Starting phenix.real_space_refine on Fri Mar 6 23:02:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7veb_31945/03_2026/7veb_31945.cif Found real_map, /net/cci-nas-00/data/ceres_data/7veb_31945/03_2026/7veb_31945.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7veb_31945/03_2026/7veb_31945.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7veb_31945/03_2026/7veb_31945.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7veb_31945/03_2026/7veb_31945.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7veb_31945/03_2026/7veb_31945.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 186 5.16 5 C 22424 2.51 5 N 6059 2.21 5 O 6861 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35530 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1218 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 156} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1274 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 166} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1225 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "D" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1271 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 166} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1, 'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1225 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "F" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1274 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 166} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1225 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "H" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 166} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1225 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "J" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1274 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 166} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1225 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "L" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1274 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 166} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1225 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "N" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1274 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 166} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 1231 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 162, 1225 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 156} Conformer: "B" Number of residues, atoms: 162, 1225 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 156} bond proxies already assigned to first conformer: 1240 Chain: "P" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1274 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 166} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1225 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "R" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1274 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 166} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1205 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 156} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "T" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1257 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 166} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'MEN:plan-2': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "U" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1225 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "V" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 166} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'MEN:plan-2': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 5 Chain: "W" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1222 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 156} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "X" Number of atoms: 1263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1263 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 166} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 1, 'MEN:plan-2': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "Y" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 495 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 58} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "Z" Number of atoms: 2132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2132 Classifications: {'peptide': 282} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 15, 'TRANS': 266} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 4, 'TRP:plan': 1, 'GLU:plan': 5, 'TYR:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 84 Chain: "a" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1430 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 9, 'TRANS': 175} Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'HIS:plan': 2, 'ARG:plan': 6, 'ASP:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 85 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.97, per 1000 atoms: 0.22 Number of scatterers: 35530 At special positions: 0 Unit cell: (128.34, 128.34, 141.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 186 16.00 O 6861 8.00 N 6059 7.00 C 22424 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.27 Conformation dependent library (CDL) restraints added in 1.4 seconds 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8464 Finding SS restraints... Secondary structure from input PDB file: 251 helices and 2 sheets defined 82.3% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 removed outlier: 3.861A pdb=" N GLN A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 47 removed outlier: 4.153A pdb=" N VAL A 35 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ALA A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN A 47 " --> pdb=" O ALA A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 63 Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 77 through 102 removed outlier: 3.591A pdb=" N VAL A 100 " --> pdb=" O THR A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 111 Processing helix chain 'A' and resid 114 through 122 Processing helix chain 'A' and resid 126 through 140 Processing helix chain 'A' and resid 145 through 174 removed outlier: 3.531A pdb=" N ALA A 149 " --> pdb=" O THR A 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 16 Processing helix chain 'B' and resid 20 through 33 Processing helix chain 'B' and resid 33 through 47 removed outlier: 3.521A pdb=" N ASN B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 63 Processing helix chain 'B' and resid 64 through 67 Processing helix chain 'B' and resid 78 through 102 Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 115 through 123 Processing helix chain 'B' and resid 125 through 145 Processing helix chain 'B' and resid 155 through 174 Processing helix chain 'C' and resid 3 through 16 removed outlier: 3.690A pdb=" N GLN C 15 " --> pdb=" O ALA C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 47 removed outlier: 4.123A pdb=" N VAL C 35 " --> pdb=" O PHE C 31 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ALA C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 63 removed outlier: 3.687A pdb=" N LEU C 51 " --> pdb=" O ASN C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 68 Processing helix chain 'C' and resid 77 through 102 Processing helix chain 'C' and resid 104 through 111 Processing helix chain 'C' and resid 114 through 122 Processing helix chain 'C' and resid 125 through 140 removed outlier: 4.131A pdb=" N TYR C 129 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 133 " --> pdb=" O TYR C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 174 Processing helix chain 'D' and resid 3 through 16 Processing helix chain 'D' and resid 20 through 33 Processing helix chain 'D' and resid 33 through 47 Processing helix chain 'D' and resid 47 through 63 Processing helix chain 'D' and resid 63 through 68 removed outlier: 4.271A pdb=" N ILE D 67 " --> pdb=" O GLN D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 102 removed outlier: 3.595A pdb=" N ALA D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 111 removed outlier: 3.553A pdb=" N ARG D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 123 Processing helix chain 'D' and resid 125 through 145 Processing helix chain 'D' and resid 155 through 174 Processing helix chain 'E' and resid 3 through 16 removed outlier: 3.807A pdb=" N GLN E 15 " --> pdb=" O ALA E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 47 removed outlier: 4.165A pdb=" N VAL E 35 " --> pdb=" O PHE E 31 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ALA E 36 " --> pdb=" O LYS E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 63 Processing helix chain 'E' and resid 64 through 68 Processing helix chain 'E' and resid 77 through 102 Processing helix chain 'E' and resid 104 through 111 Processing helix chain 'E' and resid 114 through 122 Processing helix chain 'E' and resid 125 through 140 removed outlier: 4.325A pdb=" N TYR E 129 " --> pdb=" O SER E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 174 removed outlier: 3.516A pdb=" N ALA E 149 " --> pdb=" O THR E 145 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 16 Processing helix chain 'F' and resid 20 through 33 Processing helix chain 'F' and resid 33 through 47 Processing helix chain 'F' and resid 47 through 63 Processing helix chain 'F' and resid 64 through 67 Processing helix chain 'F' and resid 78 through 102 removed outlier: 3.593A pdb=" N ALA F 82 " --> pdb=" O ASN F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 110 Processing helix chain 'F' and resid 114 through 123 Processing helix chain 'F' and resid 125 through 146 Processing helix chain 'F' and resid 155 through 174 Processing helix chain 'G' and resid 3 through 15 removed outlier: 3.841A pdb=" N GLN G 15 " --> pdb=" O ALA G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 47 removed outlier: 4.235A pdb=" N VAL G 35 " --> pdb=" O PHE G 31 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ALA G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 63 Processing helix chain 'G' and resid 64 through 68 Processing helix chain 'G' and resid 77 through 102 Processing helix chain 'G' and resid 104 through 111 Processing helix chain 'G' and resid 114 through 122 Processing helix chain 'G' and resid 125 through 140 removed outlier: 4.301A pdb=" N TYR G 129 " --> pdb=" O SER G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 174 Processing helix chain 'H' and resid 3 through 16 Processing helix chain 'H' and resid 20 through 33 Processing helix chain 'H' and resid 33 through 47 Processing helix chain 'H' and resid 47 through 63 Processing helix chain 'H' and resid 64 through 67 Processing helix chain 'H' and resid 78 through 102 removed outlier: 3.552A pdb=" N ILE H 91 " --> pdb=" O ASP H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 111 removed outlier: 3.540A pdb=" N CYS H 111 " --> pdb=" O LEU H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 123 Processing helix chain 'H' and resid 125 through 145 Processing helix chain 'H' and resid 155 through 174 Processing helix chain 'I' and resid 3 through 16 removed outlier: 3.650A pdb=" N GLN I 15 " --> pdb=" O ALA I 11 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 47 removed outlier: 4.133A pdb=" N VAL I 35 " --> pdb=" O PHE I 31 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ALA I 36 " --> pdb=" O LYS I 32 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN I 47 " --> pdb=" O ALA I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 63 Processing helix chain 'I' and resid 64 through 68 Processing helix chain 'I' and resid 77 through 102 removed outlier: 3.724A pdb=" N GLY I 89 " --> pdb=" O ALA I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 104 through 111 Processing helix chain 'I' and resid 114 through 122 removed outlier: 3.535A pdb=" N SER I 120 " --> pdb=" O SER I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 140 removed outlier: 4.115A pdb=" N TYR I 129 " --> pdb=" O SER I 125 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 174 removed outlier: 3.572A pdb=" N ALA I 149 " --> pdb=" O THR I 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 16 Processing helix chain 'J' and resid 20 through 33 Processing helix chain 'J' and resid 33 through 47 removed outlier: 3.732A pdb=" N ARG J 37 " --> pdb=" O GLU J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 63 Processing helix chain 'J' and resid 64 through 67 Processing helix chain 'J' and resid 78 through 102 Processing helix chain 'J' and resid 104 through 110 Processing helix chain 'J' and resid 114 through 123 Processing helix chain 'J' and resid 125 through 145 Processing helix chain 'J' and resid 155 through 174 Processing helix chain 'K' and resid 3 through 15 removed outlier: 3.783A pdb=" N GLN K 15 " --> pdb=" O ALA K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 47 removed outlier: 4.091A pdb=" N VAL K 35 " --> pdb=" O PHE K 31 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ALA K 36 " --> pdb=" O LYS K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 63 removed outlier: 3.504A pdb=" N ALA K 55 " --> pdb=" O LEU K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 68 removed outlier: 3.620A pdb=" N THR K 68 " --> pdb=" O TYR K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 102 Processing helix chain 'K' and resid 104 through 111 Processing helix chain 'K' and resid 114 through 122 Processing helix chain 'K' and resid 125 through 139 removed outlier: 4.250A pdb=" N TYR K 129 " --> pdb=" O SER K 125 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 174 Processing helix chain 'L' and resid 3 through 16 removed outlier: 3.657A pdb=" N ARG L 15 " --> pdb=" O GLN L 11 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 33 Processing helix chain 'L' and resid 33 through 47 removed outlier: 3.564A pdb=" N ARG L 37 " --> pdb=" O GLU L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 63 Processing helix chain 'L' and resid 78 through 102 removed outlier: 3.884A pdb=" N ILE L 91 " --> pdb=" O ASP L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 111 removed outlier: 3.622A pdb=" N CYS L 111 " --> pdb=" O LEU L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 123 Processing helix chain 'L' and resid 125 through 146 removed outlier: 3.535A pdb=" N VAL L 129 " --> pdb=" O PRO L 125 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA L 130 " --> pdb=" O GLY L 126 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA L 139 " --> pdb=" O LYS L 135 " (cutoff:3.500A) Processing helix chain 'L' and resid 155 through 174 Processing helix chain 'M' and resid 3 through 15 removed outlier: 3.626A pdb=" N GLN M 15 " --> pdb=" O ALA M 11 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 47 removed outlier: 4.123A pdb=" N VAL M 35 " --> pdb=" O PHE M 31 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ALA M 36 " --> pdb=" O LYS M 32 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN M 47 " --> pdb=" O ALA M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 47 through 63 Processing helix chain 'M' and resid 64 through 68 Processing helix chain 'M' and resid 77 through 102 Processing helix chain 'M' and resid 104 through 111 Processing helix chain 'M' and resid 114 through 122 Processing helix chain 'M' and resid 125 through 140 removed outlier: 4.166A pdb=" N TYR M 129 " --> pdb=" O SER M 125 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 174 Processing helix chain 'N' and resid 3 through 16 Processing helix chain 'N' and resid 20 through 33 Processing helix chain 'N' and resid 33 through 47 removed outlier: 3.628A pdb=" N ASN N 47 " --> pdb=" O ARG N 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 47 through 63 Processing helix chain 'N' and resid 64 through 67 Processing helix chain 'N' and resid 78 through 102 Processing helix chain 'N' and resid 104 through 110 Processing helix chain 'N' and resid 115 through 123 Processing helix chain 'N' and resid 125 through 145 Processing helix chain 'N' and resid 155 through 174 Processing helix chain 'O' and resid 3 through 15 removed outlier: 3.914A pdb=" N GLN O 15 " --> pdb=" O ALA O 11 " (cutoff:3.500A) Processing helix chain 'O' and resid 20 through 47 removed outlier: 4.003A pdb=" N VAL O 35 " --> pdb=" O PHE O 31 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ALA O 36 " --> pdb=" O LYS O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 47 through 63 Processing helix chain 'O' and resid 64 through 68 Processing helix chain 'O' and resid 77 through 102 Processing helix chain 'O' and resid 104 through 111 Processing helix chain 'O' and resid 114 through 123 Processing helix chain 'O' and resid 125 through 140 removed outlier: 4.388A pdb=" N TYR O 129 " --> pdb=" O SER O 125 " (cutoff:3.500A) Processing helix chain 'O' and resid 146 through 174 Processing helix chain 'P' and resid 3 through 16 Processing helix chain 'P' and resid 20 through 33 Processing helix chain 'P' and resid 33 through 47 removed outlier: 3.596A pdb=" N ARG P 37 " --> pdb=" O GLU P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 47 through 63 Processing helix chain 'P' and resid 64 through 67 Processing helix chain 'P' and resid 78 through 102 Processing helix chain 'P' and resid 104 through 111 removed outlier: 3.646A pdb=" N CYS P 111 " --> pdb=" O LEU P 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 114 through 123 Processing helix chain 'P' and resid 125 through 146 Processing helix chain 'P' and resid 155 through 174 Processing helix chain 'Q' and resid 3 through 16 removed outlier: 3.955A pdb=" N GLN Q 15 " --> pdb=" O ALA Q 11 " (cutoff:3.500A) Processing helix chain 'Q' and resid 20 through 47 removed outlier: 4.298A pdb=" N VAL Q 35 " --> pdb=" O PHE Q 31 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ALA Q 36 " --> pdb=" O LYS Q 32 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN Q 47 " --> pdb=" O ALA Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 63 removed outlier: 3.563A pdb=" N ASP Q 53 " --> pdb=" O GLN Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 67 removed outlier: 3.505A pdb=" N THR Q 67 " --> pdb=" O PRO Q 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 64 through 67' Processing helix chain 'Q' and resid 77 through 102 Processing helix chain 'Q' and resid 104 through 111 Processing helix chain 'Q' and resid 114 through 122 removed outlier: 3.535A pdb=" N ILE Q 118 " --> pdb=" O GLY Q 114 " (cutoff:3.500A) Processing helix chain 'Q' and resid 125 through 140 removed outlier: 4.373A pdb=" N TYR Q 129 " --> pdb=" O SER Q 125 " (cutoff:3.500A) Processing helix chain 'Q' and resid 145 through 174 removed outlier: 3.510A pdb=" N ALA Q 149 " --> pdb=" O THR Q 145 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP Q 167 " --> pdb=" O ASN Q 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 16 Processing helix chain 'R' and resid 20 through 33 removed outlier: 3.596A pdb=" N ASN R 29 " --> pdb=" O ASP R 25 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU R 30 " --> pdb=" O ALA R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 47 removed outlier: 3.740A pdb=" N ARG R 37 " --> pdb=" O GLU R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 63 Processing helix chain 'R' and resid 64 through 67 Processing helix chain 'R' and resid 78 through 102 Processing helix chain 'R' and resid 104 through 111 Processing helix chain 'R' and resid 114 through 123 removed outlier: 3.981A pdb=" N THR R 118 " --> pdb=" O GLY R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 146 Processing helix chain 'R' and resid 155 through 174 Processing helix chain 'S' and resid 3 through 15 removed outlier: 3.747A pdb=" N GLN S 15 " --> pdb=" O ALA S 11 " (cutoff:3.500A) Processing helix chain 'S' and resid 20 through 47 removed outlier: 4.135A pdb=" N VAL S 35 " --> pdb=" O PHE S 31 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ALA S 36 " --> pdb=" O LYS S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 47 through 63 removed outlier: 3.584A pdb=" N ASP S 53 " --> pdb=" O GLN S 49 " (cutoff:3.500A) Processing helix chain 'S' and resid 64 through 69 Processing helix chain 'S' and resid 77 through 102 Processing helix chain 'S' and resid 104 through 111 Processing helix chain 'S' and resid 114 through 122 removed outlier: 3.521A pdb=" N SER S 120 " --> pdb=" O SER S 116 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR S 121 " --> pdb=" O GLU S 117 " (cutoff:3.500A) Processing helix chain 'S' and resid 125 through 140 removed outlier: 4.128A pdb=" N TYR S 129 " --> pdb=" O SER S 125 " (cutoff:3.500A) Processing helix chain 'S' and resid 145 through 174 removed outlier: 3.628A pdb=" N ALA S 149 " --> pdb=" O THR S 145 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 16 Processing helix chain 'T' and resid 20 through 33 Processing helix chain 'T' and resid 33 through 47 removed outlier: 3.686A pdb=" N ARG T 37 " --> pdb=" O GLU T 33 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN T 47 " --> pdb=" O ARG T 43 " (cutoff:3.500A) Processing helix chain 'T' and resid 47 through 63 removed outlier: 3.593A pdb=" N ALA T 58 " --> pdb=" O ASN T 54 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA T 61 " --> pdb=" O ARG T 57 " (cutoff:3.500A) Processing helix chain 'T' and resid 63 through 68 removed outlier: 4.336A pdb=" N ILE T 67 " --> pdb=" O GLN T 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 102 Processing helix chain 'T' and resid 104 through 110 Processing helix chain 'T' and resid 114 through 123 Processing helix chain 'T' and resid 125 through 145 Processing helix chain 'T' and resid 155 through 174 Processing helix chain 'U' and resid 3 through 15 Processing helix chain 'U' and resid 20 through 47 removed outlier: 4.164A pdb=" N VAL U 35 " --> pdb=" O PHE U 31 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ALA U 36 " --> pdb=" O LYS U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 63 Processing helix chain 'U' and resid 64 through 68 Processing helix chain 'U' and resid 77 through 102 Processing helix chain 'U' and resid 104 through 111 Processing helix chain 'U' and resid 114 through 122 Processing helix chain 'U' and resid 125 through 140 removed outlier: 4.196A pdb=" N TYR U 129 " --> pdb=" O SER U 125 " (cutoff:3.500A) Processing helix chain 'U' and resid 146 through 174 Processing helix chain 'V' and resid 3 through 16 Processing helix chain 'V' and resid 20 through 33 Processing helix chain 'V' and resid 33 through 47 removed outlier: 3.625A pdb=" N ARG V 37 " --> pdb=" O GLU V 33 " (cutoff:3.500A) Processing helix chain 'V' and resid 47 through 63 Processing helix chain 'V' and resid 64 through 67 Processing helix chain 'V' and resid 79 through 102 Processing helix chain 'V' and resid 104 through 110 Processing helix chain 'V' and resid 114 through 123 removed outlier: 3.553A pdb=" N GLN V 120 " --> pdb=" O ARG V 116 " (cutoff:3.500A) Processing helix chain 'V' and resid 125 through 146 Processing helix chain 'V' and resid 155 through 174 removed outlier: 3.524A pdb=" N ALA V 174 " --> pdb=" O ALA V 170 " (cutoff:3.500A) Processing helix chain 'W' and resid 3 through 16 removed outlier: 3.662A pdb=" N GLN W 15 " --> pdb=" O ALA W 11 " (cutoff:3.500A) Processing helix chain 'W' and resid 20 through 47 removed outlier: 4.034A pdb=" N VAL W 35 " --> pdb=" O PHE W 31 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ALA W 36 " --> pdb=" O LYS W 32 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER W 37 " --> pdb=" O ARG W 33 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET W 38 " --> pdb=" O ALA W 34 " (cutoff:3.500A) Processing helix chain 'W' and resid 47 through 63 Processing helix chain 'W' and resid 63 through 69 Processing helix chain 'W' and resid 77 through 102 removed outlier: 3.515A pdb=" N TYR W 97 " --> pdb=" O ARG W 93 " (cutoff:3.500A) Processing helix chain 'W' and resid 104 through 111 Processing helix chain 'W' and resid 114 through 122 Processing helix chain 'W' and resid 125 through 140 removed outlier: 4.404A pdb=" N TYR W 129 " --> pdb=" O SER W 125 " (cutoff:3.500A) Processing helix chain 'W' and resid 145 through 174 Processing helix chain 'X' and resid 3 through 16 Processing helix chain 'X' and resid 20 through 33 Processing helix chain 'X' and resid 33 through 47 Processing helix chain 'X' and resid 47 through 63 Processing helix chain 'X' and resid 64 through 67 Processing helix chain 'X' and resid 76 through 102 removed outlier: 3.966A pdb=" N ARG X 80 " --> pdb=" O TYR X 76 " (cutoff:3.500A) Processing helix chain 'X' and resid 104 through 111 Processing helix chain 'X' and resid 114 through 123 Processing helix chain 'X' and resid 125 through 145 Processing helix chain 'X' and resid 155 through 174 removed outlier: 4.043A pdb=" N GLU X 161 " --> pdb=" O ALA X 157 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE X 162 " --> pdb=" O LEU X 158 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA X 174 " --> pdb=" O ALA X 170 " (cutoff:3.500A) Processing helix chain 'Y' and resid 54 through 66 Processing helix chain 'Z' and resid 30 through 44 Processing helix chain 'Z' and resid 50 through 54 Processing helix chain 'Z' and resid 55 through 65 removed outlier: 3.553A pdb=" N LEU Z 61 " --> pdb=" O SER Z 57 " (cutoff:3.500A) Processing helix chain 'Z' and resid 68 through 79 Processing helix chain 'Z' and resid 79 through 86 removed outlier: 3.646A pdb=" N LYS Z 85 " --> pdb=" O LEU Z 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 91 through 104 Processing helix chain 'Z' and resid 110 through 124 removed outlier: 4.162A pdb=" N VAL Z 114 " --> pdb=" O ASP Z 110 " (cutoff:3.500A) Processing helix chain 'Z' and resid 125 through 136 Processing helix chain 'Z' and resid 136 through 143 Processing helix chain 'Z' and resid 162 through 172 removed outlier: 3.936A pdb=" N ASN Z 166 " --> pdb=" O THR Z 162 " (cutoff:3.500A) Processing helix chain 'Z' and resid 191 through 197 removed outlier: 3.679A pdb=" N THR Z 196 " --> pdb=" O ARG Z 192 " (cutoff:3.500A) Processing helix chain 'Z' and resid 217 through 221 removed outlier: 3.834A pdb=" N ASP Z 220 " --> pdb=" O PRO Z 217 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL Z 221 " --> pdb=" O SER Z 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 217 through 221' Processing helix chain 'Z' and resid 266 through 278 Processing helix chain 'a' and resid 38 through 54 removed outlier: 3.572A pdb=" N GLU a 44 " --> pdb=" O SER a 40 " (cutoff:3.500A) Processing helix chain 'a' and resid 65 through 72 Processing helix chain 'a' and resid 78 through 89 Processing helix chain 'a' and resid 89 through 96 Processing helix chain 'a' and resid 101 through 113 removed outlier: 3.740A pdb=" N GLU a 107 " --> pdb=" O TYR a 103 " (cutoff:3.500A) Processing helix chain 'a' and resid 120 through 135 removed outlier: 4.065A pdb=" N ILE a 129 " --> pdb=" O LEU a 125 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ARG a 130 " --> pdb=" O ALA a 126 " (cutoff:3.500A) Processing helix chain 'a' and resid 135 through 145 Processing helix chain 'a' and resid 146 through 154 Processing helix chain 'a' and resid 169 through 174 Processing helix chain 'a' and resid 180 through 185 removed outlier: 3.564A pdb=" N ASP a 183 " --> pdb=" O TYR a 180 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Y' and resid 46 through 50 removed outlier: 4.079A pdb=" N THR Y 46 " --> pdb=" O VAL Y 24 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER Y 71 " --> pdb=" O GLU Y 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Z' and resid 258 through 263 2648 hydrogen bonds defined for protein. 