Starting phenix.real_space_refine on Mon Jul 6 12:26:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7veb_31945/07_2026/7veb_31945.cif Found real_map, /net/cci-nas-00/data/ceres_data/7veb_31945/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7veb_31945/07_2026/7veb_31945.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7veb_31945/07_2026/7veb_31945.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7veb_31945/07_2026/7veb_31945.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7veb_31945/07_2026/7veb_31945.map" model { file = "/net/cci-nas-00/data/ceres_data/7veb_31945/07_2026/7veb_31945.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7veb_31945/07_2026/7veb_31945.cif" } 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): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 7.78, 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: 3.22 Conformation dependent library (CDL) restraints added in 1.6 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: 0.83 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: 6.60 Time building geometry restraints manager: 4.14 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: 19667 17.99 - 35.99: 1314 35.99 - 53.98: 287 53.98 - 71.97: 88 71.97 - 89.96: 31 Dihedral angle restraints: 21387 sinusoidal: 8192 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 21384 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: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.510 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 31.530 Find NCS groups from input model: 1.230 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.210 ------------------------------------------------------------------------------- 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 : 13.693 89.965 12923 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/Z covalent geometry : bond 0.01104 / 0.55 (36155) covalent geometry : angle 1.36749 / 0.53 (49243) hydrogen bonds : bond 0.13563 / 9.19 ( 2648) hydrogen bonds : angle 5.56725 / 4.08 ( 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 : 0.898 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: 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: 0.7653 (ptp-110) REVERT: A 18 PHE cc_start: 0.8095 (m-80) cc_final: 0.7338 (m-80) REVERT: A 33 ARG cc_start: 0.9176 (mmm160) cc_final: 0.8804 (tpt170) REVERT: A 38 MET cc_start: 0.9117 (mmt) cc_final: 0.8212 (tmm) REVERT: A 39 GLU cc_start: 0.9641 (tp30) cc_final: 0.9101 (mm-30) REVERT: A 49 GLN cc_start: 0.9267 (tp40) cc_final: 0.9026 (tp-100) REVERT: A 63 PHE cc_start: 0.9009 (m-80) cc_final: 0.8632 (m-10) REVERT: A 87 ASP cc_start: 0.9161 (m-30) cc_final: 0.8885 (m-30) REVERT: A 90 TYR cc_start: 0.9265 (m-10) cc_final: 0.8940 (m-80) REVERT: A 91 TYR cc_start: 0.9053 (m-80) cc_final: 0.8837 (m-10) REVERT: A 122 PHE cc_start: 0.8741 (m-80) cc_final: 0.8385 (m-10) 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: 0.9450 (mm) REVERT: A 167 ASP cc_start: 0.9188 (t0) cc_final: 0.8560 (t0) REVERT: A 170 ILE cc_start: 0.9391 (mt) cc_final: 0.9029 (mt) REVERT: B 27 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9141 (mm) REVERT: B 29 ASN cc_start: 0.8286 (m-40) cc_final: 0.8054 (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: 0.9297 (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: 0.8975 (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: 0.8177 (tm-30) REVERT: B 129 VAL cc_start: 0.9721 (t) cc_final: 0.9520 (t) REVERT: B 145 ASN cc_start: 0.9248 (t0) cc_final: 0.8692 (p0) REVERT: C 3 THR cc_start: 0.8823 (m) cc_final: 0.8494 (p) REVERT: C 20 SER cc_start: 0.9369 (p) cc_final: 0.9126 (p) REVERT: C 31 PHE cc_start: 0.9400 (m-80) cc_final: 0.9117 (m-80) REVERT: C 65 TYR cc_start: 0.7492 (p90) cc_final: 0.7197 (p90) REVERT: C 69 MET cc_start: 0.7416 (ttm) cc_final: 0.6750 (ttm) REVERT: C 87 ASP cc_start: 0.9692 (m-30) cc_final: 0.9475 (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: 0.8838 (m-10) REVERT: C 125 SER cc_start: 0.9513 (t) cc_final: 0.9137 (p) REVERT: C 128 TRP cc_start: 0.8340 (m-10) cc_final: 0.8075 (m-10) REVERT: D 13 ASP cc_start: 0.8701 (t70) cc_final: 0.8417 (t0) REVERT: D 24 PHE cc_start: 0.8362 (m-80) cc_final: 0.8064 (m-80) REVERT: D 32 LYS cc_start: 0.9418 (ptmt) cc_final: 0.9145 (pttt) REVERT: D 46 SER cc_start: 0.8931 (m) cc_final: 0.8686 (m) REVERT: D 59 LEU cc_start: 0.9400 (tp) cc_final: 0.9183 (tt) REVERT: D 79 ARG cc_start: 0.7929 (tmt170) cc_final: 0.7682 (tpt170) REVERT: D 110 ARG cc_start: 0.9051 (mtt-85) cc_final: 0.8762 (mtm-85) REVERT: D 124 THR cc_start: 0.9076 (m) cc_final: 0.8415 (m) REVERT: D 137 LYS cc_start: 0.8454 (ttpt) cc_final: 0.8148 (tttm) REVERT: D 143 ILE cc_start: 0.9287 (pp) cc_final: 0.9055 (mm) REVERT: D 154 ASP cc_start: 0.7857 (t0) cc_final: 0.7572 (t0) REVERT: D 155 CYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7242 (m) REVERT: D 165 TYR cc_start: 0.8487 (m-10) cc_final: 0.8235 (m-10) REVERT: E 9 ILE cc_start: 0.9324 (mt) cc_final: 0.9045 (tt) REVERT: E 25 GLN cc_start: 0.9207 (mt0) cc_final: 0.8827 (mt0) REVERT: E 38 MET cc_start: 0.8751 (mmt) cc_final: 0.8242 (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: 0.8667 (t) REVERT: E 73 GLN cc_start: 0.9237 (pm20) cc_final: 0.8976 (pm20) REVERT: E 74 TYR cc_start: 0.8855 (m-80) cc_final: 0.8384 (m-10) REVERT: E 81 LYS cc_start: 0.8793 (tttp) cc_final: 0.8593 (mttm) REVERT: E 109 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8855 (tt0) REVERT: E 115 LEU cc_start: 0.9418 (tp) cc_final: 0.9161 (tt) REVERT: E 122 PHE cc_start: 0.9615 (m-80) cc_final: 0.9218 (m-10) REVERT: E 123 ASP cc_start: 0.9348 (m-30) cc_final: 0.9088 (t70) REVERT: E 167 ASP cc_start: 0.9256 (t0) cc_final: 0.8810 (t0) REVERT: E 173 LEU cc_start: 0.9618 (mm) cc_final: 0.9312 (tp) REVERT: F 21 ASN cc_start: 0.8500 (m-40) cc_final: 0.7992 (t0) REVERT: F 25 ASP cc_start: 0.9214 (m-30) cc_final: 0.8588 (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: 0.8960 (m110) REVERT: F 33 GLU cc_start: 0.9238 (mt-10) cc_final: 0.8968 (mp0) REVERT: F 35 ASN cc_start: 0.9283 (m-40) cc_final: 0.8972 (m-40) REVERT: F 62 GLU cc_start: 0.9614 (tt0) cc_final: 0.9356 (tm-30) REVERT: F 65 GLN cc_start: 0.9341 (pm20) cc_final: 0.8970 (mm-40) REVERT: F 76 TYR cc_start: 0.8863 (t80) cc_final: 0.8543 (t80) REVERT: F 93 ARG cc_start: 0.9332 (ttp80) cc_final: 0.8818 (ttp-110) REVERT: F 103 ASP cc_start: 0.9022 (t0) cc_final: 0.8601 (t0) REVERT: F 115 LEU cc_start: 0.9145 (tp) cc_final: 0.8719 (tp) REVERT: F 117 GLU cc_start: 0.9525 (pp20) cc_final: 0.9004 (pp20) REVERT: F 118 THR cc_start: 0.9623 (m) cc_final: 0.9237 (p) REVERT: F 131 VAL cc_start: 0.8606 (t) cc_final: 0.8312 (t) REVERT: F 136 MET cc_start: 0.8922 (mtm) cc_final: 0.8637 (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: 0.8791 (t0) REVERT: F 158 LEU cc_start: 0.8763 (tp) cc_final: 0.8254 (tt) REVERT: F 159 MET cc_start: 0.9074 (mmp) cc_final: 0.8751 (mmt) REVERT: F 165 TYR cc_start: 0.9296 (m-80) cc_final: 0.8940 (m-10) REVERT: G 18 PHE cc_start: 0.8365 (m-80) cc_final: 0.6659 (m-80) REVERT: G 42 ARG cc_start: 0.7986 (mtt-85) cc_final: 0.7706 (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: 0.9133 (tppt) REVERT: G 74 TYR cc_start: 0.8954 (m-80) cc_final: 0.8636 (m-10) REVERT: G 79 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8898 (pp20) REVERT: G 94 MET cc_start: 0.9177 (mmm) cc_final: 0.8924 (mtt) REVERT: G 97 TYR cc_start: 0.9529 (m-10) cc_final: 0.9126 (m-10) REVERT: G 122 PHE cc_start: 0.9312 (m-80) cc_final: 0.8896 (m-10) REVERT: G 124 LEU cc_start: 0.9124 (mt) cc_final: 0.8892 (mt) REVERT: G 129 TYR cc_start: 0.9132 (m-80) cc_final: 0.8467 (m-80) REVERT: G 161 GLU cc_start: 0.9533 (mt-10) cc_final: 0.9300 (mt-10) REVERT: G 166 ILE cc_start: 0.9341 (mt) cc_final: 0.9121 (tt) REVERT: G 167 ASP cc_start: 0.9273 (t0) cc_final: 0.8792 (t0) REVERT: G 170 ILE cc_start: 0.9536 (mt) cc_final: 0.9221 (pt) REVERT: H 3 ASP cc_start: 0.9618 (p0) cc_final: 0.9072 (m-30) REVERT: H 15 ARG cc_start: 0.8360 (mmm160) cc_final: 0.7911 (mmt-90) REVERT: H 24 PHE cc_start: 0.8708 (m-80) cc_final: 0.8332 (m-10) REVERT: H 42 ASN cc_start: 0.9106 (t0) cc_final: 0.8882 (t0) REVERT: H 60 PHE cc_start: 0.8763 (m-80) cc_final: 0.8360 (m-10) REVERT: H 63 GLN cc_start: 0.9338 (mt0) cc_final: 0.8848 (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 103 ASP cc_start: 0.9194 (t0) cc_final: 0.8992 (t0) 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: 0.8332 (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: 0.8183 (t0) REVERT: H 159 MET cc_start: 0.9025 (mmt) cc_final: 0.8542 (mmt) REVERT: I 51 LEU cc_start: 0.9421 (mt) cc_final: 0.9202 (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: 0.8893 (tptt) REVERT: I 91 TYR cc_start: 0.8929 (m-80) cc_final: 0.8720 (m-80) REVERT: I 107 MET cc_start: 0.9275 (tpp) cc_final: 0.9003 (tpt) REVERT: I 110 TYR cc_start: 0.9249 (m-10) cc_final: 0.8737 (m-10) REVERT: I 111 LEU cc_start: 0.9400 (tp) cc_final: 0.8874 (tp) REVERT: I 115 LEU cc_start: 0.9144 (tp) cc_final: 0.8936 (tp) REVERT: I 118 ILE cc_start: 0.9432 (mm) cc_final: 0.9225 (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: 0.8305 (mtp-110) REVERT: J 17 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8148 (mp0) REVERT: J 35 ASN cc_start: 0.9114 (m110) cc_final: 0.8404 (t0) REVERT: J 38 LEU cc_start: 0.9411 (mt) cc_final: 0.9034 (mp) REVERT: J 60 PHE cc_start: 0.9212 (m-80) cc_final: 0.8959 (m-80) REVERT: J 97 TYR cc_start: 0.8736 (m-10) cc_final: 0.8270 (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: 0.8538 (m-80) REVERT: K 19 LEU cc_start: 0.9293 (mt) cc_final: 0.8902 (tt) REVERT: K 21 ASN cc_start: 0.8925 (p0) cc_final: 0.8663 (t0) REVERT: K 33 ARG cc_start: 0.8774 (mtp85) cc_final: 0.8292 (tpm170) REVERT: K 38 MET cc_start: 0.8981 (mmt) cc_final: 0.8737 (mmp) REVERT: K 61 GLN cc_start: 0.9090 (mt0) cc_final: 0.8663 (mt0) REVERT: K 98 CYS cc_start: 0.8734 (t) cc_final: 0.8438 (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: 0.8524 (tp) REVERT: K 122 PHE cc_start: 0.8509 (m-10) cc_final: 0.8253 (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: 0.9168 (mt) REVERT: K 140 HIS cc_start: 0.8938 (p-80) cc_final: 0.8617 (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: 0.8541 (t0) REVERT: L 60 PHE cc_start: 0.9052 (m-80) cc_final: 0.8717 (m-10) REVERT: L 65 GLN cc_start: 0.9305 (pt0) cc_final: 0.8935 (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: 0.8850 (mtt180) REVERT: L 89 GLU cc_start: 0.9053 (pp20) cc_final: 0.8642 (pp20) REVERT: L 90 ILE cc_start: 0.9373 (mt) cc_final: 0.8792 (mm) REVERT: L 93 ARG cc_start: 0.8926 (ttp80) cc_final: 0.8543 (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: 0.9249 (ttmt) REVERT: L 159 MET cc_start: 0.8953 (mmp) cc_final: 0.8709 (mmt) REVERT: L 165 TYR cc_start: 0.9098 (m-80) cc_final: 0.8874 (m-80) REVERT: M 1 MET cc_start: 0.8127 (mpp) cc_final: 0.7656 (ptp) REVERT: M 2 LYS cc_start: 0.8665 (tttp) cc_final: 0.8450 (ttmm) REVERT: M 33 ARG cc_start: 0.9240 (mmt180) cc_final: 0.8503 (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: 0.9159 (tpt) REVERT: M 81 LYS cc_start: 