_final: 0.7233 (tp) REVERT: 2 141 GLU cc_start: 0.7009 (tt0) cc_final: 0.6437 (tm-30) REVERT: 2 150 GLN cc_start: 0.7711 (mt0) cc_final: 0.6725 (mm110) REVERT: 2 157 MET cc_start: 0.8150 (tmm) cc_final: 0.7915 (tmm) REVERT: 2 163 LYS cc_start: 0.8106 (mppt) cc_final: 0.7659 (mmtm) REVERT: 2 164 CYS cc_start: 0.7899 (t) cc_final: 0.7294 (m) REVERT: 2 181 ASN cc_start: 0.7352 (t0) cc_final: 0.6656 (t0) REVERT: 2 262 GLU cc_start: 0.6479 (mp0) cc_final: 0.6126 (mp0) REVERT: 2 286 ASN cc_start: 0.8665 (t0) cc_final: 0.8186 (t0) REVERT: 3 34 ASP cc_start: 0.7482 (m-30) cc_final: 0.6969 (m-30) REVERT: 3 38 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7654 (mm) REVERT: 3 39 GLU cc_start: 0.7115 (mp0) cc_final: 0.6609 (mp0) REVERT: 3 46 MET cc_start: 0.8243 (tpt) cc_final: 0.7775 (tpp) REVERT: 3 61 LYS cc_start: 0.8006 (tptp) cc_final: 0.7676 (tptt) REVERT: 3 96 GLU cc_start: 0.7379 (tm-30) cc_final: 0.7155 (tm-30) REVERT: 3 118 ARG cc_start: 0.7779 (ttm170) cc_final: 0.7549 (ttt180) REVERT: 3 135 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7767 (mm-30) REVERT: 3 143 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7372 (ppt170) REVERT: 3 157 MET cc_start: 0.7726 (ttm) cc_final: 0.7027 (tpp) REVERT: 3 173 TYR cc_start: 0.8565 (p90) cc_final: 0.8163 (p90) REVERT: 3 175 LYS cc_start: 0.7973 (ttmt) cc_final: 0.7598 (ttmm) REVERT: 3 181 ASN cc_start: 0.7659 (t0) cc_final: 0.7226 (t0) REVERT: 3 195 ARG cc_start: 0.7892 (ptp-110) cc_final: 0.7534 (mtp-110) REVERT: 3 207 LYS cc_start: 0.8098 (tttt) cc_final: 0.7404 (ttmm) REVERT: 3 214 ASP cc_start: 0.7983 (t70) cc_final: 0.7775 (t0) REVERT: 3 220 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6574 (pm20) REVERT: 3 225 LEU cc_start: 0.7685 (mp) cc_final: 0.7474 (mt) REVERT: 3 233 LYS cc_start: 0.7464 (mtpt) cc_final: 0.6984 (mtmm) REVERT: 3 241 ASN cc_start: 0.7046 (m-40) cc_final: 0.6532 (t0) REVERT: 3 247 ASN cc_start: 0.8170 (m-40) cc_final: 0.7898 (m-40) REVERT: 3 259 ASN cc_start: 0.7028 (OUTLIER) cc_final: 0.6488 (p0) REVERT: 3 268 ASP cc_start: 0.6902 (p0) cc_final: 0.6536 (p0) REVERT: 3 279 ASP cc_start: 0.7334 (p0) cc_final: 0.7128 (p0) REVERT: 3 282 ASN cc_start: 0.8010 (t0) cc_final: 0.7710 (t0) REVERT: 3 300 ARG cc_start: 0.8274 (mtm-85) cc_final: 0.7944 (ptp90) REVERT: 4 19 THR cc_start: 0.7623 (OUTLIER) cc_final: 0.7182 (p) REVERT: 4 23 ARG cc_start: 0.6947 (mtm180) cc_final: 0.6562 (mtm110) REVERT: 4 24 LYS cc_start: 0.7212 (tttt) cc_final: 0.6862 (tptp) REVERT: 4 29 MET cc_start: 0.7566 (mtt) cc_final: 0.7094 (mmp) REVERT: 4 62 TYR cc_start: 0.7833 (t80) cc_final: 0.7477 (t80) REVERT: 4 83 GLU cc_start: 0.7539 (tt0) cc_final: 0.6585 (tt0) REVERT: 4 114 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7336 (ttp80) REVERT: 4 118 ARG cc_start: 0.7010 (ttm170) cc_final: 0.6776 (mtp180) REVERT: 4 133 ILE cc_start: 0.7052 (mt) cc_final: 0.6823 (mm) REVERT: 4 137 GLN cc_start: 0.7730 (pm20) cc_final: 0.6542 (pt0) REVERT: 4 149 THR cc_start: 0.5393 (OUTLIER) cc_final: 0.4772 (t) REVERT: 4 154 TRP cc_start: 0.7587 (t60) cc_final: 0.7231 (t60) REVERT: 4 155 LEU cc_start: 0.8273 (mt) cc_final: 0.8033 (mm) REVERT: 4 171 MET cc_start: 0.8245 (mtp) cc_final: 0.7639 (mtp) REVERT: 4 194 LEU cc_start: 0.7549 (tt) cc_final: 0.7333 (tt) REVERT: 4 242 MET cc_start: 0.7978 (tpp) cc_final: 0.7679 (tpt) REVERT: 4 247 ASN cc_start: 0.7579 (m-40) cc_final: 0.7260 (t0) REVERT: 4 253 SER cc_start: 0.7826 (p) cc_final: 0.7607 (p) REVERT: 4 255 GLU cc_start: 0.6570 (tp30) cc_final: 0.6363 (tp30) REVERT: 4 262 GLU cc_start: 0.6950 (mp0) cc_final: 0.6564 (mp0) REVERT: 4 271 PHE cc_start: 0.7610 (t80) cc_final: 0.7408 (t80) REVERT: 4 286 ASN cc_start: 0.7892 (t0) cc_final: 0.7608 (t0) REVERT: 4 295 THR cc_start: 0.8105 (p) cc_final: 0.7886 (t) REVERT: 4 298 MET cc_start: 0.6394 (mtt) cc_final: 0.6168 (mtt) REVERT: 4 304 LYS cc_start: 0.7192 (tppt) cc_final: 0.6890 (tppt) REVERT: 4 311 TYR cc_start: 0.5967 (t80) cc_final: 0.5714 (t80) REVERT: 5 55 LYS cc_start: 0.6541 (mtmm) cc_final: 0.6028 (mtmm) REVERT: 5 60 LYS cc_start: 0.7226 (mmmt) cc_final: 0.6959 (mmtt) REVERT: 5 84 LEU cc_start: 0.6902 (mp) cc_final: 0.6661 (mt) REVERT: 5 105 LEU cc_start: 0.6783 (OUTLIER) cc_final: 0.6367 (mm) REVERT: 5 129 LYS cc_start: 0.7551 (mtpt) cc_final: 0.6733 (mptt) REVERT: 5 171 MET cc_start: 0.7723 (mtp) cc_final: 0.6938 (mtp) REVERT: 5 215 LYS cc_start: 0.7413 (mmtt) cc_final: 0.6991 (tmtt) REVERT: 6 19 THR cc_start: 0.7398 (OUTLIER) cc_final: 0.7176 (p) REVERT: 6 30 ASP cc_start: 0.6735 (m-30) cc_final: 0.6458 (m-30) REVERT: 6 37 ASP cc_start: 0.6786 (p0) cc_final: 0.6507 (p0) REVERT: 6 41 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7819 (mm-30) REVERT: 6 46 MET cc_start: 0.8052 (tpt) cc_final: 0.7755 (tpt) REVERT: 6 64 ASN cc_start: 0.5830 (m-40) cc_final: 0.5603 (m110) REVERT: 6 111 ASP cc_start: 0.7398 (t70) cc_final: 0.6884 (t0) REVERT: 6 134 ASP cc_start: 0.7029 (t0) cc_final: 0.6581 (t0) REVERT: 6 135 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7287 (mm-30) REVERT: 6 141 GLU cc_start: 0.6879 (tt0) cc_final: 0.6268 (tt0) REVERT: 6 143 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7399 (ppt170) REVERT: 6 144 SER cc_start: 0.6506 (p) cc_final: 0.5052 (p) REVERT: 6 146 ARG cc_start: 0.7501 (ptm160) cc_final: 0.7301 (ptm-80) REVERT: 6 149 THR cc_start: 0.7467 (OUTLIER) cc_final: 0.7173 (p) REVERT: 6 150 GLN cc_start: 0.7533 (mt0) cc_final: 0.7269 (mt0) REVERT: 6 158 ILE cc_start: 0.6895 (tp) cc_final: 0.6599 (mm) REVERT: 6 175 LYS cc_start: 0.7761 (ttmt) cc_final: 0.7481 (ttmm) REVERT: 6 189 SER cc_start: 0.8623 (p) cc_final: 0.8153 (t) REVERT: 6 198 SER cc_start: 0.7647 (p) cc_final: 0.7132 (t) REVERT: 6 233 LYS cc_start: 0.7773 (mtpt) cc_final: 0.7571 (mmtp) REVERT: 6 246 ARG cc_start: 0.7540 (mmm-85) cc_final: 0.7293 (mmm-85) REVERT: 6 268 ASP cc_start: 0.7847 (p0) cc_final: 0.6734 (p0) REVERT: 6 283 SER cc_start: 0.8241 (p) cc_final: 0.8028 (t) REVERT: 7 8 ARG cc_start: 0.7749 (mtm180) cc_final: 0.7517 (mtm-85) REVERT: 7 14 ARG cc_start: 0.7951 (mtm-85) cc_final: 0.7162 (mtt90) REVERT: 7 24 LYS cc_start: 0.7582 (tttt) cc_final: 0.7163 (ttpp) REVERT: 7 39 GLU cc_start: 0.7655 (mp0) cc_final: 0.6752 (mp0) REVERT: 7 43 THR cc_start: 0.7639 (OUTLIER) cc_final: 0.7376 (m) REVERT: 7 44 CYS cc_start: 0.8076 (m) cc_final: 0.7758 (m) REVERT: 7 48 TYR cc_start: 0.8079 (m-80) cc_final: 0.7813 (m-80) REVERT: 7 60 LYS cc_start: 0.7475 (mtpp) cc_final: 0.7216 (mttp) REVERT: 7 83 GLU cc_start: 0.6989 (tt0) cc_final: 0.6744 (mt-10) REVERT: 7 86 ASP cc_start: 0.8105 (t70) cc_final: 0.7748 (t0) REVERT: 7 111 ASP cc_start: 0.7110 (t70) cc_final: 0.6850 (t70) REVERT: 7 129 LYS cc_start: 0.7890 (mmmm) cc_final: 0.7622 (mttp) REVERT: 7 146 ARG cc_start: 0.7644 (ptm160) cc_final: 0.7355 (ptm160) REVERT: 7 166 ILE cc_start: 0.8311 (mt) cc_final: 0.7994 (tp) REVERT: 7 181 ASN cc_start: 0.7404 (t0) cc_final: 0.6980 (t0) REVERT: 7 193 GLU cc_start: 0.8017 (tp30) cc_final: 0.7797 (tp30) REVERT: 7 232 LYS cc_start: 0.7434 (ttmm) cc_final: 0.6805 (ttpp) REVERT: 7 271 PHE cc_start: 0.7979 (t80) cc_final: 0.7696 (t80) outliers start: 124 outliers final: 61 residues processed: 721 average time/residue: 0.3965 time to fit residues: 397.2390 Evaluate side-chains 701 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 626 time to evaluate : 1.937 ------------------------------------------------------------------------------- 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 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 158 ILE 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 211 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 38 LEU Chi-restraints excluded: chain 3 residue 110 THR 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 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 19 THR Chi-restraints excluded: chain 4 residue 27 SER Chi-restraints excluded: chain 4 residue 60 LYS Chi-restraints excluded: chain 4 residue 110 THR Chi-restraints excluded: chain 4 residue 114 ARG Chi-restraints excluded: chain 4 residue 119 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 211 GLU Chi-restraints excluded: chain 4 residue 231 GLN 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 97 LEU Chi-restraints excluded: chain 5 residue 99 VAL Chi-restraints excluded: chain 5 residue 105 LEU Chi-restraints excluded: chain 5 residue 110 THR 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 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 99 VAL 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 149 THR Chi-restraints excluded: chain 6 residue 168 ILE 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 77 ILE Chi-restraints excluded: chain 7 residue 99 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 111 optimal weight: 0.0980 chunk 62 optimal weight: 0.2980 chunk 167 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 201 optimal weight: 0.9980 chunk 217 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 199 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 161 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 64 ASN 1 87 ASN 1 138 HIS 1 231 GLN ** 3 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 259 ASN 6 160 ASN 6 183 GLN 6 227 ASN 7 87 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18772 Z= 0.223 Angle : 0.651 10.991 25612 Z= 0.330 Chirality : 0.042 0.354 2863 Planarity : 0.004 0.060 3122 Dihedral : 17.209 89.124 3141 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 5.97 % Allowed : 25.21 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.18), residues: 2163 helix: 0.41 (0.15), residues: 1183 sheet: -2.85 (0.33), residues: 238 loop : -2.44 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP 6 154 HIS 0.003 0.001 HIS 1 261 PHE 0.018 0.002 PHE 6 271 TYR 0.020 0.002 TYR 3 199 ARG 0.008 0.001 ARG 1 33 *********************** 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 741 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 629 time to evaluate : 2.055 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 14 ARG cc_start: 0.7122 (mtm-85) cc_final: 0.6887 (mtm-85) REVERT: 1 19 THR cc_start: 0.7553 (OUTLIER) cc_final: 0.7130 (t) REVERT: 1 23 ARG cc_start: 0.7836 (mtm110) cc_final: 0.7597 (mtm110) REVERT: 1 30 ASP cc_start: 0.7053 (m-30) cc_final: 0.6711 (m-30) REVERT: 1 37 ASP cc_start: 0.7954 (p0) cc_final: 0.7143 (p0) REVERT: 1 39 GLU cc_start: 0.6320 (mp0) cc_final: 0.5283 (mp0) REVERT: 1 45 MET cc_start: 0.8523 (ttm) cc_final: 0.8236 (ttp) REVERT: 1 46 MET cc_start: 0.7997 (tpt) cc_final: 0.7727 (tpp) REVERT: 1 65 GLN cc_start: 0.7398 (pt0) cc_final: 0.7093 (pp30) REVERT: 1 83 GLU cc_start: 0.7886 (tt0) cc_final: 0.7394 (mt-10) REVERT: 1 92 ASP cc_start: 0.7265 (t0) cc_final: 0.6981 (t0) REVERT: 1 100 GLU cc_start: 0.7553 (tm-30) cc_final: 0.7021 (tm-30) REVERT: 1 101 MET cc_start: 0.8061 (ttp) cc_final: 0.7665 (ttp) REVERT: 1 105 LEU cc_start: 0.7750 (pp) cc_final: 0.7276 (mp) REVERT: 1 109 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6581 (tt0) REVERT: 1 129 LYS cc_start: 0.8248 (mtpt) cc_final: 0.7951 (mtpt) REVERT: 1 134 ASP cc_start: 0.7440 (t0) cc_final: 0.6952 (t0) REVERT: 1 150 GLN cc_start: 0.7848 (mt0) cc_final: 0.7604 (mt0) REVERT: 1 168 ILE cc_start: 0.8184 (pt) cc_final: 0.7956 (pt) REVERT: 1 175 LYS cc_start: 0.7390 (ttmt) cc_final: 0.7031 (ttpp) REVERT: 1 179 GLN cc_start: 0.7381 (mt0) cc_final: 0.7096 (mt0) REVERT: 1 192 VAL cc_start: 0.8226 (t) cc_final: 0.7851 (m) REVERT: 1 193 GLU cc_start: 0.8023 (tp30) cc_final: 0.7513 (tp30) REVERT: 1 269 PHE cc_start: 0.6730 (OUTLIER) cc_final: 0.6399 (m-80) REVERT: 1 274 LYS cc_start: 0.8050 (mttt) cc_final: 0.7759 (mtpp) REVERT: 1 279 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7624 (p0) REVERT: 1 285 LYS cc_start: 0.7434 (tppt) cc_final: 0.6912 (tppt) REVERT: 1 300 ARG cc_start: 0.8010 (mtm-85) cc_final: 0.7605 (mtm-85) REVERT: 1 310 ASP cc_start: 0.7466 (m-30) cc_final: 0.7148 (m-30) REVERT: 2 6 GLU cc_start: 0.7040 (pm20) cc_final: 0.6054 (tm-30) REVERT: 2 33 ARG cc_start: 0.7829 (ttp80) cc_final: 0.7606 (ttp-170) REVERT: 2 37 ASP cc_start: 0.7696 (p0) cc_final: 0.7444 (p0) REVERT: 2 39 GLU cc_start: 0.6281 (mp0) cc_final: 0.5877 (mp0) REVERT: 2 40 SER cc_start: 0.7650 (m) cc_final: 0.7045 (t) REVERT: 2 41 GLU cc_start: 0.7976 (tt0) cc_final: 0.7560 (mm-30) REVERT: 2 46 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7729 (ttt) REVERT: 2 89 LYS cc_start: 0.7478 (mmmt) cc_final: 0.6994 (mmmt) REVERT: 2 96 GLU cc_start: 0.7522 (tm-30) cc_final: 0.7162 (tp30) REVERT: 2 100 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7359 (tm-30) REVERT: 2 101 MET cc_start: 0.6854 (OUTLIER) cc_final: 0.6550 (ptm) REVERT: 2 111 ASP cc_start: 0.6845 (t0) cc_final: 0.6566 (t0) REVERT: 2 122 LEU cc_start: 0.7536 (tp) cc_final: 0.7268 (tp) REVERT: 2 141 GLU cc_start: 0.7010 (tt0) cc_final: 0.6266 (tm-30) REVERT: 2 146 ARG cc_start: 0.7357 (ptm-80) cc_final: 0.7149 (ptm-80) REVERT: 2 157 MET cc_start: 0.8239 (tmm) cc_final: 0.7971 (tmm) REVERT: 2 163 LYS cc_start: 0.8065 (mppt) cc_final: 0.7630 (mmtm) REVERT: 2 242 MET cc_start: 0.7059 (mmm) cc_final: 0.6635 (tmm) REVERT: 2 262 GLU cc_start: 0.6567 (mp0) cc_final: 0.6130 (mp0) REVERT: 2 286 ASN cc_start: 0.8651 (t0) cc_final: 0.8300 (t0) REVERT: 2 309 GLU cc_start: 0.6736 (pm20) cc_final: 0.6315 (pm20) REVERT: 3 27 SER cc_start: 0.8211 (m) cc_final: 0.7758 (p) REVERT: 3 30 ASP cc_start: 0.7895 (m-30) cc_final: 0.7483 (m-30) REVERT: 3 34 ASP cc_start: 0.7563 (m-30) cc_final: 0.6994 (m-30) REVERT: 3 38 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7589 (mm) REVERT: 3 39 GLU cc_start: 0.7041 (mp0) cc_final: 0.6540 (mp0) REVERT: 3 61 LYS cc_start: 0.7994 (tptp) cc_final: 0.7637 (tptp) REVERT: 3 65 GLN cc_start: 0.8267 (pt0) cc_final: 0.7672 (pp30) REVERT: 3 87 ASN cc_start: 0.7915 (t0) cc_final: 0.7496 (t0) REVERT: 3 92 ASP cc_start: 0.7570 (t0) cc_final: 0.7261 (t0) REVERT: 3 96 GLU cc_start: 0.7413 (tm-30) cc_final: 0.7153 (tm-30) REVERT: 3 109 GLU cc_start: 0.7650 (tt0) cc_final: 0.7381 (tt0) REVERT: 3 121 GLU cc_start: 0.6326 (mt-10) cc_final: 0.6067 (mt-10) REVERT: 3 135 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7800 (mm-30) REVERT: 3 157 MET cc_start: 0.7713 (ttm) cc_final: 0.7094 (tpp) REVERT: 3 175 LYS cc_start: 0.7830 (ttmt) cc_final: 0.7505 (ttmm) REVERT: 3 181 ASN cc_start: 0.7676 (t0) cc_final: 0.7192 (t0) REVERT: 3 207 LYS cc_start: 0.8168 (tttt) cc_final: 0.7404 (ttmm) REVERT: 3 225 LEU cc_start: 0.7719 (mp) cc_final: 0.7506 (mt) REVERT: 3 233 LYS cc_start: 0.7491 (mtpt) cc_final: 0.7016 (mtmm) REVERT: 3 239 GLN cc_start: 0.7480 (mp10) cc_final: 0.7250 (mm-40) REVERT: 3 241 ASN cc_start: 0.6910 (m-40) cc_final: 0.6470 (t0) REVERT: 3 242 MET cc_start: 0.7948 (mmm) cc_final: 0.7691 (tmm) REVERT: 3 247 ASN cc_start: 0.8181 (m-40) cc_final: 0.7936 (m-40) REVERT: 3 250 TYR cc_start: 