7847 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.64 Time building geometry restraints manager: 4.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.35: 11941 1.35 - 1.51: 10743 1.51 - 1.67: 13160 1.67 - 1.83: 291 1.83 - 1.99: 20 Bond restraints: 36155 Sorted by residual: bond pdb=" OB CYC T 201 " pdb=" C4B CYC T 201 " ideal model delta sigma weight residual 1.217 1.363 -0.146 2.00e-02 2.50e+03 5.35e+01 bond pdb=" OB CYC Q 201 " pdb=" C4B CYC Q 201 " ideal model delta sigma weight residual 1.217 1.363 -0.146 2.00e-02 2.50e+03 5.34e+01 bond pdb=" OB CYC X 201 " pdb=" C4B CYC X 201 " ideal model delta sigma weight residual 1.217 1.363 -0.146 2.00e-02 2.50e+03 5.33e+01 bond pdb=" OB CYC V 201 " pdb=" C4B CYC V 201 " ideal model delta sigma weight residual 1.217 1.362 -0.145 2.00e-02 2.50e+03 5.28e+01 bond pdb=" OB CYC S 201 " pdb=" C4B CYC S 201 " ideal model delta sigma weight residual 1.217 1.362 -0.145 2.00e-02 2.50e+03 5.26e+01 ... (remaining 36150 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.88: 49017 8.88 - 17.75: 223 17.75 - 26.63: 0 26.63 - 35.50: 0 35.50 - 44.38: 3 Bond angle restraints: 49243 Sorted by residual: angle pdb=" CBA CYC Q 201 " pdb=" CGA CYC Q 201 " pdb=" O2A CYC Q 201 " ideal model delta sigma weight residual 115.71 160.09 -44.38 3.00e+00 1.11e-01 2.19e+02 angle pdb=" CBA CYC Q 201 " pdb=" CGA CYC Q 201 " pdb=" O1A CYC Q 201 " ideal model delta sigma weight residual 117.88 74.34 43.54 3.00e+00 1.11e-01 2.11e+02 angle pdb=" O1A CYC Q 201 " pdb=" CGA CYC Q 201 " pdb=" O2A CYC Q 201 " ideal model delta sigma weight residual 126.41 85.75 40.66 3.00e+00 1.11e-01 1.84e+02 angle pdb=" CA CYS X 155 " pdb=" CB CYS X 155 " pdb=" SG CYS X 155 " ideal model delta sigma weight residual 114.40 131.93 -17.53 2.30e+00 1.89e-01 5.81e+01 angle pdb=" CA CYS H 155 " pdb=" CB CYS H 155 " pdb=" SG CYS H 155 " ideal model delta sigma weight residual 114.40 130.11 -15.71 2.30e+00 1.89e-01 4.66e+01 ... (remaining 49238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 20693 17.99 - 35.99: 1353 35.99 - 53.98: 298 53.98 - 71.97: 92 71.97 - 89.96: 31 Dihedral angle restraints: 22467 sinusoidal: 9272 harmonic: 13195 Sorted by residual: dihedral pdb=" CA PHE Z 15 " pdb=" C PHE Z 15 " pdb=" N SER Z 16 " pdb=" CA SER Z 16 " ideal model delta harmonic sigma weight residual 180.00 -159.35 -20.65 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA TYR Z 250 " pdb=" C TYR Z 250 " pdb=" N PRO Z 251 " pdb=" CA PRO Z 251 " ideal model delta harmonic sigma weight residual 180.00 159.86 20.14 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA LEU E 111 " pdb=" C LEU E 111 " pdb=" N ILE E 112 " pdb=" CA ILE E 112 " ideal model delta harmonic sigma weight residual -180.00 -161.78 -18.22 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 22464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 5397 0.148 - 0.297: 33 0.297 - 0.445: 13 0.445 - 0.594: 3 0.594 - 0.742: 2 Chirality restraints: 5448 Sorted by residual: chirality pdb=" C2C CYC C 201 " pdb=" C1C CYC C 201 " pdb=" C3C CYC C 201 " pdb=" CMC CYC C 201 " both_signs ideal model delta sigma weight residual False -2.52 -1.78 -0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" C2C CYC B 202 " pdb=" C1C CYC B 202 " pdb=" C3C CYC B 202 " pdb=" CMC CYC B 202 " both_signs ideal model delta sigma weight residual False -2.52 -1.90 -0.62 2.00e-01 2.50e+01 9.67e+00 chirality pdb=" C2C CYC I 201 " pdb=" C1C CYC I 201 " pdb=" C3C CYC I 201 " pdb=" CMC CYC I 201 " both_signs ideal model delta sigma weight residual False -2.52 -1.94 -0.58 2.00e-01 2.50e+01 8.46e+00 ... (remaining 5445 not shown) Planarity restraints: 6402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE Z 165 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.68e+00 pdb=" C PHE Z 165 " -0.037 2.00e-02 2.50e+03 pdb=" O PHE Z 165 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN Z 166 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU V 112 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.27e+00 pdb=" C LEU V 112 " 0.036 2.00e-02 2.50e+03 pdb=" O LEU V 112 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN V 113 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET Z 271 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.40e+00 pdb=" C MET Z 271 " -0.032 2.00e-02 2.50e+03 pdb=" O MET Z 271 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN Z 272 " 0.011 2.00e-02 2.50e+03 ... (remaining 6399 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1144 2.71 - 3.26: 39509 3.26 - 3.81: 63189 3.81 - 4.35: 75277 4.35 - 4.90: 122149 Nonbonded interactions: 301268 Sorted by model distance: nonbonded pdb=" OG1 THR Z 156 " pdb=" OB CYC L 201 " model vdw 2.165 3.040 nonbonded pdb=" OH TYR R 76 " pdb=" NH2 ARG S 93 " model vdw 2.229 3.120 nonbonded pdb=" NH1 ARG B 79 " pdb=" O ASN Y 30 " model vdw 2.244 3.120 nonbonded pdb=" O TYR R 76 " pdb=" OG1 THR R 77 " model vdw 2.279 3.040 nonbonded pdb=" O TYR L 76 " pdb=" OG1 THR L 77 " model vdw 2.284 3.040 ... (remaining 301263 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB )) or resid 31 through 52 or (resid 53 and (name N or name \ CA or name C or name O or name CB )) or resid 54 through 56 or resid 58 through \ 107 or (resid 108 through 109 and (name N or name CA or name C or name O or nam \ e CB )) or resid 110 through 122 or (resid 123 and (name N or name CA or name C \ or name O or name CB )) or resid 124 through 201)) selection = (chain 'C' and (resid 1 through 6 or (resid 7 through 8 and (name N or name CA o \ r name C or name O or name CB )) or resid 9 through 27 or (resid 28 and (name N \ or name CA or name C or name O or name CB )) or resid 29 or (resid 30 and (name \ N or name CA or name C or name O or name CB )) or resid 31 through 52 or (resid \ 53 and (name N or name CA or name C or name O or name CB )) or resid 54 through \ 56 or resid 58 through 107 or (resid 108 through 109 and (name N or name CA or n \ ame C or name O or name CB )) or resid 110 through 122 or (resid 123 and (name N \ or name CA or name C or name O or name CB )) or resid 124 through 201)) selection = (chain 'E' and (resid 1 through 6 or (resid 7 through 8 and (name N or name CA o \ r name C or name O or name CB )) or resid 9 through 27 or (resid 28 and (name N \ or name CA or name C or name O or name CB )) or resid 29 or (resid 30 and (name \ N or name CA or name C or name O or name CB )) or resid 31 through 52 or (resid \ 53 and (name N or name CA or name C or name O or name CB )) or resid 54 through \ 56 or resid 58 through 107 or (resid 108 through 109 and (name N or name CA or n \ ame C or name O or name CB )) or resid 110 through 122 or (resid 123 and (name N \ or name CA or name C or name O or name CB )) or resid 124 through 201)) selection = (chain 'G' and (resid 1 through 6 or (resid 7 through 8 and (name N or name CA o \ r name C or name O or name CB )) or resid 9 through 27 or (resid 28 and (name N \ or name CA or name C or name O or name CB )) or resid 29 or (resid 30 and (name \ N or name CA or name C or name O or name CB )) or resid 31 through 52 or (resid \ 53 and (name N or name CA or name C or name O or name CB )) or resid 54 through \ 56 or resid 58 through 107 or (resid 108 through 109 and (name N or name CA or n \ ame C or name O or name CB )) or resid 110 through 122 or (resid 123 and (name N \ or name CA or name C or name O or name CB )) or resid 124 through 201)) selection = (chain 'I' and (resid 1 through 6 or (resid 7 through 8 and (name N or name CA o \ r name C or name O or name CB )) or resid 9 through 27 or (resid 28 and (name N \ or name CA or name C or name O or name CB )) or resid 29 or (resid 30 and (name \ N or name CA or name C or name O or name CB )) or resid 31 through 52 or (resid \ 53 and (name N or name CA or name C or name O or name CB )) or resid 54 through \ 56 or resid 58 through 107 or (resid 108 through 109 and (name N or name CA or n \ ame C or name O or name CB )) or resid 110 through 122 or (resid 123 and (name N \ or name CA or name C or name O or name CB )) or resid 124 through 201)) selection = (chain 'K' and (resid 1 through 6 or (resid 7 through 8 and (name N or name CA o \ r name C or name O or name CB )) or resid 9 through 27 or (resid 28 and (name N \ or name CA or name C or name O or name CB )) or resid 29 or (resid 30 and (name \ N or name CA or name C or name O or name CB )) or resid 31 through 52 or (resid \ 53 and (name N or name CA or name C or name O or name CB )) or resid 54 through \ 56 or resid 58 through 107 or (resid 108 through 109 and (name N or name CA or n \ ame C or name O or name CB )) or resid 110 through 122 or (resid 123 and (name N \ or name CA or name C or name O or name CB )) or resid 124 through 201)) selection = (chain 'M' and (resid 1 through 6 or (resid 7 through 8 and (name N or name CA o \ r name C or name O or name CB )) or resid 9 through 27 or (resid 28 and (name N \ or name CA or name C or name O or name CB )) or resid 29 or (resid 30 and (name \ N or name CA or name C or name O or name CB )) or resid 31 through 52 or (resid \ 53 and (name N or name CA or name C or name O or name CB )) or resid 54 through \ 56 or resid 58 through 107 or (resid 108 through 109 and (name N or name CA or n \ ame C or name O or name CB )) or resid 110 through 122 or (resid 123 and (name N \ or name CA or name C or name O or name CB )) or resid 124 through 201)) selection = (chain 'O' and (resid 1 through 6 or (resid 7 through 8 and (name N or name CA o \ r name C or name O or name CB )) or resid 9 through 27 or (resid 28 and (name N \ or name CA or name C or name O or name CB )) or resid 29 or (resid 30 and (name \ N or name CA or name C or name O or name CB )) or resid 31 through 52 or (resid \ 53 and (name N or name CA or name C or name O or name CB )) or resid 54 through \ 56 or resid 58 through 107 or (resid 108 through 109 and (name N or name CA or n \ ame C or name O or name CB )) or resid 110 through 122 or (resid 123 and (name N \ or name CA or name C or name O or name CB )) or resid 124 through 201)) selection = (chain 'Q' and (resid 1 through 6 or (resid 7 through 8 and (name N or name CA o \ r name C or name O or name CB )) or resid 9 through 27 or (resid 28 and (name N \ or name CA or name C or name O or name CB )) or resid 29 or (resid 30 and (name \ N or name CA or name C or name O or name CB )) or resid 31 through 52 or (resid \ 53 and (name N or name CA or name C or name O or name CB )) or resid 54 through \ 56 or resid 58 through 107 or (resid 108 through 109 and (name N or name CA or n \ ame C or name O or name CB )) or resid 110 through 122 or (resid 123 and (name N \ or name CA or name C or name O or name CB )) or resid 124 through 201)) selection = (chain 'S' and (resid 1 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 52 or (resid 53 and (name N or name \ CA or name C or name O or name CB )) or resid 54 through 56 or resid 58 through \ 201)) selection = (chain 'U' and (resid 1 through 6 or (resid 7 through 8 and (name N or name CA o \ r name C or name O or name CB )) or resid 9 through 27 or (resid 28 and (name N \ or name CA or name C or name O or name CB )) or resid 29 or (resid 30 and (name \ N or name CA or name C or name O or name CB )) or resid 31 through 52 or (resid \ 53 and (name N or name CA or name C or name O or name CB )) or resid 54 through \ 56 or resid 58 through 107 or (resid 108 through 109 and (name N or name CA or n \ ame C or name O or name CB )) or resid 110 through 122 or (resid 123 and (name N \ or name CA or name C or name O or name CB )) or resid 124 through 201)) selection = (chain 'W' and (resid 1 through 6 or (resid 7 through 8 and (name N or name CA o \ r name C or name O or name CB )) or resid 9 through 27 or (resid 28 and (name N \ or name CA or name C or name O or name CB )) or resid 29 or (resid 30 and (name \ N or name CA or name C or name O or name CB )) or resid 31 through 56 or resid 5 \ 8 through 107 or (resid 108 through 109 and (name N or name CA or name C or name \ O or name CB )) or resid 110 through 122 or (resid 123 and (name N or name CA o \ r name C or name O or name CB )) or resid 124 through 201)) } ncs_group { reference = (chain 'B' and (resid 1 through 38 or (resid 39 through 40 and (name N or name C \ A or name C or name O or name CB )) or resid 41 through 102 or (resid 103 and (n \ ame N or name CA or name C or name O or name CB )) or resid 104 through 107 or ( \ resid 108 and (name N or name CA or name C or name O or name CB )) or resid 109 \ through 119 or (resid 120 through 122 and (name N or name CA or name C or name O \ or name CB )) or resid 123 through 133 or (resid 134 and (name N or name CA or \ name C or name O or name CB )) or resid 135 through 136 or (resid 137 and (name \ N or name CA or name C or name O or name CB )) or resid 138 through 202)) selection = (chain 'D' and (resid 1 through 102 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 107 or (resid 108 and (name N or \ name CA or name C or name O or name CB )) or resid 109 through 119 or (resid 12 \ 0 through 122 and (name N or name CA or name C or name O or name CB )) or resid \ 123 through 133 or (resid 134 and (name N or name CA or name C or name O or name \ CB )) or resid 135 through 136 or (resid 137 and (name N or name CA or name C o \ r name O or name CB )) or resid 138 through 202)) selection = (chain 'F' and (resid 1 through 38 or (resid 39 through 40 and (name N or name C \ A or name C or name O or name CB )) or resid 41 through 102 or (resid 103 and (n \ ame N or name CA or name C or name O or name CB )) or resid 104 through 107 or ( \ resid 108 and (name N or name CA or name C or name O or name CB )) or resid 109 \ through 119 or (resid 120 through 122 and (name N or name CA or name C or name O \ or name CB )) or resid 123 through 133 or (resid 134 and (name N or name CA or \ name C or name O or name CB )) or resid 135 through 136 or (resid 137 and (name \ N or name CA or name C or name O or name CB )) or resid 138 through 202)) selection = (chain 'H' and (resid 1 through 38 or (resid 39 through 40 and (name N or name C \ A or name C or name O or name CB )) or resid 41 through 102 or (resid 103 and (n \ ame N or name CA or name C or name O or name CB )) or resid 104 through 107 or ( \ resid 108 and (name N or name CA or name C or name O or name CB )) or resid 109 \ through 119 or (resid 120 through 122 and (name N or name CA or name C or name O \ or name CB )) or resid 123 through 133 or (resid 134 and (name N or name CA or \ name C or name O or name CB )) or resid 135 through 202)) selection = (chain 'J' and (resid 1 through 38 or (resid 39 through 40 and (name N or name C \ A or name C or name O or name CB )) or resid 41 through 102 or (resid 103 and (n \ ame N or name CA or name C or name O or name CB )) or resid 104 through 107 or ( \ resid 108 and (name N or name CA or name C or name O or name CB )) or resid 109 \ through 119 or (resid 120 through 122 and (name N or name CA or name C or name O \ or name CB )) or resid 123 through 133 or (resid 134 and (name N or name CA or \ name C or name O or name CB )) or resid 135 through 136 or (resid 137 and (name \ N or name CA or name C or name O or name CB )) or resid 138 through 202)) selection = (chain 'L' and (resid 1 through 38 or (resid 39 through 40 and (name N or name C \ A or name C or name O or name CB )) or resid 41 through 102 or (resid 103 and (n \ ame N or name CA or name C or name O or name CB )) or resid 104 through 107 or ( \ resid 108 and (name N or name CA or name C or name O or name CB )) or resid 109 \ through 119 or (resid 120 through 122 and (name N or name CA or name C or name O \ or name CB )) or resid 123 through 133 or (resid 134 and (name N or name CA or \ name C or name O or name CB )) or resid 135 through 136 or (resid 137 and (name \ N or name CA or name C or name O or name CB )) or resid 138 through 202)) selection = (chain 'N' and (resid 1 through 38 or (resid 39 through 40 and (name N or name C \ A or name C or name O or name CB )) or resid 41 through 102 or (resid 103 and (n \ ame N or name CA or name C or name O or name CB )) or resid 104 through 107 or ( \ resid 108 and (name N or name CA or name C or name O or name CB )) or resid 109 \ through 119 or (resid 120 through 122 and (name N or name CA or name C or name O \ or name CB )) or resid 123 through 133 or (resid 134 and (name N or name CA or \ name C or name O or name CB )) or resid 135 through 136 or (resid 137 and (name \ N or name CA or name C or name O or name CB )) or resid 138 through 202)) selection = (chain 'P' and (resid 1 through 38 or (resid 39 through 40 and (name N or name C \ A or name C or name O or name CB )) or resid 41 through 102 or (resid 103 and (n \ ame N or name CA or name C or name O or name CB )) or resid 104 through 107 or ( \ resid 108 and (name N or name CA or name C or name O or name CB )) or resid 109 \ through 119 or (resid 120 through 122 and (name N or name CA or name C or name O \ or name CB )) or resid 123 through 133 or (resid 134 and (name N or name CA or \ name C or name O or name CB )) or resid 135 through 136 or (resid 137 and (name \ N or name CA or name C or name O or name CB )) or resid 138 through 202)) selection = (chain 'R' and (resid 1 through 38 or (resid 39 through 40 and (name N or name C \ A or name C or name O or name CB )) or resid 41 through 102 or (resid 103 and (n \ ame N or name CA or name C or name O or name CB )) or resid 104 through 107 or ( \ resid 108 and (name N or name CA or name C or name O or name CB )) or resid 109 \ through 119 or (resid 120 through 122 and (name N or name CA or name C or name O \ or name CB )) or resid 123 through 133 or (resid 134 and (name N or name CA or \ name C or name O or name CB )) or resid 135 through 136 or (resid 137 and (name \ N or name CA or name C or name O or name CB )) or resid 138 through 202)) selection = (chain 'T' and (resid 1 through 38 or (resid 39 through 40 and (name N or name C \ A or name C or name O or name CB )) or resid 41 through 119 or (resid 120 throug \ h 122 and (name N or name CA or name C or name O or name CB )) or resid 123 thro \ ugh 202)) selection = (chain 'V' and (resid 1 through 38 or (resid 39 through 40 and (name N or name C \ A or name C or name O or name CB )) or resid 41 through 102 or (resid 103 and (n \ ame N or name CA or name C or name O or name CB )) or resid 104 through 107 or ( \ resid 108 and (name N or name CA or name C or name O or name CB )) or resid 109 \ through 121 or (resid 122 and (name N or name CA or name C or name O or name CB \ )) or resid 123 through 133 or (resid 134 and (name N or name CA or name C or na \ me O or name CB )) or resid 135 through 136 or (resid 137 and (name N or name CA \ or name C or name O or name CB )) or resid 138 through 202)) selection = (chain 'X' and (resid 1 through 102 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 107 or (resid 108 and (name N or \ name CA or name C or name O or name CB )) or resid 109 through 119 or (resid 12 \ 0 through 122 and (name N or name CA or name C or name O or name CB )) or resid \ 123 through 202)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.140 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: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 30.790 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 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 : 0.011 0.177 36155 Z= 0.547 Angle : 1.367 44.378 49243 Z= 0.534 Chirality : 0.049 0.742 5448 Planarity : 0.004 0.034 6402 Dihedral : 13.452 89.965 14003 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.61 % Favored : 97.37 % Rotamer: Outliers : 0.74 % Allowed : 4.78 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.12), residues: 4448 helix: 1.02 (0.08), residues: 3365 sheet: 0.83 (0.98), residues: 28 loop : -1.22 (0.20), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 86 TYR 0.021 0.001 TYR D 76 PHE 0.020 0.002 PHE a 82 TRP 0.014 0.002 TRP C 128 HIS 0.005 0.001 HIS G 140 Details of bonding type rmsd covalent geometry : bond 0.01104 (36155) covalent geometry : angle 1.36749 (49243) hydrogen bonds : bond 0.13563 ( 2648) hydrogen bonds : angle 5.56725 ( 7847) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2195 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 2170 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ASP cc_start: 0.9023 (t70) cc_final: 0.8545 (t70) REVERT: A 17 ARG cc_start: 0.8503 (ptp-170) cc_final: 0.7655 (ptp-110) REVERT: A 18 PHE cc_start: 0.8095 (m-80) cc_final: 0.7339 (m-80) REVERT: A 33 ARG cc_start: 0.9176 (mmm160) cc_final: 0.8805 (tpt170) REVERT: A 38 MET cc_start: 0.9117 (mmt) cc_final: 0.8213 (tmm) REVERT: A 39 GLU cc_start: 0.9641 (tp30) cc_final: 0.9100 (mm-30) REVERT: A 49 GLN cc_start: 0.9267 (tp40) cc_final: 0.9023 (tp-100) REVERT: A 63 PHE cc_start: 0.9009 (m-80) cc_final: 0.8635 (m-10) REVERT: A 87 ASP cc_start: 0.9161 (m-30) cc_final: 0.8893 (m-30) REVERT: A 90 TYR cc_start: 0.9265 (m-10) cc_final: 0.8953 (m-80) REVERT: A 119 ASN cc_start: 0.9514 (m-40) cc_final: 0.9305 (p0) REVERT: A 124 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.8939 (mp) REVERT: A 166 ILE cc_start: 0.9772 (mt) cc_final: 0.9449 (mm) REVERT: A 167 ASP cc_start: 0.9188 (t0) cc_final: 0.8569 (t0) REVERT: A 170 ILE cc_start: 0.9391 (mt) cc_final: 0.9035 (mt) REVERT: B 27 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9142 (mm) REVERT: B 29 ASN cc_start: 0.8286 (m-40) cc_final: 0.8056 (t0) REVERT: B 32 LYS cc_start: 0.9038 (ttpp) cc_final: 0.8645 (tppt) REVERT: B 33 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8846 (mm-30) REVERT: B 49 SER cc_start: 0.9630 (m) cc_final: 0.9298 (p) REVERT: B 67 ILE cc_start: 0.9362 (pt) cc_final: 0.9137 (mm) REVERT: B 89 GLU cc_start: 0.9563 (pt0) cc_final: 0.9332 (tt0) REVERT: B 93 ARG cc_start: 0.9481 (ttp80) cc_final: 0.8957 (mtp180) REVERT: B 112 LEU cc_start: 0.9343 (mt) cc_final: 0.8974 (mp) REVERT: B 119 TYR cc_start: 0.9330 (m-80) cc_final: 0.8750 (m-80) REVERT: B 120 GLN cc_start: 0.8762 (mt0) cc_final: 0.8176 (tm-30) REVERT: B 129 VAL cc_start: 0.9721 (t) cc_final: 0.9519 (t) REVERT: B 145 ASN cc_start: 0.9248 (t0) cc_final: 0.8693 (p0) REVERT: C 3 THR cc_start: 0.8823 (m) cc_final: 0.8500 (p) REVERT: C 20 SER cc_start: 0.9369 (p) cc_final: 0.9141 (p) REVERT: C 31 PHE cc_start: 0.9400 (m-80) cc_final: 0.9123 (m-80) REVERT: C 60 TYR cc_start: 0.8042 (m-10) cc_final: 0.7794 (m-80) REVERT: C 65 TYR cc_start: 0.7492 (p90) cc_final: 0.7196 (p90) REVERT: C 69 MET cc_start: 0.7416 (ttm) cc_final: 0.6750 (ttm) REVERT: C 86 ARG cc_start: 0.9472 (ttp-170) cc_final: 0.9271 (ttp-170) REVERT: C 87 ASP cc_start: 0.9692 (m-30) cc_final: 0.9476 (m-30) REVERT: C 94 MET cc_start: 0.9533 (mmt) cc_final: 0.9142 (mmm) REVERT: C 122 PHE cc_start: 0.9067 (m-10) cc_final: 0.8852 (m-10) REVERT: C 125 SER cc_start: 0.9513 (t) cc_final: 0.9133 (p) REVERT: C 128 TRP cc_start: 0.8340 (m-10) cc_final: 0.8074 (m-10) REVERT: D 13 ASP cc_start: 0.8701 (t70) cc_final: 0.8416 (t0) REVERT: D 24 PHE cc_start: 0.8362 (m-80) cc_final: 0.8067 (m-80) REVERT: D 32 LYS cc_start: 0.9418 (ptmt) cc_final: 0.9142 (pttt) REVERT: D 46 SER cc_start: 0.8931 (m) cc_final: 0.8633 (m) REVERT: D 59 LEU cc_start: 0.9400 (tp) cc_final: 0.9175 (tt) REVERT: D 79 ARG cc_start: 0.7929 (tmt170) cc_final: 0.7681 (tpt170) REVERT: D 97 TYR cc_start: 0.9508 (m-10) cc_final: 0.9274 (m-80) REVERT: D 110 ARG cc_start: 0.9051 (mtt-85) cc_final: 0.8758 (mtm-85) REVERT: D 124 THR cc_start: 0.9076 (m) cc_final: 0.8412 (m) REVERT: D 137 LYS cc_start: 0.8454 (ttpt) cc_final: 0.8153 (tttm) REVERT: D 154 ASP cc_start: 0.7857 (t0) cc_final: 0.7557 (t0) REVERT: D 155 CYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7208 (m) REVERT: D 161 GLU cc_start: 0.8214 (tt0) cc_final: 0.7958 (tt0) REVERT: D 165 TYR cc_start: 0.8487 (m-10) cc_final: 0.8187 (m-80) REVERT: E 9 ILE cc_start: 0.9324 (mt) cc_final: 0.9046 (tt) REVERT: E 25 GLN cc_start: 0.9207 (mt0) cc_final: 0.8828 (mt0) REVERT: E 38 MET cc_start: 0.8751 (mmt) cc_final: 0.8243 (tmm) REVERT: E 62 LYS cc_start: 0.9648 (tptt) cc_final: 0.9393 (tppt) REVERT: E 72 SER cc_start: 0.8976 (m) cc_final: 0.8665 (t) REVERT: E 73 GLN cc_start: 0.9237 (pm20) cc_final: 0.8977 (pm20) REVERT: E 74 TYR cc_start: 0.8855 (m-80) cc_final: 0.8385 (m-10) REVERT: E 109 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8853 (tt0) REVERT: E 115 LEU cc_start: 0.9418 (tp) cc_final: 0.9160 (tt) REVERT: E 122 PHE cc_start: 0.9615 (m-80) cc_final: 0.9216 (m-10) REVERT: E 123 ASP cc_start: 0.9348 (m-30) cc_final: 0.9087 (t70) REVERT: E 167 ASP cc_start: 0.9256 (t0) cc_final: 0.8808 (t0) REVERT: E 173 LEU cc_start: 0.9618 (mm) cc_final: 0.9311 (tp) REVERT: F 21 ASN cc_start: 0.8500 (m-40) cc_final: 0.7989 (t0) REVERT: F 25 ASP cc_start: 0.9214 (m-30) cc_final: 0.8585 (m-30) REVERT: F 27 LEU cc_start: 0.9327 (mt) cc_final: 0.8751 (pp) REVERT: F 29 ASN cc_start: 0.9315 (m-40) cc_final: 0.8957 (m110) REVERT: F 33 GLU cc_start: 0.9238 (mt-10) cc_final: 0.8965 (mp0) REVERT: F 35 ASN cc_start: 0.9283 (m-40) cc_final: 0.8971 (m-40) REVERT: F 62 GLU cc_start: 0.9614 (tt0) cc_final: 0.9359 (tm-30) REVERT: F 65 GLN cc_start: 0.9341 (pm20) cc_final: 0.8972 (mm-40) REVERT: F 76 TYR cc_start: 0.8863 (t80) cc_final: 0.8378 (t80) REVERT: F 93 ARG cc_start: 0.9332 (ttp80) cc_final: 0.8819 (ttp-110) REVERT: F 103 ASP cc_start: 0.9022 (t0) cc_final: 0.8593 (t0) REVERT: F 115 LEU cc_start: 0.9145 (tp) cc_final: 0.8720 (tp) REVERT: F 117 GLU cc_start: 0.9525 (pp20) cc_final: 0.9002 (pp20) REVERT: F 118 THR cc_start: 0.9623 (m) cc_final: 0.9240 (p) REVERT: F 131 VAL cc_start: 0.8606 (t) cc_final: 0.8325 (t) REVERT: F 136 MET cc_start: 0.8922 (mtm) cc_final: 0.8638 (ttp) REVERT: F 138 ASP cc_start: 0.9007 (m-30) cc_final: 0.8697 (t70) REVERT: F 146 ASP cc_start: 0.9000 (t0) cc_final: 0.8783 (t0) REVERT: F 158 LEU cc_start: 0.8763 (tp) cc_final: 0.8264 (tt) REVERT: F 159 MET cc_start: 0.9074 (mmp) cc_final: 0.8790 (mmt) REVERT: F 165 TYR cc_start: 0.9296 (m-80) cc_final: 0.8941 (m-10) REVERT: G 18 PHE cc_start: 0.8365 (m-80) cc_final: 0.6662 (m-80) REVERT: G 42 ARG cc_start: 0.7986 (mtt-85) cc_final: 0.7705 (ttt90) REVERT: G 53 ASP cc_start: 0.9266 (m-30) cc_final: 0.9003 (p0) REVERT: G 62 LYS cc_start: 0.9424 (tptm) cc_final: 0.9130 (tppt) REVERT: G 74 TYR cc_start: 0.8954 (m-80) cc_final: 0.8673 (m-10) REVERT: G 79 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8894 (pp20) REVERT: G 94 MET cc_start: 0.9177 (mmm) cc_final: 0.8927 (mtt) REVERT: G 97 TYR cc_start: 0.9529 (m-10) cc_final: 0.9129 (m-10) REVERT: G 122 PHE cc_start: 0.9312 (m-80) cc_final: 0.8898 (m-10) REVERT: G 124 LEU cc_start: 0.9124 (mt) cc_final: 0.8886 (mt) REVERT: G 129 TYR cc_start: 0.9132 (m-80) cc_final: 0.8473 (m-80) REVERT: G 161 GLU cc_start: 0.9533 (mt-10) cc_final: 0.9303 (mt-10) REVERT: G 166 ILE cc_start: 0.9341 (mt) cc_final: 0.9120 (tt) REVERT: G 167 ASP cc_start: 