0.8987 (tmtt) cc_final: 0.8737 (mtpp) REVERT: M 91 TYR cc_start: 0.9271 (m-80) cc_final: 0.8921 (m-10) REVERT: M 129 TYR cc_start: 0.8963 (m-80) cc_final: 0.8657 (m-80) REVERT: M 135 TYR cc_start: 0.8994 (t80) cc_final: 0.8730 (t80) REVERT: M 161 GLU cc_start: 0.9461 (tt0) cc_final: 0.9153 (mt-10) REVERT: N 3 ASP cc_start: 0.8751 (p0) cc_final: 0.8537 (p0) REVERT: N 19 LEU cc_start: 0.8470 (mt) cc_final: 0.8234 (mm) REVERT: N 35 ASN cc_start: 0.9352 (m-40) cc_final: 0.9126 (t0) REVERT: N 36 LYS cc_start: 0.8569 (mttt) cc_final: 0.8312 (mmtt) REVERT: N 62 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8368 (tm-30) REVERT: N 67 ILE cc_start: 0.9720 (pt) cc_final: 0.9251 (mt) REVERT: N 80 ARG cc_start: 0.9408 (mtm-85) cc_final: 0.8453 (mtm-85) REVERT: N 88 MET cc_start: 0.9055 (ttp) cc_final: 0.8757 (ttp) REVERT: N 95 VAL cc_start: 0.9780 (t) cc_final: 0.9542 (p) REVERT: N 103 ASP cc_start: 0.8495 (t0) cc_final: 0.8180 (t0) REVERT: N 115 LEU cc_start: 0.9594 (tp) cc_final: 0.9323 (tp) REVERT: N 148 ASN cc_start: 0.9041 (m-40) cc_final: 0.8838 (p0) REVERT: N 165 TYR cc_start: 0.8824 (m-80) cc_final: 0.8353 (m-10) REVERT: N 167 ASP cc_start: 0.9300 (m-30) cc_final: 0.9046 (m-30) REVERT: O 13 ASP cc_start: 0.9286 (t70) cc_final: 0.9069 (t70) REVERT: O 25 GLN cc_start: 0.8456 (mt0) cc_final: 0.8254 (mt0) REVERT: O 32 LYS cc_start: 0.9210 (mmmt) cc_final: 0.8868 (mmmm) REVERT: O 47 ASN cc_start: 0.9300 (m-40) cc_final: 0.9093 (p0) REVERT: O 99 LEU cc_start: 0.9183 (mt) cc_final: 0.8886 (tp) REVERT: O 104 THR cc_start: 0.9207 (p) cc_final: 0.8866 (p) REVERT: O 118 ILE cc_start: 0.8858 (mt) cc_final: 0.8658 (mt) REVERT: O 129 TYR cc_start: 0.8843 (m-80) cc_final: 0.8226 (m-80) REVERT: O 131 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8842 (tm-30) REVERT: O 166 ILE cc_start: 0.9120 (mt) cc_final: 0.8870 (tt) REVERT: P 1 MET cc_start: 0.6960 (ptt) cc_final: 0.6580 (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: 0.8418 (mt0) REVERT: P 23 GLN cc_start: 0.8424 (mt0) cc_final: 0.8157 (mt0) REVERT: P 67 ILE cc_start: 0.9154 (pt) cc_final: 0.8793 (tp) REVERT: P 93 ARG cc_start: 0.9210 (ttp80) cc_final: 0.8426 (ttp-170) REVERT: P 94 TYR cc_start: 0.9219 (m-80) cc_final: 0.8404 (m-80) REVERT: P 97 TYR cc_start: 0.9182 (m-10) cc_final: 0.8578 (m-80) REVERT: P 104 SER cc_start: 0.9362 (p) cc_final: 0.9105 (p) REVERT: P 110 ARG cc_start: 0.8087 (mtt180) cc_final: 0.7781 (mtp85) REVERT: P 156 SER cc_start: 0.8692 (t) cc_final: 0.8358 (m) REVERT: P 159 MET cc_start: 0.9175 (mmm) cc_final: 0.8269 (tmm) REVERT: P 162 ILE cc_start: 0.9528 (pt) cc_final: 0.9278 (pt) REVERT: Q 14 THR cc_start: 0.8687 (p) cc_final: 0.8188 (t) REVERT: Q 15 GLN cc_start: 0.8509 (mm110) cc_final: 0.8222 (mm110) REVERT: Q 24 LEU cc_start: 0.8432 (mt) cc_final: 0.7748 (mt) REVERT: Q 37 SER cc_start: 0.7989 (m) cc_final: 0.7148 (p) REVERT: Q 53 ASP cc_start: 0.7168 (m-30) cc_final: 0.6729 (m-30) REVERT: Q 57 GLN cc_start: 0.6950 (mm110) cc_final: 0.6678 (mm-40) REVERT: Q 73 GLN cc_start: 0.7797 (pm20) cc_final: 0.7084 (pm20) REVERT: Q 86 ARG cc_start: 0.5640 (OUTLIER) cc_final: 0.4764 (mmt90) REVERT: Q 107 MET cc_start: 0.8564 (ttm) cc_final: 0.8000 (mtp) REVERT: Q 108 ASP cc_start: 0.8587 (m-30) cc_final: 0.8205 (m-30) REVERT: R 38 LEU cc_start: 0.8563 (mt) cc_final: 0.8268 (mp) REVERT: R 39 ASP cc_start: 0.7872 (m-30) cc_final: 0.7661 (m-30) REVERT: R 87 ASP cc_start: 0.7926 (m-30) cc_final: 0.7655 (m-30) REVERT: R 88 MET cc_start: 0.9649 (mmm) cc_final: 0.9054 (mtp) REVERT: R 103 ASP cc_start: 0.7354 (t0) cc_final: 0.6883 (t0) REVERT: R 111 CYS cc_start: 0.8829 (t) cc_final: 0.8615 (t) REVERT: R 115 LEU cc_start: 0.9287 (tt) cc_final: 0.8835 (tt) REVERT: R 159 MET cc_start: 0.8829 (mmp) cc_final: 0.8077 (ptt) REVERT: S 37 SER cc_start: 0.8987 (t) cc_final: 0.8766 (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: 0.9065 (mm-40) REVERT: S 73 GLN cc_start: 0.9059 (pt0) cc_final: 0.8828 (pm20) REVERT: S 74 TYR cc_start: 0.9331 (m-80) cc_final: 0.8955 (m-80) REVERT: S 79 GLU cc_start: 0.8643 (mp0) cc_final: 0.8403 (tm-30) REVERT: S 83 LYS cc_start: 0.8721 (mmtp) cc_final: 0.8262 (mmtm) REVERT: S 90 TYR cc_start: 0.8802 (m-10) cc_final: 0.8297 (m-10) REVERT: S 115 LEU cc_start: 0.9076 (tp) cc_final: 0.8870 (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: 0.9057 (p) REVERT: T 13 ASP cc_start: 0.8990 (t70) cc_final: 0.8666 (t0) REVERT: T 15 ARG cc_start: 0.8141 (mtp85) cc_final: 0.7121 (mmt-90) REVERT: T 18 PHE cc_start: 0.8218 (m-80) cc_final: 0.7952 (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: 0.8263 (mp10) REVERT: T 35 ASN cc_start: 0.8016 (m-40) cc_final: 0.7760 (p0) REVERT: T 76 TYR cc_start: 0.4893 (t80) cc_final: 0.4633 (t80) REVERT: T 87 ASP cc_start: 0.8707 (m-30) cc_final: 0.8491 (m-30) REVERT: U 18 PHE cc_start: 0.8657 (m-80) cc_final: 0.8426 (m-80) REVERT: U 25 GLN cc_start: 0.9058 (mt0) cc_final: 0.8706 (tt0) REVERT: U 61 GLN cc_start: 0.8053 (mt0) cc_final: 0.7604 (pp30) REVERT: U 62 LYS cc_start: 0.9275 (tppp) cc_final: 0.9046 (tptt) REVERT: U 69 MET cc_start: 0.7094 (mtt) cc_final: 0.6507 (tpp) REVERT: U 87 ASP cc_start: 0.7572 (m-30) cc_final: 0.7274 (m-30) REVERT: U 94 MET cc_start: 0.9494 (tpp) cc_final: 0.9208 (tpp) REVERT: U 117 GLU cc_start: 0.9116 (tt0) cc_final: 0.8854 (mp0) REVERT: U 123 ASP cc_start: 0.8994 (t0) cc_final: 0.8723 (t70) REVERT: U 140 HIS cc_start: 0.9408 (p-80) cc_final: 0.9192 (p-80) REVERT: U 173 LEU cc_start: 0.9398 (mt) cc_final: 0.8934 (mt) REVERT: V 5 PHE cc_start: 0.8626 (m-10) cc_final: 0.8300 (m-10) REVERT: V 11 GLN cc_start: 0.8841 (tt0) cc_final: 0.8459 (tp40) REVERT: V 13 ASP cc_start: 0.9198 (t70) cc_final: 0.8698 (t0) REVERT: V 15 ARG cc_start: 0.9393 (mtm110) cc_final: 0.9060 (mtm-85) REVERT: V 17 GLU cc_start: 0.8531 (mp0) cc_final: 0.8274 (mp0) REVERT: V 60 PHE cc_start: 0.8876 (m-80) cc_final: 0.8622 (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: 0.8537 (tpp) REVERT: V 93 ARG cc_start: 0.9403 (ttp80) cc_final: 0.8924 (ttp80) REVERT: V 97 TYR cc_start: 0.9288 (m-10) cc_final: 0.8861 (m-80) REVERT: V 108 ASP cc_start: 0.9303 (m-30) cc_final: 0.9068 (t0) REVERT: V 159 MET cc_start: 0.9029 (mmp) cc_final: 0.8617 (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: 0.9290 (p) REVERT: W 33 ARG cc_start: 0.8119 (mtp85) cc_final: 0.7883 (tmm160) REVERT: W 42 ARG cc_start: 0.6776 (tpp80) cc_final: 0.6286 (tpp80) REVERT: W 46 ASN cc_start: 0.7349 (m-40) cc_final: 0.6971 (p0) REVERT: W 65 TYR cc_start: 0.8423 (p90) cc_final: 0.7729 (p90) REVERT: W 69 MET cc_start: 0.4555 (mtp) cc_final: 0.4112 (mmm) REVERT: W 96 THR cc_start: 0.7919 (p) cc_final: 0.7677 (t) 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: 0.8485 (mmm) REVERT: W 111 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7686 (pt) REVERT: X 5 PHE cc_start: 0.8067 (m-80) cc_final: 0.7499 (m-80) REVERT: X 38 LEU cc_start: 0.9434 (mt) cc_final: 0.9180 (mt) REVERT: X 79 ARG cc_start: 0.7878 (ttm170) cc_final: 0.7321 (tpm170) REVERT: X 89 GLU cc_start: 0.8940 (tt0) cc_final: 0.8639 (tm-30) REVERT: X 119 TYR cc_start: 0.8045 (m-80) cc_final: 0.7833 (m-80) REVERT: X 136 MET cc_start: 0.7261 (mtm) cc_final: 0.6612 (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: 0.6911 (mmt) REVERT: Y 37 GLU cc_start: 0.8665 (tp30) cc_final: 0.8385 (tm-30) REVERT: Y 50 VAL cc_start: 0.9558 (t) cc_final: 0.9257 (p) REVERT: Y 55 MET cc_start: 0.9156 (ttp) cc_final: 0.8735 (ttp) REVERT: Z 9 ARG cc_start: 0.7964 (mmt180) cc_final: 0.7699 (mmm160) REVERT: Z 42 GLN cc_start: 0.9071 (tp40) cc_final: 0.8792 (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: 0.8368 (pt0) REVERT: Z 64 ASN cc_start: 0.9151 (t0) cc_final: 0.8861 (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: 0.8099 (t80) REVERT: Z 93 THR cc_start: 0.9479 (m) cc_final: 0.9260 (m) REVERT: Z 101 LYS cc_start: 0.9308 (tttt) cc_final: 0.9029 (ttpp) REVERT: Z 109 TYR cc_start: 0.7807 (m-10) cc_final: 0.7480 (m-10) REVERT: Z 119 ASP cc_start: 0.9445 (m-30) cc_final: 0.8946 (m-30) REVERT: Z 127 ASP cc_start: 0.8993 (m-30) cc_final: 0.8462 (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: 0.7690 (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: 0.8307 (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: 0.9013 (mtp) REVERT: Z 196 THR cc_start: 0.9607 (p) cc_final: 0.9357 (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: 0.9060 (tptt) REVERT: Z 275 GLN cc_start: 0.9113 (mm-40) cc_final: 0.8434 (mm-40) REVERT: a 3 ILE cc_start: 0.7564 (mm) cc_final: 0.6827 (mm) REVERT: a 21 GLU cc_start: 0.8911 (pt0) cc_final: 0.7832 (tp30) REVERT: a 38 ASP cc_start: 0.7895 (p0) cc_final: 0.7495 (p0) REVERT: a 74 ASN cc_start: 0.9413 (t0) cc_final: 0.8990 (p0) REVERT: a 82 PHE cc_start: 0.9062 (t80) cc_final: 0.8768 (t80) REVERT: a 88 LYS cc_start: 0.9607 (pttt) cc_final: 0.9206 (tptp) REVERT: a 124 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7942 (tt0) REVERT: a 152 ASN cc_start: 0.9214 (m-40) cc_final: 0.9003 (t0) REVERT: a 165 TYR cc_start: 0.5759 (t80) cc_final: 0.5344 (m-10) REVERT: a 170 PHE cc_start: 0.8396 (m-10) cc_final: 0.7933 (m-80) outliers start: 25 outliers final: 8 residues processed: 2180 average time/residue: 0.2357 time to fit residues: 816.0690 Evaluate side-chains 1583 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 1569 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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: 0.8980 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 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: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 70 GLN ** K 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 15 GLN M 140 HIS ** O 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 47 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** U 163 ASN ** V 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 21 ASN ** W 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 ASN 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: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.114828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.097212 restraints weight = 101142.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.100905 restraints weight = 50747.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.103285 restraints weight = 29313.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.104922 restraints weight = 18977.