0.7517 (t80) cc_final: 0.6947 (t80) REVERT: 3 259 ASN cc_start: 0.7401 (OUTLIER) cc_final: 0.6724 (p0) REVERT: 3 268 ASP cc_start: 0.7082 (p0) cc_final: 0.6622 (p0) REVERT: 3 269 PHE cc_start: 0.6454 (OUTLIER) cc_final: 0.4888 (t80) REVERT: 3 282 ASN cc_start: 0.8138 (t0) cc_final: 0.7859 (t0) REVERT: 3 300 ARG cc_start: 0.8331 (mtm-85) cc_final: 0.8096 (mtm-85) REVERT: 4 19 THR cc_start: 0.7651 (OUTLIER) cc_final: 0.7224 (p) REVERT: 4 23 ARG cc_start: 0.6679 (mtm180) cc_final: 0.6398 (mtm180) REVERT: 4 24 LYS cc_start: 0.7323 (tttt) cc_final: 0.6983 (tptm) REVERT: 4 29 MET cc_start: 0.7541 (mtt) cc_final: 0.7006 (mmp) REVERT: 4 33 ARG cc_start: 0.7617 (ttp80) cc_final: 0.7379 (ttp80) REVERT: 4 45 MET cc_start: 0.7843 (ttp) cc_final: 0.7059 (ttp) REVERT: 4 62 TYR cc_start: 0.7678 (t80) cc_final: 0.7277 (t80) REVERT: 4 83 GLU cc_start: 0.7521 (tt0) cc_final: 0.6603 (tt0) REVERT: 4 109 GLU cc_start: 0.7814 (pm20) cc_final: 0.7511 (pm20) REVERT: 4 133 ILE cc_start: 0.7076 (mt) cc_final: 0.6830 (mm) REVERT: 4 149 THR cc_start: 0.5494 (OUTLIER) cc_final: 0.4876 (t) REVERT: 4 154 TRP cc_start: 0.7531 (t60) cc_final: 0.7123 (t60) REVERT: 4 155 LEU cc_start: 0.8281 (mt) cc_final: 0.8053 (mm) REVERT: 4 178 LEU cc_start: 0.6974 (tp) cc_final: 0.6660 (pp) REVERT: 4 190 ILE cc_start: 0.8024 (mt) cc_final: 0.7704 (pt) REVERT: 4 193 GLU cc_start: 0.7363 (tp30) cc_final: 0.7100 (tp30) REVERT: 4 228 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7459 (tm-30) REVERT: 4 242 MET cc_start: 0.7952 (tpp) cc_final: 0.7741 (tpp) REVERT: 4 247 ASN cc_start: 0.7614 (m-40) cc_final: 0.7252 (t0) REVERT: 4 255 GLU cc_start: 0.6591 (tp30) cc_final: 0.6366 (tp30) REVERT: 4 262 GLU cc_start: 0.6994 (mp0) cc_final: 0.6561 (mp0) REVERT: 4 271 PHE cc_start: 0.7832 (t80) cc_final: 0.7473 (t80) REVERT: 4 274 LYS cc_start: 0.7778 (mttt) cc_final: 0.7195 (mtmm) REVERT: 4 286 ASN cc_start: 0.7904 (t0) cc_final: 0.7631 (t0) REVERT: 4 304 LYS cc_start: 0.7352 (tppt) cc_final: 0.6958 (tppt) REVERT: 4 311 TYR cc_start: 0.6104 (t80) cc_final: 0.5798 (t80) REVERT: 5 55 LYS cc_start: 0.6540 (mtmm) cc_final: 0.6029 (mtmm) REVERT: 5 60 LYS cc_start: 0.7237 (mmmt) cc_final: 0.6999 (mmtt) REVERT: 5 105 LEU cc_start: 0.6652 (OUTLIER) cc_final: 0.6216 (mm) REVERT: 5 129 LYS cc_start: 0.7605 (mtpt) cc_final: 0.7365 (mtpt) REVERT: 5 171 MET cc_start: 0.7698 (mtp) cc_final: 0.7025 (mtp) REVERT: 5 215 LYS cc_start: 0.7402 (mmtt) cc_final: 0.6967 (tmtt) REVERT: 6 5 ARG cc_start: 0.5277 (tpp80) cc_final: 0.4961 (tpp-160) REVERT: 6 30 ASP cc_start: 0.6559 (m-30) cc_final: 0.6343 (m-30) REVERT: 6 37 ASP cc_start: 0.6951 (p0) cc_final: 0.6734 (p0) REVERT: 6 41 GLU cc_start: 0.8289 (mm-30) cc_final: 0.8014 (mm-30) REVERT: 6 46 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7749 (tpt) REVERT: 6 64 ASN cc_start: 0.5858 (m-40) cc_final: 0.5633 (m-40) REVERT: 6 96 GLU cc_start: 0.7227 (tm-30) cc_final: 0.6891 (tm-30) REVERT: 6 111 ASP cc_start: 0.7425 (t70) cc_final: 0.7181 (t0) REVERT: 6 115 LEU cc_start: 0.6791 (pp) cc_final: 0.6449 (tp) REVERT: 6 134 ASP cc_start: 0.7110 (t0) cc_final: 0.6762 (t0) REVERT: 6 135 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7115 (mm-30) REVERT: 6 146 ARG cc_start: 0.7548 (ptm160) cc_final: 0.7308 (ptm160) REVERT: 6 149 THR cc_start: 0.7642 (OUTLIER) cc_final: 0.7271 (p) REVERT: 6 150 GLN cc_start: 0.7562 (mt0) cc_final: 0.7225 (mt0) REVERT: 6 164 CYS cc_start: 0.7870 (t) cc_final: 0.7404 (p) REVERT: 6 175 LYS cc_start: 0.7759 (ttmt) cc_final: 0.7448 (ttmm) REVERT: 6 189 SER cc_start: 0.8472 (p) cc_final: 0.8007 (m) REVERT: 6 192 VAL cc_start: 0.8391 (OUTLIER) cc_final: 0.8184 (t) REVERT: 6 198 SER cc_start: 0.7633 (p) cc_final: 0.7361 (p) REVERT: 6 230 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7354 (tp) REVERT: 6 242 MET cc_start: 0.8054 (tpp) cc_final: 0.7807 (mmm) REVERT: 6 259 ASN cc_start: 0.5702 (OUTLIER) cc_final: 0.5350 (p0) REVERT: 6 268 ASP cc_start: 0.7508 (p0) cc_final: 0.7297 (p0) REVERT: 7 14 ARG cc_start: 0.8039 (mtm-85) cc_final: 0.7750 (mtt90) REVERT: 7 24 LYS cc_start: 0.7596 (tttt) cc_final: 0.7307 (ttpt) REVERT: 7 39 GLU cc_start: 0.7598 (mp0) cc_final: 0.6806 (mp0) REVERT: 7 43 THR cc_start: 0.7453 (OUTLIER) cc_final: 0.7168 (m) REVERT: 7 44 CYS cc_start: 0.7973 (m) cc_final: 0.7656 (m) REVERT: 7 48 TYR cc_start: 0.8185 (m-80) cc_final: 0.7843 (m-80) REVERT: 7 61 LYS cc_start: 0.7810 (tptp) cc_final: 0.7544 (ttmm) REVERT: 7 83 GLU cc_start: 0.7054 (tt0) cc_final: 0.6747 (mt-10) REVERT: 7 129 LYS cc_start: 0.7905 (mmmm) cc_final: 0.7657 (mttp) REVERT: 7 146 ARG cc_start: 0.7699 (ptm160) cc_final: 0.7423 (ptm160) REVERT: 7 162 THR cc_start: 0.7704 (OUTLIER) cc_final: 0.7372 (p) REVERT: 7 166 ILE cc_start: 0.8314 (mt) cc_final: 0.7997 (tp) REVERT: 7 181 ASN cc_start: 0.7589 (t0) cc_final: 0.7159 (t0) REVERT: 7 193 GLU cc_start: 0.8025 (tp30) cc_final: 0.7777 (tp30) REVERT: 7 232 LYS cc_start: 0.7440 (ttmm) cc_final: 0.6777 (ttpp) REVERT: 7 254 ILE cc_start: 0.7855 (pt) cc_final: 0.7468 (mm) REVERT: 7 271 PHE cc_start: 0.7982 (t80) cc_final: 0.7643 (t80) outliers start: 112 outliers final: 64 residues processed: 688 average time/residue: 0.3779 time to fit residues: 363.1211 Evaluate side-chains 698 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 615 time to evaluate : 1.983 ------------------------------------------------------------------------------- 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 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 176 VAL Chi-restraints excluded: chain 1 residue 269 PHE Chi-restraints excluded: chain 1 residue 275 LEU 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 46 MET Chi-restraints excluded: chain 2 residue 101 MET Chi-restraints excluded: chain 2 residue 213 LEU 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 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 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 192 VAL 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 97 LEU Chi-restraints excluded: chain 5 residue 105 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 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 46 MET 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 149 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 269 PHE Chi-restraints excluded: chain 6 residue 304 LYS Chi-restraints excluded: chain 7 residue 19 THR Chi-restraints excluded: chain 7 residue 43 THR 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 214 ASP 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 198 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 95 optimal weight: 0.0470 chunk 135 optimal weight: 0.8980 chunk 201 optimal weight: 0.9980 chunk 213 optimal weight: 1.9990 chunk 105 optimal weight: 0.3980 chunk 191 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 64 ASN ** 1 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 282 ASN 2 181 ASN 2 183 GLN ** 2 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 259 ASN 6 227 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18772 Z= 0.199 Angle : 0.622 11.388 25612 Z= 0.314 Chirality : 0.041 0.292 2863 Planarity : 0.004 0.033 3122 Dihedral : 16.674 88.577 3120 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 5.92 % Allowed : 25.11 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.18), residues: 2163 helix: 0.78 (0.15), residues: 1190 sheet: -2.64 (0.34), residues: 238 loop : -2.26 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP 6 154 HIS 0.003 0.001 HIS 3 185 PHE 0.015 0.002 PHE 1 237 TYR 0.022 0.002 TYR 5 62 ARG 0.007 0.001 ARG 4 14 *********************** 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 727 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 616 time to evaluate : 2.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 30 ASP cc_start: 0.7277 (m-30) cc_final: 0.6999 (m-30) REVERT: 1 33 ARG cc_start: 0.8002 (ttp80) cc_final: 0.7739 (tmm-80) REVERT: 1 37 ASP cc_start: 0.7764 (p0) cc_final: 0.6912 (p0) REVERT: 1 38 LEU cc_start: 0.7739 (mt) cc_final: 0.7416 (mt) REVERT: 1 39 GLU cc_start: 0.6245 (mp0) cc_final: 0.5236 (mp0) REVERT: 1 45 MET cc_start: 0.8497 (ttm) cc_final: 0.8275 (ttp) REVERT: 1 46 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7620 (tpp) REVERT: 1 65 GLN cc_start: 0.7378 (pt0) cc_final: 0.7101 (pp30) REVERT: 1 83 GLU cc_start: 0.7928 (tt0) cc_final: 0.7401 (mt-10) REVERT: 1 92 ASP cc_start: 0.7300 (t0) cc_final: 0.6990 (t0) REVERT: 1 100 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7049 (tm-30) REVERT: 1 101 MET cc_start: 0.8058 (ttp) cc_final: 0.7720 (ttp) REVERT: 1 105 LEU cc_start: 0.7599 (pp) cc_final: 0.7207 (mp) REVERT: 1 129 LYS cc_start: 0.8265 (mtpt) cc_final: 0.7933 (mtpt) REVERT: 1 134 ASP cc_start: 0.7491 (t0) cc_final: 0.7015 (t0) REVERT: 1 168 ILE cc_start: 0.8236 (pt) cc_final: 0.8002 (pt) REVERT: 1 171 MET cc_start: 0.8219 (mtp) cc_final: 0.7763 (mmm) REVERT: 1 175 LYS cc_start: 0.7371 (ttmt) cc_final: 0.7042 (ttpp) REVERT: 1 179 GLN cc_start: 0.7390 (mt0) cc_final: 0.7096 (mt0) REVERT: 1 192 VAL cc_start: 0.8210 (t) cc_final: 0.7834 (m) REVERT: 1 193 GLU cc_start: 0.8030 (tp30) cc_final: 0.7578 (tp30) REVERT: 1 269 PHE cc_start: 0.6581 (OUTLIER) cc_final: 0.6327 (m-80) REVERT: 1 274 LYS cc_start: 0.8052 (mttt) cc_final: 0.7765 (mtpp) REVERT: 1 279 ASP cc_start: 0.7852 (p0) cc_final: 0.7395 (p0) REVERT: 1 285 LYS cc_start: 0.7519 (tppt) cc_final: 0.6979 (tppt) REVERT: 1 297 ASP cc_start: 0.7691 (t0) cc_final: 0.7438 (t0) REVERT: 1 300 ARG cc_start: 0.7970 (mtm-85) cc_final: 0.7436 (ttm-80) REVERT: 1 310 ASP cc_start: 0.7421 (m-30) cc_final: 0.7132 (m-30) REVERT: 2 23 ARG cc_start: 0.7272 (mtm110) cc_final: 0.6674 (mtm-85) REVERT: 2 33 ARG cc_start: 0.7954 (ttp80) cc_final: 0.7607 (ttp-170) REVERT: 2 39 GLU cc_start: 0.6339 (mp0) cc_final: 0.5912 (mp0) REVERT: 2 40 SER cc_start: 0.7718 (m) cc_final: 0.7339 (t) REVERT: 2 41 GLU cc_start: 0.7941 (tt0) cc_final: 0.7553 (mm-30) REVERT: 2 46 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7807 (ttt) REVERT: 2 89 LYS cc_start: 0.7446 (mmmt) cc_final: 0.7245 (mptt) REVERT: 2 96 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7171 (tp30) REVERT: 2 100 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7413 (tm-30) REVERT: 2 111 ASP cc_start: 0.7032 (t0) cc_final: 0.6698 (t0) REVERT: 2 116 THR cc_start: 0.7346 (m) cc_final: 0.7104 (p) REVERT: 2 121 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7204 (mt-10) REVERT: 2 122 LEU cc_start: 0.7507 (tp) cc_final: 0.7268 (tp) REVERT: 2 129 LYS cc_start: 0.8191 (mmpt) cc_final: 0.7919 (mmmt) REVERT: 2 141 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6101 (tm-30) REVERT: 2 146 ARG cc_start: 0.7456 (ptm-80) cc_final: 0.7192 (ptm-80) REVERT: 2 150 GLN cc_start: 0.7723 (mt0) cc_final: 0.7106 (mt0) REVERT: 2 157 MET cc_start: 0.8292 (tmm) cc_final: 0.8043 (tmm) REVERT: 2 162 THR cc_start: 0.7917 (OUTLIER) cc_final: 0.7654 (p) REVERT: 2 163 LYS cc_start: 0.8088 (mppt) cc_final: 0.7467 (mmtm) REVERT: 2 175 LYS cc_start: 0.8467 (ttmt) cc_final: 0.8157 (ttmm) REVERT: 2 183 GLN cc_start: 0.7613 (mm110) cc_final: 0.7343 (mm-40) REVERT: 2 193 GLU cc_start: 0.8016 (tp30) cc_final: 0.7807 (tp30) REVERT: 2 235 TYR cc_start: 0.7405 (t80) cc_final: 0.7043 (t80) REVERT: 2 242 MET cc_start: 0.7133 (mmm) cc_final: 0.6249 (tmm) REVERT: 2 262 GLU cc_start: 0.6622 (mp0) cc_final: 0.6286 (mp0) REVERT: 2 286 ASN cc_start: 0.8624 (t0) cc_final: 0.8206 (t0) REVERT: 2 309 GLU cc_start: 0.6874 (pm20) cc_final: 0.6456 (pm20) REVERT: 3 24 LYS cc_start: 0.7929 (tttt) cc_final: 0.7462 (ttpp) REVERT: 3 27 SER cc_start: 0.8121 (m) cc_final: 0.7668 (p) REVERT: 3 30 ASP cc_start: 0.7901 (m-30) cc_final: 0.7467 (m-30) REVERT: 3 34 ASP cc_start: 0.7678 (m-30) cc_final: 0.7140 (m-30) REVERT: 3 39 GLU cc_start: 0.7034 (mp0) cc_final: 0.6535 (mp0) REVERT: 3 46 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7978 (tpt) REVERT: 3 61 LYS cc_start: 0.7977 (tptp) cc_final: 0.7614 (tptt) REVERT: 3 65 GLN cc_start: 0.8240 (pt0) cc_final: 0.7440 (pp30) REVERT: 3 87 ASN cc_start: 0.7955 (t0) cc_final: 0.7669 (t0) REVERT: 3 92 ASP cc_start: 0.7597 (t0) cc_final: 0.7266 (t0) REVERT: 3 96 GLU cc_start: 0.7434 (tm-30) cc_final: 0.7186 (tm-30) REVERT: 3 109 GLU cc_start: 0.7720 (tt0) cc_final: 0.7407 (tt0) REVERT: 3 135 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7816 (mm-30) REVERT: 3 149 THR cc_start: 0.7594 (p) cc_final: 0.7292 (p) REVERT: 3 157 MET cc_start: 0.7694 (ttm) cc_final: 0.7031 (tpp) REVERT: 3 175 LYS cc_start: 0.7842 (ttmt) cc_final: 0.7569 (ttmm) REVERT: 3 181 ASN cc_start: 0.7673 (t0) cc_final: 0.7166 (t0) REVERT: 3 207 LYS cc_start: 0.8219 (tttt) cc_final: 0.7445 (ttmm) REVERT: 3 230 LEU cc_start: 0.6969 (tp) cc_final: 0.6653 (tp) REVERT: 3 233 LYS cc_start: 0.7458 (mtpt) cc_final: 0.6955 (mtmm) REVERT: 3 239 GLN cc_start: 0.7511 (mp10) cc_final: 0.7280 (mm-40) REVERT: 3 241 ASN cc_start: 0.7034 (m-40) cc_final: 0.6728 (t0) REVERT: 3 242 MET cc_start: 0.7943 (mmm) cc_final: 0.7577 (tmm) REVERT: 3 250 TYR cc_start: 0.7565 (t80) cc_final: 0.7009 (t80) REVERT: 3 255 GLU cc_start: 0.7667 (tp30) cc_final: 0.7182 (tp30) REVERT: 3 259 ASN cc_start: 0.7125 (OUTLIER) cc_final: 0.6631 (p0) REVERT: 3 268 ASP cc_start: 0.7117 (p0) cc_final: 0.6667 (p0) REVERT: 3 269 PHE cc_start: 0.6472 (OUTLIER) cc_final: 0.4926 (t80) REVERT: 3 282 ASN cc_start: 0.8149 (t0) cc_final: 0.7880 (t0) REVERT: 3 300 ARG cc_start: 0.8350 (mtm-85) cc_final: 0.8112 (ptp90) REVERT: 4 14 ARG cc_start: 0.8150 (mtm-85) cc_final: 0.7724 (mtm-85) REVERT: 4 19 THR cc_start: 0.7645 (p) cc_final: 0.7305 (p) REVERT: 4 23 ARG cc_start: 0.6774 (mtm180) cc_final: 0.6490 (mtm180) REVERT: 4 25 ILE cc_start: 0.7172 (mm) cc_final: 0.6921 (tp) REVERT: 4 29 MET cc_start: 0.7551 (mtt) cc_final: 0.7003 (mmp) REVERT: 4 45 MET cc_start: 0.7765 (ttp) cc_final: 0.7085 (ttp) REVERT: 4 62 TYR cc_start: 0.7657 (t80) cc_final: 0.7200 (t80) REVERT: 4 83 GLU cc_start: 0.7541 (tt0) cc_final: 0.6542 (tt0) REVERT: 4 133 ILE cc_start: 0.7149 (mt) cc_final: 0.6892 (mm) REVERT: 4 146 ARG cc_start: 0.6839 (ptm160) cc_final: 0.6294 (ptm160) REVERT: 4 154 TRP cc_start: 0.7578 (t60) cc_final: 0.7198 (t60) REVERT: 4 155 LEU cc_start: 0.8295 (mt) cc_final: 0.8072 (mm) REVERT: 4 171 MET cc_start: 0.8256 (mtp) cc_final: 0.7796 (mtp) REVERT: 4 178 LEU cc_start: 0.7028 (tp) cc_final: 0.6708 (pp) REVERT: 4 190 ILE cc_start: 0.8012 (mt) cc_final: 0.7676 (pt) REVERT: 4 193 GLU cc_start: 0.7369 (tp30) cc_final: 0.7043 (tp30) REVERT: 4 242 MET cc_start: 0.7989 (tpp) cc_final: 0.7767 (tpp) REVERT: 4 247 ASN cc_start: 0.7611 (m-40) cc_final: 0.7279 (t0) REVERT: 4 255 GLU cc_start: 0.6699 (tp30) cc_final: 0.6407 (tp30) REVERT: 4 262 GLU cc_start: 0.7018 (mp0) cc_final: 0.6795 (mp0) REVERT: 4 271 PHE cc_start: 0.7837 (t80) cc_final: 0.7463 (t80) REVERT: 4 274 LYS cc_start: 0.7769 (mttt) cc_final: 