0.9273 (t0) cc_final: 0.8803 (t0) REVERT: G 170 ILE cc_start: 0.9536 (mt) cc_final: 0.9225 (pt) REVERT: H 15 ARG cc_start: 0.8360 (mmm160) cc_final: 0.7910 (mmt-90) REVERT: H 24 PHE cc_start: 0.8708 (m-80) cc_final: 0.8331 (m-10) REVERT: H 42 ASN cc_start: 0.9106 (t0) cc_final: 0.8881 (t0) REVERT: H 60 PHE cc_start: 0.8763 (m-80) cc_final: 0.8362 (m-10) REVERT: H 63 GLN cc_start: 0.9338 (mt0) cc_final: 0.8847 (mt0) REVERT: H 87 ASP cc_start: 0.9278 (m-30) cc_final: 0.8588 (m-30) REVERT: H 97 TYR cc_start: 0.9368 (m-10) cc_final: 0.8779 (m-10) REVERT: H 107 LEU cc_start: 0.9666 (tp) cc_final: 0.9448 (tt) REVERT: H 117 GLU cc_start: 0.9054 (tp30) cc_final: 0.8334 (tp30) REVERT: H 141 ILE cc_start: 0.9359 (tp) cc_final: 0.8839 (tp) REVERT: H 146 ASP cc_start: 0.8432 (t0) cc_final: 0.8187 (t0) REVERT: H 159 MET cc_start: 0.9025 (mmt) cc_final: 0.8543 (mmt) REVERT: I 51 LEU cc_start: 0.9421 (mt) cc_final: 0.9128 (mt) REVERT: I 60 TYR cc_start: 0.8359 (m-10) cc_final: 0.7923 (m-80) REVERT: I 62 LYS cc_start: 0.9367 (tptm) cc_final: 0.8895 (tptt) REVERT: I 91 TYR cc_start: 0.8929 (m-80) cc_final: 0.8727 (m-80) REVERT: I 107 MET cc_start: 0.9275 (tpp) cc_final: 0.9004 (tpt) REVERT: I 110 TYR cc_start: 0.9249 (m-10) cc_final: 0.8742 (m-10) REVERT: I 111 LEU cc_start: 0.9400 (tp) cc_final: 0.8824 (tp) REVERT: I 115 LEU cc_start: 0.9144 (tp) cc_final: 0.8934 (tp) REVERT: I 118 ILE cc_start: 0.9432 (mm) cc_final: 0.9226 (mm) REVERT: I 167 ASP cc_start: 0.9685 (m-30) cc_final: 0.9441 (m-30) REVERT: J 15 ARG cc_start: 0.8579 (mtm180) cc_final: 0.8267 (mtp-110) REVERT: J 17 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8092 (mp0) REVERT: J 35 ASN cc_start: 0.9114 (m110) cc_final: 0.8403 (t0) REVERT: J 38 LEU cc_start: 0.9411 (mt) cc_final: 0.9035 (mp) REVERT: J 60 PHE cc_start: 0.9212 (m-80) cc_final: 0.8961 (m-80) REVERT: J 97 TYR cc_start: 0.8736 (m-10) cc_final: 0.8273 (m-10) REVERT: J 141 ILE cc_start: 0.8572 (tt) cc_final: 0.7785 (tp) REVERT: K 18 PHE cc_start: 0.8859 (m-80) cc_final: 0.8536 (m-80) REVERT: K 19 LEU cc_start: 0.9293 (mt) cc_final: 0.8903 (tt) REVERT: K 21 ASN cc_start: 0.8925 (p0) cc_final: 0.8664 (t0) REVERT: K 33 ARG cc_start: 0.8774 (mtp85) cc_final: 0.8291 (tpm170) REVERT: K 38 MET cc_start: 0.8981 (mmt) cc_final: 0.8736 (mmp) REVERT: K 61 GLN cc_start: 0.9090 (mt0) cc_final: 0.8662 (mt0) REVERT: K 98 CYS cc_start: 0.8734 (t) cc_final: 0.8440 (t) REVERT: K 107 MET cc_start: 0.9095 (tpp) cc_final: 0.8754 (tpp) REVERT: K 115 LEU cc_start: 0.9005 (tp) cc_final: 0.8522 (tp) REVERT: K 122 PHE cc_start: 0.8509 (m-10) cc_final: 0.8248 (m-10) REVERT: K 125 SER cc_start: 0.9260 (t) cc_final: 0.8920 (p) REVERT: K 133 LEU cc_start: 0.9435 (mt) cc_final: 0.9170 (mt) REVERT: K 140 HIS cc_start: 0.8938 (p-80) cc_final: 0.8618 (p-80) REVERT: K 163 ASN cc_start: 0.9456 (m-40) cc_final: 0.8962 (m110) REVERT: K 167 ASP cc_start: 0.9484 (t70) cc_final: 0.9180 (m-30) REVERT: L 13 ASP cc_start: 0.9092 (t70) cc_final: 0.8542 (t0) REVERT: L 60 PHE cc_start: 0.9052 (m-80) cc_final: 0.8719 (m-10) REVERT: L 65 GLN cc_start: 0.9305 (pt0) cc_final: 0.8621 (pm20) REVERT: L 68 GLN cc_start: 0.9452 (mt0) cc_final: 0.9225 (pp30) REVERT: L 80 ARG cc_start: 0.9079 (mtm-85) cc_final: 0.8848 (mtt180) REVERT: L 89 GLU cc_start: 0.9053 (pp20) cc_final: 0.8643 (pp20) REVERT: L 90 ILE cc_start: 0.9373 (mt) cc_final: 0.8794 (mm) REVERT: L 93 ARG cc_start: 0.8926 (ttp80) cc_final: 0.8545 (ttp-170) REVERT: L 113 ASN cc_start: 0.9189 (t0) cc_final: 0.8432 (t0) REVERT: L 137 LYS cc_start: 0.9607 (tttt) cc_final: 0.9250 (ttmt) REVERT: L 159 MET cc_start: 0.8953 (mmp) cc_final: 0.8705 (mmt) REVERT: L 165 TYR cc_start: 0.9098 (m-80) cc_final: 0.8870 (m-80) REVERT: M 1 MET cc_start: 0.8127 (mpp) cc_final: 0.7641 (ptp) REVERT: M 2 LYS cc_start: 0.8665 (tttp) cc_final: 0.8456 (ttmm) REVERT: M 17 ARG cc_start: 0.9078 (ptp-110) cc_final: 0.8669 (mtm110) REVERT: M 33 ARG cc_start: 0.9240 (mmt180) cc_final: 0.8494 (tpp-160) REVERT: M 57 GLN cc_start: 0.9602 (mm-40) cc_final: 0.9380 (mm-40) REVERT: M 69 MET cc_start: 0.9518 (tpt) cc_final: 0.9256 (tpp) REVERT: M 74 TYR cc_start: 0.9567 (m-80) cc_final: 0.9365 (m-10) REVERT: M 81 LYS cc_start: 0.8987 (tmtt) cc_final: 0.8736 (mtpp) REVERT: M 91 TYR cc_start: 0.9271 (m-80) cc_final: 0.8927 (m-10) REVERT: M 129 TYR cc_start: 0.8963 (m-80) cc_final: 0.8656 (m-80) REVERT: M 135 TYR cc_start: 0.8994 (t80) cc_final: 0.8699 (t80) REVERT: M 161 GLU cc_start: 0.9461 (tt0) cc_final: 0.9152 (mt-10) REVERT: N 3 ASP cc_start: 0.8751 (p0) cc_final: 0.8536 (p0) REVERT: N 19 LEU cc_start: 0.8470 (mt) cc_final: 0.8223 (mm) REVERT: N 35 ASN cc_start: 0.9352 (m-40) cc_final: 0.9122 (t0) REVERT: N 36 LYS cc_start: 0.8569 (mttt) cc_final: 0.8315 (mmtt) REVERT: N 62 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8509 (tm-30) REVERT: N 67 ILE cc_start: 0.9720 (pt) cc_final: 0.9243 (mt) REVERT: N 80 ARG cc_start: 0.9408 (mtm-85) cc_final: 0.8456 (mtm-85) REVERT: N 88 MET cc_start: 0.9055 (ttp) cc_final: 0.8104 (ttp) REVERT: N 95 VAL cc_start: 0.9780 (t) cc_final: 0.9544 (p) REVERT: N 103 ASP cc_start: 0.8495 (t0) cc_final: 0.8176 (t0) REVERT: N 115 LEU cc_start: 0.9594 (tp) cc_final: 0.9297 (tp) REVERT: N 148 ASN cc_start: 0.9041 (m-40) cc_final: 0.8837 (p0) REVERT: N 165 TYR cc_start: 0.8824 (m-80) cc_final: 0.8363 (m-10) REVERT: N 167 ASP cc_start: 0.9300 (m-30) cc_final: 0.9044 (m-30) REVERT: O 13 ASP cc_start: 0.9286 (t70) cc_final: 0.9067 (t70) REVERT: O 25 GLN cc_start: 0.8456 (mt0) cc_final: 0.8253 (mt0) REVERT: O 32 LYS cc_start: 0.9210 (mmmt) cc_final: 0.8867 (mmmm) REVERT: O 47 ASN cc_start: 0.9300 (m-40) cc_final: 0.9094 (p0) REVERT: O 99 LEU cc_start: 0.9183 (mt) cc_final: 0.8885 (tp) REVERT: O 104 THR cc_start: 0.9207 (p) cc_final: 0.8868 (p) REVERT: O 129 TYR cc_start: 0.8843 (m-80) cc_final: 0.8225 (m-80) REVERT: O 131 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8832 (tm-30) REVERT: O 166 ILE cc_start: 0.9120 (mt) cc_final: 0.8859 (tt) REVERT: P 1 MET cc_start: 0.6960 (ptt) cc_final: 0.6583 (ptt) REVERT: P 9 VAL cc_start: 0.9724 (t) cc_final: 0.9498 (p) REVERT: P 11 GLN cc_start: 0.8735 (mt0) cc_final: 0.8416 (mt0) REVERT: P 23 GLN cc_start: 0.8424 (mt0) cc_final: 0.8142 (mt0) REVERT: P 67 ILE cc_start: 0.9154 (pt) cc_final: 0.8795 (tp) REVERT: P 93 ARG cc_start: 0.9210 (ttp80) cc_final: 0.8425 (ttp-170) REVERT: P 94 TYR cc_start: 0.9219 (m-80) cc_final: 0.8407 (m-80) REVERT: P 97 TYR cc_start: 0.9182 (m-10) cc_final: 0.8571 (m-80) REVERT: P 104 SER cc_start: 0.9362 (p) cc_final: 0.9106 (p) REVERT: P 110 ARG cc_start: 0.8087 (mtt180) cc_final: 0.7785 (mtp85) REVERT: P 156 SER cc_start: 0.8692 (t) cc_final: 0.8362 (m) REVERT: P 159 MET cc_start: 0.9175 (mmm) cc_final: 0.8273 (tmm) REVERT: P 162 ILE cc_start: 0.9528 (pt) cc_final: 0.9280 (pt) REVERT: Q 14 THR cc_start: 0.8687 (p) cc_final: 0.8197 (t) REVERT: Q 15 GLN cc_start: 0.8509 (mm110) cc_final: 0.8226 (mm110) REVERT: Q 24 LEU cc_start: 0.8432 (mt) cc_final: 0.7757 (mt) REVERT: Q 37 SER cc_start: 0.7989 (m) cc_final: 0.7147 (p) REVERT: Q 53 ASP cc_start: 0.7168 (m-30) cc_final: 0.6732 (m-30) REVERT: Q 57 GLN cc_start: 0.6950 (mm110) cc_final: 0.6684 (mm-40) REVERT: Q 73 GLN cc_start: 0.7797 (pm20) cc_final: 0.7101 (pm20) REVERT: Q 86 ARG cc_start: 0.5640 (OUTLIER) cc_final: 0.4756 (mmt90) REVERT: Q 107 MET cc_start: 0.8564 (ttm) cc_final: 0.7980 (mtp) REVERT: Q 108 ASP cc_start: 0.8587 (m-30) cc_final: 0.8284 (m-30) REVERT: Q 168 TYR cc_start: 0.8393 (t80) cc_final: 0.8029 (t80) REVERT: R 38 LEU cc_start: 0.8563 (mt) cc_final: 0.8275 (mp) REVERT: R 39 ASP cc_start: 0.7872 (m-30) cc_final: 0.7649 (m-30) REVERT: R 87 ASP cc_start: 0.7926 (m-30) cc_final: 0.7662 (m-30) REVERT: R 88 MET cc_start: 0.9649 (mmm) cc_final: 0.9078 (mtp) REVERT: R 89 GLU cc_start: 0.9569 (pt0) cc_final: 0.9288 (tm-30) REVERT: R 103 ASP cc_start: 0.7354 (t0) cc_final: 0.6860 (t0) REVERT: R 111 CYS cc_start: 0.8829 (t) cc_final: 0.8617 (t) REVERT: R 115 LEU cc_start: 0.9287 (tt) cc_final: 0.8834 (tt) REVERT: R 136 MET cc_start: 0.9230 (ttp) cc_final: 0.8770 (ttt) REVERT: R 159 MET cc_start: 0.8829 (mmp) cc_final: 0.8063 (ptt) REVERT: S 37 SER cc_start: 0.8987 (t) cc_final: 0.8765 (p) REVERT: S 44 LEU cc_start: 0.9496 (mt) cc_final: 0.8674 (tp) REVERT: S 57 GLN cc_start: 0.9277 (mm-40) cc_final: 0.9064 (mm-40) REVERT: S 73 GLN cc_start: 0.9059 (pt0) cc_final: 0.8829 (pm20) REVERT: S 74 TYR cc_start: 0.9331 (m-80) cc_final: 0.8957 (m-80) REVERT: S 79 GLU cc_start: 0.8643 (mp0) cc_final: 0.8404 (tm-30) REVERT: S 83 LYS cc_start: 0.8721 (mmtp) cc_final: 0.8260 (mmtm) REVERT: S 90 TYR cc_start: 0.8802 (m-10) cc_final: 0.8301 (m-10) REVERT: S 115 LEU cc_start: 0.9076 (tp) cc_final: 0.8868 (tp) REVERT: S 118 ILE cc_start: 0.9581 (OUTLIER) cc_final: 0.9365 (pp) REVERT: T 9 VAL cc_start: 0.9299 (t) cc_final: 0.9054 (p) REVERT: T 13 ASP cc_start: 0.8990 (t70) cc_final: 0.8665 (t0) REVERT: T 15 ARG cc_start: 0.8141 (mtp85) cc_final: 0.7122 (mmt-90) REVERT: T 18 PHE cc_start: 0.8218 (m-80) cc_final: 0.7956 (m-80) REVERT: T 19 LEU cc_start: 0.8129 (mt) cc_final: 0.7754 (mm) REVERT: T 23 GLN cc_start: 0.8537 (mt0) cc_final: 0.8266 (mp10) REVERT: T 35 ASN cc_start: 0.8016 (m-40) cc_final: 0.7763 (p0) REVERT: T 76 TYR cc_start: 0.4893 (t80) cc_final: 0.4620 (t80) REVERT: T 87 ASP cc_start: 0.8707 (m-30) cc_final: 0.8498 (m-30) REVERT: U 18 PHE cc_start: 0.8657 (m-80) cc_final: 0.8431 (m-80) REVERT: U 25 GLN cc_start: 0.9058 (mt0) cc_final: 0.8643 (tt0) REVERT: U 42 ARG cc_start: 0.8035 (ttm-80) cc_final: 0.7518 (mtt180) REVERT: U 61 GLN cc_start: 0.8053 (mt0) cc_final: 0.7606 (pp30) REVERT: U 62 LYS cc_start: 0.9275 (tppp) cc_final: 0.9070 (tptt) REVERT: U 69 MET cc_start: 0.7094 (mtt) cc_final: 0.6480 (tpp) REVERT: U 87 ASP cc_start: 0.7572 (m-30) cc_final: 0.7286 (m-30) REVERT: U 94 MET cc_start: 0.9494 (tpp) cc_final: 0.9209 (tpp) REVERT: U 117 GLU cc_start: 0.9116 (tt0) cc_final: 0.8856 (mp0) REVERT: U 123 ASP cc_start: 0.8994 (t0) cc_final: 0.8741 (t70) REVERT: U 140 HIS cc_start: 0.9408 (p-80) cc_final: 0.9191 (p-80) REVERT: U 173 LEU cc_start: 0.9398 (mt) cc_final: 0.8938 (mt) REVERT: V 5 PHE cc_start: 0.8626 (m-10) cc_final: 0.8301 (m-10) REVERT: V 11 GLN cc_start: 0.8841 (tt0) cc_final: 0.8464 (tp40) REVERT: V 13 ASP cc_start: 0.9198 (t70) cc_final: 0.8700 (t0) REVERT: V 15 ARG cc_start: 0.9393 (mtm110) cc_final: 0.9062 (mtm-85) REVERT: V 17 GLU cc_start: 0.8531 (mp0) cc_final: 0.8283 (mp0) REVERT: V 19 LEU cc_start: 0.9313 (mt) cc_final: 0.9075 (mt) REVERT: V 60 PHE cc_start: 0.8876 (m-80) cc_final: 0.8625 (m-80) REVERT: V 62 GLU cc_start: 0.9214 (tm-30) cc_final: 0.8855 (tm-30) REVERT: V 81 MET cc_start: 0.8779 (tpp) cc_final: 0.8538 (tpp) REVERT: V 93 ARG cc_start: 0.9403 (ttp80) cc_final: 0.8939 (ttp80) REVERT: V 108 ASP cc_start: 0.9303 (m-30) cc_final: 0.9065 (t0) REVERT: V 159 MET cc_start: 0.9029 (mmp) cc_final: 0.8615 (tmm) REVERT: V 168 ARG cc_start: 0.9109 (ttt90) cc_final: 0.8898 (mmm-85) REVERT: W 22 THR cc_start: 0.9502 (p) cc_final: 0.9293 (p) REVERT: W 33 ARG cc_start: 0.8119 (mtp85) cc_final: 0.7875 (tmm160) REVERT: W 42 ARG cc_start: 0.6776 (tpp80) cc_final: 0.6285 (tpp80) REVERT: W 46 ASN cc_start: 0.7349 (m-40) cc_final: 0.6973 (p0) REVERT: W 65 TYR cc_start: 0.8423 (p90) cc_final: 0.7706 (p90) REVERT: W 69 MET cc_start: 0.4555 (mtp) cc_final: 0.4130 (mmm) REVERT: W 97 TYR cc_start: 0.8508 (m-10) cc_final: 0.7985 (m-80) REVERT: W 107 MET cc_start: 0.8741 (mmp) cc_final: 0.8483 (mmm) REVERT: W 111 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7685 (pt) REVERT: W 165 TYR cc_start: 0.8335 (m-80) cc_final: 0.8071 (m-80) REVERT: X 5 PHE cc_start: 0.8067 (m-80) cc_final: 0.7495 (m-80) REVERT: X 38 LEU cc_start: 0.9434 (mt) cc_final: 0.9185 (mt) REVERT: X 79 ARG cc_start: 0.7878 (ttm170) cc_final: 0.7331 (tpm170) REVERT: X 89 GLU cc_start: 0.8940 (tt0) cc_final: 0.8641 (tm-30) REVERT: X 119 TYR cc_start: 0.8045 (m-80) cc_final: 0.7834 (m-80) REVERT: X 136 MET cc_start: 0.7261 (mtm) cc_final: 0.6608 (mtp) REVERT: X 166 PHE cc_start: 0.8073 (m-80) cc_final: 0.7574 (m-80) REVERT: Y 20 PHE cc_start: 0.8967 (m-80) cc_final: 0.8137 (m-10) REVERT: Y 36 MET cc_start: 0.7412 (ttp) cc_final: 0.6907 (mmt) REVERT: Y 37 GLU cc_start: 0.8665 (tp30) cc_final: 0.8386 (tm-30) REVERT: Y 50 VAL cc_start: 0.9558 (t) cc_final: 0.9259 (p) REVERT: Y 55 MET cc_start: 0.9156 (ttp) cc_final: 0.8736 (ttp) REVERT: Z 9 ARG cc_start: 0.7964 (mmt180) cc_final: 0.7696 (mmm160) REVERT: Z 42 GLN cc_start: 0.9071 (tp40) cc_final: 0.8796 (tp40) REVERT: Z 44 LEU cc_start: 0.9176 (mt) cc_final: 0.8939 (mt) REVERT: Z 59 GLU cc_start: 0.8954 (mp0) cc_final: 0.8371 (pt0) REVERT: Z 64 ASN cc_start: 0.9151 (t0) cc_final: 0.8865 (t0) REVERT: Z 78 LYS cc_start: 0.9246 (mttt) cc_final: 0.8672 (ttpt) REVERT: Z 91 PHE cc_start: 0.9165 (t80) cc_final: 0.8103 (t80) REVERT: Z 93 THR cc_start: 0.9479 (m) cc_final: 0.9261 (m) REVERT: Z 101 LYS cc_start: 0.9308 (tttt) cc_final: 0.9034 (ttpp) REVERT: Z 109 TYR cc_start: 0.7807 (m-10) cc_final: 0.7208 (m-10) REVERT: Z 119 ASP cc_start: 0.9445 (m-30) cc_final: 0.8943 (m-30) REVERT: Z 127 ASP cc_start: 0.8993 (m-30) cc_final: 0.8463 (t0) REVERT: Z 150 TYR cc_start: 0.8672 (p90) cc_final: 0.8456 (p90) REVERT: Z 160 GLN cc_start: 0.7989 (pt0) cc_final: 0.7693 (pt0) REVERT: Z 179 ASP cc_start: 0.9431 (m-30) cc_final: 0.8981 (m-30) REVERT: Z 182 GLN cc_start: 0.8526 (tt0) cc_final: 0.8303 (tt0) REVERT: Z 184 GLU cc_start: 0.9131 (pt0) cc_final: 0.8816 (mp0) REVERT: Z 187 MET cc_start: 0.9344 (tmt) cc_final: 0.9007 (mtp) REVERT: Z 196 THR cc_start: 0.9607 (p) cc_final: 0.9359 (t) REVERT: Z 264 TYR cc_start: 0.9255 (t80) cc_final: 0.8861 (t80) REVERT: Z 270 LYS cc_start: 0.9423 (tppt) cc_final: 0.9062 (tptt) REVERT: Z 275 GLN cc_start: 0.9113 (mm-40) cc_final: 0.8436 (mm-40) REVERT: a 3 ILE cc_start: 0.7564 (mm) cc_final: 0.6825 (mm) REVERT: a 21 GLU cc_start: 0.8911 (pt0) cc_final: 0.7828 (tp30) REVERT: a 38 ASP cc_start: 0.7895 (p0) cc_final: 0.7499 (p0) REVERT: a 74 ASN cc_start: 0.9413 (t0) cc_final: 0.8987 (p0) REVERT: a 82 PHE cc_start: 0.9062 (t80) cc_final: 0.8764 (t80) REVERT: a 88 LYS cc_start: 0.9607 (pttt) cc_final: 0.9202 (tptp) REVERT: a 124 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7947 (tt0) REVERT: a 152 ASN cc_start: 0.9214 (m-40) cc_final: 0.9006 (t0) REVERT: a 165 TYR cc_start: 0.5759 (t80) cc_final: 0.5341 (m-10) outliers start: 25 outliers final: 8 residues processed: 2180 average time/residue: 0.2314 time to fit residues: 797.6923 Evaluate side-chains 1570 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 1556 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 432 optimal weight: 0.9980 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 4.9990 chunk 424 optimal weight: 6.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 ASN C 25 GLN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN G 61 GLN G 171 ASN H 145 ASN I 15 GLN ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 49 GLN K 61 GLN K 70 GLN ** K 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 15 GLN M 140 HIS O 73 GLN ** O 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 47 ASN Q 21 ASN R 63 GLN R 134 GLN S 15 GLN ** S 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 21 ASN U 15 GLN U 119 ASN ** U 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 21 ASN ** W 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 ASN ** X 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 92 GLN Z 266 GLN a 13 GLN ** a 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.114341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.096941 restraints weight = 100777.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.100625 restraints weight = 50231.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.103023 restraints weight = 28921.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.104584 restraints weight = 18533.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.105587 restraints weight = 13083.353| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3372 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 36155 Z= 0.183 Angle : 0.791 43.034 49243 Z= 0.373 Chirality : 0.040 0.247 5448 Planarity : 0.005 0.057 6402 Dihedral : 10.816 89.643 6599 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.82 % Favored : 98.11 % Rotamer: Outliers : 0.24 % Allowed : 3.75 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.12), residues: 4448 helix: 1.30 (0.08), residues: 3390 sheet: 1.78 (1.01), residues: 28 loop : -0.69 (0.21), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 30 TYR 0.041 0.002 TYR M 97 PHE 0.029 0.002 PHE V 166 TRP 0.017 0.002 TRP U 128 HIS 0.005 0.002 HIS K 140 Details of bonding type rmsd covalent geometry : bond 0.00400 (36155) covalent geometry : angle 0.79065 (49243) hydrogen bonds : bond 0.05424 ( 2648) hydrogen bonds : angle 4.47489 ( 7847) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1837 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 1829 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.8406 (ttpt) cc_final: 0.8166 (ttpt) REVERT: A 18 PHE cc_start: 0.7872 (m-80) cc_final: 0.6954 (m-80) REVERT: A 30 ARG cc_start: 0.8450 (tpt-90) cc_final: 0.8018 (tmt170) REVERT: A 33 ARG cc_start: 0.8811 (mmm160) cc_final: 0.8478 (tpt170) REVERT: A 38 MET cc_start: 0.8536 (mmt) cc_final: 0.7874 (tmm) REVERT: A 39 GLU cc_start: 0.8197 (tp30) cc_final: 0.7815 (mm-30) REVERT: A 62 LYS cc_start: 0.8888 (tptt) cc_final: 0.8570 (tptt) REVERT: A 63 PHE cc_start: 0.8774 (m-80) cc_final: 0.8175 (m-80) REVERT: A 90 TYR cc_start: 0.8655 (m-10) cc_final: 0.8265 (m-80) REVERT: A 109 GLU cc_start: 0.7885 (mt-10) cc_final: 0.6791 (mt-10) REVERT: A 129 TYR cc_start: 0.8768 (m-80) cc_final: 0.8517 (m-80) REVERT: A 167 ASP cc_start: 0.7736 (t0) cc_final: 0.7165 (t0) REVERT: A 173 LEU cc_start: 0.8555 (mm) cc_final: 0.8334 (mm) REVERT: B 27 LEU cc_start: 0.8035 (mm) cc_final: 0.7791 (mm) REVERT: B 29 ASN cc_start: 0.8358 (m-40) cc_final: 0.8048 (t0) REVERT: B 44 ILE cc_start: 0.9357 (mt) cc_final: 0.9085 (tp) REVERT: B 89 GLU cc_start: 0.8833 (pt0) cc_final: 0.8197 (tt0) REVERT: B 99 ILE cc_start: 0.9365 (mt) cc_final: 0.9011 (mt) REVERT: B 119 TYR cc_start: 0.9067 (m-80) cc_final: 0.8438 (m-80) REVERT: B 120 GLN cc_start: 0.7571 (mt0) cc_final: 0.7298 (tm-30) REVERT: B 136 MET cc_start: 0.7766 (mtt) cc_final: 0.4171 (mtt) REVERT: B 167 ASP cc_start: 0.8163 (t0) cc_final: 0.7958 (t70) REVERT: C 63 PHE cc_start: 0.9073 (m-80) cc_final: 0.8718 (m-10) REVERT: C 69 MET cc_start: 0.7477 (ttm) cc_final: 0.7055 (ttm) REVERT: C 87 ASP cc_start: 0.9331 (m-30) cc_final: 0.9009 (m-30) REVERT: C 91 TYR cc_start: 0.9039 (m-80) cc_final: 0.8773 (m-80) REVERT: C 94 MET cc_start: 0.9290 (mmt) cc_final: 0.8935 (mmm) REVERT: C 115 LEU cc_start: 0.8018 (pp) cc_final: 0.7503 (pp) REVERT: C 117 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8585 (mm-30) REVERT: C 119 ASN cc_start: 0.7764 (m-40) cc_final: 0.6987 (p0) REVERT: D 3 ASP cc_start: 0.7825 (p0) cc_final: 0.7607 (p0) REVERT: D 37 ARG cc_start: 0.8580 (mtp85) cc_final: 0.8338 (mmm-85) REVERT: D 49 SER cc_start: 0.9196 (p) cc_final: 0.8816 (p) REVERT: D 86 ARG cc_start: 0.8939 (ttp-110) cc_final: 0.8641 (ttp-110) REVERT: D 88 MET cc_start: 0.8119 (ttm) cc_final: 0.7670 (mmm) REVERT: D 97 TYR cc_start: 0.8776 (m-10) cc_final: 0.7590 (m-80) REVERT: D 146 ASP cc_start: 0.8984 (t0) cc_final: 0.8688 (t0) REVERT: D 154 ASP cc_start: 0.6671 (t0) cc_final: 0.6417 (t0) REVERT: E 7 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7825 (mm-30) REVERT: E 15 GLN cc_start: 0.8213 (mt0) cc_final: 0.7832 (mt0) REVERT: E 25 GLN cc_start: 0.8511 (mt0) cc_final: 0.8032 (mm-40) REVERT: E 28 ASP cc_start: 0.8577 (t70) cc_final: 0.8245 (t0) REVERT: E 38 MET cc_start: 0.8227 (mmt) cc_final: 0.7942 (tmm) REVERT: E 62 LYS cc_start: 0.9246 (tptt) cc_final: 0.8854 (tppt) REVERT: E 72 SER cc_start: 0.9038 (m) cc_final: 0.8468 (t) REVERT: E 83 LYS cc_start: 0.9401 (tppt) cc_final: 0.9086 (tppp) REVERT: E 137 LYS cc_start: 0.8807 (tttp) cc_final: 0.8560 (tttp) REVERT: E 140 HIS cc_start: 0.8530 (p90) cc_final: 0.8230 (p-80) REVERT: E 167 ASP cc_start: 0.7988 (t0) cc_final: 0.7070 (t0) REVERT: F 21 ASN cc_start: 0.8061 (m-40) cc_final: 0.7028 (t0) REVERT: F 32 LYS cc_start: 0.8965 (pttm) cc_final: 0.8572 (ptpp) REVERT: F 81 MET cc_start: 0.9236 (tpp) cc_final: 0.8825 (tpp) REVERT: F 129 VAL cc_start: 0.9727 (t) cc_final: 0.9510 (t) REVERT: F 165 TYR cc_start: 0.9212 (m-80) cc_final: 0.8338 (m-10) REVERT: G 9 ILE cc_start: 0.9542 (tp) cc_final: 0.9316 (tp) REVERT: G 49 GLN cc_start: 0.8847 (pp30) cc_final: 0.8583 (pp30) REVERT: G 61 GLN cc_start: 0.8595 (mt0) cc_final: 0.8389 (mp10) REVERT: G 62 LYS cc_start: 0.9155 (tptm) cc_final: 0.8776 (tppt) REVERT: G 65 TYR cc_start: 0.8055 (p90) cc_final: 0.7766 (p90) REVERT: G 70 GLN cc_start: 0.7186 (tm-30) cc_final: 0.6703 (pp30) REVERT: G 95 VAL cc_start: 0.9684 (t) cc_final: 0.8938 (t) REVERT: G 97 TYR cc_start: 0.9063 (m-10) cc_final: 0.8665 (m-10) REVERT: G 99 LEU cc_start: 0.8957 (tp) cc_final: 0.8491 (tp) REVERT: G 117 GLU cc_start: 0.7602 (tp30) cc_final: 0.7283 (tp30) REVERT: G 122 PHE cc_start: 0.8886 (m-80) cc_final: 0.8438 (m-10) REVERT: G 124 LEU cc_start: 0.8933 (mt) cc_final: 0.8479 (mt) REVERT: G 129 TYR cc_start: 0.8863 (m-80) cc_final: 0.7969 (m-80) REVERT: G 137 LYS cc_start: 0.9112 (ptmt) cc_final: 0.8860 (ttpp) REVERT: G 161 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8254 (mt-10) REVERT: H 17 GLU cc_start: 0.8301 (pm20) cc_final: 0.7939 (pm20) REVERT: H 42 ASN cc_start: 0.8713 (t0) cc_final: 0.8460 (t0) REVERT: H 63 GLN cc_start: 0.8910 (mt0) cc_final: 0.8366 (mt0) REVERT: H 67 ILE cc_start: 0.9484 (pt) cc_final: 0.9212 (tt) REVERT: H 91 ILE cc_start: 0.9495 (mm) cc_final: 0.8979 (tp) REVERT: H 145 ASN cc_start: 0.7993 (OUTLIER) cc_final: 0.7692 (m-40) REVERT: I 13 ASP cc_start: 0.8814 (t0) cc_final: 0.8579 (t70) REVERT: I 62 LYS cc_start: 0.9226 (tptm) cc_final: 0.8686 (tptt) REVERT: I 73 GLN cc_start: 0.9236 (pm20) cc_final: 0.8817 (pm20) REVERT: I 90 TYR cc_start: 0.7618 (m-10) cc_final: 0.7031 (m-10) REVERT: I 107 MET cc_start: 0.8846 (tpp) cc_final: 0.8530 (tpt) REVERT: I 110 TYR cc_start: 0.7815 (m-80) cc_final: 0.7445 (m-10) REVERT: I 119 ASN cc_start: 0.8470 (m110) cc_final: 0.7653 (m110) REVERT: I 135 TYR cc_start: 0.8733 (t80) cc_final: 0.8518 (t80) REVERT: I 163 ASN cc_start: 0.9138 (m110) cc_final: 0.8164 (m110) REVERT: I 166 ILE cc_start: 0.9763 (tt) cc_final: 0.9508 (tt) REVERT: J 24 PHE cc_start: 0.7058 (m-80) cc_final: 0.6672 (m-80) REVERT: J 35 ASN cc_start: 0.8458 (m110) cc_final: 0.7917 (t0) REVERT: J 91 ILE cc_start: 0.9418 (tp) cc_final: 0.9077 (tp) REVERT: J 97 TYR cc_start: 0.8973 (m-10) cc_final: 0.8334 (m-10) REVERT: J 141 ILE cc_start: 0.8878 (tt) cc_final: 0.8460 (tp) REVERT: J 145 ASN cc_start: 0.8247 (t0) cc_final: 0.7976 (t0) REVERT: K 49 GLN cc_start: 0.8229 (mm110) cc_final: 0.8023 (tp40) REVERT: K 115 LEU cc_start: 0.8971 (tp) cc_final: 0.8750 (tp) REVERT: K 165 TYR cc_start: 0.9015 (m-10) cc_final: 0.8724 (m-10) REVERT: L 2 LEU cc_start: 0.9213 (mt) cc_final: 0.8580 (mt) REVERT: L 7 LYS cc_start: 0.9069 (ttpp) cc_final: 0.8829 (ptmm) REVERT: L 13 ASP cc_start: 0.8414 (t70) cc_final: 0.8138 (t0) REVERT: L 59 LEU cc_start: 0.9531 (tp) cc_final: 0.9232 (tp) REVERT: L 65 GLN cc_start: 0.8162 (pt0) cc_final: 0.7914 (pm20) REVERT: L 80 ARG cc_start: 0.8060 (mtm-85) cc_final: 0.7834 (mtt180) REVERT: L 81 MET cc_start: 0.9061 (tpp) cc_final: 0.8415 (tpp) REVERT: L 87 ASP cc_start: 0.9084 (m-30) cc_final: 0.8740 (m-30) REVERT: L 89 GLU cc_start: 0.7766 (pp20) cc_final: 0.7368 (tm-30) REVERT: L 90 ILE cc_start: 0.9355 (mt) cc_final: 0.9023 (tt) REVERT: L 93 ARG cc_start: 0.8550 (ttp80) cc_final: 0.8230 (ttp80) REVERT: L 103 ASP cc_start: 0.8368 (m-30) cc_final: 0.7125 (m-30) REVERT: L 120 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8352 (tm-30) REVERT: L 135 LYS cc_start: 0.8669 (mmtm) cc_final: 0.8388 (mttm) REVERT: L 137 LYS cc_start: 0.9442 (tttt) cc_final: 0.8972 (ttmt) REVERT: L 161 GLU cc_start: 0.8247 (tt0) cc_final: 0.7835 (tp30) REVERT: M 9 ILE cc_start: 0.9134 (tp) cc_final: 0.8553 (tp) REVERT: M 33 ARG cc_start: 0.7660 (tpt-90) cc_final: 0.5649 (tpp-160) REVERT: M 98 CYS cc_start: 0.7008 (m) cc_final: 0.6355 (m) REVERT: M 115 LEU cc_start: 0.8876 (tt) cc_final: 0.7798 (tp) REVERT: M 129 TYR cc_start: 0.8415 (m-80) cc_final: 0.8085 (m-80) REVERT: M 135 TYR cc_start: 0.9012 (t80) cc_final: 0.8716 (t80) REVERT: M 171 ASN cc_start: 0.8592 (p0) cc_final: 0.7931 (p0) REVERT: N 3 ASP cc_start: 0.8501 (p0) cc_final: 0.8171 (p0) REVERT: N 36 LYS cc_start: 0.8420 (mttt) cc_final: 0.7666 (mttt) REVERT: N 45 THR cc_start: 0.8285 (t) cc_final: 0.8072 (t) REVERT: N 65 GLN cc_start: 0.7841 (mp10) cc_final: 0.7509 (mp10) REVERT: N 80 ARG cc_start: 0.9155 (mtm-85) cc_final: 0.8812 (mtm-85) REVERT: N 97 TYR cc_start: 0.8684 (m-10) cc_final: 0.7874 (m-80) REVERT: N 103 ASP cc_start: 0.7400 (t0) cc_final: 0.7000 (t0) REVERT: N 105 SER cc_start: 0.8545 (t) cc_final: 0.8220 (t) REVERT: N 136 MET cc_start: 0.8602 (mtm) cc_final: 0.7445 (mtm) REVERT: N 162 ILE cc_start: 0.9495 (mt) cc_final: 0.9092 (mt) REVERT: O 25 GLN cc_start: 0.7263 (mt0) cc_final: 0.6955 (mt0) REVERT: O 59 VAL cc_start: 0.8748 (m) cc_final: 0.8534 (m) REVERT: O 99 LEU cc_start: 0.9240 (mt) cc_final: 0.8954 (tp) REVERT: O 104 THR cc_start: 0.8651 (p) cc_final: 0.8014 (p) REVERT: O 129 TYR cc_start: 0.8516 (m-80) cc_final: 0.7639 (m-80) REVERT: O 150 VAL cc_start: 0.9448 (m) cc_final: 0.9220 (p) REVERT: P 1 MET cc_start: 0.6207 (ptt) cc_final: 0.5936 (ptt) REVERT: P 5 PHE cc_start: 0.8759 (m-10) cc_final: 0.8493 (m-10) REVERT: P 29 ASN cc_start: 0.8139 (m-40) cc_final: 0.7517 (m110) REVERT: P 59 LEU cc_start: 0.9019 (tp) cc_final: 0.8815 (tp) REVERT: P 93 ARG cc_start: 0.8724 (ttp80) cc_final: 0.8326 (ttp-170) REVERT: P 95 VAL cc_start: 0.9145 (t) cc_final: 0.8638 (m) REVERT: P 97 TYR cc_start: 0.8916 (m-10) cc_final: 0.8179 (m-10) REVERT: P 137 LYS cc_start: 0.9012 (tppt) cc_final: 0.8751 (tppt) REVERT: P 158 LEU cc_start: 0.8975 (mm) cc_final: 0.8586 (mt) REVERT: P 159 MET cc_start: 0.8697 (mmm) cc_final: 0.8000 (ppp) REVERT: Q 7 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8060 (mm-30) REVERT: Q 14 THR cc_start: 0.8730 (p) cc_final: 0.8410 (t) REVERT: Q 25 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7717 (mm-40) REVERT: Q 37 SER cc_start: 0.7888 (m) cc_final: 0.7239 (p) REVERT: Q 94 MET cc_start: 0.4795 (tpp) cc_final: 0.4540 (tpp) REVERT: Q 98 CYS cc_start: 0.8110 (m) cc_final: 0.7592 (m) REVERT: Q 107 MET cc_start: 0.8238 (ttm) cc_final: 0.7882 (mtp) REVERT: R 38 LEU cc_start: 0.8584 (mt) cc_final: 0.8271 (mp) REVERT: R 49 SER cc_start: 0.9309 (p) cc_final: 0.9003 (t) REVERT: R 85 LEU cc_start: 0.9433 (mt) cc_final: 0.9130 (tp) REVERT: R 128 SER cc_start: 0.8664 (m) cc_final: 0.8232 (m) REVERT: R 159 MET cc_start: 0.8240 (mmp) cc_final: 0.7879 (ptt) REVERT: S 28 ASP cc_start: 0.7885 (t0) cc_final: 0.7493 (t0) REVERT: S 38 MET cc_start: 0.8381 (mtm) cc_final: 0.8179 (mtt) REVERT: S 49 GLN cc_start: 0.8449 (tp-100) cc_final: 0.7706 (pm20) REVERT: S 79 GLU cc_start: 0.7914 (mp0) cc_final: 0.7657 (tm-30) REVERT: S 90 TYR cc_start: 0.8043 (m-10) cc_final: 0.7462 (m-10) REVERT: S 98 CYS cc_start: 0.8170 (m) cc_final: 0.6633 (m) REVERT: S 115 LEU cc_start: 0.8225 (tp) cc_final: 0.7862 (tp) REVERT: S 133 LEU cc_start: 0.8951 (mt) cc_final: 0.8708 (mt) REVERT: S 134 LYS cc_start: 0.9472 (mmpt) cc_final: 0.9236 (mmmm) REVERT: S 137 LYS cc_start: 0.9295 (ttpt) cc_final: 0.8890 (tptt) REVERT: T 15 ARG cc_start: 0.7719 (mtp85) cc_final: 0.6914 (mmm160) REVERT: T 19 LEU cc_start: 0.8105 (mt) cc_final: 0.7544 (mm) REVERT: T 23 GLN cc_start: 0.8429 (mt0) cc_final: 0.8085 (mp10) REVERT: T 25 ASP cc_start: 0.8569 (m-30) cc_final: 0.8307 (m-30) REVERT: T 47 ASN cc_start: 0.7840 (t0) cc_final: 0.7411 (t0) REVERT: T 136 MET cc_start: 0.7683 (tpt) cc_final: 0.7342 (tpp) REVERT: T 156 SER cc_start: 0.8321 (m) cc_final: 0.8021 (m) REVERT: U 28 ASP cc_start: 0.7810 (t0) cc_final: 0.7163 (t0) REVERT: U 42 ARG cc_start: 0.7771 (ttm-80) cc_final: 0.7376 (ttm170) REVERT: U 61 GLN cc_start: 0.8471 (mt0) cc_final: 0.7595 (tm-30) REVERT: U 69 MET cc_start: 0.6805 (mtt) cc_final: 0.6566 (tpp) REVERT: U 115 LEU cc_start: 0.8224 (tp) cc_final: 0.8013 (tp) REVERT: U 123 ASP cc_start: 0.8122 (t0) cc_final: 0.7862 (t70) REVERT: U 171 ASN cc_start: 0.8751 (t0) cc_final: 0.8297 (t0) REVERT: V 11 GLN cc_start: 0.8500 (tt0) cc_final: 0.8147 (tp40) REVERT: V 68 GLN cc_start: 0.8278 (pt0) cc_final: 0.8003 (pt0) REVERT: V 78 ASN cc_start: 0.6743 (t0) cc_final: 0.6038 (t0) REVERT: V 113 ASN cc_start: 0.8722 (t0) cc_final: 0.8051 (t0) REVERT: V 124 THR cc_start: 0.8846 (m) cc_final: 0.8265 (p) REVERT: V 154 ASP cc_start: 0.8133 (t0) cc_final: 0.7552 (t0) REVERT: V 162 ILE cc_start: 0.8745 (mt) cc_final: 0.8407 (mt) REVERT: W 2 LYS cc_start: 0.7512 (mmtm) cc_final: 0.7137 (mmtm) REVERT: W 7 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7812 (mm-30) REVERT: W 69 MET cc_start: 0.3931 (mtp) cc_final: 0.3726 (mmm) REVERT: W 97 TYR cc_start: 0.7604 (m-10) cc_final: 0.6548 (m-80) REVERT: W 111 LEU cc_start: 0.8075 (pt) cc_final: 0.7635 (pp) REVERT: W 115 LEU cc_start: 0.7912 (mt) cc_final: 0.7556 (mt) REVERT: W 122 PHE cc_start: 0.5928 (m-80) cc_final: 0.5698 (m-80) REVERT: W 163 ASN cc_start: 0.7681 (m-40) cc_final: 0.7317 (m-40) REVERT: X 38 LEU cc_start: 0.9483 (mt) cc_final: 0.9282 (mt) REVERT: X 166 PHE cc_start: 0.7726 (m-80) cc_final: 0.7514 (m-80) REVERT: Y 50 VAL cc_start: 0.9279 (t) cc_final: 0.9031 (p) REVERT: Y 55 MET cc_start: 0.8487 (ttp) cc_final: 0.8224 (ttp) REVERT: Z 64 ASN cc_start: 0.8486 (t0) cc_final: 0.8205 (t0) REVERT: Z 93 THR cc_start: 0.9242 (m) cc_final: 0.8888 (p) REVERT: Z 96 ILE cc_start: 0.9032 (mm) cc_final: 0.8821 (mm) REVERT: Z 98 LEU cc_start: 0.8969 (mt) cc_final: 0.8750 (mm) REVERT: Z 115 ILE cc_start: 0.8857 (mt) cc_final: 0.8581 (mm) REVERT: Z 133 TYR cc_start: 0.8014 (m-80) cc_final: 0.7625 (m-80) REVERT: Z 146 TRP cc_start: 0.8316 (m-90) cc_final: 0.8008 (m-90) REVERT: Z 157 GLN cc_start: 0.7680 (tp40) cc_final: 0.7166 (tp40) REVERT: Z 166 ASN cc_start: 0.8960 (m110) cc_final: 0.8721 (m110) REVERT: Z 175 TYR cc_start: 0.8511 (t80) cc_final: 0.8097 (t80) REVERT: Z 196 THR cc_start: 0.9091 (p) cc_final: 0.8802 (t) REVERT: Z 264 TYR cc_start: 0.8944 (t80) cc_final: 0.8661 (t80) REVERT: a 2 THR cc_start: 0.6974 (p) cc_final: 0.6429 (t) REVERT: a 44 GLU cc_start: 0.7527 (tt0) cc_final: 0.7313 (tt0) REVERT: a 65 GLN cc_start: 0.7987 (tt0) cc_final: 0.7751 (tt0) REVERT: a 74 ASN cc_start: 0.9108 (t0) cc_final: 0.8859 (p0) REVERT: a 77 ILE cc_start: 0.8489 (pt) cc_final: 0.7918 (pt) REVERT: a 104 ARG cc_start: 0.8459 (ttt90) cc_final: 0.7707 (ttp80) REVERT: a 119 TYR cc_start: 0.7825 (m-80) cc_final: 0.6848 (m-10) REVERT: a 152 ASN cc_start: 0.8252 (m-40) cc_final: 0.7766 (m-40) REVERT: a 177 TYR cc_start: 0.8221 (p90) cc_final: 0.7750 (p90) outliers start: 8 outliers final: 1 residues processed: 1832 average time/residue: 0.2172 time to fit residues: 641.9183 Evaluate side-chains 1460 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1458 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 44 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 375 optimal weight: 6.9990 chunk 347 optimal weight: 5.9990 chunk 301 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 341 optimal weight: 0.9990 chunk 328 optimal weight: 6.9990 chunk 377 optimal weight: 9.9990 chunk 400 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 GLN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN E 163 ASN F 11 GLN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 ASN G 25 GLN ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN O 119 ASN ** P 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 171 ASN ** R 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 119 ASN U 139 ASN V 23 GLN ** V 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 61 GLN ** W 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 ASN ** Z 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 200 ASN Z 266 GLN ** Z 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.111707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.094187 restraints weight = 110576.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.097808 restraints weight = 54884.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.100208 restraints weight = 31659.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.101781 restraints weight = 20384.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.102816 restraints weight = 14431.481| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3328 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3328 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 36155 Z= 0.204 Angle : 0.799 43.210 49243 Z= 0.381 Chirality : 0.041 0.271 5448 Planarity : 0.005 0.061 6402 Dihedral : 10.790 88.587 6599 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.52 % Favored : 97.41 % Rotamer: Outliers : 0.15 % Allowed : 4.45 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.12), residues: 4448 helix: 1.13 (0.08), residues: 3397 sheet: 1.86 (0.92), residues: 28 loop : -0.67 (0.22), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 30 TYR 0.053 0.002 TYR M 97 PHE 0.037 0.002 PHE Z 143 TRP 0.016 0.002 TRP C 128 HIS 0.008 0.002 HIS Z 117 Details of bonding type rmsd covalent geometry : bond 0.00448 (36155) covalent geometry : angle 0.79910 (49243) hydrogen bonds : bond 0.05113 ( 2648) hydrogen bonds : angle 4.50621 ( 7847) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1689 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1684 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 PHE cc_start: 0.7963 (m-80) cc_final: 0.7046 (m-80) REVERT: A 38 MET cc_start: 0.8500 (mmt) cc_final: 0.7636 (tmm) REVERT: A 39 GLU cc_start: 0.8243 (tp30) cc_final: 0.7693 (mm-30) REVERT: A 62 LYS cc_start: 0.8979 (tptt) cc_final: 0.8568 (tptt) REVERT: A 63 PHE cc_start: 0.8771 (m-80) cc_final: 0.8002 (m-80) REVERT: A 109 GLU cc_start: 0.7675 (mt-10) cc_final: 0.6782 (mt-10) REVERT: A 131 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7264 (tm-30) REVERT: A 134 LYS cc_start: 0.8739 (ttmm) cc_final: 0.8081 (mtpp) REVERT: A 136 ILE cc_start: 0.9275 (mm) cc_final: 0.9036 (tp) REVERT: A 165 TYR cc_start: 0.8580 (m-10) cc_final: 0.8378 (m-80) REVERT: A 167 ASP cc_start: 0.8186 (t0) cc_final: 0.7340 (t0) REVERT: A 171 ASN cc_start: 0.8785 (m-40) cc_final: 0.8547 (m-40) REVERT: B 44 ILE cc_start: 0.9406 (mt) cc_final: 0.9149 (tp) REVERT: B 89 GLU cc_start: 0.8825 (pt0) cc_final: 0.8097 (tt0) REVERT: B 99 ILE cc_start: 0.9217 (mt) cc_final: 0.8977 (mt) REVERT: B 120 GLN cc_start: 0.7787 (mt0) cc_final: 0.7392 (tm-30) REVERT: B 136 MET cc_start: 0.7504 (mtt) cc_final: 0.6502 (mtt) REVERT: C 17 ARG cc_start: 0.8464 (ptt90) cc_final: 0.8112 (ptt90) REVERT: C 63 PHE cc_start: 0.9086 (m-80) cc_final: 0.8468 (m-10) REVERT: C 69 MET cc_start: 0.7600 (ttm) cc_final: 0.7127 (ttm) REVERT: C 94 MET cc_start: 0.9433 (mmt) cc_final: 0.8985 (mmm) REVERT: C 117 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8477 (mm-30) REVERT: C 133 LEU cc_start: 0.8641 (mp) cc_final: 0.8369 (tp) REVERT: D 32 LYS cc_start: 0.9391 (pttt) cc_final: 0.9128 (pttm) REVERT: D 49 SER cc_start: 0.9115 (p) cc_final: 0.8818 (p) REVERT: D 81 MET cc_start: 0.7644 (tpp) cc_final: 0.7402 (ttt) REVERT: D 88 MET cc_start: 0.8364 (ttm) cc_final: 0.7996 (mmm) REVERT: D 97 TYR cc_start: 0.8616 (m-10) cc_final: 0.7499 (m-10) REVERT: D 112 LEU cc_start: 0.8797 (pp) cc_final: 0.8525 (pp) REVERT: D 134 GLN cc_start: 0.8200 (mt0) cc_final: 0.7886 (mt0) REVERT: D 146 ASP cc_start: 0.9125 (t0) cc_final: 0.8882 (t0) REVERT: D 154 ASP cc_start: 0.6575 (t0) cc_final: 0.6310 (t0) REVERT: D 162 ILE cc_start: 0.9129 (mm) cc_final: 0.8901 (mm) REVERT: E 25 GLN cc_start: 0.8240 (mt0) cc_final: 0.8024 (mm-40) REVERT: E 28 ASP cc_start: 0.8670 (t70) cc_final: 0.8419 (t0) REVERT: E 38 MET cc_start: 0.8137 (mmt) cc_final: 0.7762 (tmm) REVERT: E 47 ASN cc_start: 0.8136 (t0) cc_final: 0.7535 (t0) REVERT: E 51 LEU cc_start: 0.9547 (mt) cc_final: 0.9332 (mp) REVERT: E 62 LYS cc_start: 0.8958 (tptt) cc_final: 0.8734 (tppt) REVERT: E 72 SER cc_start: 0.9015 (m) cc_final: 0.8590 (t) REVERT: E 73 GLN cc_start: 0.8765 (pm20) cc_final: 0.8123 (pm20) REVERT: E 93 ARG cc_start: 0.8547 (ttp80) cc_final: 0.8216 (ttp-110) REVERT: E 121 THR cc_start: 0.9235 (p) cc_final: 0.8743 (t) REVERT: E 129 TYR cc_start: 0.8532 (m-10) cc_final: 0.8092 (m-10) REVERT: E 140 HIS cc_start: 0.8565 (p90) cc_final: 0.8334 (p-80) REVERT: E 167 ASP cc_start: 0.8004 (t0) cc_final: 0.6995 (t0) REVERT: E 171 ASN cc_start: 0.8719 (p0) cc_final: 0.8469 (p0) REVERT: E 173 LEU cc_start: 0.9179 (mm) cc_final: 0.8971 (mm) REVERT: F 11 GLN cc_start: 0.9102 (tt0) cc_final: 0.8505 (tt0) REVERT: F 25 ASP cc_start: 0.8841 (m-30) cc_final: 0.8547 (m-30) REVERT: F 81 MET cc_start: 0.9269 (tpp) cc_final: 0.8961 (tpp) REVERT: F 117 GLU cc_start: 0.8558 (pp20) cc_final: 0.8247 (pp20) REVERT: F 146 ASP cc_start: 0.8398 (t0) cc_final: 0.8168 (t0) REVERT: F 159 MET cc_start: 0.7003 (mmm) cc_final: 0.6671 (mmt) REVERT: F 161 GLU cc_start: 0.8248 (tp30) cc_final: 0.7578 (tp30) REVERT: G 49 GLN cc_start: 0.8804 (pp30) cc_final: 0.8568 (pp30) REVERT: G 61 GLN cc_start: 0.8606 (mt0) cc_final: 0.8348 (mp10) REVERT: G 62 LYS cc_start: 0.9061 (tptm) cc_final: 0.8730 (tppt) REVERT: G 70 GLN cc_start: 0.7559 (tm-30) cc_final: 0.7289 (pp30) REVERT: G 97 TYR cc_start: 0.8895 (m-10) cc_final: 0.8572 (m-10) REVERT: G 119 ASN cc_start: 0.9368 (m110) cc_final: 0.9118 (m-40) REVERT: G 122 PHE cc_start: 0.8853 (m-80) cc_final: 0.8651 (m-80) REVERT: G 123 ASP cc_start: 0.8073 (t0) cc_final: 0.7775 (t70) REVERT: G 124 LEU cc_start: 0.9022 (mt) cc_final: 0.8409 (mt) REVERT: G 135 TYR cc_start: 0.8754 (t80) cc_final: 0.8480 (t80) REVERT: G 137 LYS cc_start: 0.9058 (ptmt) cc_final: 0.8660 (ttpp) REVERT: G 161 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8078 (mt-10) REVERT: G 163 ASN cc_start: 0.9121 (m-40) cc_final: 0.8737 (m-40) REVERT: H 3 ASP cc_start: 0.8391 (p0) cc_final: 0.7705 (p0) REVERT: H 67 ILE cc_start: 0.9529 (pt) cc_final: 0.9184 (tt) REVERT: H 88 MET cc_start: 0.7963 (mtm) cc_final: 0.7585 (mtm) REVERT: H 159 MET cc_start: 0.8403 (mmm) cc_final: 0.8018 (mmm) REVERT: I 51 LEU cc_start: 0.8935 (mt) cc_final: 0.8670 (mt) REVERT: I 62 LYS cc_start: 0.9226 (tptm) cc_final: 0.8845 (tptt) REVERT: I 90 TYR cc_start: 0.7851 (m-10) cc_final: 0.7354 (m-10) REVERT: I 119 ASN cc_start: 0.8518 (m110) cc_final: 0.7711 (m110) REVERT: I 127 SER cc_start: 0.9274 (p) cc_final: 0.9048 (p) REVERT: I 129 TYR cc_start: 0.8849 (m-10) cc_final: 0.8459 (m-10) REVERT: I 166 ILE cc_start: 0.9802 (tt) cc_final: 0.9294 (tt) REVERT: I 173 LEU cc_start: 0.9516 (mt) cc_final: 0.9111 (tt) REVERT: J 17 GLU cc_start: 0.8127 (mp0) cc_final: 0.7892 (mp0) REVERT: J 35 ASN cc_start: 0.8511 (m110) cc_final: 0.8127 (t0) REVERT: J 91 ILE cc_start: 0.9396 (tp) cc_final: 0.9106 (tt) REVERT: J 97 TYR cc_start: 0.8932 (m-10) cc_final: 0.8327 (m-10) REVERT: J 112 LEU cc_start: 0.9467 (mp) cc_final: 0.8868 (mm) REVERT: K 90 TYR cc_start: 0.9043 (m-10) cc_final: 0.8737 (m-80) REVERT: K 139 ASN cc_start: 0.8049 (m110) cc_final: 0.7845 (t0) REVERT: K 161 GLU cc_start: 0.8433 (tp30) cc_final: 0.8073 (tp30) REVERT: L 2 LEU cc_start: 0.9355 (mt) cc_final: 0.8697 (mt) REVERT: L 13 ASP cc_start: 0.8442 (t70) cc_final: 0.8040 (t0) REVERT: L 59 LEU cc_start: 0.9541 (tp) cc_final: 0.9304 (tp) REVERT: L 80 ARG cc_start: 0.8125 (mtm-85) cc_final: 0.7799 (mtt-85) REVERT: L 81 MET cc_start: 0.8996 (tpp) cc_final: 0.8319 (tpp) REVERT: L 88 MET cc_start: 0.8131 (mtm) cc_final: 0.7848 (mtp) REVERT: L 89 GLU cc_start: 0.7766 (pp20) cc_final: 0.7392 (tm-30) REVERT: L 103 ASP cc_start: 0.8362 (m-30) cc_final: 0.8077 (m-30) REVERT: L 116 ARG cc_start: 0.8110 (tpp80) cc_final: 0.7786 (tpp80) REVERT: L 117 GLU cc_start: 0.8755 (tp30) cc_final: 0.8540 (tp30) REVERT: L 120 GLN cc_start: 0.8888 (tm-30) cc_final: 0.8371 (tm-30) REVERT: L 137 LYS cc_start: 0.9527 (tttt) cc_final: 0.8892 (ttmt) REVERT: L 159 MET cc_start: 0.8679 (mmt) cc_final: 0.8449 (mmt) REVERT: M 9 ILE cc_start: 0.9287 (tp) cc_final: 0.8390 (tp) REVERT: M 107 MET cc_start: 0.8024 (mmm) cc_final: 0.7610 (mmm) REVERT: M 118 ILE cc_start: 0.9539 (tp) cc_final: 0.9128 (tp) REVERT: M 129 TYR cc_start: 0.8145 (m-80) cc_final: 0.7868 (m-80) REVERT: M 135 TYR cc_start: 0.9001 (t80) cc_final: 0.8709 (t80) REVERT: M 171 ASN cc_start: 0.7998 (p0) cc_final: 0.7567 (p0) REVERT: N 36 LYS cc_start: 0.8303 (mttt) cc_final: 0.8095 (mttt) REVERT: N 65 GLN cc_start: 0.7562 (mp10) cc_final: 0.7266 (mp10) REVERT: N 66 LEU cc_start: 0.8948 (mt) cc_final: 0.8698 (mt) REVERT: N 80 ARG cc_start: 0.8954 (mtm-85) cc_final: 0.8480 (mtm-85) REVERT: N 97 TYR cc_start: 0.8621 (m-10) cc_final: 0.7925 (m-80) REVERT: N 103 ASP cc_start: 0.6788 (t0) cc_final: 0.6311 (t0) REVERT: N 105 SER cc_start: 0.8347 (t) cc_final: 0.8117 (t) REVERT: N 136 MET cc_start: 0.8740 (mtm) cc_final: 0.8458 (mtm) REVERT: N 141 ILE cc_start: 0.9176 (tp) cc_final: 0.8867 (tp) REVERT: O 3 THR cc_start: 0.8153 (m) cc_final: 0.7908 (m) REVERT: O 25 GLN cc_start: 0.7555 (mt0) cc_final: 0.7317 (mt0) REVERT: O 52 ILE cc_start: 0.7956 (pt) cc_final: 0.7721 (pt) REVERT: O 96 THR cc_start: 0.9282 (p) cc_final: 0.9048 (t) REVERT: O 99 LEU cc_start: 0.9294 (mt) cc_final: 0.9048 (tp) REVERT: O 104 THR cc_start: 0.8677 (p) cc_final: 0.7913 (p) REVERT: O 112 ILE cc_start: 0.9347 (mp) cc_final: 0.8960 (mp) REVERT: O 129 TYR cc_start: 0.8520 (m-80) cc_final: 0.7905 (m-80) REVERT: O 130 ILE cc_start: 0.9105 (mm) cc_final: 0.8896 (mm) REVERT: O 131 GLU cc_start: 0.8724 (pt0) cc_final: 0.8514 (pt0) REVERT: O 163 ASN cc_start: 0.8413 (m-40) cc_final: 0.7902 (m-40) REVERT: P 1 MET cc_start: 0.5823 (ptt) cc_final: 0.5203 (ptt) REVERT: P 39 ASP cc_start: 0.7121 (m-30) cc_final: 0.6919 (m-30) REVERT: P 81 MET cc_start: 0.8390 (tpp) cc_final: 0.8189 (tpp) REVERT: P 97 TYR cc_start: 0.8751 (m-10) cc_final: 0.8259 (m-10) REVERT: P 159 MET cc_start: 0.9041 (mmm) cc_final: 0.8389 (mmm) REVERT: Q 14 THR cc_start: 0.8720 (p) cc_final: 0.8439 (t) REVERT: Q 37 SER cc_start: 0.7896 (m) cc_final: 0.7224 (p) REVERT: Q 53 ASP cc_start: 0.5643 (m-30) cc_final: 0.5287 (m-30) REVERT: Q 62 LYS cc_start: 0.7410 (ttmt) cc_final: 0.7131 (tttm) REVERT: Q 73 GLN cc_start: 0.8305 (pm20) cc_final: 0.7773 (pm20) REVERT: Q 94 MET cc_start: 0.5525 (tpp) cc_final: 0.5114 (tpp) REVERT: Q 98 CYS cc_start: 0.8384 (m) cc_final: 0.7783 (m) REVERT: Q 107 MET cc_start: 0.7988 (ttm) cc_final: 0.7731 (mtp) REVERT: Q 108 ASP cc_start: 0.8371 (m-30) cc_final: 0.7957 (m-30) REVERT: R 39 ASP cc_start: 0.8036 (m-30) cc_final: 0.7467 (m-30) REVERT: R 49 SER cc_start: 0.9147 (p) cc_final: 0.8919 (t) REVERT: R 59 LEU cc_start: 0.9031 (tt) cc_final: 0.8788 (tt) REVERT: R 80 ARG cc_start: 0.8492 (mtm-85) cc_final: 0.8165 (mtm-85) REVERT: R 85 LEU cc_start: 0.9587 (mt) cc_final: 0.9274 (tp) REVERT: R 93 ARG cc_start: 0.8293 (ttp80) cc_final: 0.8060 (ttp80) REVERT: R 111 CYS cc_start: 0.7282 (t) cc_final: 0.6708 (t) REVERT: R 118 THR cc_start: 0.8636 (p) cc_final: 0.7443 (p) REVERT: R 128 SER cc_start: 0.8655 (m) cc_final: 0.8275 (m) REVERT: R 134 GLN cc_start: 0.7671 (mm110) cc_final: 0.7099 (mm110) REVERT: R 135 LYS cc_start: 0.7716 (mtmm) cc_final: 0.7465 (ptpp) REVERT: R 159 MET cc_start: 0.8251 (mmp) cc_final: 0.7552 (ptt) REVERT: R 168 ARG cc_start: 0.8653 (ttt90) cc_final: 0.8303 (tpp80) REVERT: S 37 SER cc_start: 0.8376 (p) cc_final: 0.7646 (t) REVERT: S 49 GLN cc_start: 0.8360 (tp-100) cc_final: 0.7619 (pm20) REVERT: S 51 LEU cc_start: 0.8545 (mp) cc_final: 0.8322 (mm) REVERT: S 52 ILE cc_start: 0.8994 (tt) cc_final: 0.8775 (tp) REVERT: S 79 GLU cc_start: 0.7751 (mp0) cc_final: 0.7481 (tm-30) REVERT: S 90 TYR cc_start: 0.8239 (m-10) cc_final: 0.7604 (m-10) REVERT: S 94 MET cc_start: 0.9512 (mmt) cc_final: 0.8612 (mmm) REVERT: S 97 TYR cc_start: 0.9090 (m-80) cc_final: 0.7717 (m-80) REVERT: S 112 ILE cc_start: 0.9537 (mm) cc_final: 0.9036 (tp) REVERT: S 115 LEU cc_start: 0.8430 (tp) cc_final: 0.8064 (tp) REVERT: S 131 GLU cc_start: 0.8295 (tm-30) cc_final: 0.8091 (tm-30) REVERT: S 133 LEU cc_start: 0.9114 (mt) cc_final: 0.8904 (mt) REVERT: S 134 LYS cc_start: 0.9513 (mmpt) cc_final: 0.9284 (mmmm) REVERT: S 137 LYS cc_start: 0.9334 (ttpt) cc_final: 0.8782 (tptt) REVERT: S 161 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7049 (mm-30) REVERT: S 165 TYR cc_start: 0.8578 (m-80) cc_final: 0.8311 (m-80) REVERT: T 13 ASP cc_start: 0.8511 (t70) cc_final: 0.7902 (t0) REVERT: T 15 ARG cc_start: 0.7925 (mtp85) cc_final: 0.7184 (mmp80) REVERT: T 19 LEU cc_start: 0.8283 (mt) cc_final: 0.7745 (mm) REVERT: T 23 GLN cc_start: 0.8390 (mt0) cc_final: 0.8046 (mp10) REVERT: T 25 ASP cc_start: 0.8628 (m-30) cc_final: 0.8320 (m-30) REVERT: T 27 LEU cc_start: 0.8849 (mt) cc_final: 0.8612 (mt) REVERT: T 47 ASN cc_start: 0.7971 (t0) cc_final: 0.7507 (t0) REVERT: T 59 LEU cc_start: 0.8950 (mt) cc_final: 0.8287 (mt) REVERT: T 76 TYR cc_start: 0.3390 (t80) cc_final: 0.3173 (t80) REVERT: T 97 TYR cc_start: 0.8839 (m-10) cc_final: 0.8378 (m-10) REVERT: T 104 SER cc_start: 0.9120 (p) cc_final: 0.8819 (p) REVERT: T 156 SER cc_start: 0.8495 (m) cc_final: 0.8072 (m) REVERT: T 162 ILE cc_start: 0.9170 (mt) cc_final: 0.8901 (mt) REVERT: T 165 TYR cc_start: 0.8655 (m-80) cc_final: 0.8081 (m-80) REVERT: U 7 GLU cc_start: 0.8384 (pm20) cc_final: 0.8154 (pm20) REVERT: U 24 LEU cc_start: 0.9296 (mt) cc_final: 0.9059 (mt) REVERT: U 28 ASP cc_start: 0.7528 (t0) cc_final: 0.7078 (t0) REVERT: U 32 LYS cc_start: 0.9230 (tmmt) cc_final: 0.8991 (tmmt) REVERT: U 42 ARG cc_start: 0.7350 (ttm-80) cc_final: 0.6748 (mtt180) REVERT: U 109 GLU cc_start: 0.8477 (tm-30) cc_final: 0.7852 (tm-30) REVERT: U 115 LEU cc_start: 0.8675 (tp) cc_final: 0.8253 (tp) REVERT: U 123 ASP cc_start: 0.8535 (t0) cc_final: 0.7821 (t0) REVERT: U 131 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8296 (mm-30) REVERT: U 134 LYS cc_start: 0.9069 (tppp) cc_final: 0.8854 (tppp) REVERT: U 137 LYS cc_start: 0.9547 (tttp) cc_final: 0.9245 (tttp) REVERT: U 150 VAL cc_start: 0.9540 (t) cc_final: 0.9314 (p) REVERT: U 163 ASN cc_start: 0.9226 (m-40) cc_final: 0.8924 (m-40) REVERT: U 171 ASN cc_start: 0.8783 (t0) cc_final: 0.8236 (t0) REVERT: U 174 SER cc_start: 0.7913 (t) cc_final: 0.7636 (t) REVERT: V 11 GLN cc_start: 0.8415 (tt0) cc_final: 0.7751 (tp40) REVERT: V 13 ASP cc_start: 0.8154 (t0) cc_final: 0.7906 (t0) REVERT: V 62 GLU cc_start: 0.7509 (pp20) cc_final: 0.5418 (pp20) REVERT: V 63 GLN cc_start: 0.8851 (mt0) cc_final: 0.8514 (mp10) REVERT: V 68 GLN cc_start: 0.8553 (pt0) cc_final: 0.8262 (pt0) REVERT: V 113 ASN cc_start: 0.9082 (t0) cc_final: 0.8222 (t0) REVERT: V 124 THR cc_start: 0.8659 (m) cc_final: 0.8100 (p) REVERT: V 162 ILE cc_start: 0.8655 (mt) cc_final: 0.8386 (mt) REVERT: W 42 ARG cc_start: 0.7527 (ttm170) cc_final: 0.6252 (tpt170) REVERT: W 69 MET cc_start: 0.3782 (mtp) cc_final: 0.3326 (mmm) REVERT: W 107 MET cc_start: 0.8020 (mmp) cc_final: 0.7379 (mmp) REVERT: W 163 ASN cc_start: 0.7577 (m-40) cc_final: 0.6984 (m-40) REVERT: X 44 ILE cc_start: 0.8057 (mm) cc_final: 0.7617 (tp) REVERT: X 88 MET cc_start: 0.8954 (ttm) cc_final: 0.8710 (ttt) REVERT: X 109 ASP cc_start: 0.8093 (t70) cc_final: 0.7820 (t70) REVERT: X 166 PHE cc_start: 0.7581 (m-80) cc_final: 0.7357 (m-80) REVERT: Y 20 PHE cc_start: 0.8041 (m-80) cc_final: 0.7677 (m-80) REVERT: Y 24 VAL cc_start: 0.8718 (t) cc_final: 0.8295 (t) REVERT: Y 28 ARG cc_start: 0.8925 (ttp-170) cc_final: 0.8676 (ttm170) REVERT: Y 50 VAL cc_start: 0.9416 (t) cc_final: 0.9170 (p) REVERT: Z 42 GLN cc_start: 0.8855 (tp40) cc_final: 0.8544 (tp40) REVERT: Z 93 THR cc_start: 0.8922 (m) cc_final: 0.8661 (p) REVERT: Z 115 ILE cc_start: 0.8795 (mt) cc_final: 0.8569 (mm) REVERT: Z 119 ASP cc_start: 0.7525 (m-30) cc_final: 0.7072 (m-30) REVERT: Z 133 TYR cc_start: 0.8595 (m-80) cc_final: 0.8263 (m-80) REVERT: Z 146 TRP cc_start: 0.8431 (m-90) cc_final: 0.8197 (m-90) REVERT: Z 179 ASP cc_start: 0.8692 (m-30) cc_final: 0.8313 (m-30) REVERT: Z 192 ARG cc_start: 0.8127 (ttp-110) cc_final: 0.7593 (ttp-110) REVERT: Z 196 THR cc_start: 0.9238 (p) cc_final: 0.8842 (t) REVERT: Z 264 TYR cc_start: 0.9246 (t80) cc_final: 0.8637 (t80) REVERT: Z 275 GLN cc_start: 0.8622 (mm110) cc_final: 0.8224 (mm-40) REVERT: a 3 ILE cc_start: 0.7269 (mm) cc_final: 0.6897 (mm) REVERT: a 74 ASN cc_start: 0.9045 (t0) cc_final: 0.8727 (p0) REVERT: a 81 ASP cc_start: 0.8300 (t70) cc_final: 0.8032 (t70) REVERT: a 119 TYR cc_start: 0.7180 (m-80) cc_final: 0.6875 (m-80) REVERT: a 151 GLN cc_start: 0.8975 (mm-40) cc_final: 0.8160 (mt0) REVERT: a 170 PHE cc_start: 0.8337 (m-10) cc_final: 0.7446 (m-80) outliers start: 5 outliers final: 0 residues processed: 1686 average time/residue: 0.2123 time to fit residues: 582.1418 Evaluate side-chains 1387 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1387 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 226 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 106 optimal weight: 0.0050 chunk 160 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 284 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 351 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 GLN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 25 GLN G 139 ASN H 47 ASN H 78 ASN ** I 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 29 ASN ** P 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 70 GLN ** R 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 ASN ** U 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 92 GLN Z 117 HIS Z 166 ASN ** Z 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.115409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.097311 restraints weight = 122384.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.101280 restraints weight = 57930.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.103898 restraints weight = 32456.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.105601 restraints weight = 20324.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.106711 restraints weight = 14016.681| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3395 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 36155 Z= 0.146 Angle : 0.760 42.916 49243 Z= 0.355 Chirality : 0.039 0.196 5448 Planarity : 0.005 0.066 6402 Dihedral : 10.752 87.341 6599 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.23 % Favored : 97.71 % Rotamer: Outliers : 0.18 % Allowed : 2.62 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.12), residues: 4448 helix: 1.22 (0.08), residues: 3394 sheet: 1.82 (0.81), residues: 28 loop : -0.64 (0.22), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Z 63 TYR 0.056 0.002 TYR M 97 PHE 0.050 0.002 PHE T 166 TRP 0.013 0.001 TRP U 128 HIS 0.006 0.002 HIS M 140 Details of bonding type rmsd covalent geometry : bond 0.00319 (36155) covalent geometry : angle 0.75963 (49243) hydrogen bonds : bond 0.04568 ( 2648) hydrogen bonds : angle 4.24937 ( 7847) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1740 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1734 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ILE cc_start: 0.9023 (mp) cc_final: 0.8816 (mm) REVERT: A 18 PHE cc_start: 0.8064 (m-80) cc_final: 0.7057 (m-80) REVERT: A 38 MET cc_start: 0.8481 (mmt) cc_final: 0.7835 (tmm) REVERT: A 39 GLU cc_start: 0.8293 (tp30) cc_final: 0.7711 (mm-30) REVERT: A 62 LYS cc_start: 0.9187 (tptt) cc_final: 0.8967 (tptt) REVERT: A 63 PHE cc_start: 0.8731 (m-80) cc_final: 0.8137 (m-80) REVERT: A 90 TYR cc_start: 0.8898 (m-10) cc_final: 0.8547 (m-80) REVERT: A 93 ARG cc_start: 0.8324 (ttp80) cc_final: 0.8068 (tpp80) REVERT: A 109 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7789 (mt-10) REVERT: A 115 LEU cc_start: 0.7564 (pp) cc_final: 0.7275 (pp) REVERT: A 131 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7140 (tm-30) REVERT: A 136 ILE cc_start: 0.9299 (mm) cc_final: 0.9085 (tp) REVERT: A 167 ASP cc_start: 0.8214 (t0) cc_final: 0.7542 (t0) REVERT: A 171 ASN cc_start: 0.8681 (m-40) cc_final: 0.8238 (m-40) REVERT: B 27 LEU cc_start: 0.7941 (mm) cc_final: 0.7735 (mm) REVERT: B 36 LYS cc_start: 0.9554 (mtmm) cc_final: 0.8582 (mppt) REVERT: B 89 GLU cc_start: 0.8594 (pt0) cc_final: 0.8296 (tt0) REVERT: B 120 GLN cc_start: 0.7787 (mt0) cc_final: 0.7280 (tm-30) REVERT: B 136 MET cc_start: 0.7426 (mtt) cc_final: 0.7019 (mtt) REVERT: C 17 ARG cc_start: 0.8507 (ptt90) cc_final: 0.8060 (ptt90) REVERT: C 69 MET cc_start: 0.7557 (ttm) cc_final: 0.7217 (ttm) REVERT: C 94 MET cc_start: 0.9395 (mmt) cc_final: 0.9134 (mmm) REVERT: C 109 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7782 (tp30) REVERT: C 117 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8677 (mm-30) REVERT: C 131 GLU cc_start: 0.8474 (tp30) cc_final: 0.8223 (mm-30) REVERT: D 29 ASN cc_start: 0.8975 (t0) cc_final: 0.8555 (t0) REVERT: D 31 VAL cc_start: 0.9589 (t) cc_final: 0.9365 (p) REVERT: D 32 LYS cc_start: 0.9333 (pttt) cc_final: 0.9094 (pttm) REVERT: D 49 SER cc_start: 0.8887 (p) cc_final: 0.8666 (p) REVERT: D 85 LEU cc_start: 0.9500 (mm) cc_final: 0.9280 (mm) REVERT: D 88 MET cc_start: 0.8371 (ttm) cc_final: 0.8148 (mmm) REVERT: D 97 TYR cc_start: 0.8605 (m-10) cc_final: 0.7369 (m-10) REVERT: D 113 ASN cc_start: 0.7849 (t0) cc_final: 0.7531 (t0) REVERT: D 115 LEU cc_start: 0.8461 (tt) cc_final: 0.8230 (tt) REVERT: D 128 SER cc_start: 0.9318 (p) cc_final: 0.8871 (m) REVERT: D 134 GLN cc_start: 0.8513 (mt0) cc_final: 0.8202 (mt0) REVERT: D 136 MET cc_start: 0.8078 (ttm) cc_final: 0.7875 (ttm) REVERT: D 146 ASP cc_start: 0.9199 (t0) cc_final: 0.8893 (t0) REVERT: D 154 ASP cc_start: 0.6794 (t0) cc_final: 0.6503 (t0) REVERT: E 7 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7579 (mm-30) REVERT: E 15 GLN cc_start: 0.7256 (mt0) cc_final: 0.6931 (mt0) REVERT: E 25 GLN cc_start: 0.8376 (mt0) cc_final: 0.8144 (mm-40) REVERT: E 28 ASP cc_start: 0.8647 (t70) cc_final: 0.8286 (t0) REVERT: E 38 MET cc_start: 0.8243 (mmt) cc_final: 0.7896 (tmm) REVERT: E 47 ASN cc_start: 0.8175 (t0) cc_final: 0.7785 (t0) REVERT: E 62 LYS cc_start: 0.8907 (tptt) cc_final: 0.8648 (tppt) REVERT: E 72 SER cc_start: 0.8850 (m) cc_final: 0.8492 (t) REVERT: E 73 GLN cc_start: 0.8553 (pm20) cc_final: 0.8283 (pm20) REVERT: E 83 LYS cc_start: 0.9232 (mmmm) cc_final: 0.8782 (mmmm) REVERT: E 109 GLU cc_start: 0.8504 (tt0) cc_final: 0.8263 (tt0) REVERT: E 121 THR cc_start: 0.9022 (p) cc_final: 0.8621 (t) REVERT: E 129 TYR