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.105936 restraints weight = 13320.736| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 36155 Z= 0.177 Angle : 0.785 43.019 49243 Z= 0.370 Chirality : 0.040 0.224 5448 Planarity : 0.005 0.112 6402 Dihedral : 11.355 89.533 5519 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.89 % Favored : 98.04 % Rotamer: Outliers : 0.27 % Allowed : 3.86 % Favored : 95.87 % 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: 1.21 (0.12), residues: 4448 helix: 1.28 (0.08), residues: 3378 sheet: 1.82 (1.02), residues: 28 loop : -0.64 (0.21), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG U 33 TYR 0.043 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/Z covalent geometry : bond 0.00376 / 0.18 (36155) covalent geometry : angle 0.78461 / 0.37 (49243) hydrogen bonds : bond 0.05378 / 3.62 ( 2648) hydrogen bonds : angle 4.47498 / 3.28 ( 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 1853 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 1844 time to evaluate : 1.311 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 18 PHE cc_start: 0.7892 (m-80) cc_final: 0.6948 (m-80) REVERT: A 25 GLN cc_start: 0.8428 (mt0) cc_final: 0.7986 (mt0) REVERT: A 30 ARG cc_start: 0.8450 (tpt-90) cc_final: 0.8241 (tmt-80) REVERT: A 33 ARG cc_start: 0.8807 (mmm160) cc_final: 0.8354 (tpt170) REVERT: A 38 MET cc_start: 0.8554 (mmt) cc_final: 0.7883 (tmm) REVERT: A 39 GLU cc_start: 0.8218 (tp30) cc_final: 0.7819 (mm-30) REVERT: A 62 LYS cc_start: 0.8893 (tptt) cc_final: 0.8571 (tptt) REVERT: A 63 PHE cc_start: 0.8733 (m-80) cc_final: 0.8190 (m-80) REVERT: A 90 TYR cc_start: 0.8623 (m-10) cc_final: 0.8268 (m-80) REVERT: A 94 MET cc_start: 0.8572 (tpp) cc_final: 0.8251 (tpp) REVERT: A 109 GLU cc_start: 0.7847 (mt-10) cc_final: 0.6990 (mt-10) REVERT: A 129 TYR cc_start: 0.8557 (m-80) cc_final: 0.8356 (m-80) REVERT: A 167 ASP cc_start: 0.7673 (t0) cc_final: 0.7002 (t0) REVERT: A 171 ASN cc_start: 0.8744 (m110) cc_final: 0.8454 (m-40) REVERT: A 173 LEU cc_start: 0.8563 (mm) cc_final: 0.8325 (mm) REVERT: B 27 LEU cc_start: 0.8044 (mm) cc_final: 0.7841 (mm) REVERT: B 29 ASN cc_start: 0.8369 (m-40) cc_final: 0.8045 (t0) REVERT: B 44 ILE cc_start: 0.9358 (mt) cc_final: 0.9084 (tp) REVERT: B 81 MET cc_start: 0.9405 (tpp) cc_final: 0.9079 (tpt) REVERT: B 89 GLU cc_start: 0.8845 (pt0) cc_final: 0.8201 (tt0) REVERT: B 99 ILE cc_start: 0.9365 (mt) cc_final: 0.9003 (mt) REVERT: B 119 TYR cc_start: 0.9067 (m-80) cc_final: 0.8435 (m-80) REVERT: B 120 GLN cc_start: 0.7587 (mt0) cc_final: 0.7296 (tm-30) REVERT: B 136 MET cc_start: 0.7808 (mtt) cc_final: 0.4189 (mtt) REVERT: C 24 LEU cc_start: 0.8582 (mt) cc_final: 0.8358 (mt) REVERT: C 44 LEU cc_start: 0.8972 (mp) cc_final: 0.8591 (mt) REVERT: C 63 PHE cc_start: 0.9048 (m-80) cc_final: 0.8796 (m-10) REVERT: C 69 MET cc_start: 0.7526 (ttm) cc_final: 0.7117 (ttm) REVERT: C 91 TYR cc_start: 0.9044 (m-80) cc_final: 0.8747 (m-80) REVERT: C 94 MET cc_start: 0.9295 (mmt) cc_final: 0.8880 (mmm) REVERT: C 115 LEU cc_start: 0.8004 (pp) cc_final: 0.7501 (pp) REVERT: C 117 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8591 (mm-30) REVERT: C 119 ASN cc_start: 0.7780 (m-40) cc_final: 0.6990 (p0) REVERT: D 49 SER cc_start: 0.9176 (p) cc_final: 0.8800 (p) REVERT: D 79 ARG cc_start: 0.7445 (tmt170) cc_final: 0.7079 (tpt170) REVERT: D 86 ARG cc_start: 0.8956 (ttp-110) cc_final: 0.8337 (ttp-110) REVERT: D 88 MET cc_start: 0.8142 (ttm) cc_final: 0.7714 (mmm) REVERT: D 97 TYR cc_start: 0.8106 (m-10) cc_final: 0.6646 (m-80) REVERT: D 154 ASP cc_start: 0.6663 (t0) cc_final: 0.6416 (t0) REVERT: E 7 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7829 (mm-30) REVERT: E 15 GLN cc_start: 0.8224 (mt0) cc_final: 0.7975 (mt0) REVERT: E 21 ASN cc_start: 0.6174 (t0) cc_final: 0.5587 (t0) REVERT: E 25 GLN cc_start: 0.8529 (mt0) cc_final: 0.7885 (mt0) REVERT: E 28 ASP cc_start: 0.8568 (t70) cc_final: 0.8214 (t0) REVERT: E 38 MET cc_start: 0.8231 (mmt) cc_final: 0.7920 (tmm) REVERT: E 62 LYS cc_start: 0.9245 (tptt) cc_final: 0.8867 (tppt) REVERT: E 72 SER cc_start: 0.9042 (m) cc_final: 0.8470 (t) REVERT: E 83 LYS cc_start: 0.9401 (tppt) cc_final: 0.9100 (tppp) REVERT: E 137 LYS cc_start: 0.8808 (tttp) cc_final: 0.8561 (tttp) REVERT: E 140 HIS cc_start: 0.8524 (p90) cc_final: 0.8230 (p-80) REVERT: E 167 ASP cc_start: 0.7999 (t0) cc_final: 0.7072 (t0) REVERT: E 173 LEU cc_start: 0.9211 (mm) cc_final: 0.8900 (mm) REVERT: F 21 ASN cc_start: 0.8068 (m-40) cc_final: 0.7035 (t0) REVERT: F 32 LYS cc_start: 0.8998 (pttm) cc_final: 0.8635 (ptpp) REVERT: F 81 MET cc_start: 0.9241 (tpp) cc_final: 0.8841 (tpp) REVERT: F 88 MET cc_start: 0.8084 (tpp) cc_final: 0.7779 (tpp) REVERT: F 129 VAL cc_start: 0.9724 (t) cc_final: 0.9512 (t) REVERT: F 145 ASN cc_start: 0.8150 (m-40) cc_final: 0.7735 (m-40) REVERT: F 165 TYR cc_start: 0.9197 (m-80) cc_final: 0.8325 (m-10) REVERT: G 9 ILE cc_start: 0.9545 (tp) cc_final: 0.9307 (tp) REVERT: G 30 ARG cc_start: 0.9338 (tmt-80) cc_final: 0.9137 (tmt-80) REVERT: G 49 GLN cc_start: 0.8884 (pp30) cc_final: 0.8652 (pp30) REVERT: G 61 GLN cc_start: 0.8616 (mt0) cc_final: 0.8412 (mp10) REVERT: G 62 LYS cc_start: 0.9155 (tptm) cc_final: 0.8840 (tppt) REVERT: G 70 GLN cc_start: 0.7181 (tm-30) cc_final: 0.6716 (pp30) REVERT: G 87 ASP cc_start: 0.8408 (m-30) cc_final: 0.8184 (m-30) REVERT: G 95 VAL cc_start: 0.9739 (t) cc_final: 0.9002 (t) REVERT: G 97 TYR cc_start: 0.9073 (m-10) cc_final: 0.8675 (m-10) REVERT: G 99 LEU cc_start: 0.8960 (tp) cc_final: 0.8596 (tp) REVERT: G 116 SER cc_start: 0.9315 (p) cc_final: 0.9093 (m) REVERT: G 117 GLU cc_start: 0.7578 (tp30) cc_final: 0.7206 (tp30) REVERT: G 122 PHE cc_start: 0.8897 (m-80) cc_final: 0.8480 (m-10) REVERT: G 124 LEU cc_start: 0.8941 (mt) cc_final: 0.8542 (mt) REVERT: G 129 TYR cc_start: 0.8895 (m-80) cc_final: 0.7994 (m-80) REVERT: G 137 LYS cc_start: 0.9120 (ptmt) cc_final: 0.8880 (ttpp) REVERT: G 161 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8270 (mt-10) REVERT: G 166 ILE cc_start: 0.9328 (mt) cc_final: 0.9110 (tp) REVERT: H 3 ASP cc_start: 0.8493 (p0) cc_final: 0.8287 (p0) REVERT: H 42 ASN cc_start: 0.8726 (t0) cc_final: 0.8456 (t0) REVERT: H 62 GLU cc_start: 0.7104 (pt0) cc_final: 0.6341 (pt0) REVERT: H 67 ILE cc_start: 0.9551 (pt) cc_final: 0.9199 (tt) REVERT: H 91 ILE cc_start: 0.9498 (mm) cc_final: 0.8970 (tp) REVERT: H 100 LEU cc_start: 0.8888 (tt) cc_final: 0.8680 (tp) REVERT: I 13 ASP cc_start: 0.8824 (t0) cc_final: 0.8587 (t70) REVERT: I 37 SER cc_start: 0.8888 (p) cc_final: 0.8559 (t) REVERT: I 38 MET cc_start: 0.8011 (tmm) cc_final: 0.7771 (tmm) REVERT: I 62 LYS cc_start: 0.9225 (tptm) cc_final: 0.8689 (tptt) REVERT: I 73 GLN cc_start: 0.9236 (pm20) cc_final: 0.8818 (pm20) REVERT: I 90 TYR cc_start: 0.7627 (m-10) cc_final: 0.7006 (m-10) REVERT: I 107 MET cc_start: 0.8853 (tpp) cc_final: 0.8510 (tpt) REVERT: I 110 TYR cc_start: 0.7797 (m-80) cc_final: 0.7446 (m-10) REVERT: I 119 ASN cc_start: 0.8472 (m110) cc_final: 0.7655 (m110) REVERT: I 133 LEU cc_start: 0.9221 (mt) cc_final: 0.8877 (mt) REVERT: I 135 TYR cc_start: 0.8726 (t80) cc_final: 0.8452 (t80) REVERT: I 136 ILE cc_start: 0.9102 (mm) cc_final: 0.8768 (tt) REVERT: I 163 ASN cc_start: 0.9129 (m110) cc_final: 0.8132 (m110) REVERT: I 166 ILE cc_start: 0.9757 (tt) cc_final: 0.9445 (tt) REVERT: I 167 ASP cc_start: 0.8023 (m-30) cc_final: 0.7822 (m-30) REVERT: J 3 ASP cc_start: 0.8365 (p0) cc_final: 0.8141 (p0) REVERT: J 35 ASN cc_start: 0.8481 (m110) cc_final: 0.7955 (t0) REVERT: J 76 TYR cc_start: 0.9164 (t80) cc_final: 0.8142 (t80) REVERT: J 91 ILE cc_start: 0.9391 (tp) cc_final: 0.9016 (tp) REVERT: J 97 TYR cc_start: 0.8970 (m-10) cc_final: 0.8328 (m-10) REVERT: J 141 ILE cc_start: 0.8890 (tt) cc_final: 0.8456 (tp) REVERT: J 145 ASN cc_start: 0.8271 (t0) cc_final: 0.8001 (t0) REVERT: K 38 MET cc_start: 0.8669 (mmt) cc_final: 0.8467 (mmp) REVERT: K 99 LEU cc_start: 0.8683 (tp) cc_final: 0.8435 (tp) REVERT: K 111 LEU cc_start: 0.9345 (tp) cc_final: 0.9133 (tp) REVERT: K 115 LEU cc_start: 0.8955 (tp) cc_final: 0.8751 (tp) REVERT: K 165 TYR cc_start: 0.9005 (m-10) cc_final: 0.8733 (m-10) REVERT: L 2 LEU cc_start: 0.9200 (mt) cc_final: 0.8575 (mt) REVERT: L 7 LYS cc_start: 0.9062 (ttpp) cc_final: 0.8824 (ptmm) REVERT: L 13 ASP cc_start: 0.8421 (t70) cc_final: 0.7926 (t0) REVERT: L 59 LEU cc_start: 0.9554 (tp) cc_final: 0.9215 (tp) REVERT: L 80 ARG cc_start: 0.8068 (mtm-85) cc_final: 0.7836 (mtt180) REVERT: L 81 MET cc_start: 0.9061 (tpp) cc_final: 0.8403 (tpp) REVERT: L 87 ASP cc_start: 0.9101 (m-30) cc_final: 0.8747 (m-30) REVERT: L 89 GLU cc_start: 0.7777 (pp20) cc_final: 0.7380 (tm-30) REVERT: L 90 ILE cc_start: 0.9358 (mt) cc_final: 0.9041 (tt) REVERT: L 93 ARG cc_start: 0.8560 (ttp80) cc_final: 0.8240 (ttp80) REVERT: L 103 ASP cc_start: 0.8367 (m-30) cc_final: 0.7127 (m-30) REVERT: L 120 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8346 (tm-30) REVERT: L 135 LYS cc_start: 0.8673 (mmtm) cc_final: 0.8388 (mttm) REVERT: L 137 LYS cc_start: 0.9443 (tttt) cc_final: 0.8965 (ttmt) REVERT: L 161 GLU cc_start: 0.8272 (tt0) cc_final: 0.7834 (tp30) REVERT: M 9 ILE cc_start: 0.9132 (tp) cc_final: 0.8555 (tp) REVERT: M 33 ARG cc_start: 0.7630 (tpt-90) cc_final: 0.5687 (tpp-160) REVERT: M 98 CYS cc_start: 0.7012 (m) cc_final: 0.6365 (m) REVERT: M 115 LEU cc_start: 0.8835 (tt) cc_final: 0.8018 (tp) REVERT: M 118 ILE cc_start: 0.9239 (mm) cc_final: 0.9034 (mm) REVERT: M 129 TYR cc_start: 0.8439 (m-80) cc_final: 0.8093 (m-80) REVERT: M 135 TYR cc_start: 0.9014 (t80) cc_final: 0.8713 (t80) REVERT: M 171 ASN cc_start: 0.8608 (p0) cc_final: 0.7969 (p0) REVERT: N 3 ASP cc_start: 0.8486 (p0) cc_final: 0.8124 (p0) REVERT: N 24 PHE cc_start: 0.8332 (m-80) cc_final: 0.8124 (m-80) REVERT: N 36 LYS cc_start: 0.8431 (mttt) cc_final: 0.7721 (mttt) REVERT: N 45 THR cc_start: 0.8331 (t) cc_final: 0.8058 (t) REVERT: N 65 GLN cc_start: 0.7836 (mp10) cc_final: 0.7471 (mp10) REVERT: N 80 ARG cc_start: 0.8988 (mtm-85) cc_final: 0.8597 (mtm-85) REVERT: N 88 MET cc_start: 0.8574 (ttp) cc_final: 0.6982 (tpt) REVERT: N 97 TYR cc_start: 0.8675 (m-10) cc_final: 0.7864 (m-80) REVERT: N 103 ASP cc_start: 0.7388 (t0) cc_final: 0.7021 (t0) REVERT: N 105 SER cc_start: 0.8543 (t) cc_final: 0.8274 (t) REVERT: N 136 MET cc_start: 0.8606 (mtm) cc_final: 0.6868 (mtm) REVERT: N 162 ILE cc_start: 0.9501 (mt) cc_final: 0.9108 (mt) REVERT: O 25 GLN cc_start: 0.7285 (mt0) cc_final: 0.6971 (mt0) REVERT: O 91 TYR cc_start: 0.9387 (m-80) cc_final: 0.8890 (m-80) REVERT: O 99 LEU cc_start: 0.9237 (mt) cc_final: 0.8931 (tp) REVERT: O 104 THR cc_start: 0.8624 (p) cc_final: 0.7976 (p) REVERT: O 129 TYR cc_start: 0.8499 (m-80) cc_final: 0.7409 (m-80) REVERT: O 150 VAL cc_start: 0.9440 (m) cc_final: 0.9209 (p) REVERT: P 1 MET cc_start: 0.6201 (ptt) cc_final: 0.5940 (ptt) REVERT: P 5 PHE cc_start: 0.8765 (m-10) cc_final: 0.8484 (m-10) REVERT: P 29 ASN cc_start: 0.8136 (m-40) cc_final: 0.7919 (m110) REVERT: P 93 ARG cc_start: 0.8746 (ttp80) cc_final: 0.8509 (ttp-170) REVERT: P 97 TYR cc_start: 0.8881 (m-10) cc_final: 0.8080 (m-10) REVERT: P 113 ASN cc_start: 0.8139 (t0) cc_final: 0.7933 (t0) REVERT: P 137 LYS cc_start: 0.9030 (tppt) cc_final: 0.8793 (tppt) REVERT: P 158 LEU cc_start: 0.8982 (mm) cc_final: 0.8601 (mt) REVERT: P 159 MET cc_start: 0.8687 (mmm) cc_final: 0.7936 (ppp) REVERT: Q 7 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8062 (mm-30) REVERT: Q 14 THR cc_start: 0.8718 (p) cc_final: 0.8421 (t) REVERT: Q 25 GLN cc_start: 0.8202 (mm-40) cc_final: 0.7682 (mm-40) REVERT: Q 37 SER cc_start: 0.7880 (m) cc_final: 0.7231 (p) REVERT: Q 53 ASP cc_start: 0.6278 (m-30) cc_final: 0.6069 (m-30) REVERT: Q 94 MET cc_start: 0.4769 (tpp) cc_final: 0.4541 (tpp) REVERT: Q 98 CYS cc_start: 0.8101 (m) cc_final: 0.7634 (m) REVERT: Q 107 MET cc_start: 0.8248 (ttm) cc_final: 0.7893 (mtp) REVERT: Q 108 ASP cc_start: 0.7898 (m-30) cc_final: 0.7687 (m-30) REVERT: Q 134 LYS cc_start: 0.6954 (tptt) cc_final: 0.6743 (tptt) REVERT: R 38 LEU cc_start: 0.8571 (mt) cc_final: 0.8256 (mp) REVERT: R 49 SER cc_start: 0.9303 (p) cc_final: 0.8998 (t) REVERT: R 85 LEU cc_start: 0.9450 (mt) cc_final: 0.9154 (tp) REVERT: R 128 SER cc_start: 0.8674 (m) cc_final: 0.8262 (m) REVERT: R 159 MET cc_start: 0.8242 (mmp) cc_final: 0.7885 (ptt) REVERT: S 18 PHE cc_start: 0.5757 (m-10) cc_final: 0.5408 (m-10) REVERT: S 28 ASP cc_start: 0.8356 (t0) cc_final: 0.7965 (t0) REVERT: S 38 MET cc_start: 0.8392 (mtm) cc_final: 0.8154 (mtt) REVERT: S 49 GLN cc_start: 0.8482 (tp-100) cc_final: 0.7724 (pm20) REVERT: S 76 SER cc_start: 0.7556 (p) cc_final: 0.7345 (p) REVERT: S 79 GLU cc_start: 0.7927 (mp0) cc_final: 0.7679 (tm-30) REVERT: S 90 TYR cc_start: 0.8036 (m-10) cc_final: 0.7421 (m-10) REVERT: S 98 CYS cc_start: 0.8190 (m) cc_final: 0.7106 (m) REVERT: S 115 LEU cc_start: 0.8240 (tp) cc_final: 0.7835 (tp) REVERT: S 134 LYS cc_start: 0.9481 (mmpt) cc_final: 0.9190 (mmmm) REVERT: S 137 LYS cc_start: 0.9300 (ttpt) cc_final: 0.8879 (tptt) REVERT: T 15 ARG cc_start: 0.7740 (mtp85) cc_final: 0.6927 (mmm160) REVERT: T 19 LEU cc_start: 0.8090 (mt) cc_final: 0.7503 (mm) REVERT: T 23 GLN cc_start: 0.8425 (mt0) cc_final: 0.8065 (mp10) REVERT: T 25 ASP cc_start: 0.8583 (m-30) cc_final: 0.8326 (m-30) REVERT: T 47 ASN cc_start: 0.7859 (t0) cc_final: 0.7377 (t0) REVERT: T 104 SER cc_start: 0.9008 (p) cc_final: 0.8758 (p) REVERT: T 136 MET cc_start: 0.7689 (tpt) cc_final: 0.7351 (tpp) REVERT: T 156 SER cc_start: 0.8449 (m) cc_final: 0.8064 (m) REVERT: T 162 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8605 (mt) REVERT: T 165 TYR cc_start: 0.8822 (m-80) cc_final: 0.8087 (m-80) REVERT: U 24 LEU cc_start: 0.9146 (mt) cc_final: 0.8926 (mt) REVERT: U 28 ASP cc_start: 0.7871 (t0) cc_final: 0.7236 (t0) REVERT: U 69 MET cc_start: 0.7627 (mtt) cc_final: 0.6909 (tpp) REVERT: U 115 LEU cc_start: 0.8194 (tp) cc_final: 0.7972 (tp) REVERT: U 123 ASP cc_start: 0.8161 (t0) cc_final: 0.7536 (t0) REVERT: U 150 VAL cc_start: 0.9524 (t) cc_final: 0.9245 (p) REVERT: U 171 ASN cc_start: 0.8745 (t0) cc_final: 0.8286 (t0) REVERT: V 11 GLN cc_start: 0.8499 (tt0) cc_final: 0.8106 (tp40) REVERT: V 68 GLN cc_start: 0.8273 (pt0) cc_final: 0.7993 (pt0) REVERT: V 78 ASN cc_start: 0.6944 (t0) cc_final: 0.6473 (t0) REVERT: V 113 ASN cc_start: 0.8712 (t0) cc_final: 0.8017 (t0) REVERT: V 124 THR cc_start: 0.8804 (m) cc_final: 0.8232 (p) REVERT: V 154 ASP cc_start: 0.8103 (t0) cc_final: 0.7498 (t0) REVERT: V 162 ILE cc_start: 0.8751 (mt) cc_final: 0.8411 (mt) REVERT: W 7 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7651 (mm-30) REVERT: W 97 TYR cc_start: 0.7647 (m-10) cc_final: 0.6585 (m-80) REVERT: W 111 LEU cc_start: 0.8040 (pt) cc_final: 0.7576 (pp) REVERT: W 115 LEU cc_start: 0.7633 (mt) cc_final: 0.7309 (mt) REVERT: W 122 PHE cc_start: 0.5934 (m-80) cc_final: 0.5686 (m-80) REVERT: W 163 ASN cc_start: 0.7698 (m-40) cc_final: 0.7365 (m-40) REVERT: X 166 PHE cc_start: 0.7723 (m-80) cc_final: 0.7501 (m-80) REVERT: Y 50 VAL cc_start: 0.9276 (t) cc_final: 0.9015 (p) REVERT: Y 55 MET cc_start: 0.8480 (ttp) cc_final: 0.8232 (ttp) REVERT: Z 30 GLU cc_start: 0.8019 (pp20) cc_final: 0.7572 (pp20) REVERT: Z 64 ASN cc_start: 0.8486 (t0) cc_final: 0.8226 (t0) REVERT: Z 86 PHE cc_start: 0.8955 (m-80) cc_final: 0.8366 (m-80) REVERT: Z 93 THR cc_start: 0.9243 (m) cc_final: 0.9001 (p) REVERT: Z 96 ILE cc_start: 0.9028 (mm) cc_final: 0.8787 (mm) REVERT: Z 98 LEU cc_start: 0.8986 (mt) cc_final: 0.8748 (mm) REVERT: Z 115 ILE cc_start: 0.8851 (mt) cc_final: 0.8599 (mm) REVERT: Z 120 LEU cc_start: 0.8991 (tp) cc_final: 0.8731 (tp) REVERT: Z 133 TYR cc_start: 0.8007 (m-80) cc_final: 0.7777 (m-80) REVERT: Z 146 TRP cc_start: 0.8316 (m-90) cc_final: 0.8014 (m-90) REVERT: Z 157 GLN cc_start: 0.7657 (tp40) cc_final: 0.7149 (tp40) REVERT: Z 166 ASN cc_start: 0.8976 (m110) cc_final: 0.8761 (m-40) REVERT: Z 168 ILE cc_start: 0.9807 (tp) cc_final: 0.9607 (tp) REVERT: Z 175 TYR cc_start: 0.8516 (t80) cc_final: 0.8103 (t80) REVERT: Z 196 THR cc_start: 0.9084 (p) cc_final: 0.8770 (t) REVERT: Z 264 TYR cc_start: 0.8945 (t80) cc_final: 0.8633 (t80) REVERT: a 2 THR cc_start: 0.6991 (p) cc_final: 0.6418 (t) REVERT: a 44 GLU cc_start: 0.7543 (tt0) cc_final: 0.7291 (tt0) REVERT: a 65 GLN cc_start: 0.7995 (tt0) cc_final: 0.7745 (tt0) REVERT: a 74 ASN cc_start: 0.9122 (t0) cc_final: 0.8851 (p0) REVERT: a 77 ILE cc_start: 0.8484 (pt) cc_final: 0.7914 (pt) REVERT: a 104 ARG cc_start: 0.8475 (ttt90) cc_final: 0.7941 (ttp80) REVERT: a 119 TYR cc_start: 0.7826 (m-80) cc_final: 0.7474 (m-10) REVERT: a 152 ASN cc_start: 0.8104 (m-40) cc_final: 0.7729 (t0) REVERT: a 170 PHE cc_start: 0.7994 (m-10) cc_final: 0.6773 (m-80) REVERT: a 177 TYR cc_start: 0.8215 (p90) cc_final: 0.7752 (p90) outliers start: 9 outliers final: 2 residues processed: 1847 average time/residue: 0.2247 time to fit residues: 671.7120 Evaluate side-chains 1468 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1465 time to evaluate : 1.335 ------------------------------------------------------------------------------- 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: 0.6980 chunk 119 optimal weight: 0.9980 chunk 375 optimal weight: 4.9990 chunk 347 optimal weight: 0.9980 chunk 301 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 chunk 341 optimal weight: 1.9990 chunk 328 optimal weight: 3.9990 chunk 377 optimal weight: 10.0000 chunk 400 optimal weight: 7.