0.7312 (mtmt) REVERT: 4 286 ASN cc_start: 0.7870 (t0) cc_final: 0.7562 (t0) REVERT: 4 295 THR cc_start: 0.8409 (t) cc_final: 0.7785 (t) REVERT: 4 298 MET cc_start: 0.6815 (OUTLIER) cc_final: 0.6174 (mpp) REVERT: 4 304 LYS cc_start: 0.7337 (tppt) cc_final: 0.6942 (tppt) REVERT: 5 30 ASP cc_start: 0.6487 (OUTLIER) cc_final: 0.6247 (t0) REVERT: 5 45 MET cc_start: 0.8272 (ttm) cc_final: 0.8041 (ttp) REVERT: 5 55 LYS cc_start: 0.6557 (mtmm) cc_final: 0.6053 (mtmm) REVERT: 5 60 LYS cc_start: 0.7247 (mmmt) cc_final: 0.6615 (tppt) REVERT: 5 105 LEU cc_start: 0.6739 (OUTLIER) cc_final: 0.6267 (mp) REVERT: 5 171 MET cc_start: 0.7591 (mtp) cc_final: 0.7053 (mtp) REVERT: 5 215 LYS cc_start: 0.7394 (mmtt) cc_final: 0.6949 (tmtt) REVERT: 6 24 LYS cc_start: 0.7598 (ttmm) cc_final: 0.7363 (ttpp) REVERT: 6 30 ASP cc_start: 0.6638 (m-30) cc_final: 0.6390 (m-30) REVERT: 6 41 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8001 (mm-30) REVERT: 6 46 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7725 (tpt) REVERT: 6 64 ASN cc_start: 0.6059 (m-40) cc_final: 0.5791 (m-40) REVERT: 6 96 GLU cc_start: 0.7183 (tm-30) cc_final: 0.6913 (tm-30) REVERT: 6 107 LEU cc_start: 0.7373 (pt) cc_final: 0.6999 (tp) REVERT: 6 115 LEU cc_start: 0.6620 (pp) cc_final: 0.6248 (tp) REVERT: 6 134 ASP cc_start: 0.7217 (t0) cc_final: 0.6844 (t0) REVERT: 6 135 GLU cc_start: 0.7503 (mm-30) cc_final: 0.6985 (mm-30) REVERT: 6 137 GLN cc_start: 0.7613 (pm20) cc_final: 0.6845 (pm20) REVERT: 6 143 ARG cc_start: 0.8141 (ppt170) cc_final: 0.7629 (ppt170) REVERT: 6 146 ARG cc_start: 0.7774 (ptm160) cc_final: 0.7439 (ptm160) REVERT: 6 149 THR cc_start: 0.7738 (p) cc_final: 0.7293 (p) REVERT: 6 150 GLN cc_start: 0.7617 (mt0) cc_final: 0.7311 (mt0) REVERT: 6 153 ASN cc_start: 0.7548 (m-40) cc_final: 0.7294 (m-40) REVERT: 6 162 THR cc_start: 0.7587 (OUTLIER) cc_final: 0.7167 (p) REVERT: 6 164 CYS cc_start: 0.7818 (t) cc_final: 0.7361 (p) REVERT: 6 175 LYS cc_start: 0.7823 (ttmt) cc_final: 0.7498 (ttmm) REVERT: 6 188 PHE cc_start: 0.7980 (m-80) cc_final: 0.7587 (m-80) REVERT: 6 237 PHE cc_start: 0.7864 (t80) cc_final: 0.7238 (t80) REVERT: 6 242 MET cc_start: 0.8039 (tpp) cc_final: 0.7304 (mmm) REVERT: 6 259 ASN cc_start: 0.5772 (OUTLIER) cc_final: 0.5530 (p0) REVERT: 6 262 GLU cc_start: 0.6593 (mp0) cc_final: 0.6045 (mp0) REVERT: 6 268 ASP cc_start: 0.7378 (p0) cc_final: 0.7114 (p0) REVERT: 6 271 PHE cc_start: 0.7647 (t80) cc_final: 0.7420 (t80) REVERT: 7 14 ARG cc_start: 0.8065 (mtm-85) cc_final: 0.7761 (mtt90) REVERT: 7 24 LYS cc_start: 0.7577 (tttt) cc_final: 0.7317 (ttpp) REVERT: 7 39 GLU cc_start: 0.7580 (mp0) cc_final: 0.6921 (mp0) REVERT: 7 44 CYS cc_start: 0.7895 (m) cc_final: 0.7660 (m) REVERT: 7 48 TYR cc_start: 0.8186 (m-80) cc_final: 0.7502 (m-10) REVERT: 7 83 GLU cc_start: 0.7171 (tt0) cc_final: 0.6954 (mt-10) REVERT: 7 111 ASP cc_start: 0.6938 (t70) cc_final: 0.6566 (t70) REVERT: 7 129 LYS cc_start: 0.7858 (mmmm) cc_final: 0.7573 (mttp) REVERT: 7 146 ARG cc_start: 0.7862 (ptm160) cc_final: 0.7625 (ptm160) REVERT: 7 162 THR cc_start: 0.7602 (OUTLIER) cc_final: 0.7234 (p) REVERT: 7 166 ILE cc_start: 0.8298 (mt) cc_final: 0.7960 (tp) REVERT: 7 175 LYS cc_start: 0.7575 (ttmt) cc_final: 0.7140 (ttmt) REVERT: 7 181 ASN cc_start: 0.7577 (t0) cc_final: 0.7145 (t0) REVERT: 7 193 GLU cc_start: 0.8002 (tp30) cc_final: 0.7558 (tp30) REVERT: 7 228 GLU cc_start: 0.7003 (tm-30) cc_final: 0.6378 (tm-30) REVERT: 7 232 LYS cc_start: 0.7397 (ttmm) cc_final: 0.6722 (ttpp) REVERT: 7 271 PHE cc_start: 0.7972 (t80) cc_final: 0.7590 (t80) REVERT: 7 313 ARG cc_start: 0.6956 (ttp-170) cc_final: 0.6742 (ttm110) outliers start: 111 outliers final: 62 residues processed: 670 average time/residue: 0.3784 time to fit residues: 354.3120 Evaluate side-chains 677 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 599 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 1 residue 46 MET 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 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 295 THR 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 46 MET Chi-restraints excluded: chain 2 residue 96 GLU Chi-restraints excluded: chain 2 residue 141 GLU Chi-restraints excluded: chain 2 residue 162 THR Chi-restraints excluded: chain 2 residue 168 ILE Chi-restraints excluded: chain 2 residue 213 LEU Chi-restraints excluded: chain 2 residue 263 THR 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 46 MET 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 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 10 SER Chi-restraints excluded: chain 4 residue 27 SER Chi-restraints excluded: chain 4 residue 60 LYS Chi-restraints excluded: chain 4 residue 79 VAL 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 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 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 30 ASP Chi-restraints excluded: chain 5 residue 97 LEU Chi-restraints excluded: chain 5 residue 105 LEU Chi-restraints excluded: chain 5 residue 142 GLU Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 158 ILE Chi-restraints excluded: chain 5 residue 168 ILE Chi-restraints excluded: chain 5 residue 211 GLU Chi-restraints excluded: chain 5 residue 299 LEU Chi-restraints excluded: chain 6 residue 46 MET Chi-restraints excluded: chain 6 residue 63 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 259 ASN Chi-restraints excluded: chain 6 residue 263 THR Chi-restraints excluded: chain 6 residue 304 LYS Chi-restraints excluded: chain 7 residue 19 THR 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 162 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 177 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 3 optimal weight: 30.0000 chunk 159 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 109 optimal weight: 0.8980 chunk 191 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 64 ASN ** 1 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 231 GLN ** 1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 282 ASN 2 181 ASN ** 2 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 261 HIS 5 150 GLN 7 247 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 18772 Z= 0.429 Angle : 0.718 9.225 25612 Z= 0.366 Chirality : 0.046 0.258 2863 Planarity : 0.005 0.042 3122 Dihedral : 16.436 89.664 3104 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 7.20 % Allowed : 25.05 % Favored : 67.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.18), residues: 2163 helix: 0.42 (0.15), residues: 1204 sheet: -2.31 (0.36), residues: 224 loop : -2.31 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP 4 154 HIS 0.010 0.001 HIS 3 261 PHE 0.019 0.002 PHE 7 188 TYR 0.025 0.003 TYR 6 199 ARG 0.008 0.001 ARG 1 95 *********************** 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 757 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 622 time to evaluate : 1.778 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: 0.7692 (mtp180) cc_final: 0.7336 (mtm-85) REVERT: 1 23 ARG cc_start: 0.7496 (mtm110) cc_final: 0.7056 (mtm110) REVERT: 1 30 ASP cc_start: 0.7286 (m-30) cc_final: 0.7026 (m-30) REVERT: 1 37 ASP cc_start: 0.8038 (p0) cc_final: 0.7608 (p0) REVERT: 1 38 LEU cc_start: 0.7628 (mt) cc_final: 0.7347 (mt) REVERT: 1 39 GLU cc_start: 0.6428 (mp0) cc_final: 0.5912 (mp0) REVERT: 1 46 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7568 (tpp) REVERT: 1 65 GLN cc_start: 0.7383 (pt0) cc_final: 0.7069 (pp30) REVERT: 1 83 GLU cc_start: 0.7971 (tt0) cc_final: 0.7504 (mt-10) REVERT: 1 92 ASP cc_start: 0.7309 (t0) cc_final: 0.7010 (t0) REVERT: 1 100 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7155 (tm-30) REVERT: 1 101 MET cc_start: 0.8071 (ttp) cc_final: 0.7792 (ttp) REVERT: 1 129 LYS cc_start: 0.8310 (mtpt) cc_final: 0.8006 (mtpt) REVERT: 1 171 MET cc_start: 0.8204 (mtp) cc_final: 0.7786 (mmm) REVERT: 1 175 LYS cc_start: 0.7303 (ttmt) cc_final: 0.7037 (ttpp) REVERT: 1 179 GLN cc_start: 0.7485 (mt0) cc_final: 0.7270 (mt0) REVERT: 1 192 VAL cc_start: 0.8210 (OUTLIER) cc_final: 0.7838 (m) REVERT: 1 193 GLU cc_start: 0.8008 (tp30) cc_final: 0.7583 (tp30) REVERT: 1 228 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7441 (tm-30) REVERT: 1 269 PHE cc_start: 0.6551 (OUTLIER) cc_final: 0.6195 (m-80) REVERT: 1 274 LYS cc_start: 0.7949 (mttt) cc_final: 0.7549 (mtpp) REVERT: 1 279 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7393 (p0) REVERT: 1 285 LYS cc_start: 0.7797 (tppt) cc_final: 0.7463 (tppt) REVERT: 1 300 ARG cc_start: 0.8189 (mtm-85) cc_final: 0.7558 (tpp80) REVERT: 1 310 ASP cc_start: 0.7378 (m-30) cc_final: 0.7080 (m-30) REVERT: 2 39 GLU cc_start: 0.6335 (mp0) cc_final: 0.5891 (mp0) REVERT: 2 40 SER cc_start: 0.7762 (m) cc_final: 0.7369 (t) REVERT: 2 41 GLU cc_start: 0.7972 (tt0) cc_final: 0.7493 (mm-30) REVERT: 2 46 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7775 (ttt) REVERT: 2 89 LYS cc_start: 0.7580 (mmmt) cc_final: 0.7093 (mmmt) REVERT: 2 96 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7281 (tp30) REVERT: 2 116 THR cc_start: 0.7930 (m) cc_final: 0.7557 (p) REVERT: 2 121 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7217 (mt-10) REVERT: 2 122 LEU cc_start: 0.7398 (tp) cc_final: 0.7031 (tp) REVERT: 2 135 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7384 (mm-30) REVERT: 2 141 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6291 (tm-30) REVERT: 2 146 ARG cc_start: 0.7465 (ptm-80) cc_final: 0.7107 (tmm-80) REVERT: 2 150 GLN cc_start: 0.7743 (mt0) cc_final: 0.7123 (mt0) REVERT: 2 162 THR cc_start: 0.7801 (OUTLIER) cc_final: 0.7539 (p) REVERT: 2 163 LYS cc_start: 0.7992 (mppt) cc_final: 0.7316 (mmtm) REVERT: 2 232 LYS cc_start: 0.8104 (tppt) cc_final: 0.7746 (mmmm) REVERT: 2 242 MET cc_start: 0.7371 (mmm) cc_final: 0.6740 (mmm) REVERT: 2 262 GLU cc_start: 0.6703 (mp0) cc_final: 0.6335 (mp0) REVERT: 2 269 PHE cc_start: 0.6935 (OUTLIER) cc_final: 0.6379 (t80) REVERT: 2 286 ASN cc_start: 0.8597 (t0) cc_final: 0.8182 (t0) REVERT: 2 309 GLU cc_start: 0.7253 (pm20) cc_final: 0.6845 (pm20) REVERT: 2 312 LEU cc_start: 0.7718 (mt) cc_final: 0.7505 (mm) REVERT: 3 27 SER cc_start: 0.8256 (m) cc_final: 0.7841 (p) REVERT: 3 34 ASP cc_start: 0.7685 (m-30) cc_final: 0.7162 (m-30) REVERT: 3 39 GLU cc_start: 0.6683 (mp0) cc_final: 0.5986 (mp0) REVERT: 3 61 LYS cc_start: 0.7987 (tptp) cc_final: 0.7332 (tptp) REVERT: 3 65 GLN cc_start: 0.8210 (pt0) cc_final: 0.7461 (pp30) REVERT: 3 92 ASP cc_start: 0.7631 (t0) cc_final: 0.7302 (t0) REVERT: 3 96 GLU cc_start: 0.7369 (tm-30) cc_final: 0.7059 (tm-30) REVERT: 3 109 GLU cc_start: 0.7871 (tt0) cc_final: 0.7552 (tt0) REVERT: 3 143 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7465 (ppt170) REVERT: 3 149 THR cc_start: 0.7742 (p) cc_final: 0.7377 (p) REVERT: 3 157 MET cc_start: 0.7757 (ttm) cc_final: 0.7079 (tpp) REVERT: 3 175 LYS cc_start: 0.7881 (ttmt) cc_final: 0.7579 (ttmm) REVERT: 3 181 ASN cc_start: 0.7750 (t0) cc_final: 0.7235 (t0) REVERT: 3 207 LYS cc_start: 0.8179 (tttt) cc_final: 0.7451 (ttmm) REVERT: 3 228 GLU cc_start: 0.6502 (tm-30) cc_final: 0.6222 (tm-30) REVERT: 3 239 GLN cc_start: 0.7772 (mp10) cc_final: 0.7570 (mm110) REVERT: 3 241 ASN cc_start: 0.7213 (m-40) cc_final: 0.6820 (m-40) REVERT: 3 255 GLU cc_start: 0.7924 (tp30) cc_final: 0.7519 (tp30) REVERT: 3 259 ASN cc_start: 0.7000 (OUTLIER) cc_final: 0.6558 (p0) REVERT: 3 268 ASP cc_start: 0.7228 (p0) cc_final: 0.6909 (p0) REVERT: 3 269 PHE cc_start: 0.6552 (OUTLIER) cc_final: 0.4990 (t80) REVERT: 3 300 ARG cc_start: 0.8408 (mtm-85) cc_final: 0.7805 (mtt-85) REVERT: 4 14 ARG cc_start: 0.8234 (mtm-85) cc_final: 0.7548 (ptp90) REVERT: 4 19 THR cc_start: 0.7831 (p) cc_final: 0.7480 (p) REVERT: 4 24 LYS cc_start: 0.7339 (tttp) cc_final: 0.6910 (tptp) REVERT: 4 29 MET cc_start: 0.7926 (mtt) cc_final: 0.7387 (mmm) REVERT: 4 45 MET cc_start: 0.7548 (ttp) cc_final: 0.7304 (ttp) REVERT: 4 62 TYR cc_start: 0.7971 (t80) cc_final: 0.7639 (t80) REVERT: 4 83 GLU cc_start: 0.7588 (tt0) cc_final: 0.6492 (tt0) REVERT: 4 131 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7457 (tp) REVERT: 4 133 ILE cc_start: 0.7355 (mt) cc_final: 0.7083 (mm) REVERT: 4 137 GLN cc_start: 0.7781 (pt0) cc_final: 0.7379 (mp10) REVERT: 4 146 ARG cc_start: 0.6809 (ptm160) cc_final: 0.6217 (ptm160) REVERT: 4 155 LEU cc_start: 0.8387 (mt) cc_final: 0.8169 (mm) REVERT: 4 178 LEU cc_start: 0.6794 (tp) cc_final: 0.6528 (pp) REVERT: 4 179 GLN cc_start: 0.7247 (mt0) cc_final: 0.6995 (mm110) REVERT: 4 193 GLU cc_start: 0.7518 (tp30) cc_final: 0.6974 (tp30) REVERT: 4 194 LEU cc_start: 0.7573 (tt) cc_final: 0.7121 (tt) REVERT: 4 195 ARG cc_start: 0.6698 (ptm160) cc_final: 0.6456 (ptp-110) REVERT: 4 242 MET cc_start: 0.8167 (tpp) cc_final: 0.7745 (tpp) REVERT: 4 247 ASN cc_start: 0.7575 (m-40) cc_final: 0.7256 (t0) REVERT: 4 262 GLU cc_start: 0.7427 (mp0) cc_final: 0.6966 (mp0) REVERT: 4 286 ASN cc_start: 0.7914 (t0) cc_final: 0.7630 (t0) REVERT: 4 295 THR cc_start: 0.8070 (t) cc_final: 0.7437 (t) REVERT: 4 298 MET cc_start: 0.6805 (OUTLIER) cc_final: 0.6154 (mpp) REVERT: 4 304 LYS cc_start: 0.7335 (tppt) cc_final: 0.6948 (tppt) REVERT: 5 38 LEU cc_start: 0.5570 (OUTLIER) cc_final: 0.5339 (tt) REVERT: 5 55 LYS cc_start: 0.5849 (mtmm) cc_final: 0.5194 (mtmm) REVERT: 5 105 LEU cc_start: 0.6724 (OUTLIER) cc_final: 0.6239 (mt) REVERT: 5 171 MET cc_start: 0.7590 (mtp) cc_final: 0.7048 (mtp) REVERT: 5 182 SER cc_start: 0.7086 (t) cc_final: 0.6698 (m) REVERT: 5 215 LYS cc_start: 0.7395 (mmtt) cc_final: 0.6947 (tmtt) REVERT: 5 241 ASN cc_start: 0.6666 (t0) cc_final: 0.6180 (t0) REVERT: 6 5 ARG cc_start: 0.5522 (tpp80) cc_final: 0.5177 (tpp-160) REVERT: 6 41 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8150 (mm-30) REVERT: 6 46 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7548 (tpt) REVERT: 6 96 GLU cc_start: 0.7226 (tm-30) cc_final: 0.6999 (tp30) REVERT: 6 107 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7067 (tp) REVERT: 6 134 ASP cc_start: 0.7116 (t0) cc_final: 0.6746 (t0) REVERT: 6 135 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7127 (mm-30) REVERT: 6 137 GLN cc_start: 0.7772 (pm20) cc_final: 0.6981 (pm20) REVERT: 6 143 ARG cc_start: 0.8143 (ppt170) cc_final: 0.7641 (ppt170) REVERT: 6 146 ARG cc_start: 0.7775 (ptm160) cc_final: 0.7400 (ptm160) REVERT: 6 150 GLN cc_start: 0.7811 (mt0) cc_final: 0.7499 (mt0) REVERT: 6 158 ILE cc_start: 0.6953 (tp) cc_final: 0.6647 (mm) REVERT: 6 162 THR cc_start: 0.7465 (OUTLIER) cc_final: 0.7265 (p) REVERT: 6 164 CYS cc_start: 0.7752 (t) cc_final: 0.7468 (m) REVERT: 6 175 LYS cc_start: 0.7767 (ttmt) cc_final: 0.7450 (ttmm) REVERT: 6 188 PHE cc_start: 0.8007 (m-80) cc_final: 0.7643 (m-80) REVERT: 6 189 SER cc_start: 0.8512 (p) cc_final: 0.8115 (m) REVERT: 6 231 GLN cc_start: 0.8577 (tt0) cc_final: 0.8231 (tt0) REVERT: 6 237 PHE cc_start: 0.7937 (t80) cc_final: 0.6894 (t80) REVERT: 6 242 MET cc_start: 0.7993 (tpp) cc_final: 0.7652 (mmm) REVERT: 6 259 ASN cc_start: 0.6208 (OUTLIER) cc_final: 0.5934 (p0) REVERT: 6 262 GLU cc_start: 0.6773 (mp0) cc_final: 0.6452 (mp0) REVERT: 6 263 THR cc_start: 0.6363 (OUTLIER) cc_final: 0.6095 (m) REVERT: 6 266 GLU cc_start: 0.7949 (tp30) cc_final: 0.7435 (tp30) REVERT: 6 271 PHE cc_start: 0.7756 (t80) cc_final: 0.7492 (t80) REVERT: 7 14 ARG cc_start: 0.8148 (mtm-85) cc_final: 0.7881 (mtt90) REVERT: 7 24 LYS cc_start: 0.7636 (tttt) cc_final: 0.7356 (ttpt) REVERT: 7 37 ASP cc_start: 0.7194 (p0) cc_final: 0.5925 (p0) REVERT: 7 39 GLU cc_start: 0.7604 (mp0) cc_final: 0.6616 (mp0) REVERT: 7 48 TYR cc_start: 0.8329 (m-80) cc_final: 0.7878 (m-10) REVERT: 7 83 GLU cc_start: 0.7334 (tt0) cc_final: 0.7069 (mt-10) REVERT: 7 111 ASP cc_start: 0.6866 (t70) cc_final: 0.6540 (t70) REVERT: 7 129 LYS cc_start: 0.7849 (mmmm) cc_final: 0.7591 (mttp) REVERT: 7 141 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7233 (mt-10) REVERT: 7 145 ASN cc_start: 0.7819 (m-40) cc_final: 0.7555 (m-40) REVERT: 7 146 ARG cc_start: 0.7823 (ptm160) cc_final: 0.7475 (ptm160) REVERT: 7 162 THR cc_start: 0.7641 (OUTLIER) cc_final: 0.7304 (p) REVERT: 7 181 ASN cc_start: 0.7655 (t0) cc_final: 0.7182 (t0) REVERT: 7 193 GLU cc_start: 0.8025 (tp30) cc_final: 0.7500 (tp30) REVERT: 7 228 GLU cc_start: 0.7138 (tm-30) cc_final: 0.6603 (tm-30) REVERT: 7 232 LYS cc_start: 0.7465 (ttmm) cc_final: 0.6801 (ttpp) REVERT: 7 271 PHE cc_start: 0.8003 (t80) cc_final: 0.7770 (t80) outliers start: 135 outliers final: 82 residues processed: 692 average time/residue: 0.3674 time to fit residues: 357.4325 Evaluate side-chains 714 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 609 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 1 residue 46 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 117 LYS Chi-restraints excluded: chain 1 residue 119 LEU Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 1 residue 158 ILE Chi-restraints excluded: chain 1 residue 176 VAL Chi-restraints excluded: chain 1 residue 192 VAL Chi-restraints excluded: chain 1 residue 215 LYS 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 46 MET Chi-restraints excluded: chain 2 residue 96 GLU Chi-restraints excluded: chain 2 residue 98 LEU Chi-restraints excluded: chain 2 residue 101 MET Chi-restraints excluded: chain 2 residue 107 LEU Chi-restraints excluded: chain 2 residue 117 LYS Chi-restraints excluded: chain 2 residue 141 GLU Chi-restraints excluded: chain 2 residue 149 THR Chi-restraints excluded: chain 2 residue 162 THR 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 263 THR Chi-restraints excluded: chain 2 residue 269 PHE 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 63 LEU Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 117 LYS 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 179 GLN 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 10 SER Chi-restraints excluded: chain 4 residue 27 SER Chi-restraints excluded: chain 4 residue 30 ASP Chi-restraints excluded: chain 4 residue 60 LYS Chi-restraints excluded: chain 4 residue 79 VAL 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 162 THR Chi-restraints excluded: chain 4 residue 192 VAL 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 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 38 LEU Chi-restraints excluded: chain 5 residue 63 LEU Chi-restraints excluded: chain 5 residue 97 LEU Chi-restraints excluded: chain 5 residue 105 LEU Chi-restraints excluded: chain 5 residue 142 GLU Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 158 ILE Chi-restraints excluded: chain 5 residue 168 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 46 MET Chi-restraints excluded: chain 6 residue 63 LEU Chi-restraints excluded: chain 6 residue 91 VAL Chi-restraints excluded: chain 6 residue 99 VAL Chi-restraints excluded: chain 6 residue 107 LEU 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 263 THR Chi-restraints excluded: chain 7 residue 40 SER Chi-restraints excluded: chain 7 residue 117 LYS Chi-restraints excluded: chain 7 residue 119 LEU Chi-restraints excluded: chain 7 residue 141 GLU Chi-restraints excluded: chain 7 residue 142 GLU 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 269 PHE 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 71 optimal weight: 0.5980 chunk 192 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 125 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 213 optimal weight: 0.6980 chunk 177 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 112 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 64 ASN 1 87 ASN 1 183 GLN ** 1 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 259 ASN 1 282 ASN 2 181 ASN ** 3 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 259 ASN ** 4 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 64 ASN ** 6 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 247 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18772 Z= 0.222 Angle : 0.652 11.189 25612 Z= 0.325 Chirality : 0.041 0.233 2863 Planarity : 0.004 0.048 3122 Dihedral : 16.157 88.371 3100 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 6.40 % Allowed : 26.49 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.18), residues: 2163 helix: 0.73 (0.15), residues: 1204 sheet: -2.10 (0.37), residues: 224 loop : -2.17 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP 6 154 HIS 0.002 0.001 HIS 6 185 PHE 0.018 0.002 PHE 4 271 TYR 0.024 0.002 TYR 4 173 ARG 0.011 0.001 ARG 5 23 *********************** 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 714 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 594 time to evaluate : 2.118 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 11 ARG cc_start: 0.7826 (mtp180) cc_final: 0.7403 (ttp-170) REVERT: 1 23 ARG cc_start: 0.7634 (mtm110) cc_final: 0.7063 (mtm110) REVERT: 1 30 ASP cc_start: 0.7232 (m-30) cc_final: 0.7025 (m-30) REVERT: 1 31 ARG cc_start: 0.6958 (OUTLIER) cc_final: 0.6681 (ttm170) REVERT: 1 37 ASP cc_start: 0.7838 (p0) cc_final: 0.6928 (p0) REVERT: 1 38 LEU cc_start: 0.7602 (mt) cc_final: 0.7279 (mt) REVERT: 1 39 GLU cc_start: 0.6364 (mp0) cc_final: 0.5446 (mp0) REVERT: 1 46 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.7329 (tpp) REVERT: 1 65 GLN cc_start: 0.7381 (pt0) cc_final: 0.7058 (pp30) REVERT: 1 83 GLU cc_start: 0.7915 (tt0) cc_final: 0.7703 (mt-10) REVERT: 1 92 ASP cc_start: 0.7284 (t0) cc_final: 0.6981 (t0) REVERT: 1 96 GLU cc_start: 0.6995 (tm-30) cc_final: 0.6716 (tm-30) REVERT: 1 100 GLU cc_start: 0.7618 (tm-30) cc_final: 0.6982 (tm-30) REVERT: 1 101 MET cc_start: 0.8082 (ttp) cc_final: 0.7799 (ttp) REVERT: 1 105 LEU cc_start: 0.7444 (pp) cc_final: 0.7107 (mp) REVERT: 1 129 LYS cc_start: 0.8279 (mtpt) cc_final: 0.7933 (mtpt) REVERT: 1 171 MET cc_start: 0.8183 (mtp) cc_final: 0.7809 (mmm) REVERT: 1 175 LYS cc_start: 0.7311 (ttmt) cc_final: 0.7036 (ttpp) REVERT: 1 179 GLN cc_start: 0.7442 (mt0) cc_final: 0.7218 (mt0) REVERT: 1 192 VAL cc_start: 0.8155 (OUTLIER) cc_final: 0.7796 (m) REVERT: 1 193 GLU cc_start: 0.7984 (tp30) cc_final: 0.7575 (tp30) REVERT: 1 228 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7578 (tm-30) REVERT: 1 261 HIS cc_start: 0.6728 (OUTLIER) cc_final: 0.6233 (m170) REVERT: 1 269 PHE cc_start: 0.6518 (OUTLIER) cc_final: 0.6212 (m-80) REVERT: 1 274 LYS cc_start: 0.8059 (mttt) cc_final: 0.7720 (mttp) REVERT: 1 285 LYS cc_start: 0.7707 (tppt) cc_final: 0.7379 (tppt) REVERT: 1 297 ASP cc_start: 0.7826 (t0) cc_final: 0.7339 (t0) REVERT: 1 300 ARG cc_start: 0.8155 (mtm-85) cc_final: 0.7705 (mtm-85) REVERT: 1 310 ASP cc_start: 0.7401 (m-30) cc_final: 0.6929 (m-30) REVERT: 2 33 ARG cc_start: 0.8202 (ttp80) cc_final: 0.7960 (ttp-110) REVERT: 2 39 GLU cc_start: 0.6357 (mp0) cc_final: 0.5937 (mp0) REVERT: 2 40 SER cc_start: 0.7756 (m) cc_final: 0.7361 (t) REVERT: 2 41 GLU cc_start: 0.7914 (tt0) cc_final: 0.7471 (mm-30) REVERT: 2 46 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7810 (ttt) REVERT: 2 89 LYS cc_start: 0.7471 (mmmt) cc_final: 0.6987 (mmmt) REVERT: 2 96 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7195 (tp30) REVERT: 2 100 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7313 (tm-30) REVERT: 2 116 THR cc_start: 0.7877 (m) cc_final: 0.7532 (p) REVERT: 2 121 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7203 (mt-10) REVERT: 2 122 LEU cc_start: 0.7251 (tp) cc_final: 0.6881 (tp) REVERT: 2 141 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6185 (tm-30) REVERT: 2 150 GLN cc_start: 0.7743 (mt0) cc_final: 0.7116 (mt0) REVERT: 2 162 THR cc_start: 0.7842 (OUTLIER) cc_final: 0.7589 (p) REVERT: 2 163 LYS cc_start: 0.7990 (mppt) cc_final: 0.7285 (mmtm) REVERT: 2 242 MET cc_start: 0.7313 (mmm) cc_final: 0.6668 (mmm) REVERT: 2 262 GLU cc_start: 0.6708 (mp0) cc_final: 0.6349 (mp0) REVERT: 2 286 ASN cc_start: 0.8568 (t0) cc_final: 0.8041 (t0) REVERT: 2 300 ARG cc_start: 0.7868 (mtm-85) cc_final: 0.7365 (mtm-85) REVERT: 2 309 GLU cc_start: 0.7261 (pm20) cc_final: 0.6900 (pm20) REVERT: 2 312 LEU cc_start: 0.7656 (mt) cc_final: 0.7453 (mm) REVERT: 3 27 SER cc_start: 0.8096 (m) cc_final: 0.7629 (p) REVERT: 3 39 GLU cc_start: 0.6708 (mp0) cc_final: 0.6044 (mp0) REVERT: 3 46 MET cc_start: 0.8126 (tpt) cc_final: 0.7659 (tpp) REVERT: 3 61 LYS cc_start: 0.7924 (tptp) cc_final: 0.7528 (tptt) REVERT: 3 65 GLN cc_start: 0.8215 (pt0) cc_final: 0.7658 (pp30) REVERT: 3 86 ASP cc_start: 0.8654 (t0) cc_final: 0.8409 (t0) REVERT: 3 92 ASP cc_start: 0.7647 (t0) cc_final: 0.7257 (t0) REVERT: 3 96 GLU cc_start: 0.7385 (tm-30) cc_final: 0.7078 (tm-30) REVERT: 3 109 GLU cc_start: 0.7822 (tt0) cc_final: 0.7469 (tt0) REVERT: 3 131 ILE cc_start: 0.7630 (mt) cc_final: 0.7428 (mp) REVERT: 3 143 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7378 (ppt170) REVERT: 3 149 THR cc_start: 0.7825 (p) cc_final: 0.7395 (p) REVERT: 3 157 MET cc_start: 0.7737 (ttm) cc_final: 0.7051 (tpp) REVERT: 3 174 SER cc_start: 0.8530 (p) cc_final: 0.8155 (t) REVERT: 3 175 LYS cc_start: 0.7878 (ttmt) cc_final: 0.7532 (ttmm) REVERT: 3 181 ASN cc_start: 0.7706 (t0) cc_final: 0.7151 (t0) REVERT: 3 207 LYS cc_start: 0.8216 (tttt) cc_final: 0.7448 (ttmm) REVERT: 3 228 GLU cc_start: 0.6494 (tm-30) cc_final: 0.6261 (tm-30) REVERT: 3 239 GLN cc_start: 0.7594 (mp10) cc_final: 0.7369 (mm110) REVERT: 3 241 ASN cc_start: 0.7178 (m-40) cc_final: 0.6757 (t0) REVERT: 3 250 TYR cc_start: 0.7388 (t80) cc_final: 0.6715 (t80) REVERT: 3 255 GLU cc_start: 0.7868 (tp30) cc_final: 0.7458 (tp30) REVERT: 3 259 ASN cc_start: 0.7268 (OUTLIER) cc_final: 0.6962 (p0) REVERT: 3 268 ASP cc_start: 0.7174 (p0) cc_final: 0.6789 (p0) REVERT: 3 269 PHE cc_start: 0.6422 (OUTLIER) cc_final: 0.4913 (t80) REVERT: 4 14 ARG cc_start: 0.8014 (mtm-85) cc_final: 0.7311 (ptp90) REVERT: 4 19 THR cc_start: 0.7703 (p) cc_final: 0.7408 (p) REVERT: 4 29 MET cc_start: 0.7641 (mtt) cc_final: 0.7232 (mmm) REVERT: 4 62 TYR cc_start: 0.7945 (t80) cc_final: 0.7598 (t80) REVERT: 4 83 GLU cc_start: 0.7552 (tt0) cc_final: 0.6283 (tt0) REVERT: 4 96 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.7045 (tp30) REVERT: 4 98 LEU cc_start: 0.8310 (mt) cc_final: 0.8062 (mm) REVERT: 4 114 ARG cc_start: 0.7831 (ttp80) cc_final: 0.7277 (ptt90) REVERT: 4 133 ILE cc_start: 0.7168 (mt) cc_final: 0.6893 (mm) REVERT: 4 146 ARG cc_start: 0.6767 (ptm160) cc_final: 0.6071 (ptm160) REVERT: 4 149 THR cc_start: 0.5645 (OUTLIER) cc_final: 0.5056 (t) REVERT: 4 154 TRP cc_start: 0.7551 (t60) cc_final: 0.7077 (t60) REVERT: 4 155 LEU cc_start: 0.8267 (mt) cc_final: 0.8061 (mm) REVERT: 4 178 LEU cc_start: 0.6822 (tp) cc_final: 0.6595 (pp) REVERT: 4 193 GLU cc_start: 0.7415 (tp30) cc_final: 0.6891 (tp30) REVERT: 4 194 LEU cc_start: 0.7501 (tt) cc_final: 0.7032 (tt) REVERT: 4 242 MET cc_start: 0.7929 (tpp) cc_final: 0.7671 (tpp) REVERT: 4 247 ASN cc_start: 0.7563 (m-40) cc_final: 0.7213 (t0) REVERT: 4 262 GLU cc_start: 0.7352 (mp0) cc_final: 0.6910 (mp0) REVERT: 4 271 PHE cc_start: 0.7548 (t80) cc_final: 0.7335 (t80) REVERT: 4 274 LYS cc_start: 0.7781 (mttt) cc_final: 0.7296 (mtmt) REVERT: 4 286 ASN cc_start: 0.7900 (t0) cc_final: 0.7599 (t0) REVERT: 5 55 LYS cc_start: 0.6095 (mtmm) cc_final: 0.5428 (mtmm) REVERT: 5 105 LEU cc_start: 0.6713 (OUTLIER) cc_final: 0.6182 (mp) REVERT: 5 171 MET cc_start: 0.7648 (mtp) cc_final: 0.7085 (mtp) REVERT: 5 182 SER cc_start: 0.7141 (t) cc_final: 0.6775 (m) REVERT: 5 215 LYS cc_start: 0.7375 (mmtt) cc_final: 0.6936 (tmtt) REVERT: 5 241 ASN cc_start: 0.6630 (t0) cc_final: 0.6019 (t0) REVERT: 6 5 ARG cc_start: 0.5393 (tpp80) cc_final: 0.5139 (tpp-160) REVERT: 6 41 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8180 (mm-30) REVERT: 6 46 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7750 (tpt) REVERT: 6 96 GLU cc_start: 0.7186 (tm-30) cc_final: 0.6964 (tp30) REVERT: 6 107 LEU cc_start: 0.7537 (pt) cc_final: 0.7097 (tp) REVERT: 6 134 ASP cc_start: 0.7139 (t0) cc_final: 0.6766 (t0) REVERT: 6 135 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7213 (mm-30) REVERT: 6 143 ARG cc_start: 0.8098 (ppt170) cc_final: 0.7646 (ppt170) REVERT: 6 146 ARG cc_start: 0.7767 (ptm160) cc_final: 0.7380 (ptm160) REVERT: 6 149 THR cc_start: 0.7802 (p) cc_final: 0.7431 (p) REVERT: 6 150 GLN cc_start: 0.7775 (mt0) cc_final: 0.7462 (mt0) REVERT: 6 158 ILE cc_start: 0.6759 (tp) cc_final: 0.6474 (mm) REVERT: 6 185 HIS cc_start: 0.7985 (t70) cc_final: 0.7621 (t70) REVERT: 6 188 PHE cc_start: 0.7955 (m-80) cc_final: 0.7558 (m-80) REVERT: 6 231 GLN cc_start: 0.8561 (tt0) cc_final: 0.8240 (tt0) REVERT: 6 242 MET cc_start: 0.7857 (tpp) cc_final: 0.7483 (mmm) REVERT: 6 259 ASN cc_start: 0.5617 (OUTLIER) cc_final: 0.5331 (p0) REVERT: 6 263 THR cc_start: 0.6192 (OUTLIER) cc_final: 0.5849 (m) REVERT: 6 269 PHE cc_start: 0.6799 (m-80) cc_final: 0.6215 (m-80) REVERT: 6 271 PHE cc_start: 0.7704 (t80) cc_final: 0.7491 (t80) REVERT: 7 5 ARG cc_start: 0.6087 (mmm-85) cc_final: 0.5832 (tpp80) REVERT: 7 14 ARG cc_start: 0.8125 (mtm-85) cc_final: 0.7844 (mtt90) REVERT: 7 24 LYS cc_start: 0.7572 (tttt) cc_final: 0.7251 (ttpt) REVERT: 7 37 ASP cc_start: 0.7211 (p0) cc_final: 0.5923 (p0) REVERT: 7 39 GLU cc_start: 0.7612 (mp0) cc_final: 0.6620 (mp0) REVERT: 7 48 TYR cc_start: 0.8139 (m-80) cc_final: 0.7701 (m-80) REVERT: 7 83 GLU cc_start: 0.7258 (tt0) cc_final: 0.7026 (mt-10) REVERT: 7 111 ASP cc_start: 0.6823 (t70) cc_final: 0.6499 (t70) REVERT: 7 129 LYS cc_start: 0.7838 (mmmm) cc_final: 0.7573 (mttm) REVERT: 7 145 ASN cc_start: 0.7770 (m-40) cc_final: 0.7498 (m-40) REVERT: 7 146 ARG cc_start: 0.7805 (ptm160) cc_final: 0.7601 (ptm160) REVERT: 7 162 THR cc_start: 0.7625 (OUTLIER) cc_final: 0.7314 (p) REVERT: 7 181 ASN cc_start: 0.7592 (t0) cc_final: 0.7137 (t0) REVERT: 7 193 GLU cc_start: 0.7939 (tp30) cc_final: 0.7424 (tp30) REVERT: 7 228 GLU cc_start: 0.7089 (tm-30) cc_final: 0.6569 (tm-30) REVERT: 7 232 LYS cc_start: 0.7408 (ttmm) cc_final: 