cc_start: 0.8619 (m-10) cc_final: 0.7912 (m-10) REVERT: E 140 HIS cc_start: 0.8552 (p90) cc_final: 0.8056 (p-80) REVERT: E 167 ASP cc_start: 0.8297 (t0) cc_final: 0.7068 (t0) REVERT: E 168 TYR cc_start: 0.8585 (t80) cc_final: 0.7991 (t80) REVERT: E 171 ASN cc_start: 0.8538 (p0) cc_final: 0.8233 (p0) REVERT: E 173 LEU cc_start: 0.9111 (mm) cc_final: 0.8840 (mm) REVERT: F 11 GLN cc_start: 0.9105 (tt0) cc_final: 0.8450 (tt0) REVERT: F 25 ASP cc_start: 0.8780 (m-30) cc_final: 0.8400 (m-30) REVERT: F 27 LEU cc_start: 0.8974 (mt) cc_final: 0.8191 (pp) REVERT: F 60 PHE cc_start: 0.8660 (m-10) cc_final: 0.8096 (m-10) REVERT: F 81 MET cc_start: 0.9095 (tpp) cc_final: 0.8694 (tpt) REVERT: F 103 ASP cc_start: 0.8082 (t0) cc_final: 0.7859 (t0) REVERT: F 146 ASP cc_start: 0.8017 (t0) cc_final: 0.7809 (t0) REVERT: F 161 GLU cc_start: 0.8240 (tp30) cc_final: 0.7974 (tp30) REVERT: G 20 SER cc_start: 0.7597 (t) cc_final: 0.6524 (m) REVERT: G 25 GLN cc_start: 0.8868 (mt0) cc_final: 0.8247 (mt0) REVERT: G 28 ASP cc_start: 0.8394 (t0) cc_final: 0.8168 (t70) REVERT: G 38 MET cc_start: 0.9333 (mtm) cc_final: 0.8460 (ttm) REVERT: G 49 GLN cc_start: 0.8856 (pp30) cc_final: 0.8591 (pp30) REVERT: G 61 GLN cc_start: 0.8562 (mt0) cc_final: 0.8327 (mp10) REVERT: G 62 LYS cc_start: 0.9044 (tptm) cc_final: 0.8775 (tppt) REVERT: G 97 TYR cc_start: 0.8966 (m-10) cc_final: 0.8713 (m-10) REVERT: G 98 CYS cc_start: 0.8495 (p) cc_final: 0.7892 (m) REVERT: G 123 ASP cc_start: 0.8016 (t0) cc_final: 0.7785 (t70) REVERT: G 124 LEU cc_start: 0.9034 (mt) cc_final: 0.8488 (mt) REVERT: G 135 TYR cc_start: 0.8375 (t80) cc_final: 0.8087 (t80) REVERT: G 161 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8138 (mt-10) REVERT: H 1 MET cc_start: 0.6235 (mpp) cc_final: 0.5847 (mpp) REVERT: H 67 ILE cc_start: 0.9516 (pt) cc_final: 0.9181 (tt) REVERT: H 87 ASP cc_start: 0.8762 (m-30) cc_final: 0.7851 (m-30) REVERT: H 103 ASP cc_start: 0.7554 (t70) cc_final: 0.7314 (t70) REVERT: I 19 LEU cc_start: 0.8651 (mt) cc_final: 0.8393 (mt) REVERT: I 51 LEU cc_start: 0.8869 (mt) cc_final: 0.8561 (mt) REVERT: I 62 LYS cc_start: 0.9238 (tptm) cc_final: 0.8914 (tptt) REVERT: I 73 GLN cc_start: 0.9223 (pm20) cc_final: 0.8868 (pm20) REVERT: I 111 LEU cc_start: 0.9104 (tp) cc_final: 0.8810 (tp) REVERT: I 115 LEU cc_start: 0.8809 (tp) cc_final: 0.8110 (tp) REVERT: I 119 ASN cc_start: 0.8578 (m110) cc_final: 0.7728 (m110) REVERT: I 129 TYR cc_start: 0.8793 (m-10) cc_final: 0.8338 (m-10) REVERT: I 173 LEU cc_start: 0.9391 (mt) cc_final: 0.9098 (tt) REVERT: J 17 GLU cc_start: 0.7979 (mp0) cc_final: 0.7766 (mp0) REVERT: J 91 ILE cc_start: 0.9410 (tp) cc_final: 0.9067 (tt) REVERT: J 97 TYR cc_start: 0.8711 (m-10) cc_final: 0.8255 (m-10) REVERT: J 112 LEU cc_start: 0.9453 (mp) cc_final: 0.8855 (mm) REVERT: K 5 ILE cc_start: 0.9225 (mm) cc_final: 0.8956 (mm) REVERT: K 30 ARG cc_start: 0.8393 (tpt-90) cc_final: 0.8176 (tpt-90) REVERT: K 90 TYR cc_start: 0.8964 (m-10) cc_final: 0.8746 (m-10) REVERT: K 111 LEU cc_start: 0.9199 (tp) cc_final: 0.8835 (tp) REVERT: K 129 TYR cc_start: 0.8613 (m-80) cc_final: 0.8168 (m-10) REVERT: K 139 ASN cc_start: 0.8318 (m110) cc_final: 0.7889 (t0) REVERT: L 2 LEU cc_start: 0.9379 (mt) cc_final: 0.8994 (mt) REVERT: L 7 LYS cc_start: 0.8746 (ptmm) cc_final: 0.8368 (ptmm) REVERT: L 13 ASP cc_start: 0.8450 (t70) cc_final: 0.8191 (t0) REVERT: L 81 MET cc_start: 0.9006 (tpp) cc_final: 0.8334 (tpp) REVERT: L 88 MET cc_start: 0.8009 (mtm) cc_final: 0.7193 (mtp) REVERT: L 89 GLU cc_start: 0.8061 (pp20) cc_final: 0.7524 (tm-30) REVERT: L 103 ASP cc_start: 0.8029 (m-30) cc_final: 0.7680 (m-30) REVERT: L 108 ASP cc_start: 0.8133 (m-30) cc_final: 0.7880 (m-30) REVERT: L 116 ARG cc_start: 0.8038 (tpp80) cc_final: 0.7679 (tpp80) REVERT: L 120 GLN cc_start: 0.8832 (tm-30) cc_final: 0.8326 (tm-30) REVERT: L 137 LYS cc_start: 0.9407 (tttt) cc_final: 0.8924 (ttmt) REVERT: L 161 GLU cc_start: 0.8547 (tt0) cc_final: 0.7788 (tp30) REVERT: M 107 MET cc_start: 0.7950 (mmm) cc_final: 0.7494 (mmm) REVERT: M 110 TYR cc_start: 0.8994 (m-10) cc_final: 0.8667 (m-10) REVERT: M 115 LEU cc_start: 0.8795 (tt) cc_final: 0.8301 (tp) REVERT: M 118 ILE cc_start: 0.9609 (tp) cc_final: 0.9174 (tp) REVERT: M 129 TYR cc_start: 0.7976 (m-80) cc_final: 0.7392 (m-10) REVERT: M 135 TYR cc_start: 0.8834 (t80) cc_final: 0.8629 (t80) REVERT: M 171 ASN cc_start: 0.7847 (p0) cc_final: 0.7350 (p0) REVERT: N 65 GLN cc_start: 0.7305 (mp10) cc_final: 0.6892 (mp10) REVERT: N 66 LEU cc_start: 0.8824 (mt) cc_final: 0.8548 (mt) REVERT: N 80 ARG cc_start: 0.8820 (mtm-85) cc_final: 0.8045 (mtm-85) REVERT: N 87 ASP cc_start: 0.8507 (m-30) cc_final: 0.8122 (m-30) REVERT: N 88 MET cc_start: 0.8285 (ttm) cc_final: 0.7911 (tpp) REVERT: N 95 VAL cc_start: 0.9607 (t) cc_final: 0.9376 (p) REVERT: N 97 TYR cc_start: 0.8560 (m-10) cc_final: 0.8006 (m-80) REVERT: N 103 ASP cc_start: 0.7004 (t0) cc_final: 0.6235 (t0) REVERT: N 118 THR cc_start: 0.9298 (p) cc_final: 0.8991 (t) REVERT: N 136 MET cc_start: 0.8861 (mtm) cc_final: 0.7708 (mtm) REVERT: O 4 PRO cc_start: 0.8694 (Cg_exo) cc_final: 0.8363 (Cg_endo) REVERT: O 19 LEU cc_start: 0.8320 (mm) cc_final: 0.7368 (tp) REVERT: O 52 ILE cc_start: 0.7990 (pt) cc_final: 0.7776 (pt) REVERT: O 61 GLN cc_start: 0.8123 (mt0) cc_final: 0.7908 (mt0) REVERT: O 96 THR cc_start: 0.9314 (p) cc_final: 0.9048 (t) REVERT: O 104 THR cc_start: 0.9024 (p) cc_final: 0.8341 (p) REVERT: O 115 LEU cc_start: 0.8369 (tp) cc_final: 0.8087 (tp) REVERT: O 130 ILE cc_start: 0.9140 (mm) cc_final: 0.8909 (mm) REVERT: P 95 VAL cc_start: 0.9210 (t) cc_final: 0.9005 (m) REVERT: P 97 TYR cc_start: 0.8781 (m-10) cc_final: 0.8447 (m-10) REVERT: P 122 LEU cc_start: 0.8299 (mm) cc_final: 0.8000 (mm) REVERT: P 158 LEU cc_start: 0.9188 (mm) cc_final: 0.8777 (mm) REVERT: Q 13 ASP cc_start: 0.8838 (t0) cc_final: 0.8629 (t0) REVERT: Q 25 GLN cc_start: 0.8717 (mm-40) cc_final: 0.7958 (mm-40) REVERT: Q 37 SER cc_start: 0.7309 (m) cc_final: 0.6613 (p) REVERT: Q 39 GLU cc_start: 0.7470 (mt-10) cc_final: 0.6776 (pt0) REVERT: Q 69 MET cc_start: 0.7390 (ptm) cc_final: 0.6693 (ptm) REVERT: Q 74 TYR cc_start: 0.7244 (m-80) cc_final: 0.6358 (m-80) REVERT: Q 94 MET cc_start: 0.6096 (tpp) cc_final: 0.5685 (tpp) REVERT: Q 98 CYS cc_start: 0.8310 (m) cc_final: 0.7818 (m) REVERT: Q 139 ASN cc_start: 0.7586 (m-40) cc_final: 0.7295 (m-40) REVERT: R 29 ASN cc_start: 0.7206 (t0) cc_final: 0.6735 (t0) REVERT: R 38 LEU cc_start: 0.8618 (mt) cc_final: 0.8077 (mp) REVERT: R 39 ASP cc_start: 0.8045 (m-30) cc_final: 0.7485 (m-30) REVERT: R 111 CYS cc_start: 0.8077 (t) cc_final: 0.7579 (t) REVERT: R 118 THR cc_start: 0.8673 (p) cc_final: 0.8454 (p) REVERT: R 128 SER cc_start: 0.8622 (m) cc_final: 0.8295 (m) REVERT: R 159 MET cc_start: 0.8228 (mmp) cc_final: 0.7624 (ptt) REVERT: S 37 SER cc_start: 0.8459 (p) cc_final: 0.7728 (t) REVERT: S 49 GLN cc_start: 0.8512 (tp-100) cc_final: 0.7806 (pm20) REVERT: S 79 GLU cc_start: 0.7796 (mp0) cc_final: 0.7462 (tm-30) REVERT: S 90 TYR cc_start: 0.8206 (m-10) cc_final: 0.7633 (m-10) REVERT: S 94 MET cc_start: 0.9480 (mmt) cc_final: 0.8632 (mmm) REVERT: S 97 TYR cc_start: 0.9085 (m-80) cc_final: 0.8073 (m-80) REVERT: S 112 ILE cc_start: 0.9488 (mm) cc_final: 0.8936 (tp) REVERT: S 115 LEU cc_start: 0.8611 (tp) cc_final: 0.8312 (tp) REVERT: S 133 LEU cc_start: 0.9074 (mt) cc_final: 0.8860 (mt) REVERT: S 134 LYS cc_start: 0.9555 (mmpt) cc_final: 0.9133 (mmmm) REVERT: S 161 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7271 (mm-30) REVERT: T 15 ARG cc_start: 0.7609 (mtp85) cc_final: 0.7092 (mmp80) REVERT: T 19 LEU cc_start: 0.8127 (mt) cc_final: 0.7545 (mm) REVERT: T 23 GLN cc_start: 0.8398 (mt0) cc_final: 0.8044 (mp10) REVERT: T 47 ASN cc_start: 0.7823 (t0) cc_final: 0.7304 (t0) REVERT: T 59 LEU cc_start: 0.9377 (mt) cc_final: 0.9070 (mt) REVERT: T 62 GLU cc_start: 0.7095 (pt0) cc_final: 0.6857 (mm-30) REVERT: T 66 LEU cc_start: 0.7923 (pt) cc_final: 0.7627 (pp) REVERT: T 104 SER cc_start: 0.9129 (p) cc_final: 0.8821 (p) REVERT: T 162 ILE cc_start: 0.8960 (mt) cc_final: 0.8739 (mt) REVERT: T 165 TYR cc_start: 0.8245 (m-80) cc_final: 0.8029 (m-80) REVERT: U 28 ASP cc_start: 0.7515 (t0) cc_final: 0.7010 (t0) REVERT: U 42 ARG cc_start: 0.7307 (ttm-80) cc_final: 0.7089 (mtt90) REVERT: U 98 CYS cc_start: 0.7993 (t) cc_final: 0.7515 (t) REVERT: U 109 GLU cc_start: 0.8343 (tm-30) cc_final: 0.7486 (tm-30) REVERT: U 115 LEU cc_start: 0.8790 (tp) cc_final: 0.8367 (tp) REVERT: U 123 ASP cc_start: 0.8391 (t0) cc_final: 0.7947 (t0) REVERT: U 137 LYS cc_start: 0.9586 (tttp) cc_final: 0.9174 (tptp) REVERT: U 140 HIS cc_start: 0.8701 (p-80) cc_final: 0.8438 (p-80) REVERT: U 171 ASN cc_start: 0.8812 (t0) cc_final: 0.8488 (t0) REVERT: U 174 SER cc_start: 0.7878 (t) cc_final: 0.7649 (t) REVERT: V 11 GLN cc_start: 0.8515 (tt0) cc_final: 0.7573 (tp40) REVERT: V 17 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7111 (mp0) REVERT: V 62 GLU cc_start: 0.7589 (pp20) cc_final: 0.7150 (pp20) REVERT: V 68 GLN cc_start: 0.8521 (pt0) cc_final: 0.8249 (pt0) REVERT: V 81 MET cc_start: 0.8669 (tpp) cc_final: 0.8152 (tpp) REVERT: V 90 ILE cc_start: 0.9501 (mm) cc_final: 0.9290 (mm) REVERT: V 103 ASP cc_start: 0.8082 (t70) cc_final: 0.7864 (p0) REVERT: V 113 ASN cc_start: 0.9128 (t0) cc_final: 0.8224 (t0) REVERT: V 124 THR cc_start: 0.8889 (m) cc_final: 0.8520 (p) REVERT: V 136 MET cc_start: 0.9197 (mtm) cc_final: 0.8923 (mtp) REVERT: V 162 ILE cc_start: 0.8636 (mt) cc_final: 0.8427 (mt) REVERT: W 42 ARG cc_start: 0.7430 (ttm170) cc_final: 0.6032 (tpt170) REVERT: W 111 LEU cc_start: 0.8471 (pt) cc_final: 0.8056 (pp) REVERT: W 163 ASN cc_start: 0.7325 (m-40) cc_final: 0.7109 (m-40) REVERT: X 32 LYS cc_start: 0.7579 (mmtp) cc_final: 0.7008 (mmmm) REVERT: X 44 ILE cc_start: 0.8061 (mm) cc_final: 0.7664 (tp) REVERT: X 52 VAL cc_start: 0.9154 (t) cc_final: 0.8882 (p) REVERT: X 88 MET cc_start: 0.8930 (ttm) cc_final: 0.8640 (ttt) REVERT: X 89 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7916 (tm-30) REVERT: X 109 ASP cc_start: 0.8242 (t70) cc_final: 0.7667 (m-30) REVERT: Y 55 MET cc_start: 0.8808 (tpt) cc_final: 0.8549 (tpt) REVERT: Z 64 ASN cc_start: 0.8972 (t0) cc_final: 0.8686 (t0) REVERT: Z 115 ILE cc_start: 0.9101 (mt) cc_final: 0.8732 (mm) REVERT: Z 120 LEU cc_start: 0.9178 (tp) cc_final: 0.7989 (tp) REVERT: Z 124 GLU cc_start: 0.7524 (pm20) cc_final: 0.6823 (pm20) REVERT: Z 196 THR cc_start: 0.9305 (p) cc_final: 0.8882 (t) REVERT: Z 264 TYR cc_start: 0.9256 (t80) cc_final: 0.8614 (t80) REVERT: Z 275 GLN cc_start: 0.8420 (mm110) cc_final: 0.8191 (mm-40) REVERT: a 5 LEU cc_start: 0.6792 (pt) cc_final: 0.6589 (pp) REVERT: a 44 GLU cc_start: 0.7721 (tt0) cc_final: 0.7499 (tt0) REVERT: a 74 ASN cc_start: 0.9023 (t0) cc_final: 0.8631 (p0) REVERT: a 84 ARG cc_start: 0.8668 (ttm110) cc_final: 0.8212 (ttm-80) REVERT: a 138 LYS cc_start: 0.9312 (mttt) cc_final: 0.8749 (mtmt) REVERT: a 151 GLN cc_start: 0.8942 (mm-40) cc_final: 0.8112 (mt0) outliers start: 6 outliers final: 0 residues processed: 1737 average time/residue: 0.2116 time to fit residues: 599.8686 Evaluate side-chains 1428 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1428 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 412 optimal weight: 5.9990 chunk 309 optimal weight: 7.9990 chunk 232 optimal weight: 0.3980 chunk 284 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 391 optimal weight: 10.0000 chunk 174 optimal weight: 4.9990 chunk 333 optimal weight: 7.9990 chunk 314 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 179 optimal weight: 0.4980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 GLN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN G 139 ASN ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 ASN ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 HIS ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN O 73 GLN O 119 ASN ** P 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 139 ASN ** R 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 92 GLN Z 141 ASN Z 166 ASN ** Z 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.113741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.095548 restraints weight = 120309.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.099441 restraints weight = 58814.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.101995 restraints weight = 33496.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.103690 restraints weight = 21264.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.104830 restraints weight = 14745.472| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 36155 Z= 0.164 Angle : 0.755 43.041 49243 Z= 0.358 Chirality : 0.039 0.215 5448 Planarity : 0.005 0.063 6402 Dihedral : 10.797 89.242 6599 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.56 % Favored : 97.37 % Rotamer: Outliers : 0.06 % Allowed : 2.30 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.13), residues: 4448 helix: 1.22 (0.08), residues: 3383 sheet: 1.80 (0.81), residues: 28 loop : -0.64 (0.22), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG T 86 TYR 0.043 0.002 TYR M 97 PHE 0.023 0.002 PHE J 166 TRP 0.014 0.001 TRP C 128 HIS 0.006 0.002 HIS Z 117 Details of bonding type rmsd covalent geometry : bond 0.00364 (36155) covalent geometry : angle 0.75480 (49243) hydrogen bonds : bond 0.04556 ( 2648) hydrogen bonds : angle 4.28773 ( 7847) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1661 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1659 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7375 (tpp) cc_final: 0.7157 (tpp) REVERT: A 15 GLN cc_start: 0.8238 (mt0) cc_final: 0.7985 (mt0) REVERT: A 18 PHE cc_start: 0.8094 (m-80) cc_final: 0.7210 (m-80) REVERT: A 38 MET cc_start: 0.8440 (mmt) cc_final: 0.7603 (tmm) REVERT: A 39 GLU cc_start: 0.8178 (tp30) cc_final: 0.7601 (mm-30) REVERT: A 49 GLN cc_start: 0.7900 (mp-120) cc_final: 0.6923 (mm-40) REVERT: A 62 LYS cc_start: 0.9174 (tptt) cc_final: 0.8924 (tptt) REVERT: A 63 PHE cc_start: 0.8755 (m-80) cc_final: 0.8207 (m-80) REVERT: A 90 TYR cc_start: 0.8913 (m-10) cc_final: 0.8501 (m-80) REVERT: A 109 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7641 (mt-10) REVERT: A 131 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7264 (tm-30) REVERT: A 167 ASP cc_start: 0.8309 (t0) cc_final: 0.7508 (t0) REVERT: A 171 ASN cc_start: 0.8576 (m-40) cc_final: 0.8175 (m-40) REVERT: B 25 ASP cc_start: 0.8192 (p0) cc_final: 0.7775 (p0) REVERT: B 35 ASN cc_start: 0.8533 (m-40) cc_final: 0.7726 (t0) REVERT: B 36 LYS cc_start: 0.9538 (mtmm) cc_final: 0.8631 (mppt) REVERT: B 88 MET cc_start: 0.6351 (tmm) cc_final: 0.5683 (tmm) REVERT: B 120 GLN cc_start: 0.7880 (mt0) cc_final: 0.7385 (tm-30) REVERT: C 17 ARG cc_start: 0.8603 (ptt90) cc_final: 0.8376 (ptt90) REVERT: C 94 MET cc_start: 0.9418 (mmt) cc_final: 0.9001 (mmm) REVERT: C 109 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8061 (tp30) REVERT: C 117 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8628 (mm-30) REVERT: C 131 GLU cc_start: 0.8505 (tp30) cc_final: 0.8196 (mm-30) REVERT: C 133 LEU cc_start: 0.8504 (mp) cc_final: 0.8203 (mp) REVERT: D 49 SER cc_start: 0.8668 (p) cc_final: 0.8422 (p) REVERT: D 88 MET cc_start: 0.8308 (ttm) cc_final: 0.6868 (mmm) REVERT: D 111 CYS cc_start: 0.7481 (t) cc_final: 0.7258 (t) REVERT: D 113 ASN cc_start: 0.8017 (t0) cc_final: 0.7698 (t0) REVERT: D 134 GLN cc_start: 0.8554 (mt0) cc_final: 0.8261 (mt0) REVERT: D 154 ASP cc_start: 0.6774 (t0) cc_final: 0.6344 (t0) REVERT: D 162 ILE cc_start: 0.8773 (mm) cc_final: 0.8426 (mm) REVERT: E 7 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7566 (mm-30) REVERT: E 28 ASP cc_start: 0.8712 (t70) cc_final: 0.8365 (t0) REVERT: E 38 MET cc_start: 0.8158 (mmt) cc_final: 0.7754 (tmm) REVERT: E 47 ASN cc_start: 0.8145 (t0) cc_final: 0.7720 (t0) REVERT: E 62 LYS cc_start: 0.8903 (tptt) cc_final: 0.8599 (tppt) REVERT: E 69 MET cc_start: 0.8427 (mtp) cc_final: 0.7871 (ttm) REVERT: E 72 SER cc_start: 0.8882 (m) cc_final: 0.8461 (t) REVERT: E 73 GLN cc_start: 0.8972 (pm20) cc_final: 0.7606 (pm20) REVERT: E 83 LYS cc_start: 0.9188 (mmmm) cc_final: 0.8759 (mmmm) REVERT: E 121 THR cc_start: 0.9176 (p) cc_final: 0.8684 (t) REVERT: E 129 TYR cc_start: 0.8529 (m-10) cc_final: 0.7966 (m-10) REVERT: E 140 HIS cc_start: 0.8598 (p90) cc_final: 0.8102 (p-80) REVERT: E 167 ASP cc_start: 0.8264 (t0) cc_final: 0.7093 (t0) REVERT: E 168 TYR cc_start: 0.8631 (t80) cc_final: 0.8195 (t80) REVERT: E 171 ASN cc_start: 0.8644 (p0) cc_final: 0.8263 (p0) REVERT: E 173 LEU cc_start: 0.8856 (mm) cc_final: 0.8636 (mm) REVERT: F 11 GLN cc_start: 0.8929 (tt0) cc_final: 0.8558 (tt0) REVERT: F 25 ASP cc_start: 0.8864 (m-30) cc_final: 0.8614 (m-30) REVERT: F 60 PHE cc_start: 0.8393 (m-10) cc_final: 0.7796 (m-10) REVERT: F 81 MET cc_start: 0.9127 (tpp) cc_final: 0.8719 (tpt) REVERT: F 88 MET cc_start: 0.8458 (tpt) cc_final: 0.8174 (mmm) REVERT: G 25 GLN cc_start: 0.8714 (mt0) cc_final: 0.8165 (mt0) REVERT: G 28 ASP cc_start: 0.8342 (t0) cc_final: 0.8139 (t70) REVERT: G 61 GLN cc_start: 0.8576 (mt0) cc_final: 0.8322 (mp10) REVERT: G 62 LYS cc_start: 0.9041 (tptm) cc_final: 0.8771 (tppt) REVERT: G 97 TYR cc_start: 0.8952 (m-10) cc_final: 0.8745 (m-10) REVERT: G 98 CYS cc_start: 0.8509 (p) cc_final: 0.7785 (m) REVERT: G 112 ILE cc_start: 0.9352 (mt) cc_final: 0.9136 (mt) REVERT: G 122 PHE cc_start: 0.8582 (m-80) cc_final: 0.8331 (m-10) REVERT: G 123 ASP cc_start: 0.8031 (t0) cc_final: 0.7765 (t0) REVERT: G 124 LEU cc_start: 0.9204 (mt) cc_final: 0.8512 (mp) REVERT: G 135 TYR cc_start: 0.8704 (t80) cc_final: 0.8273 (t80) REVERT: H 1 MET cc_start: 0.6323 (mpp) cc_final: 0.6055 (mpp) REVERT: H 88 MET cc_start: 0.7769 (mtm) cc_final: 0.7408 (mtm) REVERT: H 91 ILE cc_start: 0.9496 (mm) cc_final: 0.9138 (tp) REVERT: H 103 ASP cc_start: 0.7639 (t70) cc_final: 0.7426 (t70) REVERT: H 112 LEU cc_start: 0.9264 (mt) cc_final: 0.8949 (mt) REVERT: H 129 VAL cc_start: 0.9186 (t) cc_final: 0.8979 (t) REVERT: H 161 GLU cc_start: 0.7497 (pm20) cc_final: 0.7283 (pm20) REVERT: I 51 LEU cc_start: 0.8919 (mt) cc_final: 0.8611 (mt) REVERT: I 62 LYS cc_start: 0.9301 (tptm) cc_final: 0.8927 (tptt) REVERT: I 73 GLN cc_start: 0.9253 (pm20) cc_final: 0.8967 (pm20) REVERT: I 115 LEU cc_start: 0.8851 (tp) cc_final: 0.8275 (tt) REVERT: I 119 ASN cc_start: 0.8630 (m110) cc_final: 0.7609 (m110) REVERT: I 144 LEU cc_start: 0.8770 (mt) cc_final: 0.8206 (mt) REVERT: I 173 LEU cc_start: 0.9394 (mt) cc_final: 0.9139 (tt) REVERT: J 17 GLU cc_start: 0.7958 (mp0) cc_final: 0.7465 (mp0) REVERT: J 24 PHE cc_start: 0.6551 (m-80) cc_final: 0.6166 (m-80) REVERT: J 28 SER cc_start: 0.9309 (t) cc_final: 0.9073 (p) REVERT: J 33 GLU cc_start: 0.7869 (pm20) cc_final: 0.7591 (mp0) REVERT: J 35 ASN cc_start: 0.8717 (m110) cc_final: 0.7928 (t0) REVERT: J 91 ILE cc_start: 0.9422 (tp) cc_final: 0.9126 (tt) REVERT: J 97 TYR cc_start: 0.8724 (m-10) cc_final: 0.8168 (m-10) REVERT: J 112 LEU cc_start: 0.9487 (mp) cc_final: 0.8974 (mm) REVERT: K 30 ARG cc_start: 0.8521 (tpt-90) cc_final: 0.8202 (tpt-90) REVERT: K 97 TYR cc_start: 0.7957 (m-10) cc_final: 0.7732 (m-80) REVERT: L 2 LEU cc_start: 0.9440 (mt) cc_final: 0.8732 (mt) REVERT: L 7 LYS cc_start: 0.8735 (ptmm) cc_final: 0.8368 (ptmm) REVERT: L 13 ASP cc_start: 0.8317 (t70) cc_final: 0.8027 (t0) REVERT: L 81 MET cc_start: 0.9023 (tpp) cc_final: 0.8345 (tpp) REVERT: L 88 MET cc_start: 0.8208 (mtm) cc_final: 0.7833 (mtp) REVERT: L 89 GLU cc_start: 0.7977 (pp20) cc_final: 0.7479 (tm-30) REVERT: L 103 ASP cc_start: 0.8010 (m-30) cc_final: 0.7645 (m-30) REVERT: L 116 ARG cc_start: 0.8097 (tpp80) cc_final: 0.7843 (tpp80) REVERT: L 120 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8342 (tm-30) REVERT: L 137 LYS cc_start: 0.9505 (tttt) cc_final: 0.8796 (ttmt) REVERT: L 146 ASP cc_start: 0.9167 (t0) cc_final: 0.8910 (t0) REVERT: L 159 MET cc_start: 0.9000 (mmt) cc_final: 0.8392 (mmt) REVERT: L 161 GLU cc_start: 0.8594 (tt0) cc_final: 0.7823 (tp30) REVERT: M 9 ILE cc_start: 0.9295 (tp) cc_final: 0.8594 (tp) REVERT: M 107 MET cc_start: 0.7949 (mmm) cc_final: 0.7497 (mmm) REVERT: M 110 TYR cc_start: 0.8971 (m-10) cc_final: 0.8745 (m-10) REVERT: M 115 LEU cc_start: 0.8909 (tt) cc_final: 0.8444 (tp) REVERT: M 118 ILE cc_start: 0.9620 (tp) cc_final: 0.9214 (tp) REVERT: M 129 TYR cc_start: 0.8068 (m-80) cc_final: 0.7773 (m-80) REVERT: M 171 ASN cc_start: 0.7663 (p0) cc_final: 0.7366 (p0) REVERT: N 45 THR cc_start: 0.8562 (t) cc_final: 0.8359 (t) REVERT: N 66 LEU cc_start: 0.8899 (mt) cc_final: 0.8474 (mt) REVERT: N 87 ASP cc_start: 0.8602 (m-30) cc_final: 0.8205 (m-30) REVERT: N 88 MET cc_start: 0.8464 (ttm) cc_final: 0.7810 (tpp) REVERT: N 97 TYR cc_start: 0.8567 (m-10) cc_final: 0.7867 (m-80) REVERT: N 103 ASP cc_start: 0.7087 (t0) cc_final: 0.6636 (t0) REVERT: N 118 THR cc_start: 0.9152 (p) cc_final: 0.8892 (t) REVERT: N 136 MET cc_start: 0.8906 (mtm) cc_final: 0.7972 (mtm) REVERT: N 162 ILE cc_start: 0.9276 (mt) cc_final: 0.8896 (mt) REVERT: O 4 PRO cc_start: 0.8768 (Cg_exo) cc_final: 0.8387 (Cg_endo) REVERT: O 19 LEU cc_start: 0.8390 (mm) cc_final: 0.7506 (tp) REVERT: O 61 GLN cc_start: 0.7507 (mt0) cc_final: 0.7284 (mt0) REVERT: O 96 THR cc_start: 0.9346 (p) cc_final: 0.9108 (t) REVERT: O 104 THR cc_start: 0.8971 (p) cc_final: 0.8181 (p) REVERT: O 130 ILE cc_start: 0.9162 (mm) cc_final: 0.8303 (mt) REVERT: O 131 GLU cc_start: 0.8015 (tt0) cc_final: 0.7788 (tt0) REVERT: O 133 LEU cc_start: 0.9244 (mt) cc_final: 0.8854 (pp) REVERT: O 163 ASN cc_start: 0.8404 (m-40) cc_final: 0.7816 (m-40) REVERT: P 29 ASN cc_start: 0.7934 (t0) cc_final: 0.7520 (t0) REVERT: P 59 LEU cc_start: 0.8573 (tt) cc_final: 0.8155 (tt) REVERT: P 97 TYR cc_start: 0.8813 (m-10) cc_final: 0.8245 (m-10) REVERT: P 158 LEU cc_start: 0.9269 (mm) cc_final: 0.8734 (mm) REVERT: P 159 MET cc_start: 0.8835 (mmp) cc_final: 0.8498 (mmm) REVERT: Q 25 GLN cc_start: 0.8819 (mm-40) cc_final: 0.7852 (mm110) REVERT: Q 39 GLU cc_start: 0.7450 (mt-10) cc_final: 0.6680 (pt0) REVERT: Q 69 MET cc_start: 0.7142 (ptm) cc_final: 0.6080 (ptm) REVERT: Q 73 GLN cc_start: 0.8255 (pm20) cc_final: 0.7545 (pm20) REVERT: Q 94 MET cc_start: 0.5757 (tpp) cc_final: 0.5407 (tpp) REVERT: Q 108 ASP cc_start: 0.8737 (m-30) cc_final: 0.8318 (m-30) REVERT: R 38 LEU cc_start: 0.8651 (mt) cc_final: 0.8226 (mp) REVERT: R 85 LEU cc_start: 0.9590 (mt) cc_final: 0.9155 (tp) REVERT: R 111 CYS cc_start: 0.8170 (t) cc_final: 0.7711 (t) REVERT: R 118 THR cc_start: 0.8800 (p) cc_final: 0.8524 (p) REVERT: R 128 SER cc_start: 0.8683 (m) cc_final: 0.8313 (m) REVERT: R 159 MET cc_start: 0.8205 (mmp) cc_final: 0.7424 (ptt) REVERT: R 160 SER cc_start: 0.9036 (t) cc_final: 0.8745 (p) REVERT: S 37 SER cc_start: 0.8572 (p) cc_final: 0.7781 (t) REVERT: S 49 GLN cc_start: 0.8449 (tp-100) cc_final: 0.7704 (pm20) REVERT: S 74 TYR cc_start: 0.8628 (m-80) cc_final: 0.8062 (m-10) REVERT: S 79 GLU cc_start: 0.7822 (mp0) cc_final: 0.7459 (tm-30) REVERT: S 90 TYR cc_start: 0.8368 (m-10) cc_final: 0.7915 (m-10) REVERT: S 97 TYR cc_start: 0.9092 (m-80) cc_final: 0.8118 (m-80) REVERT: S 107 MET cc_start: 0.7475 (ptp) cc_final: 0.7272 (ptp) REVERT: S 112 ILE cc_start: 0.9503 (mm) cc_final: 0.8913 (tp) REVERT: S 115 LEU cc_start: 0.8596 (tp) cc_final: 0.8318 (tp) REVERT: T 15 ARG cc_start: 0.7736 (mtp85) cc_final: 0.7206 (mmp80) REVERT: T 19 LEU cc_start: 0.8120 (mt) cc_final: 0.7483 (mm) REVERT: T 23 GLN cc_start: 0.8447 (mt0) cc_final: 0.8021 (mp10) REVERT: T 47 ASN cc_start: 0.7424 (t0) cc_final: 0.6235 (t0) REVERT: T 50 THR cc_start: 0.9226 (m) cc_final: 0.8976 (p) REVERT: T 104 SER cc_start: 0.9112 (p) cc_final: 0.8902 (p) REVERT: U 28 ASP cc_start: 0.7400 (t0) cc_final: 0.6997 (t0) REVERT: U 109 GLU cc_start: 0.8404 (tm-30) cc_final: 0.7474 (tm-30) REVERT: U 115 LEU cc_start: 0.8698 (tp) cc_final: 0.8312 (tp) REVERT: U 137 LYS cc_start: 0.9586 (tttp) cc_final: 0.9193 (tptp) REVERT: U 171 ASN cc_start: 0.8830 (t0) cc_final: 0.8492 (t0) REVERT: U 174 SER cc_start: 0.7709 (t) cc_final: 0.7444 (t) REVERT: V 11 GLN cc_start: 0.8427 (tt0) cc_final: 0.7824 (tp40) REVERT: V 35 ASN cc_start: 0.8289 (m110) cc_final: 0.7981 (t0) REVERT: V 60 PHE cc_start: 0.8686 (m-80) cc_final: 0.8386 (m-80) REVERT: V 62 GLU cc_start: 0.7839 (pp20) cc_final: 0.7619 (pp20) REVERT: V 68 GLN cc_start: 0.8365 (pt0) cc_final: 0.7859 (pt0) REVERT: V 78 ASN cc_start: 0.6392 (t0) cc_final: 0.6099 (t0) REVERT: V 81 MET cc_start: 0.8522 (tpp) cc_final: 0.7778 (tpp) REVERT: V 103 ASP cc_start: 0.8149 (t70) cc_final: 0.7940 (p0) REVERT: V 113 ASN cc_start: 0.9003 (t0) cc_final: 0.8359 (t0) REVERT: V 124 THR cc_start: 0.8927 (m) cc_final: 0.8568 (p) REVERT: V 162 ILE cc_start: 0.8591 (mt) cc_final: 0.8384 (mt) REVERT: W 7 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8077 (mm-30) REVERT: W 24 LEU cc_start: 0.8836 (mt) cc_final: 0.8603 (mt) REVERT: W 42 ARG cc_start: 0.7408 (ttm170) cc_final: 0.6049 (tpt170) REVERT: W 111 LEU cc_start: 0.8199 (pt) cc_final: 0.7711 (pp) REVERT: W 163 ASN cc_start: 0.7508 (m-40) cc_final: 0.7232 (m-40) REVERT: X 3 ASP cc_start: 0.7796 (p0) cc_final: 0.7432 (p0) REVERT: X 32 LYS cc_start: 0.7882 (mmtp) cc_final: 0.7116 (mmmm) REVERT: X 44 ILE cc_start: 0.8080 (mm) cc_final: 0.7704 (tp) REVERT: X 52 VAL cc_start: 0.9202 (t) cc_final: 0.8877 (p) REVERT: X 88 MET cc_start: 0.8783 (ttm) cc_final: 0.8358 (ttt) REVERT: X 89 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8118 (tm-30) REVERT: X 109 ASP cc_start: 0.7954 (t70) cc_final: 0.7744 (t70) REVERT: X 110 ARG cc_start: 0.8217 (ttm110) cc_final: 0.7994 (ttm170) REVERT: Y 20 PHE cc_start: 0.8374 (m-10) cc_final: 0.8097 (m-10) REVERT: Y 23 GLU cc_start: 0.7999 (mp0) cc_final: 0.7777 (mp0) REVERT: Z 47 ASP cc_start: 0.7774 (t0) cc_final: 0.7549 (t0) REVERT: Z 59 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7855 (pm20) REVERT: Z 115 ILE cc_start: 0.9045 (mt) cc_final: 0.8690 (mm) REVERT: Z 120 LEU cc_start: 0.9239 (tp) cc_final: 0.8520 (tp) REVERT: Z 177 ASN cc_start: 0.8998 (t0) cc_final: 0.8617 (t0) REVERT: Z 196 THR cc_start: 0.9124 (p) cc_final: 0.8651 (m) REVERT: Z 264 TYR cc_start: 0.9216 (t80) cc_final: 0.8552 (t80) REVERT: Z 275 GLN cc_start: 0.8436 (mm110) cc_final: 0.8226 (mm-40) REVERT: a 68 LEU cc_start: 0.7995 (mp) cc_final: 0.7576 (mp) REVERT: a 74 ASN cc_start: 0.9102 (t0) cc_final: 0.8651 (p0) REVERT: a 84 ARG cc_start: 0.8968 (ttm110) cc_final: 0.8323 (ttm-80) REVERT: a 134 ASP cc_start: 0.8590 (m-30) cc_final: 0.8108 (m-30) REVERT: a 138 LYS cc_start: 0.9356 (mttt) cc_final: 0.8771 (mtmt) REVERT: a 151 GLN cc_start: 0.8976 (mm-40) cc_final: 0.8127 (mt0) outliers start: 2 outliers final: 0 residues processed: 1661 average time/residue: 0.2100 time to fit residues: 568.4759 Evaluate side-chains 1384 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1383 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 96 optimal weight: 0.0980 chunk 253 optimal weight: 4.9990 chunk 310 optimal weight: 7.9990 chunk 312 optimal weight: 4.9990 chunk 431 optimal weight: 0.2980 chunk 198 optimal weight: 10.0000 chunk 429 optimal weight: 0.3980 chunk 348 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 227 optimal weight: 0.7980 chunk 334 optimal weight: 0.9990 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 GLN D 23 GLN E 15 GLN ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN F 134 GLN ** H 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 139 ASN K 147 GLN ** L 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 HIS ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 70 GLN Q 119 ASN Q 139 ASN ** R 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 53 ASN Z 90 ASN Z 92 GLN Z 166 ASN Z 177 ASN ** a 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.116603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.098138 restraints weight = 124458.