0.6751 (ttpp) REVERT: 7 271 PHE cc_start: 0.7968 (t80) cc_final: 0.7506 (t80) REVERT: 7 313 ARG cc_start: 0.6993 (ttp-170) cc_final: 0.6734 (ttm110) outliers start: 120 outliers final: 68 residues processed: 656 average time/residue: 0.3718 time to fit residues: 342.0131 Evaluate side-chains 677 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 590 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 31 ARG Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 1 residue 46 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 117 LYS Chi-restraints excluded: chain 1 residue 119 LEU Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 1 residue 158 ILE Chi-restraints excluded: chain 1 residue 176 VAL Chi-restraints excluded: chain 1 residue 192 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 309 GLU Chi-restraints excluded: chain 2 residue 22 VAL Chi-restraints excluded: chain 2 residue 45 MET Chi-restraints excluded: chain 2 residue 46 MET Chi-restraints excluded: chain 2 residue 96 GLU Chi-restraints excluded: chain 2 residue 98 LEU Chi-restraints excluded: chain 2 residue 117 LYS Chi-restraints excluded: chain 2 residue 141 GLU Chi-restraints excluded: chain 2 residue 162 THR Chi-restraints excluded: chain 2 residue 192 VAL Chi-restraints excluded: chain 2 residue 213 LEU Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 19 THR Chi-restraints excluded: chain 3 residue 45 MET 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 115 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 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 309 GLU Chi-restraints excluded: chain 3 residue 312 LEU Chi-restraints excluded: chain 4 residue 10 SER Chi-restraints excluded: chain 4 residue 30 ASP Chi-restraints excluded: chain 4 residue 60 LYS Chi-restraints excluded: chain 4 residue 79 VAL 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 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 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 5 residue 97 LEU Chi-restraints excluded: chain 5 residue 105 LEU Chi-restraints excluded: chain 5 residue 142 GLU Chi-restraints excluded: chain 5 residue 158 ILE Chi-restraints excluded: chain 5 residue 168 ILE Chi-restraints excluded: chain 5 residue 259 ASN Chi-restraints excluded: chain 6 residue 46 MET Chi-restraints excluded: chain 6 residue 63 LEU Chi-restraints excluded: chain 6 residue 115 LEU Chi-restraints excluded: chain 6 residue 142 GLU Chi-restraints excluded: chain 6 residue 148 LEU Chi-restraints excluded: chain 6 residue 168 ILE Chi-restraints excluded: chain 6 residue 200 GLN Chi-restraints excluded: chain 6 residue 259 ASN Chi-restraints excluded: chain 6 residue 263 THR 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 148 LEU Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 214 ASP Chi-restraints excluded: chain 7 residue 263 THR Chi-restraints excluded: chain 7 residue 305 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 206 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 156 optimal weight: 0.0470 chunk 120 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 64 ASN 1 87 ASN ** 1 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 282 ASN ** 2 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 81 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 18772 Z= 0.312 Angle : 0.694 14.404 25612 Z= 0.344 Chirality : 0.043 0.217 2863 Planarity : 0.004 0.043 3122 Dihedral : 16.063 88.721 3093 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 6.02 % Allowed : 26.49 % Favored : 67.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.18), residues: 2163 helix: 0.62 (0.15), residues: 1211 sheet: -2.05 (0.37), residues: 224 loop : -2.12 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP 6 154 HIS 0.006 0.001 HIS 3 185 PHE 0.015 0.002 PHE 4 209 TYR 0.032 0.002 TYR 2 235 ARG 0.009 0.001 ARG 1 33 *********************** 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 714 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 601 time to evaluate : 1.905 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 11 ARG cc_start: 0.7723 (mtp180) cc_final: 0.7324 (ttp-170) REVERT: 1 19 THR cc_start: 0.7561 (OUTLIER) cc_final: 0.6925 (t) REVERT: 1 22 VAL cc_start: 0.6501 (t) cc_final: 0.6233 (p) REVERT: 1 23 ARG cc_start: 0.7610 (mtm110) cc_final: 0.7094 (mtm110) REVERT: 1 30 ASP cc_start: 0.7323 (m-30) cc_final: 0.7084 (m-30) REVERT: 1 31 ARG cc_start: 0.6995 (OUTLIER) cc_final: 0.6545 (ttm170) REVERT: 1 37 ASP cc_start: 0.8024 (p0) cc_final: 0.7006 (p0) REVERT: 1 38 LEU cc_start: 0.7593 (mt) cc_final: 0.7331 (mm) REVERT: 1 39 GLU cc_start: 0.6381 (mp0) cc_final: 0.5477 (mp0) REVERT: 1 65 GLN cc_start: 0.7365 (pt0) cc_final: 0.7035 (pp30) REVERT: 1 83 GLU cc_start: 0.7944 (tt0) cc_final: 0.7742 (mt-10) REVERT: 1 92 ASP cc_start: 0.7304 (t0) cc_final: 0.6914 (t0) REVERT: 1 96 GLU cc_start: 0.7004 (tm-30) cc_final: 0.6702 (tm-30) REVERT: 1 100 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7066 (tm-30) REVERT: 1 101 MET cc_start: 0.8095 (ttp) cc_final: 0.7865 (ttp) REVERT: 1 105 LEU cc_start: 0.7452 (pp) cc_final: 0.7072 (mp) REVERT: 1 129 LYS cc_start: 0.8316 (mtpt) cc_final: 0.7967 (mtpt) REVERT: 1 171 MET cc_start: 0.8188 (mtp) cc_final: 0.7836 (mmm) REVERT: 1 175 LYS cc_start: 0.7384 (ttmt) cc_final: 0.7137 (ttpp) REVERT: 1 179 GLN cc_start: 0.7546 (mt0) cc_final: 0.7324 (mt0) REVERT: 1 193 GLU cc_start: 0.7985 (tp30) cc_final: 0.7621 (tp30) REVERT: 1 228 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7604 (tm-30) REVERT: 1 261 HIS cc_start: 0.6663 (OUTLIER) cc_final: 0.6188 (m170) REVERT: 1 274 LYS cc_start: 0.8076 (mttt) cc_final: 0.7676 (mtpp) REVERT: 1 285 LYS cc_start: 0.7792 (tppt) cc_final: 0.7432 (tppt) REVERT: 1 296 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7226 (tm-30) REVERT: 1 297 ASP cc_start: 0.7870 (t0) cc_final: 0.7449 (t0) REVERT: 1 300 ARG cc_start: 0.8125 (mtm-85) cc_final: 0.7645 (mtm-85) REVERT: 1 310 ASP cc_start: 0.7389 (m-30) cc_final: 0.6919 (m-30) REVERT: 2 33 ARG cc_start: 0.8254 (ttp80) cc_final: 0.7969 (ttp-110) REVERT: 2 39 GLU cc_start: 0.6363 (mp0) cc_final: 0.5920 (mp0) REVERT: 2 40 SER cc_start: 0.7753 (m) cc_final: 0.7440 (t) REVERT: 2 46 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7822 (ttt) REVERT: 2 89 LYS cc_start: 0.7458 (mmmt) cc_final: 0.6998 (mmmt) REVERT: 2 100 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7392 (tm-30) REVERT: 2 116 THR cc_start: 0.7824 (m) cc_final: 0.7492 (p) REVERT: 2 121 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7382 (mt-10) REVERT: 2 129 LYS cc_start: 0.8021 (mmpt) cc_final: 0.7816 (mmpt) REVERT: 2 143 ARG cc_start: 0.6429 (OUTLIER) cc_final: 0.6010 (ppt-90) REVERT: 2 150 GLN cc_start: 0.7762 (mt0) cc_final: 0.7148 (mt0) REVERT: 2 162 THR cc_start: 0.7800 (OUTLIER) cc_final: 0.7531 (p) REVERT: 2 163 LYS cc_start: 0.7918 (mppt) cc_final: 0.7360 (mmtm) REVERT: 2 242 MET cc_start: 0.7388 (mmm) cc_final: 0.6922 (mmm) REVERT: 2 262 GLU cc_start: 0.6950 (mp0) cc_final: 0.6558 (mp0) REVERT: 2 269 PHE cc_start: 0.6930 (OUTLIER) cc_final: 0.6320 (t80) REVERT: 2 286 ASN cc_start: 0.8542 (t0) cc_final: 0.7994 (t0) REVERT: 2 300 ARG cc_start: 0.7902 (mtm-85) cc_final: 0.7380 (mtm-85) REVERT: 2 312 LEU cc_start: 0.7672 (mt) cc_final: 0.7469 (mm) REVERT: 3 27 SER cc_start: 0.8094 (m) cc_final: 0.7620 (p) REVERT: 3 39 GLU cc_start: 0.6800 (mp0) cc_final: 0.6138 (mp0) REVERT: 3 46 MET cc_start: 0.8158 (tpt) cc_final: 0.7706 (tpp) REVERT: 3 61 LYS cc_start: 0.7935 (tptp) cc_final: 0.7501 (tptt) REVERT: 3 65 GLN cc_start: 0.8199 (pt0) cc_final: 0.7605 (pp30) REVERT: 3 86 ASP cc_start: 0.8534 (t0) cc_final: 0.8323 (t0) REVERT: 3 92 ASP cc_start: 0.7681 (t0) cc_final: 0.7288 (t0) REVERT: 3 96 GLU cc_start: 0.7383 (tm-30) cc_final: 0.7108 (tm-30) REVERT: 3 109 GLU cc_start: 0.7847 (tt0) cc_final: 0.7518 (tt0) REVERT: 3 143 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7405 (ppt170) REVERT: 3 149 THR cc_start: 0.7841 (p) cc_final: 0.7474 (p) REVERT: 3 157 MET cc_start: 0.7756 (ttm) cc_final: 0.7067 (tpp) REVERT: 3 174 SER cc_start: 0.8515 (p) cc_final: 0.8190 (t) REVERT: 3 175 LYS cc_start: 0.7854 (ttmt) cc_final: 0.7512 (ttmm) REVERT: 3 181 ASN cc_start: 0.7716 (t0) cc_final: 0.7160 (t0) REVERT: 3 207 LYS cc_start: 0.8223 (tttt) cc_final: 0.7460 (ttmm) REVERT: 3 228 GLU cc_start: 0.6776 (tm-30) cc_final: 0.6492 (tm-30) REVERT: 3 239 GLN cc_start: 0.7719 (mp10) cc_final: 0.7471 (mm110) REVERT: 3 241 ASN cc_start: 0.7355 (m-40) cc_final: 0.6945 (t0) REVERT: 3 255 GLU cc_start: 0.7802 (tp30) cc_final: 0.7517 (tp30) REVERT: 3 259 ASN cc_start: 0.7385 (OUTLIER) cc_final: 0.6660 (p0) REVERT: 3 268 ASP cc_start: 0.7184 (p0) cc_final: 0.6860 (p0) REVERT: 3 269 PHE cc_start: 0.6468 (OUTLIER) cc_final: 0.4979 (t80) REVERT: 4 19 THR cc_start: 0.7744 (p) cc_final: 0.7399 (p) REVERT: 4 23 ARG cc_start: 0.6713 (mtm180) cc_final: 0.6302 (mtm110) REVERT: 4 29 MET cc_start: 0.7678 (mtt) cc_final: 0.7231 (mmm) REVERT: 4 62 TYR cc_start: 0.7916 (t80) cc_final: 0.7569 (t80) REVERT: 4 83 GLU cc_start: 0.7563 (tt0) cc_final: 0.6260 (tt0) REVERT: 4 96 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7035 (tp30) REVERT: 4 98 LEU cc_start: 0.8284 (mt) cc_final: 0.8028 (mm) REVERT: 4 133 ILE cc_start: 0.7220 (mt) cc_final: 0.6933 (mm) REVERT: 4 146 ARG cc_start: 0.6825 (OUTLIER) cc_final: 0.6263 (ptm160) REVERT: 4 154 TRP cc_start: 0.7628 (t60) cc_final: 0.7174 (t60) REVERT: 4 155 LEU cc_start: 0.8289 (mt) cc_final: 0.8081 (mm) REVERT: 4 178 LEU cc_start: 0.6790 (tp) cc_final: 0.6540 (pp) REVERT: 4 193 GLU cc_start: 0.7545 (tp30) cc_final: 0.7218 (tp30) REVERT: 4 194 LEU cc_start: 0.7514 (tt) cc_final: 0.7042 (tt) REVERT: 4 207 LYS cc_start: 0.7883 (tttt) cc_final: 0.7351 (tppt) REVERT: 4 242 MET cc_start: 0.8182 (tpp) cc_final: 0.7792 (tpp) REVERT: 4 247 ASN cc_start: 0.7553 (m-40) cc_final: 0.7211 (t0) REVERT: 4 262 GLU cc_start: 0.7422 (mp0) cc_final: 0.6875 (mp0) REVERT: 4 263 THR cc_start: 0.8065 (m) cc_final: 0.7712 (p) REVERT: 4 286 ASN cc_start: 0.7894 (t0) cc_final: 0.7573 (t0) REVERT: 4 298 MET cc_start: 0.7143 (OUTLIER) cc_final: 0.6611 (mpp) REVERT: 5 55 LYS cc_start: 0.5889 (mtmm) cc_final: 0.5261 (mtmm) REVERT: 5 105 LEU cc_start: 0.6675 (OUTLIER) cc_final: 0.6136 (mp) REVERT: 5 171 MET cc_start: 0.7675 (mtp) cc_final: 0.7109 (mtp) REVERT: 5 182 SER cc_start: 0.7112 (t) cc_final: 0.6760 (m) REVERT: 5 215 LYS cc_start: 0.7390 (mmtt) cc_final: 0.6922 (tmtt) REVERT: 5 241 ASN cc_start: 0.6650 (t0) cc_final: 0.6155 (t0) REVERT: 5 242 MET cc_start: 0.5522 (tpp) cc_final: 0.5077 (tmm) REVERT: 6 13 LYS cc_start: 0.8067 (tppt) cc_final: 0.7520 (tptp) REVERT: 6 41 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8197 (mm-30) REVERT: 6 46 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7733 (tpt) REVERT: 6 60 LYS cc_start: 0.7819 (mmmt) cc_final: 0.7379 (tmtt) REVERT: 6 80 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.6329 (mt) REVERT: 6 96 GLU cc_start: 0.7204 (tm-30) cc_final: 0.6958 (tp30) REVERT: 6 107 LEU cc_start: 0.7574 (pt) cc_final: 0.7319 (tp) REVERT: 6 134 ASP cc_start: 0.7155 (t0) cc_final: 0.6769 (t0) REVERT: 6 135 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7153 (mm-30) REVERT: 6 143 ARG cc_start: 0.8104 (ppt170) cc_final: 0.7655 (ppt170) REVERT: 6 146 ARG cc_start: 0.7583 (ptm160) cc_final: 0.7179 (ptm160) REVERT: 6 150 GLN cc_start: 0.7796 (mt0) cc_final: 0.7504 (mt0) REVERT: 6 158 ILE cc_start: 0.6814 (tp) cc_final: 0.6572 (mm) REVERT: 6 188 PHE cc_start: 0.7972 (m-80) cc_final: 0.7560 (m-80) REVERT: 6 231 GLN cc_start: 0.8549 (tt0) cc_final: 0.7830 (mt0) REVERT: 6 242 MET cc_start: 0.7877 (tpp) cc_final: 0.7464 (mmm) REVERT: 6 259 ASN cc_start: 0.5696 (OUTLIER) cc_final: 0.5406 (p0) REVERT: 6 262 GLU cc_start: 0.6677 (mp0) cc_final: 0.6419 (mp0) REVERT: 6 263 THR cc_start: 0.6232 (OUTLIER) cc_final: 0.5956 (m) REVERT: 6 271 PHE cc_start: 0.7742 (t80) cc_final: 0.7439 (t80) REVERT: 6 304 LYS cc_start: 0.8127 (tppt) cc_final: 0.7693 (mtpp) REVERT: 7 5 ARG cc_start: 0.6111 (mmm-85) cc_final: 0.5858 (tpp80) REVERT: 7 14 ARG cc_start: 0.8158 (mtm-85) cc_final: 0.7847 (mtt90) REVERT: 7 24 LYS cc_start: 0.7599 (tttt) cc_final: 0.7321 (ttpt) REVERT: 7 37 ASP cc_start: 0.7234 (p0) cc_final: 0.5969 (p0) REVERT: 7 39 GLU cc_start: 0.7610 (mp0) cc_final: 0.6649 (mp0) REVERT: 7 48 TYR cc_start: 0.8245 (m-80) cc_final: 0.7804 (m-80) REVERT: 7 83 GLU cc_start: 0.7294 (tt0) cc_final: 0.7047 (mt-10) REVERT: 7 111 ASP cc_start: 0.6951 (t70) cc_final: 0.6599 (t70) REVERT: 7 129 LYS cc_start: 0.7833 (mmmm) cc_final: 0.7581 (mttp) REVERT: 7 141 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7391 (mt-10) REVERT: 7 146 ARG cc_start: 0.7803 (ptm160) cc_final: 0.7509 (ptm160) REVERT: 7 162 THR cc_start: 0.7615 (OUTLIER) cc_final: 0.7320 (p) REVERT: 7 181 ASN cc_start: 0.7676 (t0) cc_final: 0.7226 (t0) REVERT: 7 193 GLU cc_start: 0.8097 (tp30) cc_final: 0.7515 (tp30) REVERT: 7 228 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6627 (tm-30) REVERT: 7 232 LYS cc_start: 0.7401 (ttmm) cc_final: 0.6735 (ttpp) REVERT: 7 250 TYR cc_start: 0.7636 (t80) cc_final: 0.7296 (t80) REVERT: 7 271 PHE cc_start: 0.7977 (t80) cc_final: 0.7471 (t80) REVERT: 7 285 LYS cc_start: 0.8408 (ttmm) cc_final: 0.7926 (tppt) REVERT: 7 313 ARG cc_start: 0.6957 (ttp-170) cc_final: 0.6709 (ttm110) outliers start: 113 outliers final: 71 residues processed: 665 average time/residue: 0.3782 time to fit residues: 352.1231 Evaluate side-chains 685 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 594 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 1 residue 31 ARG Chi-restraints excluded: chain 1 residue 63 LEU 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 148 LEU Chi-restraints excluded: chain 1 residue 158 ILE Chi-restraints excluded: chain 1 residue 178 LEU Chi-restraints excluded: chain 1 residue 217 LEU Chi-restraints excluded: chain 1 residue 261 HIS 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 46 MET Chi-restraints excluded: chain 2 residue 98 LEU Chi-restraints excluded: chain 2 residue 117 LYS Chi-restraints excluded: chain 2 residue 143 ARG Chi-restraints excluded: chain 2 residue 162 THR Chi-restraints excluded: chain 2 residue 192 VAL Chi-restraints excluded: chain 2 residue 213 LEU Chi-restraints excluded: chain 2 residue 263 THR Chi-restraints excluded: chain 2 residue 269 PHE Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 19 THR Chi-restraints excluded: chain 3 residue 45 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 143 ARG Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 179 GLN 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 309 GLU Chi-restraints excluded: chain 3 residue 312 LEU Chi-restraints excluded: chain 4 residue 10 SER Chi-restraints excluded: chain 4 residue 27 SER Chi-restraints excluded: chain 4 residue 30 ASP Chi-restraints excluded: chain 4 residue 60 LYS Chi-restraints excluded: chain 4 residue 79 VAL 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 142 GLU Chi-restraints excluded: chain 4 residue 146 ARG 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 192 VAL Chi-restraints excluded: chain 4 residue 221 LYS 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 38 LEU Chi-restraints excluded: chain 5 residue 97 LEU Chi-restraints excluded: chain 5 residue 105 LEU Chi-restraints excluded: chain 5 residue 123 ILE Chi-restraints excluded: chain 5 residue 142 GLU Chi-restraints excluded: chain 5 residue 147 VAL Chi-restraints excluded: chain 5 residue 168 ILE Chi-restraints excluded: chain 5 residue 299 LEU Chi-restraints excluded: chain 6 residue 46 MET 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 142 GLU Chi-restraints excluded: chain 6 residue 148 LEU Chi-restraints excluded: chain 6 residue 168 ILE Chi-restraints excluded: chain 6 residue 178 LEU Chi-restraints excluded: chain 6 residue 200 GLN Chi-restraints excluded: chain 6 residue 259 ASN Chi-restraints excluded: chain 6 residue 263 THR 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 141 GLU 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 263 THR Chi-restraints excluded: chain 7 residue 269 PHE 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 131 optimal weight: 4.9990 chunk 85 optimal weight: 0.0970 chunk 127 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 135 optimal weight: 0.7980 chunk 145 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 193 optimal weight: 0.6980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** 2 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 259 ASN ** 6 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 231 GLN ** 6 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 247 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18772 Z= 0.216 Angle : 0.670 13.816 25612 Z= 0.330 Chirality : 0.041 0.210 2863 Planarity : 0.004 0.039 3122 Dihedral : 15.836 87.696 3087 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 5.38 % Allowed : 27.61 % Favored : 67.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.19), residues: 2163 helix: 0.83 (0.15), residues: 1204 sheet: -1.90 (0.38), residues: 224 loop : -2.02 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP 6 154 HIS 0.003 0.001 HIS 6 185 PHE 0.017 0.002 PHE 4 209 TYR 0.025 0.002 TYR 2 235 ARG 0.008 0.001 ARG 7 33 *********************** 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 706 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 605 time to evaluate : 2.041 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 11 ARG cc_start: 0.7852 (mtp180) cc_final: 0.7433 (ttp-170) REVERT: 1 23 ARG cc_start: 0.7577 (mtm110) cc_final: 0.7033 (mtm-85) REVERT: 1 30 ASP cc_start: 0.7253 (m-30) cc_final: 0.7018 (m-30) REVERT: 1 31 ARG cc_start: 0.6946 (OUTLIER) cc_final: 0.6620 (ttm170) REVERT: 1 37 ASP cc_start: 0.7824 (p0) cc_final: 0.7316 (p0) REVERT: 1 48 TYR cc_start: 0.8468 (m-80) cc_final: 0.7780 (m-80) REVERT: 1 57 THR cc_start: 0.7526 (t) cc_final: 0.7256 (t) REVERT: 1 65 GLN cc_start: 0.7358 (pt0) cc_final: 0.7026 (pp30) REVERT: 1 81 HIS cc_start: 0.7869 (t70) cc_final: 0.7601 (t-170) REVERT: 1 92 ASP cc_start: 0.7288 (t0) cc_final: 0.6895 (t0) REVERT: 1 96 GLU cc_start: 0.6979 (tm-30) cc_final: 0.6715 (tm-30) REVERT: 1 100 GLU cc_start: 0.7553 (tm-30) cc_final: 0.6991 (tm-30) REVERT: 1 101 MET cc_start: 0.8126 (ttp) cc_final: 0.7918 (ttp) REVERT: 1 105 LEU cc_start: 0.7413 (pp) cc_final: 0.7049 (mp) REVERT: 1 109 GLU cc_start: 0.7593 (tt0) cc_final: 0.7215 (tt0) REVERT: 1 129 LYS cc_start: 0.8326 (mtpt) cc_final: 0.7949 (mtpt) REVERT: 1 171 MET cc_start: 0.8178 (mtp) cc_final: 0.7842 (mmm) REVERT: 1 179 GLN cc_start: 0.7520 (mt0) cc_final: 0.7265 (mt0) REVERT: 1 193 GLU cc_start: 0.7962 (tp30) cc_final: 0.7604 (tp30) REVERT: 1 228 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7604 (tm-30) REVERT: 1 261 HIS cc_start: 0.6680 (OUTLIER) cc_final: 0.6221 (m170) REVERT: 1 269 PHE cc_start: 0.6707 (OUTLIER) cc_final: 0.6322 (m-80) REVERT: 1 274 LYS cc_start: 0.8072 (mttt) cc_final: 0.7672 (mtpp) REVERT: 1 285 LYS cc_start: 0.7736 (tppt) cc_final: 0.7376 (tppt) REVERT: 1 293 GLU cc_start: 0.6643 (OUTLIER) cc_final: 0.6302 (tm-30) REVERT: 1 296 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7211 (tm-30) REVERT: 1 297 ASP cc_start: 0.7856 (t0) cc_final: 0.7426 (t0) REVERT: 1 300 ARG cc_start: 0.8114 (mtm-85) cc_final: 0.7707 (mtm-85) REVERT: 1 310 ASP cc_start: 0.7397 (m-30) cc_final: 0.6927 (m-30) REVERT: 2 33 ARG cc_start: 0.8145 (ttp80) cc_final: 0.7800 (ttp-110) REVERT: 2 39 GLU cc_start: 0.6355 (mp0) cc_final: 0.5948 (mp0) REVERT: 2 46 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7829 (ttt) REVERT: 2 89 LYS cc_start: 0.7418 (mmmt) cc_final: 0.6964 (mmmt) REVERT: 2 100 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7333 (tm-30) REVERT: 2 116 THR cc_start: 0.7792 (m) cc_final: 0.7493 (p) REVERT: 2 121 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7405 (mt-10) REVERT: 2 129 LYS cc_start: 0.8020 (mmpt) cc_final: 0.7699 (mmpt) REVERT: 2 143 ARG cc_start: 0.6284 (OUTLIER) cc_final: 0.5919 (ppt-90) REVERT: 2 150 GLN cc_start: 0.7737 (mt0) cc_final: 0.7104 (mt0) REVERT: 2 162 THR cc_start: 0.7814 (OUTLIER) cc_final: 0.7575 (p) REVERT: 2 163 LYS cc_start: 0.7917 (mppt) cc_final: 0.7361 (mmtm) REVERT: 2 235 TYR cc_start: 0.7599 (t80) cc_final: 0.6981 (t80) REVERT: 2 242 MET cc_start: 0.7232 (mmm) cc_final: 0.6754 (mmm) REVERT: 2 262 GLU cc_start: 0.6917 (mp0) cc_final: 0.6542 (mp0) REVERT: 2 286 ASN cc_start: 0.8514 (t0) cc_final: 0.7967 (t0) REVERT: 2 300 ARG cc_start: 0.7893 (mtm-85) cc_final: 0.7457 (mtm-85) REVERT: 2 312 LEU cc_start: 0.7656 (mt) cc_final: 0.7454 (mm) REVERT: 3 27 SER cc_start: 0.8065 (m) cc_final: 0.7643 (p) REVERT: 3 39 GLU cc_start: 0.6786 (mp0) cc_final: 0.6124 (mp0) REVERT: 3 46 MET cc_start: 0.8182 (tpt) cc_final: 0.7740 (tpp) REVERT: 3 61 LYS cc_start: 0.7903 (tptp) cc_final: 0.7467 (tptt) REVERT: 3 65 GLN cc_start: 0.8190 (pt0) cc_final: 0.7313 (pp30) REVERT: 3 86 ASP cc_start: 0.8654 (t0) cc_final: 0.8314 (t0) REVERT: 3 92 ASP cc_start: 0.7663 (t0) cc_final: 0.7250 (t0) REVERT: 3 96 GLU cc_start: 0.7396 (tm-30) cc_final: 0.7150 (tm-30) REVERT: 3 109 GLU cc_start: 0.7793 (tt0) cc_final: 0.7475 (tt0) REVERT: 3 143 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7367 (ppt170) REVERT: 3 149 THR cc_start: 0.7730 (p) cc_final: 0.7157 (p) REVERT: 3 150 GLN cc_start: 0.7618 (mt0) cc_final: 0.7151 (mm110) REVERT: 3 157 MET cc_start: 0.7739 (ttm) cc_final: 0.7166 (tpp) REVERT: 3 174 SER cc_start: 0.8518 (p) cc_final: 0.8245 (t) REVERT: 3 175 LYS cc_start: 0.7854 (ttmt) cc_final: 0.7486 (ttmm) REVERT: 3 181 ASN cc_start: 0.7704 (t0) cc_final: 0.7137 (t0) REVERT: 3 207 LYS cc_start: 0.8218 (tttt) cc_final: 0.7449 (ttmm) REVERT: 3 228 GLU cc_start: 0.6765 (tm-30) cc_final: 0.6508 (tm-30) REVERT: 3 239 GLN cc_start: 0.7590 (mp10) cc_final: 0.7327 (mm110) REVERT: 3 241 ASN cc_start: 0.7249 (m-40) cc_final: 0.6883 (t0) REVERT: 3 250 TYR cc_start: 0.7359 (t80) cc_final: 0.6748 (t80) REVERT: 3 255 GLU cc_start: 0.7877 (tp30) cc_final: 0.7518 (tp30) REVERT: 3 259 ASN cc_start: 0.7135 (OUTLIER) cc_final: 0.6867 (p0) REVERT: 3 268 ASP cc_start: 0.7173 (p0) cc_final: 0.6818 (p0) REVERT: 3 269 PHE cc_start: 0.6435 (OUTLIER) cc_final: 0.4949 (t80) REVERT: 4 19 THR cc_start: 0.7693 (p) cc_final: 0.7382 (p) REVERT: 4 29 MET cc_start: 0.7676 (mtt) cc_final: 0.7232 (mmm) REVERT: 4 62 TYR cc_start: 0.7908 (t80) cc_final: 0.7554 (t80) REVERT: 4 96 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7042 (tp30) REVERT: 4 118 ARG cc_start: 0.6983 (mtp180) cc_final: 0.6723 (mtp180) REVERT: 4 133 ILE cc_start: 0.7191 (mt) cc_final: 0.6904 (mm) REVERT: 4 146 ARG cc_start: 0.6802 (ptm160) cc_final: 0.6111 (ptm160) REVERT: 4 154 TRP cc_start: 0.7575 (t60) cc_final: 0.7170 (t60) REVERT: 4 178 LEU cc_start: 0.6768 (tp) cc_final: 0.6518 (pp) REVERT: 4 193 GLU cc_start: 0.7507 (tp30) cc_final: 0.7197 (tp30) REVERT: 4 194 LEU cc_start: 0.7488 (tt) cc_final: 0.6984 (tt) REVERT: 4 221 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7219 (tmmt) REVERT: 4 242 MET cc_start: 0.7920 (tpp) cc_final: 0.7676 (tpp) REVERT: 4 247 ASN cc_start: 0.7530 (m-40) cc_final: 0.7162 (t0) REVERT: 4 262 GLU cc_start: 0.7372 (mp0) cc_final: 0.6903 (mp0) REVERT: 4 286 ASN cc_start: 0.7886 (t0) cc_final: 0.7552 (t0) REVERT: 4 298 MET cc_start: 0.6948 (OUTLIER) cc_final: 0.6358 (mpp) REVERT: 4 304 LYS cc_start: 0.7394 (tppt) cc_final: 0.6628 (tppt) REVERT: 5 23 ARG cc_start: 0.5875 (mpp80) cc_final: 0.5624 (mpp80) REVERT: 5 29 MET cc_start: 0.5730 (tpp) cc_final: 0.5526 (tpp) REVERT: 5 55 LYS cc_start: 0.6111 (mtmm) cc_final: 0.5512 (mtmm) REVERT: 5 105 LEU cc_start: 0.6668 (OUTLIER) cc_final: 0.6117 (mt) REVERT: 5 171 MET cc_start: 0.7685 (mtp) cc_final: 0.7113 (mtp) REVERT: 5 175 LYS cc_start: 0.6750 (ttmt) cc_final: 0.6307 (ttmt) REVERT: 5 182 SER cc_start: 0.7112 (t) cc_final: 0.6776 (m) REVERT: 5 215 LYS cc_start: 0.7385 (mmtt) cc_final: 0.6903 (tmtt) REVERT: 5 241 ASN cc_start: 0.6625 (t0) cc_final: 0.6126 (t0) REVERT: 5 242 MET cc_start: 0.5465 (tpp) cc_final: 0.5027 (tmm) REVERT: 6 13 LYS cc_start: 0.8069 (tppt) cc_final: 0.7514 (tptp) REVERT: 6 41 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8132 (mm-30) REVERT: 6 46 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7717 (tpt) REVERT: 6 60 LYS cc_start: 0.7793 (mmmt) cc_final: 0.7365 (tmtt) REVERT: 6 96 GLU cc_start: 0.7165 (tm-30) cc_final: 0.6946 (tp30) REVERT: 6 107 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7216 (tp) REVERT: 6 134 ASP cc_start: 0.7156 (t0) cc_final: 0.6780 (t0) REVERT: 6 135 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7179 (mm-30) REVERT: 6 143 ARG cc_start: 0.8128 (ppt170) cc_final: 0.7654 (ppt170) REVERT: 6 146 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7218 (ptm160) REVERT: 6 149 THR cc_start: 0.7540 (p) cc_final: 0.7175 (p) REVERT: 6 150 GLN cc_start: 0.7703 (mt0) cc_final: 0.7266 (mt0) REVERT: 6 158 ILE cc_start: 0.6770 (tp) cc_final: 0.6536 (mm) REVERT: 6 185 HIS cc_start: 0.7988 (t70) cc_final: 0.7599 (t70) REVERT: 6 188 PHE cc_start: 0.7959 (m-80) cc_final: 0.7511 (m-80) REVERT: 6 242 MET cc_start: 0.7749 (tpp) cc_final: 0.7352 (mmm) REVERT: 6 248 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7574 (tp) REVERT: 6 259 ASN cc_start: 0.5615 (OUTLIER) cc_final: 0.5352 (p0) REVERT: 6 262 GLU cc_start: 0.6748 (mp0) cc_final: 0.6395 (mp0) REVERT: 6 263 THR cc_start: 0.6154 (OUTLIER) cc_final: 0.5880 (m) REVERT: 6 269 PHE cc_start: 0.6585 (m-80) cc_final: 0.5852 (m-80) REVERT: 6 271 PHE cc_start: 0.7739 (t80) cc_final: 0.7420 (t80) REVERT: 7 5 ARG cc_start: 0.6046 (mmm-85) cc_final: 0.5842 (tpp80) REVERT: 7 14 ARG cc_start: 0.8135 (mtm-85) cc_final: 0.7829 (mtt90) REVERT: 7 24 LYS cc_start: 0.7582 (tttt) cc_final: 0.7302 (ttpt) REVERT: 7 37 ASP cc_start: 0.7258 (p0) cc_final: 0.5937 (p0) REVERT: 7 39 GLU cc_start: 0.7620 (mp0) cc_final: 0.6670 (mp0) REVERT: 7 48 TYR cc_start: 0.8045 (m-80) cc_final: 0.7572 (m-80) REVERT: 7 83 GLU cc_start: 0.7274 (tt0) cc_final: 0.7024 (mt-10) REVERT: 7 95 ARG cc_start: 0.7705 (ptp90) cc_final: 0.7332 (ptm160) REVERT: 7 111 ASP cc_start: 0.6878 (t70) cc_final: 0.6529 (t70) REVERT: 7 129 LYS cc_start: 0.7795 (mmmm) cc_final: 0.7534 (mttm) REVERT: 7 145 ASN cc_start: 0.7811 (m-40) cc_final: 0.7543 (m-40) REVERT: 7 146 ARG cc_start: 0.7804 (ptm160) cc_final: 0.7597 (ptm160) REVERT: 7 162 THR cc_start: 0.7549 (OUTLIER) cc_final: 0.7246 (p) REVERT: 7 181 ASN cc_start: 0.7633 (t0) cc_final: 0.7203 (t0) REVERT: 7 193 GLU cc_start: 0.8064 (tp30) cc_final: 0.7448 (tp30) REVERT: 7 228 GLU cc_start: 0.7079 (tm-30) cc_final: 0.6585 (tm-30) REVERT: 7 232 LYS cc_start: 0.7325 (ttmm) cc_final: 0.6618 (ttpp) REVERT: 7 250 TYR cc_start: 0.7781 (t80) cc_final: 0.7492 (t80) REVERT: 7 271 PHE cc_start: 0.7953 (t80) cc_final: 0.7454 (t80) REVERT: 7 285 LYS cc_start: 0.8379 (ttmm) cc_final: 0.7920 (tppt) REVERT: 7 305 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7626 (m-30) outliers start: 101 outliers final: 67 residues processed: 657 average time/residue: 0.3812 time to fit residues: 348.2263 Evaluate side-chains 678 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 589 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 31 ARG 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 148 LEU Chi-restraints excluded: chain 1 residue 158 ILE Chi-restraints excluded: chain 1 residue 178 LEU 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 275 LEU Chi-restraints excluded: chain 1 residue 279 ASP Chi-restraints excluded: chain 1 residue 293 GLU 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 46 MET Chi-restraints excluded: chain 2 residue 98 LEU Chi-restraints excluded: chain 2 residue 101 MET Chi-restraints excluded: chain 2 residue 141 GLU Chi-restraints excluded: chain 2 residue 143 ARG Chi-restraints excluded: chain 2 residue 162 THR 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 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 45 MET 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 115 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 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 10 SER Chi-restraints excluded: chain 4 residue 27 SER Chi-restraints excluded: chain 4 residue 30 ASP Chi-restraints excluded: chain 4 residue 60 LYS Chi-restraints excluded: chain 4 residue 79 VAL Chi-restraints excluded: chain 4 residue 96 GLU Chi-restraints excluded: chain 4 residue 110 THR 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 221 LYS 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 97 LEU Chi-restraints excluded: chain 5 residue 105 LEU Chi-restraints excluded: chain 5 residue 142 GLU Chi-restraints excluded: chain 5 residue 168 ILE Chi-restraints excluded: chain 5 residue 259 ASN Chi-restraints excluded: chain 5 residue 299 LEU Chi-restraints excluded: chain 6 residue 46 MET Chi-restraints excluded: chain 6 residue 63 LEU Chi-restraints excluded: chain 6 residue 107 LEU Chi-restraints excluded: chain 6 residue 115 LEU Chi-restraints excluded: chain 6 residue 142 GLU Chi-restraints excluded: chain 6 residue 146 ARG Chi-restraints excluded: chain 6 residue 148 LEU Chi-restraints excluded: chain 6 residue 168 ILE Chi-restraints excluded: chain 6 residue 175 LYS Chi-restraints excluded: chain 6 residue 200 GLN Chi-restraints excluded: chain 6 residue 248 LEU Chi-restraints excluded: chain 6 residue 259 ASN Chi-restraints excluded: chain 6 residue 263 THR Chi-restraints excluded: chain 7 residue 107 LEU Chi-restraints excluded: chain 7 residue 109 GLU 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 214 ASP Chi-restraints excluded: chain 7 residue 263 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 204 optimal weight: 2.9990 chunk 186 optimal weight: 0.9980 chunk 198 optimal weight: 0.0470 chunk 119 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 155 optimal weight: 0.0970 chunk 60 optimal weight: 0.8980 chunk 179 optimal weight: 0.9980 chunk 187 optimal weight: 0.6980 chunk 197 optimal weight: 0.0970 chunk 130 optimal weight: 1.9990 overall best weight: 0.3274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** 2 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 259 ASN ** 6 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 247 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18772 Z= 0.187 Angle : 0.670 13.523 25612 Z= 0.329 Chirality : 0.041 0.204 2863 Planarity : 0.004 0.040 3122 Dihedral : 15.647 87.986 3085 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 5.17 % Allowed : 28.30 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.19), residues: 2163 helix: 0.93 (0.15), residues: 1197 sheet: -1.77 (0.39), residues: 224 loop : -1.94 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP 6 154 HIS 0.005 0.000 HIS 3 261 PHE 0.017 0.002 PHE 4 209 TYR 0.022 0.001 TYR 6 199 ARG 0.007 0.001 ARG 7 33 *********************** 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 691 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 594 time to evaluate : 2.095 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: 0.7860 (mtp180) cc_final: 0.7430 (ttp-170) REVERT: 1 19 THR cc_start: 0.7294 (OUTLIER) cc_final: 0.6891 (t) REVERT: 1 23 ARG cc_start: 0.7616 (mtm110) cc_final: 0.7075 (mtm110) REVERT: 1 30 ASP cc_start: 0.7245 (m-30) cc_final: 0.7021 (m-30) REVERT: 1 33 ARG cc_start: 0.7995 (ttp80) cc_final: 0.7778 (tmm-80) REVERT: 1 37 ASP cc_start: 0.7808 (p0) cc_final: 0.7310 (p0) REVERT: 1 48 TYR cc_start: 0.8418 (m-80) cc_final: 0.7777 (m-80) REVERT: 1 57 THR cc_start: 0.7565 (t) cc_final: 0.7278 (t) REVERT: 1 65 GLN cc_start: 0.7354 (pt0) cc_final: 0.7025 (pp30) REVERT: 1 83 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7472 (mt-10) REVERT: 1 92 ASP cc_start: 0.7262 (t0) cc_final: 0.6875 (t0) REVERT: 1 100 GLU cc_start: 0.7477 (tm-30) cc_final: 0.6966 (tm-30) REVERT: 1 101 MET cc_start: 0.8138 (ttp) cc_final: 0.7933 (ttp) REVERT: 1 105 LEU cc_start: 0.7369 (pp) cc_final: 0.7002 (mp) REVERT: 1 109 GLU cc_start: 0.7586 (tt0) cc_final: 0.7212 (tt0) REVERT: 1 129 LYS cc_start: 0.8296 (mtpt) cc_final: 0.7885 (mtpt) REVERT: 1 171 MET cc_start: 0.8186 (mtp) cc_final: 0.7853 (mmm) REVERT: 1 179 GLN cc_start: 0.7547 (mt0) cc_final: 0.7326 (mt0) REVERT: 1 193 GLU cc_start: 0.7911 (tp30) cc_final: 0.7532 (tp30) REVERT: 1 228 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7592 (tm-30) REVERT: 1 261 HIS cc_start: 0.6644 (OUTLIER) cc_final: 0.6200 (m170) REVERT: 1 269 PHE cc_start: 0.6728 (OUTLIER) cc_final: 0.6368 (m-80) REVERT: 1 285 LYS cc_start: 0.7680 (tppt) cc_final: 0.7330 (tppt) REVERT: 1 293 GLU cc_start: 0.6632 (tm-30) cc_final: 0.6291 (tm-30) REVERT: 1 296 GLU cc_start: 0.7548 (tm-30) cc_final: 0.7180 (tm-30) REVERT: 1 297 ASP cc_start: 0.7848 (t0) cc_final: 0.7400 (t0) REVERT: 1 300 ARG cc_start: 0.8112 (mtm-85) cc_final: 0.7703 (mtm-85) REVERT: 1 310 ASP cc_start: 0.7414 (m-30) cc_final: 0.6951 (m-30) REVERT: 2 33 ARG cc_start: 0.8116 (ttp80) cc_final: 0.7888 (ttp-110) REVERT: 2 39 GLU cc_start: 0.6357 (mp0) cc_final: 0.5929 (mp0) REVERT: 2 46 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7743 (ttt) REVERT: 2 89 LYS cc_start: 0.7385 (mmmt) cc_final: 0.6936 (mmmt) REVERT: 2 100 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7431 (tm-30) REVERT: 2 116 THR cc_start: 0.7806 (m) cc_final: 0.7499 (p) REVERT: 2 121 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7394 (mt-10) REVERT: 2 122 LEU cc_start: 0.7523 (tp) cc_final: 0.7209 (tp) REVERT: 2 129 LYS cc_start: 0.7992 (mmpt) cc_final: 0.7638 (mmpt) REVERT: 2 143 ARG cc_start: 0.6289 (OUTLIER) cc_final: 0.5854 (ppt-90) REVERT: 2 150 GLN cc_start: 0.7713 (mt0) cc_final: 0.7087 (mt0) REVERT: 2 162 THR cc_start: 0.7801 (OUTLIER) cc_final: 0.7566 (p) REVERT: 2 163 LYS cc_start: 0.7929 (mppt) cc_final: 0.7365 (mmtm) REVERT: 2 235 TYR cc_start: 0.7457 (t80) cc_final: 0.6920 (t80) REVERT: 2 242 MET cc_start: 0.7220 (mmm) cc_final: 0.6743 (mmm) REVERT: 2 262 GLU cc_start: 0.6842 (mp0) cc_final: 0.6464 (mp0) REVERT: 2 286 ASN cc_start: 0.8476 (t0) cc_final: 0.7934 (t0) REVERT: 2 298 MET cc_start: 0.7129 (mtm) cc_final: 0.6891 (ptp) REVERT: 2 300 ARG cc_start: 0.7897 (mtm-85) cc_final: 0.7535 (mtm-85) REVERT: 3 24 LYS cc_start: 0.7983 (tttt) cc_final: 0.7526 (ttpp) REVERT: 3 27 SER cc_start: 0.8054 (m) cc_final: 0.7638 (p) REVERT: 3 39 GLU cc_start: 0.6781 (mp0) cc_final: 0.6125 (mp0) REVERT: 3 46 MET cc_start: 0.8152 (tpt) cc_final: 0.7722 (tpp) REVERT: 3 61 LYS cc_start: 0.7878 (tptp) cc_final: 0.7465 (tptt) REVERT: 3 65 GLN cc_start: 0.8168 (pt0) cc_final: 0.7276 (pp30) REVERT: 3 86 ASP cc_start: 0.8585 (t0) cc_final: 0.8242 (t0) REVERT: 3 92 ASP cc_start: 0.7648 (t0) cc_final: 0.7252 (t0) REVERT: 3 96 GLU cc_start: 0.7395 (tm-30) cc_final: 0.7097 (tm-30) REVERT: 3 109 GLU cc_start: 0.7764 (tt0) cc_final: 0.7430 (tt0) REVERT: 3 143 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7292 (ppt170) REVERT: 3 149 THR cc_start: 0.7589 (p) cc_final: 0.7035 (p) REVERT: 3 150 GLN cc_start: 0.7612 (mt0) cc_final: 0.7150 (mm110) REVERT: 3 157 MET cc_start: 0.7727 (ttm) cc_final: 0.7151 (tpp) REVERT: 3 174 SER cc_start: 0.8518 (p) cc_final: 0.8278 (t) REVERT: 3 175 LYS cc_start: 0.7844 (ttmt) cc_final: 0.7514 (ttmm) REVERT: 3 181 ASN cc_start: 0.7702 (t0) cc_final: 0.7123 (t0) REVERT: 3 207 LYS cc_start: 0.8192 (tttt) cc_final: 0.7499 (ttmm) REVERT: 3 228 GLU cc_start: 0.6743 (tm-30) cc_final: 0.6501 (tm-30) REVERT: 3 239 GLN cc_start: 0.7552 (mp10) cc_final: 0.7276 (mm110) REVERT: 3 241 ASN cc_start: 0.7162 (m-40) cc_final: 0.6805 (t0) REVERT: 3 250 TYR cc_start: 0.7323 (t80) cc_final: 0.6931 (t80) REVERT: 3 255 GLU cc_start: 0.8025 (tp30) cc_final: 0.7628 (tp30) REVERT: 3 269 PHE cc_start: 0.6371 (OUTLIER) cc_final: 0.4903 (t80) REVERT: 3 309 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6610 (mm-30) REVERT: 4 19 THR cc_start: 0.7673 (p) cc_final: 0.7322 (p) REVERT: 4 23 ARG cc_start: 0.6790 (mtm180) cc_final: 0.6432 (mtm110) REVERT: 4 29 MET cc_start: 0.7676 (mtt) cc_final: 0.7237 (mmm) REVERT: 4 62 TYR cc_start: 0.7902 (t80) cc_final: 0.7547 (t80) REVERT: 4 96 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7087 (tp30) REVERT: 4 114 ARG cc_start: 0.7787 (ttp80) cc_final: 0.7201 (ptt90) REVERT: 4 133 ILE cc_start: 0.7214 (mt) cc_final: 0.6937 (mm) REVERT: 4 146 ARG cc_start: 0.6803 (OUTLIER) cc_final: 0.6112 (ptm160) REVERT: 4 154 TRP cc_start: 0.7622 (t60) cc_final: 0.7406 (t60) REVERT: 4 178 LEU cc_start: 0.6745 (tp) cc_final: 0.6505 (pp) REVERT: 4 193 GLU cc_start: 0.7259 (tp30) cc_final: 0.7026 (tp30) REVERT: 4 194 LEU cc_start: 0.7478 (tt) cc_final: 0.6963 (tt) REVERT: 4 207 LYS cc_start: 0.7874 (tttt) cc_final: 0.7364 (tppt) REVERT: 4 221 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7206 (tmmt) REVERT: 4 242 MET cc_start: 0.7931 (tpp) cc_final: 0.7661 (tpt) REVERT: 4 247 ASN cc_start: 0.7517 (m-40) cc_final: 0.7142 (t0) REVERT: 4 262 GLU cc_start: 0.7426 (mp0) cc_final: 0.6915 (mp0) REVERT: 4 286 ASN cc_start: 0.7880 (t0) cc_final: 0.7525 (t0) REVERT: 4 298 MET cc_start: 0.6959 (OUTLIER) cc_final: 0.6381 (mpp) REVERT: 4 304 LYS cc_start: 0.7338 (tppt) cc_final: 0.6573 (tppt) REVERT: 5 55 LYS cc_start: 0.6158 (mtmm) cc_final: 0.5524 (mtmm) REVERT: 5 105 LEU cc_start: 0.6643 (OUTLIER) cc_final: 0.6090 (mt) REVERT: 5 171 MET cc_start: 0.7696 (mtp) cc_final: 0.7110 (mtp) REVERT: 5 175 LYS cc_start: 0.6759 (ttmt) cc_final: 0.6308 (ttmt) REVERT: 5 182 SER cc_start: 0.6854 (t) cc_final: 0.6502 (m) REVERT: 5 215 LYS cc_start: 0.7386 (mmtt) cc_final: 0.6896 (tmtt) REVERT: 5 241 ASN cc_start: 0.6600 (t0) cc_final: 0.5975 (t0) REVERT: 5 242 MET cc_start: 0.5409 (tpp) cc_final: 0.4973 (tmm) REVERT: 6 13 LYS cc_start: 0.8085 (tppt) cc_final: 0.7516 (tptp) REVERT: 6 41 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8136 (mm-30) REVERT: 6 46 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7714 (tpt) REVERT: 6 60 LYS cc_start: 0.7769 (mmmt) cc_final: 0.7348 (tmtt) REVERT: 6 96 GLU cc_start: 0.7219 (tm-30) cc_final: 0.6988 (tp30) REVERT: 6 107 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7205 (tp) REVERT: 6 134 ASP cc_start: 0.7146 (t0) cc_final: 0.6820 (t0) REVERT: 6 135 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7192 (mm-30) REVERT: 6 137 GLN cc_start: 0.7733 (pm20) cc_final: 0.7087 (pm20) REVERT: 6 143 ARG cc_start: 0.8134 (ppt170) cc_final: 0.7657 (ppt170) REVERT: 6 146 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7274 (ptm160) REVERT: 6 149 THR cc_start: 0.7448 (p) cc_final: 0.7164 (p) REVERT: 6 150 GLN cc_start: 0.7572 (mt0) cc_final: 0.7262 (mt0) REVERT: 6 158 ILE cc_start: 0.6706 (tp) cc_final: 0.6457 (mm) REVERT: 6 188 PHE cc_start: 0.7949 (m-80) cc_final: 0.7549 (m-80) REVERT: 6 242 MET cc_start: 0.7734 (tpp) cc_final: 0.7347 (mmm) REVERT: 6 248 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7573 (tp) REVERT: 6 259 ASN cc_start: 0.5628 (OUTLIER) cc_final: 0.5198 (p0) REVERT: 6 262 GLU cc_start: 0.6755 (mp0) cc_final: 0.6408 (mp0) REVERT: 6 263 THR cc_start: 0.6101 (OUTLIER) cc_final: 0.5813 (m) REVERT: 6 269 PHE cc_start: 0.6633 (m-80) cc_final: 0.5988 (m-80) REVERT: 6 271 PHE cc_start: 0.7765 (t80) cc_final: 0.7488 (t80) REVERT: 7 14 ARG cc_start: 0.8105 (mtm-85) cc_final: 0.7792 (mtt90) REVERT: 7 24 LYS cc_start: 0.7577 (tttt) cc_final: 0.7304 (ttpt) REVERT: 7 37 ASP cc_start: 0.7252 (p0) cc_final: 0.5946 (p0) REVERT: 7 39 GLU cc_start: 0.7616 (mp0) cc_final: 0.6690 (mp0) REVERT: 7 83 GLU cc_start: 0.7277 (tt0) cc_final: 0.7015 (mt-10) REVERT: 7 98 LEU cc_start: 0.6810 (mt) cc_final: 0.6591 (mm) REVERT: 7 111 ASP cc_start: 0.6926 (t70) cc_final: 0.6588 (t70) REVERT: 7 129 LYS cc_start: 0.7766 (mmmm) cc_final: 0.7505 (mttp) REVERT: 7 145 ASN cc_start: 0.7766 (m-40) cc_final: 0.7499 (m-40) REVERT: 7 146 ARG cc_start: 0.7836 (ptm160) cc_final: 0.7616 (ptm160) REVERT: 7 162 THR cc_start: 0.7512 (OUTLIER) cc_final: 0.7210 (p) REVERT: 7 181 ASN cc_start: 0.7598 (t0) cc_final: 0.7178 (t0) REVERT: 7 193 GLU cc_start: 0.8052 (tp30) cc_final: 0.7445 (tp30) REVERT: 7 228 GLU cc_start: 0.7035 (tm-30) cc_final: 0.6532 (tm-30) REVERT: 7 232 LYS cc_start: 0.7316 (ttmm) cc_final: 0.6597 (ttpp) REVERT: 7 250 TYR cc_start: 0.7777 (t80) cc_final: 0.7423 (t80) REVERT: 7 271 PHE cc_start: 0.7942 (t80) cc_final: 0.7470 (t80) REVERT: 7 285 LYS cc_start: 0.8363 (ttmm) cc_final: 0.7917 (tppt) REVERT: 7 305 ASP cc_start: 0.7804 (m-30) cc_final: 0.7539 (m-30) outliers start: 97 outliers final: 62 residues processed: 647 average time/residue: 0.3960 time to fit residues: 356.4159 Evaluate side-chains 668 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 585 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 1 residue 34 ASP Chi-restraints excluded: chain 1 residue 107 LEU Chi-restraints excluded: chain 1 residue 110 THR Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 1 residue 178 LEU 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 309 GLU Chi-restraints excluded: chain 2 residue 22 VAL Chi-restraints excluded: chain 2 residue 46 MET Chi-restraints excluded: chain 2 residue 83 GLU Chi-restraints excluded: chain 2 residue 98 LEU Chi-restraints excluded: chain 2 residue 101 MET Chi-restraints excluded: chain 2 residue 141 GLU Chi-restraints excluded: chain 2 residue 143 ARG Chi-restraints excluded: chain 2 residue 162 THR Chi-restraints excluded: chain 2 residue 192 VAL Chi-restraints excluded: chain 2 residue 213 LEU 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 45 MET 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 115 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 193 GLU Chi-restraints excluded: chain 3 residue 269 PHE Chi-restraints excluded: chain 3 residue 270 VAL Chi-restraints excluded: chain 3 residue 309 GLU Chi-restraints excluded: chain 3 residue 312 LEU Chi-restraints excluded: chain 4 residue 10 SER Chi-restraints excluded: chain 4 residue 27 SER Chi-restraints excluded: chain 4 residue 79 VAL Chi-restraints excluded: chain 4 residue 96 GLU Chi-restraints excluded: chain 4 residue 110 THR Chi-restraints excluded: chain 4 residue 142 GLU Chi-restraints excluded: chain 4 residue 146 ARG Chi-restraints excluded: chain 4 residue 148 LEU Chi-restraints excluded: chain 4 residue 149 THR Chi-restraints excluded: chain 4 residue 221 LYS 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 298 MET Chi-restraints excluded: chain 5 residue 38 LEU Chi-restraints excluded: chain 5 residue 97 LEU Chi-restraints excluded: chain 5 residue 99 VAL Chi-restraints excluded: chain 5 residue 105 LEU Chi-restraints excluded: chain 5 residue 114 ARG Chi-restraints excluded: chain 5 residue 123 ILE Chi-restraints excluded: chain 5 residue 142 GLU Chi-restraints excluded: chain 5 residue 147 VAL Chi-restraints excluded: chain 5 residue 168 ILE Chi-restraints excluded: chain 5 residue 299 LEU Chi-restraints excluded: chain 6 residue 46 MET Chi-restraints excluded: chain 6 residue 63 LEU Chi-restraints excluded: chain 6 residue 99 VAL Chi-restraints excluded: chain 6 residue 107 LEU Chi-restraints excluded: chain 6 residue 115 LEU Chi-restraints excluded: chain 6 residue 142 GLU Chi-restraints excluded: chain 6 residue 146 ARG Chi-restraints excluded: chain 6 residue 148 LEU Chi-restraints excluded: chain 6 residue 168 ILE Chi-restraints excluded: chain 6 residue 175 LYS Chi-restraints excluded: chain 6 residue 248 LEU Chi-restraints excluded: chain 6 residue 259 ASN Chi-restraints excluded: chain 6 residue 263 THR Chi-restraints excluded: chain 7 residue 107 LEU Chi-restraints excluded: chain 7 residue 109 GLU 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 214 ASP Chi-restraints excluded: chain 7 residue 263 THR Chi-restraints excluded: chain 7 residue 269 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 209 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 145 optimal weight: 4.9990 chunk 220 optimal weight: 0.5980 chunk 202 optimal weight: 1.9990 chunk 175 optimal weight: 0.0570 chunk 18 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 139 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 64 ASN ** 1 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 282 ASN ** 2 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 183 GLN ** 3 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 231 GLN 7 247 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 18772 Z= 0.225 Angle : 0.683 13.190 25612 Z= 0.336 Chirality : 0.042 0.203 2863 Planarity : 0.004 0.040 3122 Dihedral : 15.591 89.196 3085 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 4.85 % Allowed : 29.05 % Favored : 66.