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.102190 restraints weight = 59739.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.104783 restraints weight = 33663.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.106536 restraints weight = 21189.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.107651 restraints weight = 14537.091| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3410 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3410 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.5629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 36155 Z= 0.143 Angle : 0.752 42.902 49243 Z= 0.356 Chirality : 0.039 0.215 5448 Planarity : 0.005 0.059 6402 Dihedral : 10.726 88.704 6599 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.68 % Favored : 97.23 % Rotamer: Outliers : 0.06 % Allowed : 2.42 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.13), residues: 4448 helix: 1.23 (0.09), residues: 3383 sheet: 1.57 (0.82), residues: 28 loop : -0.61 (0.22), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG T 86 TYR 0.034 0.002 TYR M 97 PHE 0.049 0.002 PHE T 166 TRP 0.013 0.001 TRP C 128 HIS 0.005 0.001 HIS Z 117 Details of bonding type rmsd covalent geometry : bond 0.00318 (36155) covalent geometry : angle 0.75183 (49243) hydrogen bonds : bond 0.04357 ( 2648) hydrogen bonds : angle 4.21541 ( 7847) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1672 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1670 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.8130 (mt0) cc_final: 0.7595 (mt0) REVERT: A 38 MET cc_start: 0.8480 (mmt) cc_final: 0.7615 (tmm) REVERT: A 63 PHE cc_start: 0.8957 (m-80) cc_final: 0.8356 (m-80) REVERT: A 90 TYR cc_start: 0.8896 (m-10) cc_final: 0.8385 (m-80) REVERT: A 109 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7748 (mt-10) REVERT: A 131 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7243 (tm-30) REVERT: A 167 ASP cc_start: 0.8330 (t0) cc_final: 0.7610 (t0) REVERT: A 171 ASN cc_start: 0.8596 (m-40) cc_final: 0.8204 (m-40) REVERT: B 35 ASN cc_start: 0.8424 (m-40) cc_final: 0.7577 (t0) REVERT: B 36 LYS cc_start: 0.9510 (mtmm) cc_final: 0.8477 (mppt) REVERT: B 120 GLN cc_start: 0.7853 (mt0) cc_final: 0.7373 (tm-30) REVERT: C 17 ARG cc_start: 0.8628 (ptt90) cc_final: 0.8106 (ptt90) REVERT: C 94 MET cc_start: 0.9380 (mmt) cc_final: 0.9026 (mmm) REVERT: C 117 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8625 (mm-30) REVERT: C 131 GLU cc_start: 0.8499 (tp30) cc_final: 0.8196 (mm-30) REVERT: D 3 ASP cc_start: 0.8305 (p0) cc_final: 0.8022 (p0) REVERT: D 49 SER cc_start: 0.8692 (p) cc_final: 0.8396 (p) REVERT: D 97 TYR cc_start: 0.8414 (m-10) cc_final: 0.7348 (m-10) REVERT: D 113 ASN cc_start: 0.8024 (t0) cc_final: 0.7739 (t0) REVERT: D 128 SER cc_start: 0.9314 (p) cc_final: 0.8933 (m) REVERT: D 134 GLN cc_start: 0.8537 (mt0) cc_final: 0.8220 (mt0) REVERT: D 146 ASP cc_start: 0.9268 (t0) cc_final: 0.8978 (t0) REVERT: D 154 ASP cc_start: 0.6663 (t0) cc_final: 0.6314 (t0) REVERT: D 159 MET cc_start: 0.8215 (mmp) cc_final: 0.8000 (mmm) REVERT: D 162 ILE cc_start: 0.8694 (mm) cc_final: 0.8486 (mm) REVERT: E 7 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7803 (mm-30) REVERT: E 28 ASP cc_start: 0.8696 (t70) cc_final: 0.8284 (t0) REVERT: E 38 MET cc_start: 0.8303 (mmt) cc_final: 0.7985 (tmm) REVERT: E 69 MET cc_start: 0.8404 (mtp) cc_final: 0.7842 (ttm) REVERT: E 72 SER cc_start: 0.8767 (m) cc_final: 0.8197 (t) REVERT: E 83 LYS cc_start: 0.9191 (mmmm) cc_final: 0.8749 (mmmm) REVERT: E 109 GLU cc_start: 0.8505 (tt0) cc_final: 0.8208 (tt0) REVERT: E 118 ILE cc_start: 0.9423 (mp) cc_final: 0.9200 (tt) REVERT: E 121 THR cc_start: 0.9174 (p) cc_final: 0.8699 (t) REVERT: E 129 TYR cc_start: 0.8554 (m-10) cc_final: 0.7839 (m-10) REVERT: E 137 LYS cc_start: 0.8833 (tttp) cc_final: 0.8392 (tptt) REVERT: E 140 HIS cc_start: 0.8544 (p90) cc_final: 0.8029 (p-80) REVERT: E 167 ASP cc_start: 0.8387 (t0) cc_final: 0.6949 (t0) REVERT: E 171 ASN cc_start: 0.8691 (p0) cc_final: 0.8261 (p0) REVERT: F 11 GLN cc_start: 0.9000 (tt0) cc_final: 0.8283 (tt0) REVERT: F 25 ASP cc_start: 0.8942 (m-30) cc_final: 0.8657 (m-30) REVERT: F 60 PHE cc_start: 0.8077 (m-10) cc_final: 0.7568 (m-10) REVERT: F 81 MET cc_start: 0.9104 (tpp) cc_final: 0.8658 (tpt) REVERT: G 20 SER cc_start: 0.7934 (t) cc_final: 0.6843 (m) REVERT: G 25 GLN cc_start: 0.8712 (mt0) cc_final: 0.8168 (mt0) REVERT: G 28 ASP cc_start: 0.8351 (t0) cc_final: 0.8134 (t70) REVERT: G 38 MET cc_start: 0.9307 (mtm) cc_final: 0.8501 (ttm) REVERT: G 62 LYS cc_start: 0.9058 (tptm) cc_final: 0.8760 (tppt) REVERT: G 98 CYS cc_start: 0.8339 (p) cc_final: 0.7775 (m) REVERT: G 122 PHE cc_start: 0.8641 (m-80) cc_final: 0.8078 (m-10) REVERT: G 124 LEU cc_start: 0.9217 (mt) cc_final: 0.8454 (mp) REVERT: G 135 TYR cc_start: 0.8721 (t80) cc_final: 0.8465 (t80) REVERT: H 3 ASP cc_start: 0.8408 (p0) cc_final: 0.8062 (p0) REVERT: H 17 GLU cc_start: 0.8611 (pm20) cc_final: 0.7606 (pm20) REVERT: H 81 MET cc_start: 0.8705 (mmm) cc_final: 0.8379 (tpp) REVERT: H 87 ASP cc_start: 0.9091 (m-30) cc_final: 0.8164 (m-30) REVERT: H 91 ILE cc_start: 0.9453 (mm) cc_final: 0.9060 (tp) REVERT: H 145 ASN cc_start: 0.7670 (m-40) cc_final: 0.7096 (m-40) REVERT: H 159 MET cc_start: 0.8131 (mmm) cc_final: 0.7659 (mmt) REVERT: H 168 ARG cc_start: 0.8066 (tpt-90) cc_final: 0.7564 (ttt180) REVERT: I 62 LYS cc_start: 0.9294 (tptm) cc_final: 0.8924 (tptt) REVERT: I 115 LEU cc_start: 0.8899 (tp) cc_final: 0.8316 (tt) REVERT: I 119 ASN cc_start: 0.8641 (m110) cc_final: 0.7635 (m110) REVERT: I 127 SER cc_start: 0.9181 (p) cc_final: 0.8940 (p) REVERT: I 129 TYR cc_start: 0.8804 (m-10) cc_final: 0.8588 (m-10) REVERT: I 135 TYR cc_start: 0.8585 (t80) cc_final: 0.8279 (t80) REVERT: I 144 LEU cc_start: 0.8737 (mt) cc_final: 0.8281 (mt) REVERT: I 173 LEU cc_start: 0.9322 (mt) cc_final: 0.9103 (tt) REVERT: J 17 GLU cc_start: 0.8090 (mp0) cc_final: 0.7556 (mp0) REVERT: J 24 PHE cc_start: 0.6515 (m-80) cc_final: 0.6226 (m-80) REVERT: J 28 SER cc_start: 0.9357 (t) cc_final: 0.9123 (p) REVERT: J 35 ASN cc_start: 0.8739 (m110) cc_final: 0.7890 (t0) REVERT: J 88 MET cc_start: 0.8816 (mmt) cc_final: 0.8430 (mmm) REVERT: J 91 ILE cc_start: 0.9366 (tp) cc_final: 0.9163 (tt) REVERT: J 97 TYR cc_start: 0.8571 (m-10) cc_final: 0.8052 (m-10) REVERT: J 112 LEU cc_start: 0.9520 (mp) cc_final: 0.8891 (mm) REVERT: K 30 ARG cc_start: 0.8530 (tpt-90) cc_final: 0.8068 (tpt-90) REVERT: K 90 TYR cc_start: 0.8992 (m-10) cc_final: 0.8733 (m-80) REVERT: K 133 LEU cc_start: 0.8692 (mt) cc_final: 0.8441 (tp) REVERT: K 139 ASN cc_start: 0.8736 (OUTLIER) cc_final: 0.8110 (t0) REVERT: L 2 LEU cc_start: 0.9423 (mt) cc_final: 0.8726 (mt) REVERT: L 81 MET cc_start: 0.8971 (tpp) cc_final: 0.8310 (tpp) REVERT: L 88 MET cc_start: 0.7689 (mtm) cc_final: 0.7013 (mtp) REVERT: L 89 GLU cc_start: 0.7671 (pp20) cc_final: 0.7429 (tm-30) REVERT: L 103 ASP cc_start: 0.7995 (m-30) cc_final: 0.7662 (m-30) REVERT: L 116 ARG cc_start: 0.8098 (tpp80) cc_final: 0.7771 (tpp80) REVERT: L 120 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8028 (tm-30) REVERT: L 137 LYS cc_start: 0.9461 (tttt) cc_final: 0.8747 (ttmt) REVERT: L 146 ASP cc_start: 0.9180 (t0) cc_final: 0.8946 (t0) REVERT: L 159 MET cc_start: 0.8986 (mmt) cc_final: 0.8702 (mtp) REVERT: L 161 GLU cc_start: 0.8686 (tt0) cc_final: 0.7809 (tp30) REVERT: M 9 ILE cc_start: 0.9164 (tp) cc_final: 0.8461 (tp) REVERT: M 57 GLN cc_start: 0.9434 (mm-40) cc_final: 0.8924 (mm-40) REVERT: M 107 MET cc_start: 0.7949 (mmm) cc_final: 0.7368 (mmm) REVERT: M 110 TYR cc_start: 0.8992 (m-10) cc_final: 0.8780 (m-10) REVERT: M 115 LEU cc_start: 0.8893 (tt) cc_final: 0.8342 (tp) REVERT: M 118 ILE cc_start: 0.9628 (tp) cc_final: 0.9248 (tp) REVERT: M 129 TYR cc_start: 0.7829 (m-80) cc_final: 0.7578 (m-80) REVERT: M 135 TYR cc_start: 0.9147 (t80) cc_final: 0.8798 (t80) REVERT: M 161 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8107 (mt-10) REVERT: M 171 ASN cc_start: 0.7547 (p0) cc_final: 0.7270 (p0) REVERT: N 42 ASN cc_start: 0.9492 (t0) cc_final: 0.8772 (t0) REVERT: N 87 ASP cc_start: 0.8968 (m-30) cc_final: 0.8636 (m-30) REVERT: N 88 MET cc_start: 0.8327 (ttm) cc_final: 0.7710 (tpp) REVERT: N 89 GLU cc_start: 0.7817 (pp20) cc_final: 0.7305 (pp20) REVERT: N 97 TYR cc_start: 0.8417 (m-10) cc_final: 0.7821 (m-80) REVERT: N 103 ASP cc_start: 0.7020 (t0) cc_final: 0.6412 (t0) REVERT: N 136 MET cc_start: 0.8832 (mtm) cc_final: 0.7712 (mtm) REVERT: N 165 TYR cc_start: 0.8634 (m-10) cc_final: 0.7682 (m-80) REVERT: O 4 PRO cc_start: 0.8734 (Cg_exo) cc_final: 0.8383 (Cg_endo) REVERT: O 19 LEU cc_start: 0.8405 (mm) cc_final: 0.7553 (tp) REVERT: O 61 GLN cc_start: 0.7583 (mt0) cc_final: 0.6884 (tm-30) REVERT: O 68 THR cc_start: 0.7155 (t) cc_final: 0.6924 (m) REVERT: O 96 THR cc_start: 0.9367 (p) cc_final: 0.9107 (t) REVERT: O 98 CYS cc_start: 0.8306 (m) cc_final: 0.7363 (p) REVERT: O 104 THR cc_start: 0.8970 (p) cc_final: 0.8284 (p) REVERT: O 130 ILE cc_start: 0.9253 (mm) cc_final: 0.8996 (mt) REVERT: O 163 ASN cc_start: 0.8516 (m-40) cc_final: 0.8176 (m110) REVERT: O 170 ILE cc_start: 0.9031 (tt) cc_final: 0.8827 (tp) REVERT: P 97 TYR cc_start: 0.8783 (m-10) cc_final: 0.8196 (m-10) REVERT: P 122 LEU cc_start: 0.8371 (mm) cc_final: 0.8048 (mm) REVERT: Q 1 MET cc_start: 0.8545 (tpp) cc_final: 0.8255 (tpt) REVERT: Q 25 GLN cc_start: 0.8918 (mm-40) cc_final: 0.8418 (mm110) REVERT: Q 39 GLU cc_start: 0.7413 (mt-10) cc_final: 0.6673 (pt0) REVERT: Q 53 ASP cc_start: 0.6364 (m-30) cc_final: 0.6140 (m-30) REVERT: Q 62 LYS cc_start: 0.7610 (ttmm) cc_final: 0.7398 (ttmm) REVERT: Q 69 MET cc_start: 0.7043 (ptm) cc_final: 0.6295 (ptm) REVERT: Q 73 GLN cc_start: 0.8248 (pm20) cc_final: 0.8025 (pm20) REVERT: Q 94 MET cc_start: 0.5713 (tpp) cc_final: 0.5374 (tpp) REVERT: Q 108 ASP cc_start: 0.8798 (m-30) cc_final: 0.8380 (m-30) REVERT: R 29 ASN cc_start: 0.7456 (t0) cc_final: 0.7239 (t0) REVERT: R 85 LEU cc_start: 0.9569 (mt) cc_final: 0.9146 (tp) REVERT: R 111 CYS cc_start: 0.8149 (t) cc_final: 0.7688 (t) REVERT: R 128 SER cc_start: 0.8734 (m) cc_final: 0.8360 (m) REVERT: R 141 ILE cc_start: 0.8685 (mm) cc_final: 0.8472 (mm) REVERT: R 160 SER cc_start: 0.9011 (t) cc_final: 0.8518 (p) REVERT: R 161 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7504 (mm-30) REVERT: S 37 SER cc_start: 0.8462 (p) cc_final: 0.7934 (t) REVERT: S 49 GLN cc_start: 0.8397 (tp-100) cc_final: 0.7764 (pm20) REVERT: S 74 TYR cc_start: 0.8699 (m-80) cc_final: 0.8080 (m-10) REVERT: S 79 GLU cc_start: 0.7864 (mp0) cc_final: 0.7493 (tm-30) REVERT: S 90 TYR cc_start: 0.8229 (m-10) cc_final: 0.7989 (m-10) REVERT: S 94 MET cc_start: 0.9428 (mmp) cc_final: 0.9032 (mmm) REVERT: S 97 TYR cc_start: 0.9079 (m-80) cc_final: 0.8230 (m-80) REVERT: S 107 MET cc_start: 0.7438 (ptp) cc_final: 0.7101 (ptp) REVERT: S 112 ILE cc_start: 0.9510 (mm) cc_final: 0.8903 (tp) REVERT: S 115 LEU cc_start: 0.8569 (tp) cc_final: 0.8222 (tp) REVERT: S 163 ASN cc_start: 0.9388 (m110) cc_final: 0.9146 (m-40) REVERT: T 19 LEU cc_start: 0.8146 (mt) cc_final: 0.7554 (mm) REVERT: T 23 GLN cc_start: 0.8406 (mt0) cc_final: 0.8071 (mp10) REVERT: T 47 ASN cc_start: 0.7646 (t0) cc_final: 0.6104 (t0) REVERT: T 50 THR cc_start: 0.9191 (m) cc_final: 0.8860 (p) REVERT: T 162 ILE cc_start: 0.8903 (mt) cc_final: 0.8648 (mt) REVERT: T 165 TYR cc_start: 0.8525 (m-80) cc_final: 0.7948 (m-80) REVERT: U 23 GLU cc_start: 0.8697 (pm20) cc_final: 0.8471 (pm20) REVERT: U 28 ASP cc_start: 0.7425 (t0) cc_final: 0.6958 (t0) REVERT: U 32 LYS cc_start: 0.9272 (tmmt) cc_final: 0.9044 (tmmt) REVERT: U 109 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7426 (tm-30) REVERT: U 115 LEU cc_start: 0.8617 (tp) cc_final: 0.8308 (tp) REVERT: U 137 LYS cc_start: 0.9435 (tttp) cc_final: 0.9032 (tptp) REVERT: U 171 ASN cc_start: 0.8910 (t0) cc_final: 0.8563 (t0) REVERT: U 174 SER cc_start: 0.7634 (t) cc_final: 0.7359 (t) REVERT: V 29 ASN cc_start: 0.8381 (m-40) cc_final: 0.8113 (t0) REVERT: V 35 ASN cc_start: 0.8251 (m110) cc_final: 0.7952 (t0) REVERT: V 60 PHE cc_start: 0.8794 (m-80) cc_final: 0.8338 (m-80) REVERT: V 62 GLU cc_start: 0.7605 (pp20) cc_final: 0.7345 (pp20) REVERT: V 68 GLN cc_start: 0.8288 (pt0) cc_final: 0.7795 (pt0) REVERT: V 78 ASN cc_start: 0.6162 (t0) cc_final: 0.5932 (t0) REVERT: V 81 MET cc_start: 0.8502 (tpp) cc_final: 0.7738 (tpp) REVERT: V 103 ASP cc_start: 0.8120 (t70) cc_final: 0.7865 (p0) REVERT: V 113 ASN cc_start: 0.9153 (t0) cc_final: 0.8318 (t0) REVERT: V 124 THR cc_start: 0.8976 (m) cc_final: 0.8725 (p) REVERT: V 134 GLN cc_start: 0.8445 (mm110) cc_final: 0.8205 (mm110) REVERT: V 162 ILE cc_start: 0.8607 (mt) cc_final: 0.8335 (mt) REVERT: V 173 VAL cc_start: 0.8238 (t) cc_final: 0.8019 (t) REVERT: W 42 ARG cc_start: 0.7353 (ttm170) cc_final: 0.6018 (tpt170) REVERT: W 69 MET cc_start: 0.3812 (mmm) cc_final: 0.3380 (tpt) REVERT: W 88 ILE cc_start: 0.8612 (mm) cc_final: 0.8308 (mm) REVERT: W 94 MET cc_start: 0.8131 (ptt) cc_final: 0.7812 (ppp) REVERT: W 111 LEU cc_start: 0.8409 (pt) cc_final: 0.7876 (pp) REVERT: X 3 ASP cc_start: 0.7840 (p0) cc_final: 0.7501 (p0) REVERT: X 32 LYS cc_start: 0.7656 (mmtp) cc_final: 0.6818 (mmmm) REVERT: X 44 ILE cc_start: 0.8113 (mm) cc_final: 0.7758 (tp) REVERT: X 52 VAL cc_start: 0.9266 (t) cc_final: 0.8959 (p) REVERT: X 88 MET cc_start: 0.8899 (ttm) cc_final: 0.8481 (ttt) REVERT: X 89 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8042 (tm-30) REVERT: X 136 MET cc_start: 0.8015 (mmm) cc_final: 0.7595 (mmm) REVERT: Y 23 GLU cc_start: 0.7895 (mp0) cc_final: 0.7418 (mp0) REVERT: Y 33 THR cc_start: 0.9095 (p) cc_final: 0.8716 (t) REVERT: Z 59 GLU cc_start: 0.8449 (pm20) cc_final: 0.7989 (pm20) REVERT: Z 115 ILE cc_start: 0.8979 (mt) cc_final: 0.8679 (mm) REVERT: Z 119 ASP cc_start: 0.7643 (m-30) cc_final: 0.7055 (m-30) REVERT: Z 120 LEU cc_start: 0.9333 (tp) cc_final: 0.8767 (tp) REVERT: Z 141 ASN cc_start: 0.8401 (m-40) cc_final: 0.7822 (m-40) REVERT: Z 168 ILE cc_start: 0.9749 (tp) cc_final: 0.9532 (tp) REVERT: Z 175 TYR cc_start: 0.8524 (t80) cc_final: 0.8066 (t80) REVERT: Z 179 ASP cc_start: 0.8537 (m-30) cc_final: 0.8242 (t70) REVERT: Z 196 THR cc_start: 0.9129 (p) cc_final: 0.8648 (m) REVERT: a 68 LEU cc_start: 0.8110 (mp) cc_final: 0.7545 (mp) REVERT: a 74 ASN cc_start: 0.9061 (t0) cc_final: 0.8842 (p0) REVERT: a 84 ARG cc_start: 0.9023 (ttm110) cc_final: 0.8585 (ttm110) REVERT: a 98 GLU cc_start: 0.8146 (pt0) cc_final: 0.7896 (pt0) REVERT: a 129 ILE cc_start: 0.8946 (tt) cc_final: 0.8455 (tp) REVERT: a 161 GLN cc_start: 0.8177 (tt0) cc_final: 0.7624 (tt0) outliers start: 2 outliers final: 1 residues processed: 1672 average time/residue: 0.2075 time to fit residues: 568.3575 Evaluate side-chains 1402 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1400 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 17 optimal weight: 9.9990 chunk 210 optimal weight: 0.9980 chunk 276 optimal weight: 7.9990 chunk 314 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 159 optimal weight: 0.3980 chunk 150 optimal weight: 0.9990 chunk 325 optimal weight: 10.0000 chunk 406 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 268 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 GLN ** D 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN F 134 GLN ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 ASN ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 63 GLN M 140 HIS M 163 ASN N 47 ASN ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 25 GLN ** P 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 139 ASN ** R 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 139 ASN ** S 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 ASN U 119 ASN ** U 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 68 GLN ** V 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 61 GLN ** W 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 90 ASN Z 166 ASN ** a 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.115615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.099733 restraints weight = 87071.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.102871 restraints weight = 45681.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.104918 restraints weight = 27298.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.106284 restraints weight = 18003.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.107258 restraints weight = 13027.252| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3406 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.5861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 36155 Z= 0.147 Angle : 0.765 42.917 49243 Z= 0.365 Chirality : 0.040 0.213 5448 Planarity : 0.005 0.077 6402 Dihedral : 10.736 89.087 6599 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.81 % Favored : 97.10 % Rotamer: Outliers : 0.06 % Allowed : 1.45 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.13), residues: 4448 helix: 1.16 (0.09), residues: 3390 sheet: 1.37 (0.83), residues: 28 loop : -0.56 (0.22), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 15 TYR 0.050 0.002 TYR R 97 PHE 0.036 0.002 PHE a 170 TRP 0.011 0.001 TRP C 128 HIS 0.008 0.002 HIS Z 117 Details of bonding type rmsd covalent geometry : bond 0.00326 (36155) covalent geometry : angle 0.76517 (49243) hydrogen bonds : bond 0.04305 ( 2648) hydrogen bonds : angle 4.25572 ( 7847) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1646 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1644 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6753 (tpp) cc_final: 0.6530 (tpp) REVERT: A 15 GLN cc_start: 0.8314 (mt0) cc_final: 0.7763 (mt0) REVERT: A 18 PHE cc_start: 0.7719 (m-80) cc_final: 0.7517 (m-80) REVERT: A 38 MET cc_start: 0.8450 (mmt) cc_final: 0.7600 (tmm) REVERT: A 39 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7853 (mt-10) REVERT: A 90 TYR cc_start: 0.8700 (m-10) cc_final: 0.8110 (m-80) REVERT: A 109 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7723 (mm-30) REVERT: A 131 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7319 (tm-30) REVERT: A 167 ASP cc_start: 0.8371 (t0) cc_final: 0.7561 (t0) REVERT: A 171 ASN cc_start: 0.8636 (m-40) cc_final: 0.8154 (m-40) REVERT: B 25 ASP cc_start: 0.7596 (p0) cc_final: 0.6701 (p0) REVERT: B 29 ASN cc_start: 0.8013 (m110) cc_final: 0.7744 (m110) REVERT: B 35 ASN cc_start: 0.8564 (m-40) cc_final: 0.7726 (t0) REVERT: B 36 LYS cc_start: 0.9453 (mtmm) cc_final: 0.8436 (mppt) REVERT: B 59 LEU cc_start: 0.9228 (tp) cc_final: 0.8644 (tt) REVERT: B 120 GLN cc_start: 0.7919 (mt0) cc_final: 0.7425 (tm-30) REVERT: B 141 ILE cc_start: 0.9302 (tt) cc_final: 0.9084 (tt) REVERT: B 159 MET cc_start: 0.8578 (mpp) cc_final: 0.8320 (mpp) REVERT: C 17 ARG cc_start: 0.8669 (ptt90) cc_final: 0.8054 (ptt90) REVERT: C 51 LEU cc_start: 0.8608 (mp) cc_final: 0.8340 (tp) REVERT: C 94 MET cc_start: 0.9374 (mmt) cc_final: 0.9118 (mmm) REVERT: C 117 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8622 (mm-30) REVERT: D 24 PHE cc_start: 0.8566 (m-80) cc_final: 0.8346 (m-80) REVERT: D 49 SER cc_start: 0.8829 (p) cc_final: 0.8410 (p) REVERT: D 81 MET cc_start: 0.7738 (ttm) cc_final: 0.7460 (ttm) REVERT: D 97 TYR cc_start: 0.8250 (m-10) cc_final: 0.7230 (m-80) REVERT: D 113 ASN cc_start: 0.8029 (t0) cc_final: 0.7678 (t0) REVERT: D 128 SER cc_start: 0.9403 (p) cc_final: 0.9132 (p) REVERT: D 134 GLN cc_start: 0.8597 (mt0) cc_final: 0.8251 (mt0) REVERT: D 154 ASP cc_start: 0.6634 (t0) cc_final: 0.6303 (t0) REVERT: E 7 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7741 (mm-30) REVERT: E 28 ASP cc_start: 0.8596 (t70) cc_final: 0.8292 (t0) REVERT: E 38 MET cc_start: 0.8150 (mmt) cc_final: 0.7819 (tmm) REVERT: E 47 ASN cc_start: 0.8464 (m110) cc_final: 0.7695 (m110) REVERT: E 69 MET cc_start: 0.8242 (mtp) cc_final: 0.7992 (ttm) REVERT: E 72 SER cc_start: 0.8770 (m) cc_final: 0.8306 (t) REVERT: E 83 LYS cc_start: 0.9199 (mmmm) cc_final: 0.8311 (mmmm) REVERT: E 86 ARG cc_start: 0.8473 (ttp80) cc_final: 0.7783 (ttp80) REVERT: E 120 SER cc_start: 0.9346 (t) cc_final: 0.9142 (t) REVERT: E 121 THR cc_start: 0.9245 (p) cc_final: 0.8722 (t) REVERT: E 129 TYR cc_start: 0.8538 (m-10) cc_final: 0.7898 (m-10) REVERT: E 137 LYS cc_start: 0.8483 (tttp) cc_final: 0.8046 (tptm) REVERT: E 140 HIS cc_start: 0.8463 (p90) cc_final: 0.7989 (p-80) REVERT: E 167 ASP cc_start: 0.8405 (t0) cc_final: 0.6974 (t0) REVERT: E 171 ASN cc_start: 0.8767 (p0) cc_final: 0.8296 (p0) REVERT: F 11 GLN cc_start: 0.8905 (tt0) cc_final: 0.8562 (tt0) REVERT: F 60 PHE cc_start: 0.8044 (m-10) cc_final: 0.7408 (m-10) REVERT: F 81 MET cc_start: 0.9224 (tpp) cc_final: 0.8748 (tpt) REVERT: F 146 ASP cc_start: 0.7739 (t70) cc_final: 0.7431 (t0) REVERT: G 1 MET cc_start: 0.7225 (tpp) cc_final: 0.6819 (tpp) REVERT: G 25 GLN cc_start: 0.8566 (mt0) cc_final: 0.8236 (mt0) REVERT: G 38 MET cc_start: 0.9260 (mtm) cc_final: 0.8405 (ttm) REVERT: G 70 GLN cc_start: 0.7740 (pp30) cc_final: 0.7489 (pp30) REVERT: G 98 CYS cc_start: 0.8232 (p) cc_final: 0.7777 (m) REVERT: G 122 PHE cc_start: 0.8632 (m-80) cc_final: 0.8057 (m-10) REVERT: G 123 ASP cc_start: 0.8273 (t0) cc_final: 0.7759 (t0) REVERT: G 124 LEU cc_start: 0.9234 (mt) cc_final: 0.8496 (mp) REVERT: G 135 TYR cc_start: 0.8670 (t80) cc_final: 0.8336 (t80) REVERT: H 3 ASP cc_start: 0.8360 (p0) cc_final: 0.8105 (p0) REVERT: H 17 GLU cc_start: 0.8640 (pm20) cc_final: 0.8144 (pm20) REVERT: H 91 ILE cc_start: 0.9535 (mm) cc_final: 0.9220 (tp) REVERT: H 112 LEU cc_start: 0.9414 (mt) cc_final: 0.9081 (mt) REVERT: H 115 LEU cc_start: 0.8306 (tt) cc_final: 0.7775 (pp) REVERT: H 159 MET cc_start: 0.8320 (mmm) cc_final: 0.7591 (mmt) REVERT: I 60 TYR cc_start: 0.7312 (m-80) cc_final: 0.7071 (m-80) REVERT: I 62 LYS cc_start: 0.9255 (tptm) cc_final: 0.8919 (tptt) REVERT: I 73 GLN cc_start: 0.9353 (pm20) cc_final: 0.8912 (pm20) REVERT: I 115 LEU cc_start: 0.8956 (tp) cc_final: 0.8419 (tt) REVERT: I 119 ASN cc_start: 0.8612 (m110) cc_final: 0.7608 (m110) REVERT: I 127 SER cc_start: 0.9170 (p) cc_final: 0.8963 (p) REVERT: I 135 TYR cc_start: 0.8684 (t80) cc_final: 0.8454 (t80) REVERT: I 144 LEU cc_start: 0.8812 (mt) cc_final: 0.8358 (mt) REVERT: I 173 LEU cc_start: 0.9324 (mt) cc_final: 0.9112 (tt) REVERT: J 17 GLU cc_start: 0.8087 (mp0) cc_final: 0.7534 (mp0) REVERT: J 24 PHE cc_start: 0.6712 (m-80) cc_final: 0.6406 (m-80) REVERT: J 28 SER cc_start: 0.9398 (t) cc_final: 0.9137 (p) REVERT: J 35 ASN cc_start: 0.8781 (m110) cc_final: 0.7883 (t0) REVERT: J 88 MET cc_start: 0.8792 (mmt) cc_final: 0.8505 (mmm) REVERT: J 91 ILE cc_start: 0.9383 (tp) cc_final: 0.9133 (tt) REVERT: J 97 TYR cc_start: 0.8493 (m-10) cc_final: 0.8032 (m-10) REVERT: J 112 LEU cc_start: 0.9542 (mp) cc_final: 0.8923 (mm) REVERT: K 30 ARG cc_start: 0.8446 (tpt-90) cc_final: 0.8228 (tpt-90) REVERT: K 97 TYR cc_start: 0.8150 (m-10) cc_final: 0.7846 (m-80) REVERT: K 133 LEU cc_start: 0.8835 (mt) cc_final: 0.8459 (tp) REVERT: K 139 ASN cc_start: 0.9062 (t0) cc_final: 0.8253 (t0) REVERT: L 2 LEU cc_start: 0.9368 (mt) cc_final: 0.8642 (mt) REVERT: L 3 ASP cc_start: 0.8739 (p0) cc_final: 0.8303 (p0) REVERT: L 62 GLU cc_start: 0.8431 (tm-30) cc_final: 0.8224 (tm-30) REVERT: L 81 MET cc_start: 0.8995 (tpp) cc_final: 0.8365 (tpp) REVERT: L 88 MET cc_start: 0.7769 (mtm) cc_final: 0.7532 (mtp) REVERT: L 89 GLU cc_start: 0.7741 (pp20) cc_final: 0.7519 (tm-30) REVERT: L 116 ARG cc_start: 0.8138 (tpp80) cc_final: 0.7835 (tpp80) REVERT: L 120 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8199 (tm-30) REVERT: L 137 LYS cc_start: 0.9462 (tttt) cc_final: 0.8962 (ttmm) REVERT: L 146 ASP cc_start: 0.9227 (t0) cc_final: 0.8974 (t0) REVERT: L 159 MET cc_start: 0.9047 (mmt) cc_final: 0.8467 (mmt) REVERT: L 161 GLU cc_start: 0.8707 (tt0) cc_final: 0.7855 (tp30) REVERT: M 57 GLN cc_start: 0.9430 (mm-40) cc_final: 0.8922 (mm-40) REVERT: M 84 CYS cc_start: 0.8247 (t) cc_final: 0.7962 (m) REVERT: M 94 MET cc_start: 0.8619 (ttm) cc_final: 0.8206 (mtp) REVERT: M 110 TYR cc_start: 0.8885 (m-10) cc_final: 0.8628 (m-10) REVERT: M 115 LEU cc_start: 0.8825 (tt) cc_final: 0.8341 (tp) REVERT: M 118 ILE cc_start: 0.9626 (tp) cc_final: 0.9135 (tp) REVERT: M 128 TRP cc_start: 0.8471 (m-10) cc_final: 0.7576 (m-10) REVERT: M 129 TYR cc_start: 0.7952 (m-80) cc_final: 0.7499 (m-80) REVERT: M 171 ASN cc_start: 0.7540 (p0) cc_final: 0.7239 (p0) REVERT: N 20 THR cc_start: 0.7902 (t) cc_final: 0.7486 (p) REVERT: N 42 ASN cc_start: 0.9497 (t0) cc_final: 0.8929 (t0) REVERT: N 65 GLN cc_start: 0.7343 (pm20) cc_final: 0.6741 (pm20) REVERT: N 66 LEU cc_start: 0.8706 (mt) cc_final: 0.8397 (mt) REVERT: N 87 ASP cc_start: 0.9007 (m-30) cc_final: 0.8732 (m-30) REVERT: N 88 MET cc_start: 0.8471 (ttm) cc_final: 0.7762 (tpp) REVERT: N 89 GLU cc_start: 0.7886 (pp20) cc_final: 0.7363 (pp20) REVERT: N 97 TYR cc_start: 0.8355 (m-10) cc_final: 0.7868 (m-80) REVERT: N 103 ASP cc_start: 0.7006 (t0) cc_final: 0.6576 (t0) REVERT: N 116 ARG cc_start: 0.7677 (ttm170) cc_final: 0.7266 (ttm170) REVERT: N 136 MET cc_start: 0.8592 (mtm) cc_final: 0.7698 (mtm) REVERT: N 137 LYS cc_start: 0.8401 (ttmm) cc_final: 0.7851 (tttt) REVERT: N 173 VAL cc_start: 0.6197 (p) cc_final: 0.5652 (t) REVERT: O 4 PRO cc_start: 0.8707 (Cg_exo) cc_final: 0.8356 (Cg_endo) REVERT: O 19 LEU cc_start: 0.8790 (mm) cc_final: 0.8035 (tp) REVERT: O 51 LEU cc_start: 0.7930 (mt) cc_final: 0.7706 (mt) REVERT: O 60 TYR cc_start: 0.6053 (m-10) cc_final: 0.5753 (m-10) REVERT: O 61 GLN cc_start: 0.7535 (mt0) cc_final: 0.6892 (tm-30) REVERT: O 68 THR cc_start: 0.7156 (t) cc_final: 0.6930 (m) REVERT: O 96 THR cc_start: 0.9403 (p) cc_final: 0.9148 (t) REVERT: O 98 CYS cc_start: 0.8378 (m) cc_final: 0.7396 (p) REVERT: O 104 THR cc_start: 0.8965 (p) cc_final: 0.8291 (p) REVERT: O 107 MET cc_start: 0.8610 (tpp) cc_final: 0.8150 (mmp) REVERT: O 130 ILE cc_start: 0.9213 (mm) cc_final: 0.8973 (mt) REVERT: O 131 GLU cc_start: 0.8701 (pt0) cc_final: 0.8458 (pt0) REVERT: O 163 ASN cc_start: 0.8502 (m-40) cc_final: 0.8205 (m-40) REVERT: O 170 ILE cc_start: 0.9028 (tt) cc_final: 0.8820 (tp) REVERT: P 93 ARG cc_start: 0.8531 (ttp80) cc_final: 0.7830 (ttp-170) REVERT: P 94 TYR cc_start: 0.8574 (m-80) cc_final: 0.8088 (m-10) REVERT: P 97 TYR cc_start: 0.8596 (m-10) cc_final: 0.7852 (m-80) REVERT: P 122 LEU cc_start: 0.8439 (mm) cc_final: 0.8156 (mm) REVERT: Q 25 GLN cc_start: 0.9024 (mm-40) cc_final: 0.8180 (mm-40) REVERT: Q 39 GLU cc_start: 0.7422 (mt-10) cc_final: 0.6703 (pt0) REVERT: Q 53 ASP cc_start: 0.6352 (m-30) cc_final: 0.6117 (m-30) REVERT: Q 62 LYS cc_start: 0.7736 (ttmm) cc_final: 0.7492 (ttmm) REVERT: Q 69 MET cc_start: 0.7215 (ptm) cc_final: 0.6549 (ptm) REVERT: Q 108 ASP cc_start: 0.8736 (m-30) cc_final: 0.8533 (m-30) REVERT: R 85 LEU cc_start: 0.9611 (mt) cc_final: 0.9183 (tp) REVERT: R 111 CYS cc_start: 0.8177 (t) cc_final: 0.7754 (t) REVERT: R 128 SER cc_start: 0.8829 (m) cc_final: 0.8497 (m) REVERT: R 141 ILE cc_start: 0.8352 (mm) cc_final: 0.7786 (pt) REVERT: S 37 SER cc_start: 