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.19), residues: 2163 helix: 0.88 (0.15), residues: 1204 sheet: -1.72 (0.39), residues: 224 loop : -1.86 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP 6 154 HIS 0.006 0.001 HIS 6 81 PHE 0.021 0.002 PHE 7 16 TYR 0.027 0.002 TYR 5 62 ARG 0.008 0.001 ARG 4 14 ********************** 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 687 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 596 time to evaluate : 1.881 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: 0.7873 (mtp180) cc_final: 0.7446 (ttp-170) REVERT: 1 19 THR cc_start: 0.7276 (OUTLIER) cc_final: 0.6871 (t) REVERT: 1 23 ARG cc_start: 0.7567 (mtm110) cc_final: 0.7093 (mtm110) REVERT: 1 30 ASP cc_start: 0.7277 (m-30) cc_final: 0.7063 (m-30) REVERT: 1 33 ARG cc_start: 0.8000 (ttp80) cc_final: 0.7762 (tmm-80) REVERT: 1 37 ASP cc_start: 0.7821 (p0) cc_final: 0.7360 (p0) REVERT: 1 48 TYR cc_start: 0.8424 (m-80) cc_final: 0.7820 (m-80) REVERT: 1 57 THR cc_start: 0.7533 (t) cc_final: 0.7323 (t) REVERT: 1 65 GLN cc_start: 0.7359 (pt0) cc_final: 0.7029 (pp30) REVERT: 1 83 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7488 (mt-10) REVERT: 1 92 ASP cc_start: 0.7257 (t0) cc_final: 0.6869 (t0) REVERT: 1 100 GLU cc_start: 0.7510 (tm-30) cc_final: 0.6978 (tm-30) REVERT: 1 105 LEU cc_start: 0.7359 (pp) cc_final: 0.6983 (mp) REVERT: 1 109 GLU cc_start: 0.7604 (tt0) cc_final: 0.7259 (tt0) REVERT: 1 129 LYS cc_start: 0.8334 (mtpt) cc_final: 0.7931 (mtpt) REVERT: 1 171 MET cc_start: 0.8194 (mtp) cc_final: 0.7844 (mmm) REVERT: 1 179 GLN cc_start: 0.7550 (mt0) cc_final: 0.7345 (mt0) REVERT: 1 193 GLU cc_start: 0.7881 (tp30) cc_final: 0.7494 (tp30) REVERT: 1 228 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7599 (tm-30) REVERT: 1 261 HIS cc_start: 0.6621 (OUTLIER) cc_final: 0.6169 (m170) REVERT: 1 269 PHE cc_start: 0.6739 (OUTLIER) cc_final: 0.6351 (m-80) REVERT: 1 285 LYS cc_start: 0.7728 (tppt) cc_final: 0.7360 (tppt) REVERT: 1 293 GLU cc_start: 0.6658 (tm-30) cc_final: 0.6310 (tm-30) REVERT: 1 296 GLU cc_start: 0.7544 (tm-30) cc_final: 0.7191 (tm-30) REVERT: 1 297 ASP cc_start: 0.7845 (t0) cc_final: 0.7415 (t0) REVERT: 1 300 ARG cc_start: 0.8075 (mtm-85) cc_final: 0.7669 (mtm-85) REVERT: 1 310 ASP cc_start: 0.7397 (m-30) cc_final: 0.6936 (m-30) REVERT: 2 33 ARG cc_start: 0.8138 (ttp80) cc_final: 0.7918 (ttp-110) REVERT: 2 39 GLU cc_start: 0.6352 (mp0) cc_final: 0.5903 (mp0) REVERT: 2 89 LYS cc_start: 0.7430 (mmmt) cc_final: 0.6991 (mmmt) REVERT: 2 100 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7367 (tm-30) REVERT: 2 116 THR cc_start: 0.7803 (m) cc_final: 0.7490 (p) REVERT: 2 121 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7379 (mt-10) REVERT: 2 122 LEU cc_start: 0.7306 (tp) cc_final: 0.7001 (tp) REVERT: 2 129 LYS cc_start: 0.7957 (mmpt) cc_final: 0.7596 (mmpt) REVERT: 2 143 ARG cc_start: 0.6325 (OUTLIER) cc_final: 0.5893 (ppt-90) REVERT: 2 150 GLN cc_start: 0.7723 (mt0) cc_final: 0.7100 (mt0) REVERT: 2 162 THR cc_start: 0.7787 (OUTLIER) cc_final: 0.7560 (p) REVERT: 2 163 LYS cc_start: 0.7936 (mppt) cc_final: 0.7379 (mmtm) REVERT: 2 235 TYR cc_start: 0.7611 (t80) cc_final: 0.7072 (t80) REVERT: 2 242 MET cc_start: 0.7246 (mmm) cc_final: 0.6712 (mmm) REVERT: 2 262 GLU cc_start: 0.6938 (mp0) cc_final: 0.6485 (mp0) REVERT: 2 286 ASN cc_start: 0.8496 (t0) cc_final: 0.7928 (t0) REVERT: 2 298 MET cc_start: 0.7073 (mtm) cc_final: 0.6807 (ptp) REVERT: 2 300 ARG cc_start: 0.7912 (mtm-85) cc_final: 0.7552 (mtm-85) REVERT: 3 24 LYS cc_start: 0.8021 (tttt) cc_final: 0.7541 (ttpp) REVERT: 3 27 SER cc_start: 0.8062 (m) cc_final: 0.7643 (p) REVERT: 3 39 GLU cc_start: 0.6782 (mp0) cc_final: 0.6127 (mp0) REVERT: 3 46 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7799 (tpp) REVERT: 3 61 LYS cc_start: 0.7897 (tptp) cc_final: 0.7448 (tptt) REVERT: 3 65 GLN cc_start: 0.8158 (pt0) cc_final: 0.7486 (pp30) REVERT: 3 86 ASP cc_start: 0.8569 (t0) cc_final: 0.8241 (t0) REVERT: 3 92 ASP cc_start: 0.7652 (t0) cc_final: 0.7259 (t0) REVERT: 3 96 GLU cc_start: 0.7378 (tm-30) cc_final: 0.7086 (tm-30) REVERT: 3 109 GLU cc_start: 0.7776 (tt0) cc_final: 0.7438 (tt0) REVERT: 3 143 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7331 (ppt170) REVERT: 3 149 THR cc_start: 0.7595 (p) cc_final: 0.7059 (p) REVERT: 3 150 GLN cc_start: 0.7606 (mt0) cc_final: 0.7146 (mm110) REVERT: 3 157 MET cc_start: 0.7730 (ttm) cc_final: 0.7151 (tpp) REVERT: 3 174 SER cc_start: 0.8499 (p) cc_final: 0.8266 (t) REVERT: 3 175 LYS cc_start: 0.7836 (ttmt) cc_final: 0.7530 (ttmm) REVERT: 3 181 ASN cc_start: 0.7705 (t0) cc_final: 0.7114 (t0) REVERT: 3 207 LYS cc_start: 0.8200 (tttt) cc_final: 0.7443 (ttmm) REVERT: 3 228 GLU cc_start: 0.6772 (tm-30) cc_final: 0.6520 (tm-30) REVERT: 3 239 GLN cc_start: 0.7561 (mp10) cc_final: 0.7357 (mm110) REVERT: 3 255 GLU cc_start: 0.7663 (tp30) cc_final: 0.7441 (tp30) REVERT: 3 269 PHE cc_start: 0.6385 (OUTLIER) cc_final: 0.4913 (t80) REVERT: 3 300 ARG cc_start: 0.8385 (mtm-85) cc_final: 0.7805 (mtm-85) REVERT: 3 309 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6662 (mt-10) REVERT: 4 14 ARG cc_start: 0.8160 (ttm110) cc_final: 0.7664 (ptp-110) REVERT: 4 19 THR cc_start: 0.7672 (p) cc_final: 0.7360 (p) REVERT: 4 23 ARG cc_start: 0.6774 (mtm180) cc_final: 0.6447 (mtm110) REVERT: 4 29 MET cc_start: 0.7686 (mtt) cc_final: 0.7288 (mmm) REVERT: 4 96 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7105 (tp30) REVERT: 4 98 LEU cc_start: 0.8210 (mt) cc_final: 0.7937 (mm) REVERT: 4 114 ARG cc_start: 0.7813 (ttp80) cc_final: 0.7199 (ptt90) REVERT: 4 133 ILE cc_start: 0.7234 (mt) cc_final: 0.6953 (mm) REVERT: 4 146 ARG cc_start: 0.6806 (OUTLIER) cc_final: 0.6201 (ptm160) REVERT: 4 154 TRP cc_start: 0.7652 (t60) cc_final: 0.7262 (t60) REVERT: 4 178 LEU cc_start: 0.6761 (tp) cc_final: 0.6524 (pp) REVERT: 4 193 GLU cc_start: 0.7527 (tp30) cc_final: 0.7227 (tp30) REVERT: 4 194 LEU cc_start: 0.7485 (tt) cc_final: 0.6989 (tt) REVERT: 4 207 LYS cc_start: 0.7885 (tttt) cc_final: 0.7348 (tppt) REVERT: 4 221 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7226 (tmmt) REVERT: 4 247 ASN cc_start: 0.7516 (m-40) cc_final: 0.7137 (t0) REVERT: 4 262 GLU cc_start: 0.7460 (mp0) cc_final: 0.6943 (mp0) REVERT: 4 286 ASN cc_start: 0.7857 (t0) cc_final: 0.7490 (t0) REVERT: 4 298 MET cc_start: 0.6954 (OUTLIER) cc_final: 0.6372 (mpp) REVERT: 4 300 ARG cc_start: 0.8061 (mtm-85) cc_final: 0.7708 (ttm-80) REVERT: 4 304 LYS cc_start: 0.7338 (tppt) cc_final: 0.6568 (tppt) REVERT: 5 55 LYS cc_start: 0.6177 (mtmm) cc_final: 0.5553 (mtmm) REVERT: 5 105 LEU cc_start: 0.6636 (OUTLIER) cc_final: 0.6075 (mt) REVERT: 5 142 GLU cc_start: 0.4380 (OUTLIER) cc_final: 0.3953 (mm-30) REVERT: 5 171 MET cc_start: 0.7715 (mtp) cc_final: 0.7086 (mtp) REVERT: 5 175 LYS cc_start: 0.6766 (ttmt) cc_final: 0.6312 (ttmt) REVERT: 5 182 SER cc_start: 0.6955 (t) cc_final: 0.6595 (m) REVERT: 5 215 LYS cc_start: 0.7385 (mmtt) cc_final: 0.6888 (tmtt) REVERT: 5 241 ASN cc_start: 0.6616 (t0) cc_final: 0.6110 (t0) REVERT: 5 242 MET cc_start: 0.5440 (tpp) cc_final: 0.5000 (tmm) REVERT: 6 5 ARG cc_start: 0.5340 (tpp80) cc_final: 0.5123 (tpp-160) REVERT: 6 13 LYS cc_start: 0.8089 (tppt) cc_final: 0.7512 (tptp) REVERT: 6 31 ARG cc_start: 0.7308 (ttm-80) cc_final: 0.7027 (ttm-80) REVERT: 6 41 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8071 (mm-30) REVERT: 6 46 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7717 (tpt) REVERT: 6 60 LYS cc_start: 0.7753 (mmmt) cc_final: 0.7327 (tmtt) REVERT: 6 96 GLU cc_start: 0.7213 (tm-30) cc_final: 0.6978 (tp30) REVERT: 6 107 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7120 (tt) REVERT: 6 117 LYS cc_start: 0.6866 (tptm) cc_final: 0.6599 (ttmm) REVERT: 6 134 ASP cc_start: 0.7166 (t0) cc_final: 0.6932 (t0) REVERT: 6 135 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7228 (mm-30) REVERT: 6 143 ARG cc_start: 0.8113 (ppt170) cc_final: 0.7672 (ppt170) REVERT: 6 146 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7263 (ptm160) REVERT: 6 149 THR cc_start: 0.7503 (p) cc_final: 0.7182 (p) REVERT: 6 150 GLN cc_start: 0.7609 (mt0) cc_final: 0.7295 (mt0) REVERT: 6 158 ILE cc_start: 0.6715 (tp) cc_final: 0.6468 (mm) REVERT: 6 188 PHE cc_start: 0.7961 (m-80) cc_final: 0.7542 (m-80) REVERT: 6 242 MET cc_start: 0.7846 (tpp) cc_final: 0.7430 (mmm) REVERT: 6 248 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7575 (tp) REVERT: 6 259 ASN cc_start: 0.5685 (OUTLIER) cc_final: 0.5203 (p0) REVERT: 6 262 GLU cc_start: 0.6765 (mp0) cc_final: 0.6433 (mp0) REVERT: 6 263 THR cc_start: 0.6099 (OUTLIER) cc_final: 0.5826 (m) REVERT: 6 269 PHE cc_start: 0.6567 (m-80) cc_final: 0.5954 (m-80) REVERT: 6 271 PHE cc_start: 0.7754 (t80) cc_final: 0.7486 (t80) REVERT: 7 8 ARG cc_start: 0.8158 (mtm180) cc_final: 0.7951 (mtm-85) REVERT: 7 14 ARG cc_start: 0.8107 (mtm-85) cc_final: 0.7807 (mtt90) REVERT: 7 24 LYS cc_start: 0.7596 (tttt) cc_final: 0.7323 (ttpt) REVERT: 7 39 GLU cc_start: 0.7627 (mp0) cc_final: 0.7036 (mp0) REVERT: 7 83 GLU cc_start: 0.7256 (tt0) cc_final: 0.6994 (mt-10) REVERT: 7 98 LEU cc_start: 0.6825 (mt) cc_final: 0.6603 (mm) REVERT: 7 111 ASP cc_start: 0.6934 (t70) cc_final: 0.6584 (t70) REVERT: 7 129 LYS cc_start: 0.7745 (mmmm) cc_final: 0.7491 (mttp) REVERT: 7 145 ASN cc_start: 0.7775 (m-40) cc_final: 0.7514 (m-40) REVERT: 7 146 ARG cc_start: 0.7840 (ptm160) cc_final: 0.7617 (ptm160) REVERT: 7 162 THR cc_start: 0.7456 (OUTLIER) cc_final: 0.7161 (p) REVERT: 7 181 ASN cc_start: 0.7612 (t0) cc_final: 0.7181 (t0) REVERT: 7 193 GLU cc_start: 0.8046 (tp30) cc_final: 0.7443 (tp30) REVERT: 7 228 GLU cc_start: 0.7044 (tm-30) cc_final: 0.6552 (tm-30) REVERT: 7 232 LYS cc_start: 0.7332 (ttmm) cc_final: 0.6603 (ttpp) REVERT: 7 250 TYR cc_start: 0.7782 (t80) cc_final: 0.7435 (t80) REVERT: 7 271 PHE cc_start: 0.7946 (t80) cc_final: 0.7486 (t80) REVERT: 7 285 LYS cc_start: 0.8374 (ttmm) cc_final: 0.7923 (tppt) REVERT: 7 305 ASP cc_start: 0.7835 (m-30) cc_final: 0.7631 (m-30) REVERT: 7 309 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7140 (mm-30) outliers start: 91 outliers final: 61 residues processed: 646 average time/residue: 0.3933 time to fit residues: 356.1357 Evaluate side-chains 674 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 591 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 1 residue 34 ASP Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 107 LEU Chi-restraints excluded: chain 1 residue 110 THR Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 1 residue 178 LEU 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 275 LEU Chi-restraints excluded: chain 1 residue 309 GLU Chi-restraints excluded: chain 2 residue 22 VAL Chi-restraints excluded: chain 2 residue 98 LEU Chi-restraints excluded: chain 2 residue 101 MET Chi-restraints excluded: chain 2 residue 141 GLU Chi-restraints excluded: chain 2 residue 143 ARG Chi-restraints excluded: chain 2 residue 162 THR 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 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 110 THR Chi-restraints excluded: chain 3 residue 115 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 193 GLU Chi-restraints excluded: chain 3 residue 269 PHE Chi-restraints excluded: chain 3 residue 270 VAL Chi-restraints excluded: chain 3 residue 309 GLU Chi-restraints excluded: chain 3 residue 312 LEU Chi-restraints excluded: chain 4 residue 10 SER Chi-restraints excluded: chain 4 residue 27 SER Chi-restraints excluded: chain 4 residue 79 VAL Chi-restraints excluded: chain 4 residue 96 GLU Chi-restraints excluded: chain 4 residue 110 THR Chi-restraints excluded: chain 4 residue 142 GLU Chi-restraints excluded: chain 4 residue 146 ARG Chi-restraints excluded: chain 4 residue 148 LEU Chi-restraints excluded: chain 4 residue 149 THR Chi-restraints excluded: chain 4 residue 221 LYS 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 298 MET Chi-restraints excluded: chain 5 residue 38 LEU Chi-restraints excluded: chain 5 residue 97 LEU Chi-restraints excluded: chain 5 residue 99 VAL Chi-restraints excluded: chain 5 residue 105 LEU Chi-restraints excluded: chain 5 residue 114 ARG Chi-restraints excluded: chain 5 residue 142 GLU Chi-restraints excluded: chain 5 residue 168 ILE Chi-restraints excluded: chain 5 residue 178 LEU Chi-restraints excluded: chain 5 residue 183 GLN Chi-restraints excluded: chain 5 residue 299 LEU Chi-restraints excluded: chain 6 residue 46 MET Chi-restraints excluded: chain 6 residue 63 LEU Chi-restraints excluded: chain 6 residue 99 VAL Chi-restraints excluded: chain 6 residue 107 LEU Chi-restraints excluded: chain 6 residue 115 LEU Chi-restraints excluded: chain 6 residue 142 GLU Chi-restraints excluded: chain 6 residue 146 ARG Chi-restraints excluded: chain 6 residue 148 LEU Chi-restraints excluded: chain 6 residue 168 ILE Chi-restraints excluded: chain 6 residue 175 LYS Chi-restraints excluded: chain 6 residue 248 LEU Chi-restraints excluded: chain 6 residue 259 ASN Chi-restraints excluded: chain 6 residue 263 THR Chi-restraints excluded: chain 7 residue 86 ASP Chi-restraints excluded: chain 7 residue 109 GLU 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 214 ASP Chi-restraints excluded: chain 7 residue 263 THR Chi-restraints excluded: chain 7 residue 269 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 0.3980 chunk 53 optimal weight: 0.8980 chunk 161 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 175 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 180 optimal weight: 0.0070 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 64 ASN ** 1 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 231 GLN 1 282 ASN 2 181 ASN ** 2 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 153 ASN 6 181 ASN ** 6 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 247 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.168465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.133545 restraints weight = 26046.308| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.22 r_work: 0.3534 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18772 Z= 0.206 Angle : 0.679 13.473 25612 Z= 0.332 Chirality : 0.041 0.200 2863 Planarity : 0.004 0.039 3122 Dihedral : 15.465 89.564 3085 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 4.90 % Allowed : 28.84 % Favored : 66.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.19), residues: 2163 helix: 0.94 (0.15), residues: 1204 sheet: -1.29 (0.42), residues: 196 loop : -1.81 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP 6 154 HIS 0.003 0.000 HIS 1 81 PHE 0.020 0.002 PHE 4 271 TYR 0.023 0.002 TYR 6 199 ARG 0.009 0.001 ARG 7 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6172.65 seconds wall clock time: 110 minutes 9.22 seconds (6609.22 seconds total)