0.8392 (p) cc_final: 0.8037 (t) REVERT: S 49 GLN cc_start: 0.8469 (tp-100) cc_final: 0.7753 (pm20) REVERT: S 74 TYR cc_start: 0.8740 (m-80) cc_final: 0.8058 (m-10) REVERT: S 79 GLU cc_start: 0.7886 (mp0) cc_final: 0.7520 (tm-30) REVERT: S 94 MET cc_start: 0.9481 (mmp) cc_final: 0.9207 (mmm) REVERT: S 97 TYR cc_start: 0.9066 (m-10) cc_final: 0.8254 (m-80) REVERT: S 107 MET cc_start: 0.7482 (ptp) cc_final: 0.7225 (ptp) REVERT: S 112 ILE cc_start: 0.9520 (mm) cc_final: 0.8862 (tp) REVERT: S 115 LEU cc_start: 0.8552 (tp) cc_final: 0.8233 (tp) REVERT: S 139 ASN cc_start: 0.8362 (OUTLIER) cc_final: 0.7820 (t0) REVERT: T 23 GLN cc_start: 0.8394 (mt0) cc_final: 0.8121 (mp10) REVERT: T 47 ASN cc_start: 0.7718 (t0) cc_final: 0.6160 (t0) REVERT: T 104 SER cc_start: 0.9145 (p) cc_final: 0.8664 (p) REVERT: T 110 ARG cc_start: 0.5728 (tpp80) cc_final: 0.5030 (mtt180) REVERT: T 165 TYR cc_start: 0.8564 (m-80) cc_final: 0.7933 (m-80) REVERT: U 23 GLU cc_start: 0.8709 (pm20) cc_final: 0.8490 (pm20) REVERT: U 28 ASP cc_start: 0.7086 (t0) cc_final: 0.6857 (t0) REVERT: U 32 LYS cc_start: 0.9240 (tmmt) cc_final: 0.8992 (tmmt) REVERT: U 97 TYR cc_start: 0.8579 (m-10) cc_final: 0.7911 (m-80) REVERT: U 98 CYS cc_start: 0.8011 (t) cc_final: 0.7486 (t) REVERT: U 109 GLU cc_start: 0.8430 (tm-30) cc_final: 0.7391 (tm-30) REVERT: U 137 LYS cc_start: 0.9500 (tttp) cc_final: 0.9082 (tptp) REVERT: U 171 ASN cc_start: 0.8893 (t0) cc_final: 0.8577 (t0) REVERT: U 174 SER cc_start: 0.7579 (t) cc_final: 0.7336 (t) REVERT: V 29 ASN cc_start: 0.8114 (m-40) cc_final: 0.7888 (t0) REVERT: V 35 ASN cc_start: 0.8368 (m110) cc_final: 0.8060 (t0) REVERT: V 60 PHE cc_start: 0.8795 (m-80) cc_final: 0.8427 (m-80) REVERT: V 62 GLU cc_start: 0.7640 (pp20) cc_final: 0.7332 (pp20) REVERT: V 68 GLN cc_start: 0.8226 (pt0) cc_final: 0.7600 (pt0) REVERT: V 81 MET cc_start: 0.8480 (tpp) cc_final: 0.7739 (tpp) REVERT: V 90 ILE cc_start: 0.9490 (mm) cc_final: 0.9258 (mm) REVERT: V 103 ASP cc_start: 0.8120 (t70) cc_final: 0.7823 (p0) REVERT: V 113 ASN cc_start: 0.9133 (t0) cc_final: 0.8291 (t0) REVERT: V 124 THR cc_start: 0.8942 (m) cc_final: 0.8740 (p) REVERT: V 162 ILE cc_start: 0.8540 (mt) cc_final: 0.8318 (mt) REVERT: W 3 THR cc_start: 0.7001 (m) cc_final: 0.6512 (m) REVERT: W 42 ARG cc_start: 0.7344 (ttm170) cc_final: 0.6026 (tpt170) REVERT: W 69 MET cc_start: 0.3896 (mmm) cc_final: 0.3424 (tpt) REVERT: W 72 SER cc_start: 0.8892 (m) cc_final: 0.8550 (p) REVERT: W 94 MET cc_start: 0.8168 (ptt) cc_final: 0.7791 (ppp) REVERT: W 107 MET cc_start: 0.8508 (mmp) cc_final: 0.6935 (mmp) REVERT: W 111 LEU cc_start: 0.8406 (pt) cc_final: 0.7821 (pp) REVERT: W 165 TYR cc_start: 0.7961 (m-80) cc_final: 0.7587 (m-80) REVERT: X 2 LEU cc_start: 0.6280 (pp) cc_final: 0.6010 (pp) REVERT: X 3 ASP cc_start: 0.7815 (p0) cc_final: 0.7471 (p0) REVERT: X 44 ILE cc_start: 0.8163 (mm) cc_final: 0.7818 (tp) REVERT: X 52 VAL cc_start: 0.9291 (t) cc_final: 0.8995 (p) REVERT: X 88 MET cc_start: 0.8788 (ttm) cc_final: 0.8426 (ttt) REVERT: X 89 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8022 (tm-30) REVERT: Y 23 GLU cc_start: 0.7732 (mp0) cc_final: 0.7252 (mp0) REVERT: Y 33 THR cc_start: 0.9095 (p) cc_final: 0.8732 (t) REVERT: Y 64 ARG cc_start: 0.8788 (mtp-110) cc_final: 0.8472 (ttm110) REVERT: Z 98 LEU cc_start: 0.9034 (mm) cc_final: 0.8738 (mm) REVERT: Z 119 ASP cc_start: 0.7678 (m-30) cc_final: 0.7079 (m-30) REVERT: Z 120 LEU cc_start: 0.9417 (tp) cc_final: 0.8741 (tp) REVERT: Z 129 ASP cc_start: 0.8771 (t0) cc_final: 0.8416 (t0) REVERT: Z 141 ASN cc_start: 0.8261 (m-40) cc_final: 0.7803 (m-40) REVERT: Z 196 THR cc_start: 0.9023 (p) cc_final: 0.8548 (m) REVERT: a 51 ARG cc_start: 0.8980 (ttp80) cc_final: 0.8597 (ptm-80) REVERT: a 68 LEU cc_start: 0.8338 (mp) cc_final: 0.7732 (mp) REVERT: a 74 ASN cc_start: 0.9161 (t0) cc_final: 0.8633 (p0) REVERT: a 84 ARG cc_start: 0.9001 (ttm110) cc_final: 0.8735 (ttm110) REVERT: a 98 GLU cc_start: 0.8238 (pt0) cc_final: 0.7724 (pt0) REVERT: a 167 ASP cc_start: 0.7785 (m-30) cc_final: 0.7525 (m-30) outliers start: 2 outliers final: 0 residues processed: 1645 average time/residue: 0.2099 time to fit residues: 565.1752 Evaluate side-chains 1380 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1379 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 264 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 437 optimal weight: 7.9990 chunk 152 optimal weight: 0.8980 chunk 174 optimal weight: 6.9990 chunk 407 optimal weight: 7.9990 chunk 177 optimal weight: 0.3980 chunk 42 optimal weight: 0.9980 chunk 287 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 199 optimal weight: 6.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 GLN D 29 ASN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 ASN ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 HIS N 47 ASN ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN ** P 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 ASN ** V 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 23 GLN Z 64 ASN ** Z 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 156 ASN ** a 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.113836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.096659 restraints weight = 102323.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.100131 restraints weight = 52850.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.102381 restraints weight = 31178.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.103895 restraints weight = 20348.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.104959 restraints weight = 14532.198| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3363 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3363 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.6065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 36155 Z= 0.184 Angle : 0.800 43.031 49243 Z= 0.387 Chirality : 0.041 0.231 5448 Planarity : 0.005 0.065 6402 Dihedral : 10.829 89.671 6599 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.95 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.13), residues: 4448 helix: 1.14 (0.09), residues: 3363 sheet: -0.22 (0.79), residues: 40 loop : -0.62 (0.22), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 33 TYR 0.053 0.002 TYR R 97 PHE 0.028 0.002 PHE T 166 TRP 0.014 0.001 TRP C 128 HIS 0.005 0.002 HIS G 140 Details of bonding type rmsd covalent geometry : bond 0.00414 (36155) covalent geometry : angle 0.80048 (49243) hydrogen bonds : bond 0.04573 ( 2648) hydrogen bonds : angle 4.40227 ( 7847) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1583 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1583 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.7750 (ttpt) cc_final: 0.7175 (ttpt) REVERT: A 15 GLN cc_start: 0.8223 (mt0) cc_final: 0.7324 (mm-40) REVERT: A 38 MET cc_start: 0.8471 (mmt) cc_final: 0.7614 (tmm) REVERT: A 39 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7513 (mt-10) REVERT: A 63 PHE cc_start: 0.8788 (m-80) cc_final: 0.8413 (m-80) REVERT: A 90 TYR cc_start: 0.8536 (m-10) cc_final: 0.8075 (m-80) REVERT: A 109 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7218 (mt-10) REVERT: A 131 GLU cc_start: 0.7442 (tm-30) cc_final: 0.7089 (tm-30) REVERT: A 167 ASP cc_start: 0.7646 (t0) cc_final: 0.7205 (t0) REVERT: A 171 ASN cc_start: 0.8450 (m-40) cc_final: 0.8208 (m-40) REVERT: B 25 ASP cc_start: 0.7689 (p0) cc_final: 0.7439 (p0) REVERT: B 29 ASN cc_start: 0.8074 (m110) cc_final: 0.7843 (m110) REVERT: B 35 ASN cc_start: 0.8745 (m-40) cc_final: 0.7813 (t0) REVERT: B 36 LYS cc_start: 0.9470 (mtmm) cc_final: 0.8485 (mppt) REVERT: B 120 GLN cc_start: 0.8027 (mt0) cc_final: 0.7578 (tm-30) REVERT: C 17 ARG cc_start: 0.8749 (ptt90) cc_final: 0.8157 (ptt90) REVERT: C 69 MET cc_start: 0.7424 (ttm) cc_final: 0.7098 (ttm) REVERT: C 74 TYR cc_start: 0.7123 (m-80) cc_final: 0.6835 (m-80) REVERT: C 94 MET cc_start: 0.9411 (mmt) cc_final: 0.9021 (mmm) REVERT: C 115 LEU cc_start: 0.8017 (pp) cc_final: 0.7432 (pp) REVERT: C 117 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8584 (mm-30) REVERT: D 49 SER cc_start: 0.8788 (p) cc_final: 0.8483 (p) REVERT: D 86 ARG cc_start: 0.8886 (ttp-110) cc_final: 0.8593 (ttp-110) REVERT: D 97 TYR cc_start: 0.8361 (m-10) cc_final: 0.6827 (m-80) REVERT: D 113 ASN cc_start: 0.8195 (t0) cc_final: 0.7876 (t0) REVERT: D 128 SER cc_start: 0.9370 (p) cc_final: 0.8685 (m) REVERT: D 134 GLN cc_start: 0.8622 (mt0) cc_final: 0.8258 (mt0) REVERT: D 135 LYS cc_start: 0.8639 (mmmm) cc_final: 0.8433 (mtpp) REVERT: D 154 ASP cc_start: 0.6757 (t0) cc_final: 0.6355 (t0) REVERT: E 28 ASP cc_start: 0.8635 (t70) cc_final: 0.8361 (t0) REVERT: E 38 MET cc_start: 0.8175 (mmt) cc_final: 0.7847 (tmm) REVERT: E 47 ASN cc_start: 0.8536 (m110) cc_final: 0.7821 (m110) REVERT: E 69 MET cc_start: 0.8252 (mtp) cc_final: 0.7945 (ttm) REVERT: E 72 SER cc_start: 0.8924 (m) cc_final: 0.8515 (t) REVERT: E 74 TYR cc_start: 0.7842 (m-10) cc_final: 0.7046 (m-10) REVERT: E 83 LYS cc_start: 0.9211 (mmmm) cc_final: 0.8951 (mmmm) REVERT: E 109 GLU cc_start: 0.8541 (tt0) cc_final: 0.8185 (tt0) REVERT: E 111 LEU cc_start: 0.9114 (mt) cc_final: 0.8865 (mt) REVERT: E 120 SER cc_start: 0.9238 (t) cc_final: 0.9025 (t) REVERT: E 121 THR cc_start: 0.9306 (p) cc_final: 0.8790 (t) REVERT: E 137 LYS cc_start: 0.8649 (tttp) cc_final: 0.8330 (tttp) REVERT: E 140 HIS cc_start: 0.8414 (p90) cc_final: 0.8068 (p90) REVERT: E 167 ASP cc_start: 0.8487 (t0) cc_final: 0.7069 (t0) REVERT: E 171 ASN cc_start: 0.8834 (p0) cc_final: 0.8429 (p0) REVERT: F 11 GLN cc_start: 0.9110 (tt0) cc_final: 0.8408 (tt0) REVERT: F 39 ASP cc_start: 0.8531 (m-30) cc_final: 0.8302 (m-30) REVERT: F 60 PHE cc_start: 0.8122 (m-10) cc_final: 0.7365 (m-10) REVERT: F 81 MET cc_start: 0.9195 (tpp) cc_final: 0.8797 (tpt) REVERT: F 117 GLU cc_start: 0.8611 (pp20) cc_final: 0.8332 (pp20) REVERT: F 146 ASP cc_start: 0.7947 (t70) cc_final: 0.7570 (t0) REVERT: F 161 GLU cc_start: 0.7955 (tp30) cc_final: 0.7744 (tp30) REVERT: G 1 MET cc_start: 0.7355 (tpp) cc_final: 0.6957 (tpp) REVERT: G 25 GLN cc_start: 0.8624 (mt0) cc_final: 0.8407 (mt0) REVERT: G 57 GLN cc_start: 0.9056 (mp10) cc_final: 0.8703 (mp10) REVERT: G 70 GLN cc_start: 0.7976 (pp30) cc_final: 0.7774 (pp30) REVERT: G 122 PHE cc_start: 0.8713 (m-80) cc_final: 0.8147 (m-10) REVERT: G 123 ASP cc_start: 0.8292 (t0) cc_final: 0.7880 (t0) REVERT: G 124 LEU cc_start: 0.9231 (mt) cc_final: 0.8674 (mt) REVERT: G 135 TYR cc_start: 0.8641 (t80) cc_final: 0.8402 (t80) REVERT: H 3 ASP cc_start: 0.8413 (p0) cc_final: 0.8191 (p0) REVERT: H 81 MET cc_start: 0.8689 (mmp) cc_final: 0.8343 (mmp) REVERT: H 91 ILE cc_start: 0.9496 (mm) cc_final: 0.9107 (tp) REVERT: H 112 LEU cc_start: 0.9326 (mt) cc_final: 0.9027 (mt) REVERT: H 115 LEU cc_start: 0.8528 (tt) cc_final: 0.8226 (tt) REVERT: H 159 MET cc_start: 0.8312 (mmm) cc_final: 0.7614 (mmt) REVERT: I 15 GLN cc_start: 0.8136 (mt0) cc_final: 0.7850 (mp10) REVERT: I 60 TYR cc_start: 0.7274 (m-80) cc_final: 0.7064 (m-80) REVERT: I 62 LYS cc_start: 0.9271 (tptm) cc_final: 0.8868 (tptt) REVERT: I 73 GLN cc_start: 0.9364 (pm20) cc_final: 0.8924 (pm20) REVERT: I 115 LEU cc_start: 0.9056 (tp) cc_final: 0.8339 (tt) REVERT: I 119 ASN cc_start: 0.8517 (m110) cc_final: 0.7604 (m110) REVERT: I 135 TYR cc_start: 0.8617 (t80) cc_final: 0.8398 (t80) REVERT: I 144 LEU cc_start: 0.9086 (mt) cc_final: 0.8543 (mt) REVERT: I 173 LEU cc_start: 0.9345 (mt) cc_final: 0.9084 (tt) REVERT: J 17 GLU cc_start: 0.8171 (mp0) cc_final: 0.7597 (mp0) REVERT: J 24 PHE cc_start: 0.6708 (m-80) cc_final: 0.6457 (m-80) REVERT: J 28 SER cc_start: 0.9384 (t) cc_final: 0.9153 (p) REVERT: J 35 ASN cc_start: 0.8773 (m110) cc_final: 0.7915 (t0) REVERT: J 91 ILE cc_start: 0.9422 (tp) cc_final: 0.9156 (tt) REVERT: J 97 TYR cc_start: 0.8732 (m-10) cc_final: 0.8412 (m-10) REVERT: J 112 LEU cc_start: 0.9549 (mp) cc_final: 0.8885 (mm) REVERT: K 30 ARG cc_start: 0.8516 (tpt-90) cc_final: 0.8060 (tpt-90) REVERT: K 87 ASP cc_start: 0.8641 (t70) cc_final: 0.8382 (t0) REVERT: K 130 ILE cc_start: 0.9360 (pt) cc_final: 0.9031 (pt) REVERT: K 139 ASN cc_start: 0.8808 (t0) cc_final: 0.8178 (t0) REVERT: K 166 ILE cc_start: 0.9379 (mm) cc_final: 0.9178 (mm) REVERT: L 2 LEU cc_start: 0.9481 (mt) cc_final: 0.8691 (mt) REVERT: L 3 ASP cc_start: 0.8737 (p0) cc_final: 0.8359 (p0) REVERT: L 62 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7911 (tm-30) REVERT: L 81 MET cc_start: 0.8819 (tpp) cc_final: 0.8068 (tpp) REVERT: L 88 MET cc_start: 0.7821 (mtm) cc_final: 0.7565 (mtp) REVERT: L 116 ARG cc_start: 0.8097 (tpp80) cc_final: 0.7813 (tpp80) REVERT: L 120 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8234 (tm-30) REVERT: L 137 LYS cc_start: 0.9483 (tttt) cc_final: 0.8799 (ttmt) REVERT: L 146 ASP cc_start: 0.9249 (t0) cc_final: 0.8975 (t0) REVERT: L 161 GLU cc_start: 0.8755 (tt0) cc_final: 0.7739 (tp30) REVERT: M 57 GLN cc_start: 0.9433 (mm-40) cc_final: 0.8947 (mm-40) REVERT: M 84 CYS cc_start: 0.8782 (t) cc_final: 0.8229 (m) REVERT: M 94 MET cc_start: 0.8989 (ttm) cc_final: 0.8307 (mtp) REVERT: M 115 LEU cc_start: 0.8928 (tt) cc_final: 0.8284 (tt) REVERT: M 118 ILE cc_start: 0.9651 (tp) cc_final: 0.9210 (tp) REVERT: M 129 TYR cc_start: 0.8073 (m-80) cc_final: 0.7770 (m-10) REVERT: M 161 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8095 (mt-10) REVERT: M 171 ASN cc_start: 0.7530 (p0) cc_final: 0.7295 (p0) REVERT: N 20 THR cc_start: 0.8015 (t) cc_final: 0.7739 (p) REVERT: N 50 THR cc_start: 0.8753 (t) cc_final: 0.8522 (t) REVERT: N 65 GLN cc_start: 0.7599 (pm20) cc_final: 0.7062 (pm20) REVERT: N 67 ILE cc_start: 0.9574 (pt) cc_final: 0.9173 (tp) REVERT: N 87 ASP cc_start: 0.8535 (m-30) cc_final: 0.8117 (m-30) REVERT: N 88 MET cc_start: 0.8687 (ttm) cc_final: 0.8017 (tpp) REVERT: N 89 GLU cc_start: 0.7846 (pp20) cc_final: 0.7360 (pp20) REVERT: N 97 TYR cc_start: 0.8501 (m-10) cc_final: 0.7906 (m-80) REVERT: N 103 ASP cc_start: 0.7237 (t0) cc_final: 0.6776 (t0) REVERT: N 116 ARG cc_start: 0.8087 (ttm170) cc_final: 0.7820 (ttm170) REVERT: O 4 PRO cc_start: 0.9177 (Cg_exo) cc_final: 0.8851 (Cg_endo) REVERT: O 19 LEU cc_start: 0.8228 (mm) cc_final: 0.7528 (tp) REVERT: O 51 LEU cc_start: 0.7924 (mt) cc_final: 0.7708 (mt) REVERT: O 61 GLN cc_start: 0.7605 (mt0) cc_final: 0.6882 (tm-30) REVERT: O 68 THR cc_start: 0.7187 (t) cc_final: 0.6918 (m) REVERT: O 96 THR cc_start: 0.9410 (p) cc_final: 0.9196 (t) REVERT: O 98 CYS cc_start: 0.8424 (m) cc_final: 0.7562 (p) REVERT: O 104 THR cc_start: 0.8986 (p) cc_final: 0.8129 (p) REVERT: O 107 MET cc_start: 0.8522 (tpp) cc_final: 0.8206 (mmp) REVERT: O 130 ILE cc_start: 0.9286 (mm) cc_final: 0.9049 (mt) REVERT: O 163 ASN cc_start: 0.8610 (m-40) cc_final: 0.8067 (m-40) REVERT: P 2 LEU cc_start: 0.8970 (mp) cc_final: 0.8175 (mp) REVERT: P 93 ARG cc_start: 0.8423 (ttp80) cc_final: 0.8172 (ttp-170) REVERT: P 97 TYR cc_start: 0.8823 (m-10) cc_final: 0.8346 (m-10) REVERT: P 113 ASN cc_start: 0.8038 (t0) cc_final: 0.7816 (t0) REVERT: P 122 LEU cc_start: 0.8520 (mm) cc_final: 0.8052 (mm) REVERT: Q 25 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8467 (mm110) REVERT: Q 39 GLU cc_start: 0.7585 (mt-10) cc_final: 0.6797 (pt0) REVERT: Q 62 LYS cc_start: 0.7779 (ttmm) cc_final: 0.7443 (ttmm) REVERT: Q 69 MET cc_start: 0.7150 (ptm) cc_final: 0.6527 (ptm) REVERT: Q 108 ASP cc_start: 0.8746 (m-30) cc_final: 0.8402 (m-30) REVERT: Q 121 THR cc_start: 0.8397 (t) cc_final: 0.7994 (p) REVERT: R 85 LEU cc_start: 0.9580 (mt) cc_final: 0.9117 (tp) REVERT: R 111 CYS cc_start: 0.8348 (t) cc_final: 0.7847 (t) REVERT: R 116 ARG cc_start: 0.8563 (ttm110) cc_final: 0.8343 (ttp-110) REVERT: R 118 THR cc_start: 0.8957 (p) cc_final: 0.7544 (p) REVERT: R 128 SER cc_start: 0.8996 (m) cc_final: 0.8673 (m) REVERT: R 160 SER cc_start: 0.9008 (t) cc_final: 0.8733 (p) REVERT: R 166 PHE cc_start: 0.8132 (m-80) cc_final: 0.7579 (m-80) REVERT: S 37 SER cc_start: 0.8375 (p) cc_final: 0.7770 (t) REVERT: S 49 GLN cc_start: 0.8617 (tp-100) cc_final: 0.7593 (pm20) REVERT: S 74 TYR cc_start: 0.8761 (m-80) cc_final: 0.7879 (m-10) REVERT: S 79 GLU cc_start: 0.7953 (mp0) cc_final: 0.7560 (tm-30) REVERT: S 93 ARG cc_start: 0.7615 (ttp80) cc_final: 0.7036 (ttp80) REVERT: S 94 MET cc_start: 0.9517 (mmp) cc_final: 0.9151 (mmm) REVERT: S 97 TYR cc_start: 0.8928 (m-10) cc_final: 0.8273 (m-80) REVERT: S 107 MET cc_start: 0.7635 (ptp) cc_final: 0.7361 (ptp) REVERT: S 112 ILE cc_start: 0.9461 (mm) cc_final: 0.8997 (tp) REVERT: S 163 ASN cc_start: 0.9294 (m110) cc_final: 0.9015 (m-40) REVERT: T 1 MET cc_start: 0.7569 (mmp) cc_final: 0.6744 (ptt) REVERT: T 3 ASP cc_start: 0.7238 (p0) cc_final: 0.7032 (p0) REVERT: T 13 ASP cc_start: 0.8671 (t70) cc_final: 0.8269 (t0) REVERT: T 15 ARG cc_start: 0.7825 (mtp85) cc_final: 0.7178 (mmp80) REVERT: T 19 LEU cc_start: 0.8050 (mt) cc_final: 0.7387 (mm) REVERT: T 23 GLN cc_start: 0.8170 (mt0) cc_final: 0.7938 (mt0) REVERT: T 25 ASP cc_start: 0.8727 (m-30) cc_final: 0.8368 (m-30) REVERT: T 141 ILE cc_start: 0.8578 (mt) cc_final: 0.8366 (mm) REVERT: U 28 ASP cc_start: 0.7142 (t0) cc_final: 0.6869 (t0) REVERT: U 32 LYS cc_start: 0.9263 (tmmt) cc_final: 0.9053 (tmmt) REVERT: U 98 CYS cc_start: 0.8040 (t) cc_final: 0.7492 (t) REVERT: U 109 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7523 (tm-30) REVERT: U 134 LYS cc_start: 0.9096 (tppp) cc_final: 0.8839 (tppt) REVERT: U 171 ASN cc_start: 0.8839 (t0) cc_final: 0.8546 (t0) REVERT: U 174 SER cc_start: 0.7851 (t) cc_final: 0.7447 (t) REVERT: V 3 ASP cc_start: 0.8710 (p0) cc_final: 0.8467 (p0) REVERT: V 29 ASN cc_start: 0.8305 (m-40) cc_final: 0.8100 (t0) REVERT: V 60 PHE cc_start: 0.8811 (m-80) cc_final: 0.8546 (m-80) REVERT: V 81 MET cc_start: 0.8488 (tpp) cc_final: 0.7828 (tpp) REVERT: V 90 ILE cc_start: 0.9521 (mm) cc_final: 0.9248 (mm) REVERT: V 103 ASP cc_start: 0.8132 (t70) cc_final: 0.7902 (p0) REVERT: V 113 ASN cc_start: 0.9245 (t0) cc_final: 0.8456 (t0) REVERT: V 124 THR cc_start: 0.8893 (m) cc_final: 0.8594 (p) REVERT: W 42 ARG cc_start: 0.7583 (ttm170) cc_final: 0.6206 (tpt170) REVERT: W 69 MET cc_start: 0.4034 (mmm) cc_final: 0.3584 (tpt) REVERT: W 72 SER cc_start: 0.8765 (m) cc_final: 0.8454 (p) REVERT: W 94 MET cc_start: 0.8348 (ptt) cc_final: 0.7828 (ppp) REVERT: W 111 LEU cc_start: 0.8422 (pt) cc_final: 0.7864 (pp) REVERT: X 3 ASP cc_start: 0.7834 (p0) cc_final: 0.7423 (p0) REVERT: X 44 ILE cc_start: 0.8143 (mm) cc_final: 0.7845 (tp) REVERT: X 52 VAL cc_start: 0.9388 (t) cc_final: 0.9040 (p) REVERT: X 88 MET cc_start: 0.8765 (ttm) cc_final: 0.8245 (ttt) REVERT: X 89 GLU cc_start: 0.8395 (tm-30) cc_final: 0.8074 (tm-30) REVERT: X 117 GLU cc_start: 0.7853 (pm20) cc_final: 0.7590 (pm20) REVERT: X 133 ILE cc_start: 0.8865 (mm) cc_final: 0.7938 (tp) REVERT: Y 23 GLU cc_start: 0.7717 (mp0) cc_final: 0.7275 (mp0) REVERT: Z 10 LEU cc_start: 0.9343 (mm) cc_final: 0.9140 (mm) REVERT: Z 59 GLU cc_start: 0.8646 (pm20) cc_final: 0.8002 (pm20) REVERT: Z 101 LYS cc_start: 0.9138 (tmtt) cc_final: 0.8656 (ttpp) REVERT: Z 120 LEU cc_start: 0.9615 (tp) cc_final: 0.8899 (tp) REVERT: Z 196 THR cc_start: 0.9046 (p) cc_final: 0.8642 (m) REVERT: a 31 TYR cc_start: 0.7834 (m-80) cc_final: 0.7601 (m-80) REVERT: a 44 GLU cc_start: 0.7548 (tt0) cc_final: 0.7340 (tt0) REVERT: a 51 ARG cc_start: 0.8976 (ttp80) cc_final: 0.8592 (ptm-80) REVERT: a 65 GLN cc_start: 0.8136 (tt0) cc_final: 0.7801 (tt0) REVERT: a 84 ARG cc_start: 0.9034 (ttm110) cc_final: 0.8591 (ttm-80) REVERT: a 88 LYS cc_start: 0.9008 (pttm) cc_final: 0.8155 (tppt) REVERT: a 98 GLU cc_start: 0.8283 (pt0) cc_final: 0.7300 (pt0) REVERT: a 107 GLU cc_start: 0.8953 (pm20) cc_final: 0.8675 (pm20) REVERT: a 127 TRP cc_start: 0.8333 (m100) cc_final: 0.8131 (m100) REVERT: a 137 GLN cc_start: 0.7982 (tp40) cc_final: 0.7186 (tp40) REVERT: a 151 GLN cc_start: 0.8866 (mm-40) cc_final: 0.7999 (mt0) REVERT: a 167 ASP cc_start: 0.7837 (m-30) cc_final: 0.7596 (m-30) REVERT: a 177 TYR cc_start: 0.8136 (p90) cc_final: 0.7233 (p90) outliers start: 0 outliers final: 0 residues processed: 1583 average time/residue: 0.2078 time to fit residues: 538.0159 Evaluate side-chains 1361 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1361 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 297 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 412 optimal weight: 3.9990 chunk 362 optimal weight: 1.9990 chunk 287 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 348 optimal weight: 1.9990 chunk 365 optimal weight: 0.9990 chunk 330 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 427 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN D 23 GLN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 78 ASN ** K 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 HIS ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 73 GLN ** R 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 139 ASN ** S 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 ASN ** U 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 63 GLN ** W 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 23 GLN X 47 ASN Z 64 ASN Z 90 ASN ** Z 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 161 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.114979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.099647 restraints weight = 79623.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.102563 restraints weight = 43236.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.104465 restraints weight = 26415.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.105800 restraints weight = 17782.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.106631 restraints weight = 12998.113| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.6241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 36155 Z= 0.158 Angle : 0.800 42.953 49243 Z= 0.387 Chirality : 0.041 0.228 5448 Planarity : 0.005 0.076 6402 Dihedral : 10.878 89.120 6599 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.92 % Favored : 97.01 % Rotamer: Outliers : 0.06 % Allowed : 0.91 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.13), residues: 4448 helix: 1.10 (0.09), residues: 3389 sheet: 1.16 (0.82), residues: 28 loop : -0.58 (0.22), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 15 TYR 0.049 0.002 TYR M 135 PHE 0.045 0.002 PHE Z 165 TRP 0.031 0.002 TRP a 29 HIS 0.004 0.001 HIS G 140 Details of bonding type rmsd covalent geometry : bond 0.00355 (36155) covalent geometry : angle 0.79955 (49243) hydrogen bonds : bond 0.04469 ( 2648) hydrogen bonds : angle 4.36753 ( 7847) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1605 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1603 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.8206 (mt0) cc_final: 0.7896 (mm110) REVERT: A 38 MET cc_start: 0.8510 (mmt) cc_final: 0.7764 (tmm) REVERT: A 63 PHE cc_start: 0.8590 (m-80) cc_final: 0.8106 (m-80) REVERT: A 90 TYR cc_start: 0.8471 (m-10) cc_final: 0.8098 (m-80) REVERT: A 94 MET cc_start: 0.8034 (tpp) cc_final: 0.6880 (tpt) REVERT: A 109 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7931 (mt-10) REVERT: A 131 GLU cc_start: 0.7395 (tm-30) cc_final: 0.7012 (tm-30) REVERT: A 161 GLU cc_start: 0.8683 (pp20) cc_final: 0.8424 (pp20) REVERT: A 163 ASN cc_start: 0.8451 (t0) cc_final: 0.8155 (t0) REVERT: A 165 TYR cc_start: 0.8542 (m-80) cc_final: 0.7778 (m-10) REVERT: A 167 ASP cc_start: 0.7492 (t0) cc_final: 0.7160 (t0) REVERT: A 171 ASN cc_start: 0.8343 (m-40) cc_final: 0.8083 (m-40) REVERT: B 25 ASP cc_start: 0.7421 (p0) cc_final: 0.7193 (p0) REVERT: B 35 ASN cc_start: 0.8716 (m-40) cc_final: 0.7812 (t0) REVERT: B 36 LYS cc_start: 0.9449 (mtmm) cc_final: 0.8440 (mppt) REVERT: B 81 MET cc_start: 0.9221 (tpp) cc_final: 0.8710 (tpt) REVERT: B 120 GLN cc_start: 0.7996 (mt0) cc_final: 0.7452 (tm-30) REVERT: C 17 ARG cc_start: 0.8732 (ptt90) cc_final: 0.8131 (ptt90) REVERT: C 69 MET cc_start: 0.7409 (ttm) cc_final: 0.7101 (ttm) REVERT: C 74 TYR cc_start: 0.7163 (m-80) cc_final: 0.6896 (m-80) REVERT: C 79 GLU cc_start: 0.6969 (pm20) cc_final: 0.6523 (pm20) REVERT: C 94 MET cc_start: 0.9379 (mmt) cc_final: 0.9065 (mmm) REVERT: C 115 LEU cc_start: 0.7934 (pp) cc_final: 0.7451 (pp) REVERT: C 119 ASN cc_start: 0.7862 (m-40) cc_final: 0.7643 (m110) REVERT: C 131 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8173 (tp30) REVERT: D 29 ASN cc_start: 0.9132 (t0) cc_final: 0.7744 (t0) REVERT: D 97 TYR cc_start: 0.8438 (m-10) cc_final: 0.6829 (m-80) REVERT: D 113 ASN cc_start: 0.8162 (t0) cc_final: 0.7736 (t0) REVERT: D 115 LEU cc_start: 0.8617 (tt) cc_final: 0.8398 (tt) REVERT: D 124 THR cc_start: 0.8870 (m) cc_final: 0.8600 (m) REVERT: D 128 SER cc_start: 0.9348 (p) cc_final: 0.8809 (m) REVERT: D 134 GLN cc_start: 0.8557 (mt0) cc_final: 0.8130 (mt0) REVERT: D 154 ASP cc_start: 0.6738 (t0) cc_final: 0.6357 (t0) REVERT: E 7 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7894 (mm-30) REVERT: E 28 ASP cc_start: 0.8569 (t70) cc_final: 0.8190 (t0) REVERT: E 38 MET cc_start: 0.8149 (mmt) cc_final: 0.7826 (tmm) REVERT: E 47 ASN cc_start: 0.8532 (m110) cc_final: 0.7772 (m110) REVERT: E 69 MET cc_start: 0.8221 (mtp) cc_final: 0.7993 (ttm) REVERT: E 72 SER cc_start: 0.8922 (m) cc_final: 0.8511 (t) REVERT: E 74 TYR cc_start: 0.7811 (m-10) cc_final: 0.7320 (m-10) REVERT: E 83 LYS cc_start: 0.9152 (mmmm) cc_final: 0.8935 (mmmm) REVERT: E 111 LEU cc_start: 0.8904 (mt) cc_final: 0.8238 (mt) REVERT: E 121 THR cc_start: 0.9301 (p) cc_final: 0.8807 (t) REVERT: E 167 ASP cc_start: 0.8500 (t0) cc_final: 0.7024 (t0) REVERT: E 171 ASN cc_start: 0.8822 (p0) cc_final: 0.8401 (p0) REVERT: F 1 MET cc_start: 0.6708 (pmm) cc_final: 0.6459 (pmm) REVERT: F 11 GLN cc_start: 0.9117 (tt0) cc_final: 0.8416 (tt0) REVERT: F 30 LEU cc_start: 0.8447 (mm) cc_final: 0.7914 (tp) REVERT: F 60 PHE cc_start: 0.8081 (m-10) cc_final: 0.7581 (m-10) REVERT: F 81 MET cc_start: 0.9211 (tpp) cc_final: 0.8829 (tpt) REVERT: F 120 GLN cc_start: 0.8790 (tt0) cc_final: 0.8578 (tt0) REVERT: F 136 MET cc_start: 0.7707 (ttt) cc_final: 0.7453 (ttp) REVERT: F 146 ASP cc_start: 0.7597 (t70) cc_final: 0.7337 (t0) REVERT: G 25 GLN cc_start: 0.8718 (mt0) cc_final: 0.8211 (mt0) REVERT: G 33 ARG cc_start: 0.7887 (mtp-110) cc_final: 0.7389 (mtp85) REVERT: G 57 GLN cc_start: 0.8865 (mp10) cc_final: 0.8449 (mp10) REVERT: G 98 CYS cc_start: 0.8424 (p) cc_final: 0.7850 (p) REVERT: G 122 PHE cc_start: 0.8657 (m-80) cc_final: 0.8051 (m-10) REVERT: G 123 ASP cc_start: 0.8288 (t0) cc_final: 0.7726 (t0) REVERT: G 124 LEU cc_start: 0.9202 (mt) cc_final: 0.8631 (mp) REVERT: G 137 LYS cc_start: 0.9134 (ttmt) cc_final: 0.8881 (ttmt) REVERT: G 163 ASN cc_start: 0.9171 (m-40) cc_final: 0.8488 (m-40) REVERT: H 3 ASP cc_start: 0.8442 (p0) cc_final: 0.8211 (p0) REVERT: H 44 ILE cc_start: 0.9503 (tt) cc_final: 0.9302 (tt) REVERT: H 88 MET cc_start: 0.8122 (ttm) cc_final: 0.7865 (ttm) REVERT: H 91 ILE cc_start: 0.9450 (mm) cc_final: 0.9140 (tp) REVERT: H 112 LEU cc_start: 0.9351 (mt) cc_final: 0.9084 (mt) REVERT: H 159 MET cc_start: 0.8223 (mmm) cc_final: 0.7576 (mmt) REVERT: I 25 GLN cc_start: 0.8975 (mm-40) cc_final: 0.8222 (pt0) REVERT: I 51 LEU cc_start: 0.8678 (mt) cc_final: 0.8404 (mt) REVERT: I 60 TYR cc_start: 0.7358 (m-80) cc_final: 0.7097 (m-80) REVERT: I 62 LYS cc_start: 0.9312 (tptm) cc_final: 0.8900 (tptt) REVERT: I 73 GLN cc_start: 0.9300 (pm20) cc_final: 0.8930 (pm20) REVERT: I 83 LYS cc_start: 0.9003 (mmtm) cc_final: 0.8688 (mmmm) REVERT: I 119 ASN cc_start: 0.8576 (m110) cc_final: 0.7903 (m110) REVERT: I 173 LEU cc_start: 0.9356 (mt) cc_final: 0.9105 (tt) REVERT: J 17 GLU cc_start: 0.8115 (mp0) cc_final: 0.7547 (mp0) REVERT: J 24 PHE cc_start: 0.6517 (m-80) cc_final: 0.6211 (m-80) REVERT: J 28 SER cc_start: 0.9420 (t) cc_final: 0.9175 (p) REVERT: J 35 ASN cc_start: 0.8775 (m110) cc_final: 0.7977 (t0) REVERT: J 76 TYR cc_start: 0.8713 (t80) cc_final: 0.8218 (t80) REVERT: J 91 ILE cc_start: 0.9405 (tp) cc_final: 0.9085 (tt) REVERT: J 97 TYR cc_start: 0.8782 (m-10) cc_final: 0.8521 (m-10) REVERT: J 112 LEU cc_start: 0.9532 (mp) cc_final: 0.8895 (mm) REVERT: K 30 ARG cc_start: 0.8598 (tpt-90) cc_final: 0.8349 (tpt-90) REVERT: K 61 GLN cc_start: 0.8765 (mt0) cc_final: 0.8556 (mt0) REVERT: K 133 LEU cc_start: 0.8785 (mt) cc_final: 0.8534 (tp) REVERT: K 139 ASN cc_start: 0.9019 (t0) cc_final: 0.8224 (t0) REVERT: K 166 ILE cc_start: 0.9381 (mm) cc_final: 0.9164 (mm) REVERT: L 2 LEU cc_start: 0.9462 (mt) cc_final: 0.8650 (mt) REVERT: L 3 ASP cc_start: 0.8749 (p0) cc_final: 0.8324 (p0) REVERT: L 63 GLN cc_start: 0.8478 (mt0) cc_final: 0.8124 (mt0) REVERT: L 81 MET cc_start: 0.8898 (tpp) cc_final: 0.8221 (tpp) REVERT: L 88 MET cc_start: 0.7481 (mtm) cc_final: 0.7232 (ptm) REVERT: L 103 ASP cc_start: 0.7161 (m-30) cc_final: 0.6936 (m-30) REVERT: L 120 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8080 (tm-30) REVERT: L 137 LYS cc_start: 0.9422 (tttt) cc_final: 0.8714 (ttmt) REVERT: L 146 ASP cc_start: 0.9442 (t0) cc_final: 0.9230 (t0) REVERT: L 161 GLU cc_start: 0.8810 (tt0) cc_final: 0.8485 (tt0) REVERT: M 57 GLN cc_start: 0.9446 (mm-40) cc_final: 0.8997 (mm-40) REVERT: M 79 GLU cc_start: 0.7996 (tp30) cc_final: 0.7402 (tm-30) REVERT: M 84 CYS cc_start: 0.8773 (t) cc_final: 0.8255 (m) REVERT: M 94 MET cc_start: 0.8690 (ttm) cc_final: 0.7633 (ppp) REVERT: M 115 LEU cc_start: 0.8903 (tt) cc_final: 0.8285 (tp) REVERT: M 118 ILE cc_start: 0.9603 (tp) cc_final: 0.9204 (tp) REVERT: M 128 TRP cc_start: 0.8559 (m-10) cc_final: 0.7675 (m-10) REVERT: M 129 TYR cc_start: 0.7981 (m-80) cc_final: 0.7677 (m-10) REVERT: M 135 TYR cc_start: 0.8963 (t80) cc_final: 0.8709 (t80) REVERT: M 171 ASN cc_start: 0.7443 (p0) cc_final: 0.7235 (p0) REVERT: N 20 THR cc_start: 0.7758 (t) cc_final: 0.7407 (p) REVERT: N 65 GLN cc_start: 0.7531 (pm20) cc_final: 0.6883 (pm20) REVERT: N 67 ILE cc_start: 0.9571 (pt) cc_final: 0.9157 (tp) REVERT: N 80 ARG cc_start: 0.8807 (mtm-85) cc_final: 0.7926 (mtm-85) REVERT: N 87 ASP cc_start: 0.8964 (m-30) cc_final: 0.8669 (m-30) REVERT: N 88 MET cc_start: 0.8570 (ttm) cc_final: 0.8020 (tpp) REVERT: N 89 GLU cc_start: 0.7841 (pp20) cc_final: 0.7308 (pp20) REVERT: N 97 TYR cc_start: 0.8435 (m-10) cc_final: 0.7925 (m-80) REVERT: N 103 ASP cc_start: 0.7471 (t0) cc_final: 0.7104 (t0) REVERT: O 19 LEU cc_start: 0.8411 (mm) cc_final: 0.7696 (tp) REVERT: O 51 LEU cc_start: 0.8084 (mt) cc_final: 0.7870 (mt) REVERT: O 61 GLN cc_start: 0.7564 (mt0) cc_final: 0.6877 (tm-30) REVERT: O 68 THR cc_start: 0.7156 (t) cc_final: 0.6946 (m) REVERT: O 96 THR cc_start: 0.9445 (p) cc_final: 0.9196 (t) REVERT: O 98 CYS cc_start: 0.8422 (m) cc_final: 0.7409 (p) REVERT: O 104 THR cc_start: 0.8862 (p) cc_final: 0.7991 (p) REVERT: O 107 MET cc_start: 0.8472 (tpp) cc_final: 0.8131 (mmp) REVERT: O 130 ILE cc_start: 0.9294 (mm) cc_final: 0.9064 (mt) REVERT: O 131 GLU cc_start: 0.8273 (tt0) cc_final: 0.7954 (tt0) REVERT: O 163 ASN cc_start: 0.8497 (m-40) cc_final: 0.8113 (m-40) REVERT: P 7 LYS cc_start: 0.9081 (tppt) cc_final: 0.8870 (mmmm) REVERT: P 67 ILE cc_start: 0.8588 (mt) cc_final: 0.8260 (tp) REVERT: P 97 TYR cc_start: 0.8800 (m-10) cc_final: 0.8365 (m-10) REVERT: P 104 SER cc_start: 0.9505 (p) cc_final: 0.9282 (p) REVERT: P 122 LEU cc_start: 0.8603 (mm) cc_final: 0.8241 (mm) REVERT: Q 1 MET cc_start: 0.7692 (tpt) cc_final: 0.7442 (tpt) REVERT: Q 13 ASP cc_start: 0.8952 (t0) cc_final: 0.8533 (t0) REVERT: Q 25 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8499 (mm110) REVERT: Q 39 GLU cc_start: 0.7495 (mt-10) cc_final: 0.6649 (pt0) REVERT: Q 57 GLN cc_start: 0.8470 (mm110) cc_final: 0.7604 (mm-40) REVERT: Q 62 LYS cc_start: 0.7515 (ttmm) cc_final: 0.7223 (ttmm) REVERT: Q 69 MET cc_start: 0.7514 (ptm) cc_final: 0.6911 (ptm) REVERT: Q 108 ASP cc_start: 0.9059 (m-30) cc_final: 0.8551 (m-30) REVERT: R 85 LEU cc_start: 0.9556 (mt) cc_final: 0.9149 (tp) REVERT: R 111 CYS cc_start: 0.8147 (t) cc_final: 0.7806 (t) REVERT: R 118 THR cc_start: 0.8965 (p) cc_final: 0.8713 (p) REVERT: R 128 SER cc_start: 0.9001 (m) cc_final: 0.8727 (m) REVERT: S 37 SER cc_start: 0.8365 (p) cc_final: 0.7813 (t) REVERT: S 49 GLN cc_start: 0.8474 (tp-100) cc_final: 0.7551 (pm20) REVERT: S 74 TYR cc_start: 0.8716 (m-80) cc_final: 0.7914 (m-10) REVERT: S 79 GLU cc_start: 0.7954 (mp0) cc_final: 0.7456 (tp30) REVERT: S 93 ARG cc_start: 0.7517 (ttp80) cc_final: 0.7142 (ttp80) REVERT: S 94 MET cc_start: 0.9547 (mmp) cc_final: 0.9197 (mmm) REVERT: S 97 TYR cc_start: 0.8922 (m-10) cc_final: 0.8279 (m-80) REVERT: S 107 MET cc_start: 0.7567 (ptp) cc_final: 0.7326 (ptp) REVERT: S 112 ILE cc_start: 0.9512 (mm) cc_final: 0.8895 (tp) REVERT: S 139 ASN cc_start: 0.8739 (OUTLIER) cc_final: 0.8205 (t0) REVERT: S 163 ASN cc_start: 0.9240 (m110) cc_final: 0.8972 (m-40) REVERT: T 3 ASP cc_start: 0.7051 (p0) cc_final: 0.6799 (p0) REVERT: T 13 ASP cc_start: 0.8645 (t70) cc_final: 0.8266 (t0) REVERT: T 15 ARG cc_start: 0.7706 (mtp85) cc_final: 0.7178 (mmp80) REVERT: T 19 LEU cc_start: 0.8325 (mt) cc_final: 0.7681 (mm) REVERT: T 23 GLN cc_start: 0.8391 (mt0) cc_final: 0.8053 (mp10) REVERT: T 25 ASP cc_start: 0.8522 (m-30) cc_final: 0.8172 (m-30) REVERT: T 93 ARG cc_start: 0.8019 (ttp-170) cc_final: 0.7065 (ttm-80) REVERT: T 141 ILE cc_start: 0.8647 (mt) cc_final: 0.8393 (mm) REVERT: U 28 ASP cc_start: 0.7106 (t0) cc_final: 0.6791 (t0) REVERT: U 32 LYS cc_start: 0.9222 (tmmt) cc_final: 0.8963 (tmmt) REVERT: U 97 TYR cc_start: 0.8583 (m-10) cc_final: 0.7958 (m-80) REVERT: U 98 CYS cc_start: 0.7875 (t) cc_final: 0.7346 (t) REVERT: U 109 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8244 (tm-30) REVERT: U 134 LYS cc_start: 0.9081 (tppp) cc_final: 0.8687 (tppt) REVERT: U 161 GLU cc_start: 0.8847 (tp30) cc_final: 0.8623 (tp30) REVERT: U 171 ASN cc_start: 0.8725 (t0) cc_final: 0.8382 (t0) REVERT: U 174 SER cc_start: 0.7730 (t) cc_final: 0.7344 (t) REVERT: V 29 ASN cc_start: 0.8246 (m-40) cc_final: 0.7762 (t0) REVERT: V 60 PHE cc_start: 0.8925 (m-80) cc_final: 0.8507 (m-80) REVERT: V 78 ASN cc_start: 0.6533 (t0) cc_final: 0.5815 (t0) REVERT: V 81 MET cc_start: 0.8439 (tpp) cc_final: 0.7796 (tpp) REVERT: V 113 ASN cc_start: 0.9183 (t0) cc_final: 0.8435 (t0) REVERT: V 124 THR cc_start: 0.8984 (m) cc_final: 0.8720 (p) REVERT: W 1 MET cc_start: 0.6033 (pmm) cc_final: 0.5296 (pmm) REVERT: W 24 LEU cc_start: 0.9063 (mt) cc_final: 0.8827 (mt) REVERT: W 49 GLN cc_start: 0.8996 (mp10) cc_final: 0.8701 (mp10) REVERT: W 69 MET cc_start: 0.4042 (mmm) cc_final: 0.3587 (tpt) REVERT: W 72 SER cc_start: 0.8711 (m) cc_final: 0.8423 (p) REVERT: W 94 MET cc_start: 0.8405 (ptt) cc_final: 0.7817 (ppp) REVERT: W 111 LEU cc_start: 0.8444 (pt) cc_final: 0.7905 (pp) REVERT: X 3 ASP cc_start: 0.7787 (p0) cc_final: 0.7410 (p0) REVERT: X 44 ILE cc_start: 0.8162 (mm) cc_final: 0.7919 (tp) REVERT: X 52 VAL cc_start: 0.9388 (t) cc_final: 0.9084 (p) REVERT: X 88 MET cc_start: 0.8613 (ttm) cc_final: 0.8013 (ttt) REVERT: X 89 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8033 (tm-30) REVERT: X 117 GLU cc_start: 0.7819 (pm20) cc_final: 0.7573 (pm20) REVERT: X 136 MET cc_start: 0.8049 (mmm) cc_final: 0.7350 (mmm) REVERT: Y 33 THR cc_start: 0.9112 (p) cc_final: 0.8837 (t) REVERT: Z 59 GLU cc_start: 0.8481 (pm20) cc_final: 0.8138 (pm20) REVERT: Z 101 LYS cc_start: 0.9185 (tmtt) cc_final: 0.8692 (ttpp) REVERT: Z 120 LEU cc_start: 0.9279 (tp) cc_final: 0.9003 (tp) REVERT: Z 196 THR cc_start: 0.8987 (p) cc_final: 0.8628 (m) REVERT: a 44 GLU cc_start: 0.7543 (tt0) cc_final: 0.7237 (tt0) REVERT: a 51 ARG cc_start: 0.8993 (ttp80) cc_final: 0.8605 (ptm-80) REVERT: a 65 GLN cc_start: 0.8246 (tt0) cc_final: 0.7765 (tt0) REVERT: a 68 LEU cc_start: 0.8733 (mp) cc_final: 0.8399 (mp) REVERT: a 69 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7873 (mt-10) REVERT: a 84 ARG cc_start: 0.8958 (ttm110) cc_final: 0.8624 (ttm-80) REVERT: a 88 LYS cc_start: 0.8623 (pttm) cc_final: 0.7958 (tppt) REVERT: a 98 GLU cc_start: 0.8206 (pt0) cc_final: 0.7819 (pt0) REVERT: a 137 GLN cc_start: 0.7858 (tp40) cc_final: 0.7238 (tp40) REVERT: a 151 GLN cc_start: 0.8861 (mm-40) cc_final: 0.8002 (mt0) REVERT: a 177 TYR cc_start: 0.8234 (p90) cc_final: 0.7599 (p90) outliers start: 2 outliers final: 0 residues processed: 1604 average time/residue: 0.2069 time to fit residues: 545.4737 Evaluate side-chains 1346 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1345 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 310 optimal weight: 0.9980 chunk 398 optimal weight: 4.9990 chunk 327 optimal weight: 20.0000 chunk 119 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 66 optimal weight: 0.3980 chunk 366 optimal weight: 0.3980 chunk 168 optimal weight: 3.9990 chunk 170 optimal weight: 0.7980 chunk 221 optimal weight: 7.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 GLN G 139 ASN ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 163 ASN N 47 ASN ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 25 GLN ** P 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 ASN ** U 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 61 GLN ** W 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 ASN Z 64 ASN Z 90 ASN ** Z 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.115525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.098362 restraints weight = 110034.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.101863 restraints weight = 56148.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.104128 restraints weight = 32905.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.105692 restraints weight = 21403.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.106767 restraints weight = 15149.742| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3398 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3398 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.6428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 36155 Z= 0.160 Angle : 0.812 42.951 49243 Z= 0.394 Chirality : 0.041 0.214 5448 Planarity : 0.005 0.061 6402 Dihedral : 10.820 89.590 6599 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.13 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.13), residues: 4448 helix: 1.11 (0.09), residues: 3375 sheet: 1.09 (0.81), residues: 28 loop : -0.51 (0.22), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 15 TYR 0.056 0.002 TYR R 97 PHE 0.036 0.002 PHE X 24 TRP 0.020 0.001 TRP a 136 HIS 0.010 0.002 HIS M 140 Details of bonding type rmsd covalent geometry : bond 0.00360 (36155) covalent geometry : angle 0.81224 (49243) hydrogen bonds : bond 0.04465 ( 2648) hydrogen bonds : angle 4.38565 ( 7847) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1586 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1586 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.7846 (ttpt) cc_final: 0.6465 (ttpt) REVERT: A 15 GLN cc_start: 0.8258 (mt0) cc_final: 0.7342 (mm110) REVERT: A 38 MET cc_start: 0.8534 (mmt) cc_final: 0.7709 (tmm) REVERT: A 39 GLU cc_start: 0.7764 (mt-10) cc_final: 0.6548 (mt-10) REVERT: A 62 LYS cc_start: 0.9253 (tmtt) cc_final: 0.8961 (tptt) REVERT: A 90 TYR cc_start: 0.8434 (m-10) cc_final: 0.8115 (m-80) REVERT: A 98 CYS cc_start: 0.8601 (t) cc_final: 0.7839 (t) REVERT: A 131 GLU cc_start: 0.7389 (tm-30) cc_final: 0.7032 (tm-30) REVERT: A 161 GLU cc_start: 0.8903 (pp20) cc_final: 0.8558 (pp20) REVERT: A 163 ASN cc_start: 0.8410 (t0) cc_final: 0.8122 (t0) REVERT: A 165 TYR cc_start: 0.8477 (m-80) cc_final: 0.7750 (m-10) REVERT: A 167 ASP cc_start: 0.7562 (t0) cc_final: 0.6985 (t0) REVERT: B 29 ASN cc_start: 0.8109 (m110) cc_final: 0.7899 (m110) REVERT: B 35 ASN cc_start: 0.8748 (m-40) cc_final: 0.7807 (t0) REVERT: B 36 LYS cc_start: 0.9461 (mtmm) cc_final: 0.8442 (mppt) REVERT: B 120 GLN cc_start: 0.8036 (mt0) cc_final: 0.7422 (tm-30) REVERT: C 17 ARG cc_start: 0.8738 (ptt90) cc_final: 0.8126 (ptt90) REVERT: C 69 MET cc_start: 0.7432 (ttm) cc_final: 0.7133 (ttm) REVERT: C 74 TYR cc_start: 0.7481 (m-80) cc_final: 0.7112 (m-80) REVERT: C 94 MET cc_start: 0.9465 (mmt) cc_final: 0.9085 (mmm) REVERT: C 115 LEU cc_start: 0.7905 (pp) cc_final: 0.7427 (pp) REVERT: C 131 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8133 (tp30) REVERT: D 29 ASN cc_start: 0.9099 (t0) cc_final: 0.7690 (t0) REVERT: D 49 SER cc_start: 0.8778 (p) cc_final: 0.8475 (p) REVERT: D 97 TYR cc_start: 0.8408 (m-10) cc_final: 0.6933 (m-80) REVERT: D 113 ASN cc_start: 0.8183 (t0) cc_final: 0.7901 (t0) REVERT: D 128 SER cc_start: 0.9369 (p) cc_final: 0.9163 (p) REVERT: D 134 GLN cc_start: 0.8235 (mt0) cc_final: 0.7902 (mt0) REVERT: D 135 LYS cc_start: 0.8475 (mmmm) cc_final: 0.8025 (mmmm) REVERT: D 137 LYS cc_start: 0.7630 (mttt) cc_final: 0.7250 (mmmt) REVERT: D 138 ASP cc_start: 0.8501 (p0) cc_final: 0.8062 (p0) REVERT: D 154 ASP cc_start: 0.6780 (t0) cc_final: 0.6399 (t0) REVERT: E 28 ASP cc_start: 0.8502 (t70) cc_final: 0.8257 (t0) REVERT: E 38 MET cc_start: 0.8149 (mmt) cc_final: 0.7802 (tmm) REVERT: E 47 ASN cc_start: 0.8557 (m110) cc_final: 0.7806 (m110) REVERT: E 69 MET cc_start: 0.8202 (mtp) cc_final: 0.7985 (ttm) REVERT: E 72 SER cc_start: 0.8937 (m) cc_final: 0.8534 (t) REVERT: E 74 TYR cc_start: 0.7808 (m-10) cc_final: 0.7293 (m-10) REVERT: E 94 MET cc_start: 0.7470 (ttm) cc_final: 0.6956 (tmm) REVERT: E 121 THR cc_start: 0.9263 (p) cc_final: 0.8776 (t) REVERT: E 167 ASP cc_start: 0.8524 (t0) cc_final: 0.7050 (t0) REVERT: E 171 ASN cc_start: 0.8830 (p0) cc_final: 0.8379 (p0) REVERT: F 11 GLN cc_start: 0.9213 (tt0) cc_final: 0.8547 (tt0) REVERT: F 29 ASN cc_start: 0.9263 (m-40) cc_final: 0.8973 (m110) REVERT: F 30 LEU cc_start: 0.8473 (mm) cc_final: 0.7899 (tp) REVERT: F 81 MET cc_start: 0.9193 (tpp) cc_final: 0.8906 (tpp) REVERT: F 120 GLN cc_start: 0.8839 (tt0) cc_final: 0.8627 (tt0) REVERT: F 145 ASN cc_start: 0.8779 (m-40) cc_final: 0.8442 (m-40) REVERT: F 146 ASP cc_start: 0.7621 (t70) cc_final: 0.7377 (t0) REVERT: G 28 ASP cc_start: 0.8380 (t70) cc_final: 0.8140 (t70) REVERT: G 33 ARG cc_start: 0.7908 (mtp-110) cc_final: 0.7604 (mtp85) REVERT: G 98 CYS cc_start: 0.8434 (p) cc_final: 0.8201 (p) REVERT: G 122 PHE cc_start: 0.8659 (m-80) cc_final: 0.8050 (m-10) REVERT: G 124 LEU cc_start: 0.9211 (mt) cc_final: 0.8697 (mt) REVERT: G 129 TYR cc_start: 0.9167 (m-10) cc_final: 0.8925 (m-10) REVERT: G 163 ASN cc_start: 0.9175 (m-40) cc_final: 0.8554 (m-40) REVERT: H 3 ASP cc_start: 0.8463 (p0) cc_final: 0.8182 (p0) REVERT: H 15 ARG cc_start: 0.7495 (mtm-85) cc_final: 0.6913 (mtm-85) REVERT: H 39 ASP cc_start: 0.7048 (m-30) cc_final: 0.6841 (m-30) REVERT: H 59 LEU cc_start: 0.8219 (tp) cc_final: 0.7987 (tt) REVERT: H 81 MET cc_start: 0.8980 (mmp) cc_final: 0.8338 (mmp) REVERT: H 87 ASP cc_start: 0.9002 (m-30) cc_final: 0.8731 (m-30) REVERT: H 91 ILE cc_start: 0.9525 (mm) cc_final: 0.9088 (tp) REVERT: H 112 LEU cc_start: 0.9352 (mt) cc_final: 0.9087 (mt) REVERT: H 161 GLU cc_start: 0.7832 (pm20) cc_final: 0.7520 (pm20) REVERT: I 25 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8285 (pt0) REVERT: I 51 LEU cc_start: 0.8717 (mt) cc_final: 0.8382 (mt) REVERT: I 60 TYR cc_start: 0.7445 (m-80) cc_final: 0.7106 (m-80) REVERT: I 62 LYS cc_start: 0.9321 (tptm) cc_final: 0.8887 (tptt) REVERT: I 73 GLN cc_start: 0.9310 (pm20) cc_final: 0.8941 (pm20) REVERT: I 83 LYS cc_start: 0.8987 (mmtm) cc_final: 0.8709 (mmmm) REVERT: I 119 ASN cc_start: 0.8554 (m110) cc_final: 0.7861 (m110) REVERT: I 167 ASP cc_start: 0.7793 (m-30) cc_final: 0.7591 (m-30) REVERT: I 173 LEU cc_start: 0.9352 (mt) cc_final: 0.9078 (tt) REVERT: J 17 GLU cc_start: 0.8110 (mp0) cc_final: 0.7529 (mp0) REVERT: J 28 SER cc_start: 0.9444 (t) cc_final: 0.9177 (p) REVERT: J 35 ASN cc_start: 0.8786 (m110) cc_final: 0.8055 (t0) REVERT: J 88 MET cc_start: 0.9132 (mmm) cc_final: 0.8670 (mmm) REVERT: J 91 ILE cc_start: 0.9421 (tp) cc_final: 0.9118 (tt) REVERT: J 97 TYR cc_start: 0.8821 (m-10) cc_final: 0.8502 (m-10) REVERT: J 112 LEU cc_start: 0.9546 (mp) cc_final: 0.8882 (mm) REVERT: K 30 ARG cc_start: 0.8426 (tpt-90) cc_final: 0.8166 (tpt-90) REVERT: K 61 GLN cc_start: 0.8730 (mt0) cc_final: 0.8528 (mt0) REVERT: K 94 MET cc_start: 0.8782 (mmt) cc_final: 0.8430 (mmt) REVERT: K 133 LEU cc_start: 0.8730 (mt) cc_final: 0.8506 (tp) REVERT: K 139 ASN cc_start: 0.9031 (t0) cc_final: 0.8295 (t0) REVERT: L 2 LEU cc_start: 0.9496 (mt) cc_final: 0.8737 (mt) REVERT: L 3 ASP cc_start: 0.8675 (p0) cc_final: 0.8323 (p0) REVERT: L 49 SER cc_start: 0.9216 (m) cc_final: 0.9015 (p) REVERT: L 62 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8242 (tm-30) REVERT: L 63 GLN cc_start: 0.8733 (mt0) cc_final: 0.8220 (mt0) REVERT: L 81 MET cc_start: 0.8918 (tpp) cc_final: 0.8257 (tpp) REVERT: L 88 MET cc_start: 0.7955 (mtm) cc_final: 0.7660 (mtp) REVERT: L 113 ASN cc_start: 0.9523 (t0) cc_final: 0.8554 (t0) REVERT: L 120 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8042 (tm-30) REVERT: L 137 LYS cc_start: 0.9391 (tttt) cc_final: 0.8858 (ttmt) REVERT: L 146 ASP cc_start: 0.9428 (t0) cc_final: 0.9126 (t0) REVERT: L 161 GLU cc_start: 0.8832 (tt0) cc_final: 0.7611 (tp30) REVERT: M 17 ARG cc_start: 0.8717 (ptm-80) cc_final: 0.8370 (ptm-80) REVERT: M 33 ARG cc_start: 0.8233 (ttt180) cc_final: 0.7990 (ttt180) REVERT: M 57 GLN cc_start: 0.9434 (mm-40) cc_final: 0.8989 (mm-40) REVERT: M 84 CYS cc_start: 0.8775 (t) cc_final: 0.8304 (m) REVERT: M 115 LEU cc_start: 0.8841 (tt) cc_final: 0.8273 (tp) REVERT: M 118 ILE cc_start: 0.9649 (tp) cc_final: 0.9239 (tp) REVERT: M 128 TRP cc_start: 0.8532 (m-10) cc_final: 0.7680 (m-10) REVERT: M 135 TYR cc_start: 0.8897 (t80) cc_final: 0.8665 (t80) REVERT: M 171 ASN cc_start: 0.7787 (p0) cc_final: 0.7571 (p0) REVERT: N 17 GLU cc_start: 0.7636 (pm20) cc_final: 0.7430 (pm20) REVERT: N 42 ASN cc_start: 0.9540 (t0) cc_final: 0.9047 (t0) REVERT: N 50 THR cc_start: 0.8713 (t) cc_final: 0.8500 (t) REVERT: N 67 ILE cc_start: 0.9567 (pt) cc_final: 0.9141 (tp) REVERT: N 87 ASP cc_start: 0.8964 (m-30) cc_final: 0.8631 (m-30) REVERT: N 88 MET cc_start: 0.8583 (ttm) cc_final: 0.7650 (mmm) REVERT: N 89 GLU cc_start: 0.7821 (pp20) cc_final: 0.7305 (pp20) REVERT: N 97 TYR cc_start: 0.8383 (m-10) cc_final: 0.7949 (m-80) REVERT: N 103 ASP cc_start: 0.7407 (t0) cc_final: 0.6978 (t0) REVERT: N 116 ARG cc_start: 0.7877 (ttm170) cc_final: 0.7434 (ttm170) REVERT: N 136 MET cc_start: 0.8225 (mtm) cc_final: 0.6903 (mtt) REVERT: O 19 LEU cc_start: 0.8397 (mm) cc_final: 0.7619 (tp) REVERT: O 61 GLN cc_start: 0.7630 (mt0) cc_final: 0.6944 (tm-30) REVERT: O 96 THR cc_start: 0.9467 (p) cc_final: 0.9210 (t) REVERT: O 98 CYS cc_start: 0.8413 (m) cc_final: 0.7407 (p) REVERT: O 104 THR cc_start: 0.8925 (p) cc_final: 0.7991 (p) REVERT: O 163 ASN cc_start: 0.8493 (m-40) cc_final: 0.8110 (m-40) REVERT: P 7 LYS cc_start: 0.9066 (tppt) cc_final: 0.8812 (mmmm) REVERT: P 38 LEU cc_start: 0.8357 (pp) cc_final: 0.8050 (tt) REVERT: P 67 ILE cc_start: 0.8479 (mt) cc_final: 0.8231 (tp) REVERT: P 95 VAL cc_start: 0.9091 (p) cc_final: 0.8877 (m) REVERT: P 97 TYR cc_start: 0.8786 (m-10) cc_final: 0.8368 (m-10) REVERT: P 104 SER cc_start: 0.9450 (p) cc_final: 0.9161 (p) REVERT: P 122 LEU cc_start: 0.8603 (mm) cc_final: 0.8287 (mm) REVERT: Q 25 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8415 (mm110) REVERT: Q 39 GLU cc_start: 0.7232 (mt-10) cc_final: 0.6418 (pt0) REVERT: Q 57 GLN cc_start: 0.8393 (mm110) cc_final: 0.7855 (mm-40) REVERT: Q 62 LYS cc_start: 0.7213 (ttmm) cc_final: 0.6934 (ttmm) REVERT: Q 63 PHE cc_start: 0.7558 (m-10) cc_final: 0.7218 (m-10) REVERT: Q 90 TYR cc_start: 0.6255 (m-80) cc_final: 0.5994 (m-10) REVERT: Q 108 ASP cc_start: 0.9020 (m-30) cc_final: 0.8596 (m-30) REVERT: R 29 ASN cc_start: 0.7419 (t0) cc_final: 0.7212 (t0) REVERT: R 85 LEU cc_start: 0.9560 (mt) cc_final: 0.9121 (tp) REVERT: R 111 CYS cc_start: 0.8275 (t) cc_final: 0.7802 (t) REVERT: R 118 THR cc_start: 0.8886 (p) cc_final: 0.7598 (p) REVERT: R 128 SER cc_start: 0.9118 (m) cc_final: 0.8827 (m) REVERT: R 166 PHE cc_start: 0.8070 (m-80) cc_final: 0.7866 (m-80) REVERT: S 37 SER cc_start: 0.8374 (p) cc_final: 0.7830 (t) REVERT: S 49 GLN cc_start: 0.8336 (tp-100) cc_final: 0.7564 (pm20) REVERT: S 74 TYR cc_start: 0.8707 (m-80) cc_final: 0.7915 (m-10) REVERT: S 79 GLU cc_start: 0.7984 (mp0) cc_final: 0.7417 (tp30) REVERT: S 81 LYS cc_start: 0.8497 (mmmm) cc_final: 0.8273 (mmmm) REVERT: S 90 TYR cc_start: 0.8375 (m-80) cc_final: 0.8022 (m-10) REVERT: S 93 ARG cc_start: 0.7566 (ttp80) cc_final: 0.7101 (ttp80) REVERT: S 94 MET cc_start: 0.9527 (mmp) cc_final: 0.9160 (mmm) REVERT: S 97 TYR cc_start: 0.9013 (m-10) cc_final: 0.8327 (m-80) REVERT: S 107 MET cc_start: 0.7531 (ptp) cc_final: 0.7263 (ptp) REVERT: S 112 ILE cc_start: 0.9512 (mm) cc_final: 0.8884 (tp) REVERT: S 134 LYS cc_start: 0.8938 (mmmm) cc_final: 0.8686 (mmmm) REVERT: S 163 ASN cc_start: 0.9199 (m110) cc_final: 0.8943 (m-40) REVERT: T 3 ASP cc_start: 0.7055 (p0) cc_final: 0.6843 (p0) REVERT: T 13 ASP cc_start: 0.8603 (t70) cc_final: 0.8203 (t0) REVERT: T 23 GLN cc_start: 0.8443 (mt0) cc_final: 0.8101 (mp10) REVERT: T 25 ASP cc_start: 0.8718 (m-30) cc_final: 0.8346 (m-30) REVERT: T 50 THR cc_start: 0.9147 (p) cc_final: 0.8905 (t) REVERT: T 51 ILE cc_start: 0.7122 (mt) cc_final: 0.6919 (mt) REVERT: T 79 ARG cc_start: 0.7908 (tmm-80) cc_final: 0.7448 (tmt-80) REVERT: T 93 ARG cc_start: 0.8048 (ttp-170) cc_final: 0.7082 (ttm-80) REVERT: T 141 ILE cc_start: 0.8616 (mt) cc_final: 0.8365 (mm) REVERT: U 32 LYS cc_start: 0.9269 (tmmt) cc_final: 0.9049 (tmmt) REVERT: U 74 TYR cc_start: 0.8240 (m-80) cc_final: 0.7846 (m-10) REVERT: U 97 TYR cc_start: 0.8591 (m-10) cc_final: 0.8058 (m-80) REVERT: U 109 GLU cc_start: 0.8417 (tm-30) cc_final: 0.6943 (mp0) REVERT: U 134 LYS cc_start: 0.9082 (tppp) cc_final: 0.8792 (tppt) REVERT: U 171 ASN cc_start: 0.8795 (t0) cc_final: 0.8424 (t0) REVERT: U 174 SER cc_start: 0.7698 (t) cc_final: 0.7317 (t) REVERT: V 17 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7316 (mt-10) REVERT: V 60 PHE cc_start: 0.8969 (m-80) cc_final: 0.8568 (m-80) REVERT: V 81 MET cc_start: 0.8502 (tpp) cc_final: 0.8167 (tpp) REVERT: V 90 ILE cc_start: 0.9398 (mm) cc_final: 0.9191 (mm) REVERT: V 113 ASN cc_start: 0.9215 (t0) cc_final: 0.8410 (t0) REVERT: V 124 THR cc_start: 0.8921 (m) cc_final: 0.8655 (p) REVERT: W 1 MET cc_start: 0.6111 (pmm) cc_final: 0.5292 (pmm) REVERT: W 24 LEU cc_start: 0.8986 (mt) cc_final: 0.8780 (mt) REVERT: W 49 GLN cc_start: 0.9013 (mp10) cc_final: 0.8723 (mp10) REVERT: W 63 PHE cc_start: 0.5557 (m-80) cc_final: 0.5250 (m-80) REVERT: W 69 MET cc_start: 0.5392 (mmm) cc_final: 0.5147 (tpt) REVERT: W 94 MET cc_start: 0.8833 (ptt) cc_final: 0.8248 (ppp) REVERT: W 111 LEU cc_start: 0.8421 (pt) cc_final: 0.7903 (pp) REVERT: X 3 ASP cc_start: 0.7708 (p0) cc_final: 0.7348 (p0) REVERT: X 25 ASP cc_start: 0.7895 (m-30) cc_final: 0.6643 (p0) REVERT: X 32 LYS cc_start: 0.8138 (mmtp) cc_final: 0.7494 (tptm) REVERT: X 44 ILE cc_start: 0.8103 (mm) cc_final: 0.7794 (tp) REVERT: X 52 VAL cc_start: 0.9274 (t) cc_final: 0.9008 (p) REVERT: X 88 MET cc_start: 0.8611 (ttm) cc_final: 0.7935 (ttt) REVERT: X 89 GLU cc_start: 0.8423 (tm-30) cc_final: 0.8038 (tm-30) REVERT: X 93 ARG cc_start: 0.8780 (ttp80) cc_final: 0.8131 (ttt90) REVERT: X 117 GLU cc_start: 0.7864 (pm20) cc_final: 0.7609 (pm20) REVERT: X 136 MET cc_start: 0.8080 (mmm) cc_final: 0.7402 (mmm) REVERT: Y 33 THR cc_start: 0.9166 (p) cc_final: 0.8861 (t) REVERT: Z 59 GLU cc_start: 0.8382 (pm20) cc_final: 0.8053 (pm20) REVERT: Z 101 LYS cc_start: 0.9174 (tmtt) cc_final: 0.8713 (ttpp) REVERT: Z 120 LEU cc_start: 0.9318 (tp) cc_final: 0.9056 (tp) REVERT: Z 165 PHE cc_start: 0.8337 (t80) cc_final: 0.7934 (t80) REVERT: Z 196 THR cc_start: 0.9012 (p) cc_final: 0.8630 (m) REVERT: Z 216 THR cc_start: 0.8092 (t) cc_final: 0.7840 (t) REVERT: a 51 ARG cc_start: 0.9022 (ttp80) cc_final: 0.8649 (ptm-80) REVERT: a 65 GLN cc_start: 0.8353 (tt0) cc_final: 0.7972 (tt0) REVERT: a 68 LEU cc_start: 0.8829 (mp) cc_final: 0.8508 (mp) REVERT: a 69 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7869 (mt-10) REVERT: a 84 ARG cc_start: 0.9020 (ttm110) cc_final: 0.8603 (ttm-80) REVERT: a 88 LYS cc_start: 0.8646 (pttm) cc_final: 0.7955 (tppt) REVERT: a 98 GLU cc_start: 0.8106 (pt0) cc_final: 0.7726 (pt0) REVERT: a 137 GLN cc_start: 0.7893 (tp40) cc_final: 0.7272 (tp40) REVERT: a 151 GLN cc_start: 0.8845 (mm-40) cc_final: 0.7872 (mt0) REVERT: a 177 TYR cc_start: 0.8310 (p90) cc_final: 0.7445 (p90) outliers start: 0 outliers final: 0 residues processed: 1586 average time/residue: 0.2063 time to fit residues: 539.0569 Evaluate side-chains 1351 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1351 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 51 optimal weight: 0.7980 chunk 430 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 160 optimal weight: 3.9990 chunk 337 optimal weight: 5.9990 chunk 420 optimal weight: 3.9990 chunk 49 optimal weight: 0.0570 chunk 438 optimal weight: 6.9990 chunk 153 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 ASN ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 147 GLN ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN S 139 ASN ** S 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 25 GLN V 78 ASN X 42 ASN Z 90 ASN ** Z 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.116879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.099535 restraints weight = 112242.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.103106 restraints weight = 56755.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.105452 restraints weight = 33165.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.107024 restraints weight = 21498.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.108156 restraints weight = 15220.651| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3418 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3418 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.6583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 36155 Z= 0.153 Angle : 0.810 43.558 49243 Z= 0.392 Chirality : 0.041 0.195 5448 Planarity : 0.005 0.092 6402 Dihedral : 10.826 89.319 6599 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.97 % Favored : 96.94 % Rotamer: Outliers : 0.03 % Allowed : 0.44 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.13), residues: 4448 helix: 1.11 (0.09), residues: 3383 sheet: 1.11 (0.82), residues: 28 loop : -0.53 (0.22), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 30 TYR 0.049 0.002 TYR M 97 PHE 0.033 0.002 PHE X 24 TRP 0.034 0.002 TRP K 128 HIS 0.011 0.002 HIS M 140 Details of bonding type rmsd covalent geometry : bond 0.00342 (36155) covalent geometry : angle 0.80964 (49243) hydrogen bonds : bond 0.04409 ( 2648) hydrogen bonds : angle 4.37442 ( 7847) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9538.86 seconds wall clock time: 163 minutes 48.68 seconds (9828.68 seconds total)