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN B 23 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 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 119 ASN O 139 ASN Q 171 ASN ** R 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 25 GLN ** S 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 ASN ** Z 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 166 ASN Z 177 ASN Z 182 GLN Z 200 ASN Z 266 GLN ** Z 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.114144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.096224 restraints weight = 109644.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.099926 restraints weight = 54431.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.102365 restraints weight = 31543.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.103989 restraints weight = 20339.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.105070 restraints weight = 14328.574| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4414 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= 0.165 Angle : 0.767 43.099 49243 Z= 0.361 Chirality : 0.040 0.234 5448 Planarity : 0.005 0.059 6402 Dihedral : 11.372 88.775 5519 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.25 % Favored : 97.68 % Rotamer: Outliers : 0.15 % Allowed : 3.51 % Favored : 96.34 % 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: 1.20 (0.12), residues: 4448 helix: 1.26 (0.08), residues: 3366 sheet: 1.99 (0.95), residues: 28 loop : -0.58 (0.21), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 30 TYR 0.033 0.002 TYR V 97 PHE 0.039 0.002 PHE Z 143 TRP 0.009 0.001 TRP S 128 HIS 0.006 0.002 HIS M 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (36155) covalent geometry : angle 0.76728 / 0.36 (49243) hydrogen bonds : bond 0.04907 / 3.28 ( 2648) hydrogen bonds : angle 4.35479 / 3.18 ( 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 1765 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1760 time to evaluate : 1.318 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 1 MET cc_start: 0.7605 (tpp) cc_final: 0.7398 (tpp) REVERT: A 18 PHE cc_start: 0.7960 (m-80) cc_final: 0.7050 (m-80) REVERT: A 30 ARG cc_start: 0.8228 (tpt-90) cc_final: 0.7954 (tmt170) REVERT: A 38 MET cc_start: 0.8530 (mmt) cc_final: 0.7905 (tmm) REVERT: A 63 PHE cc_start: 0.8745 (m-80) cc_final: 0.8300 (m-80) REVERT: A 129 TYR cc_start: 0.8666 (m-80) cc_final: 0.8380 (m-80) REVERT: A 131 GLU cc_start: 0.7467 (tm-30) cc_final: 0.7222 (tm-30) REVERT: A 134 LYS cc_start: 0.8670 (ttmm) cc_final: 0.8035 (mtpp) REVERT: A 136 ILE cc_start: 0.9276 (mm) cc_final: 0.9033 (tp) REVERT: A 167 ASP cc_start: 0.8066 (t0) cc_final: 0.7243 (t0) REVERT: A 171 ASN cc_start: 0.8860 (m-40) cc_final: 0.8638 (m-40) REVERT: B 44 ILE cc_start: 0.9350 (mt) cc_final: 0.9064 (tp) REVERT: B 89 GLU cc_start: 0.8809 (pt0) cc_final: 0.8135 (tt0) REVERT: B 119 TYR cc_start: 0.9332 (m-80) cc_final: 0.8736 (m-80) REVERT: B 120 GLN cc_start: 0.7666 (mt0) cc_final: 0.7346 (tm-30) REVERT: B 136 MET cc_start: 0.7455 (mtt) cc_final: 0.6492 (mtt) REVERT: C 17 ARG cc_start: 0.8331 (ptt90) cc_final: 0.7879 (ptt90) REVERT: C 60 TYR cc_start: 0.6460 (m-80) cc_final: 0.6252 (m-80) REVERT: C 63 PHE cc_start: 0.9031 (m-80) cc_final: 0.8560 (m-10) REVERT: C 69 MET cc_start: 0.7542 (ttm) cc_final: 0.7138 (ttm) REVERT: C 91 TYR cc_start: 0.9091 (m-80) cc_final: 0.8718 (m-80) REVERT: C 94 MET cc_start: 0.9418 (mmt) cc_final: 0.9004 (mmm) REVERT: C 117 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8515 (mm-30) REVERT: D 49 SER cc_start: 0.9078 (p) cc_final: 0.8821 (p) REVERT: D 81 MET cc_start: 0.7703 (tpp) cc_final: 0.7449 (ttt) REVERT: D 85 LEU cc_start: 0.9515 (mp) cc_final: 0.9311 (mm) REVERT: D 88 MET cc_start: 0.8295 (ttm) cc_final: 0.7764 (mmm) REVERT: D 97 TYR cc_start: 0.7910 (m-10) cc_final: 0.6726 (m-80) REVERT: D 113 ASN cc_start: 0.7656 (t0) cc_final: 0.7394 (t0) REVERT: D 128 SER cc_start: 0.9203 (p) cc_final: 0.8973 (p) REVERT: D 134 GLN cc_start: 0.8175 (mt0) cc_final: 0.7839 (mt0) REVERT: D 136 MET cc_start: 0.8098 (ttm) cc_final: 0.7774 (ttm) REVERT: D 154 ASP cc_start: 0.6487 (t0) cc_final: 0.6220 (t0) REVERT: D 162 ILE cc_start: 0.9080 (mm) cc_final: 0.8792 (mm) REVERT: E 25 GLN cc_start: 0.8596 (mt0) cc_final: 0.8047 (mt0) REVERT: E 28 ASP cc_start: 0.8590 (t70) cc_final: 0.8263 (t0) REVERT: E 38 MET cc_start: 0.8118 (mmt) cc_final: 0.7741 (tmm) REVERT: E 47 ASN cc_start: 0.8106 (t0) cc_final: 0.7749 (t0) REVERT: E 62 LYS cc_start: 0.9287 (tptt) cc_final: 0.8932 (tppt) REVERT: E 72 SER cc_start: 0.9052 (m) cc_final: 0.8659 (t) REVERT: E 73 GLN cc_start: 0.8930 (pm20) cc_final: 0.8230 (pm20) REVERT: E 93 ARG cc_start: 0.8353 (ttp80) cc_final: 0.7350 (ttp80) REVERT: E 121 THR cc_start: 0.9121 (p) cc_final: 0.8693 (t) REVERT: E 140 HIS cc_start: 0.8517 (p90) cc_final: 0.8255 (p-80) REVERT: E 167 ASP cc_start: 0.7924 (t0) cc_final: 0.7000 (t0) REVERT: E 173 LEU cc_start: 0.9149 (mm) cc_final: 0.8929 (mm) REVERT: F 11 GLN cc_start: 0.9075 (tt0) cc_final: 0.8469 (tt0) REVERT: F 21 ASN cc_start: 0.8082 (m-40) cc_final: 0.6705 (t0) REVERT: F 25 ASP cc_start: 0.8807 (m-30) cc_final: 0.8483 (m-30) REVERT: F 32 LYS cc_start: 0.8788 (pttm) cc_final: 0.8524 (ptpp) REVERT: F 33 GLU cc_start: 0.8801 (mp0) cc_final: 0.8573 (mp0) REVERT: F 81 MET cc_start: 0.9217 (tpp) cc_final: 0.8984 (tpt) REVERT: F 146 ASP cc_start: 0.8237 (t0) cc_final: 0.7999 (t0) REVERT: F 161 GLU cc_start: 0.8243 (tp30) cc_final: 0.7611 (tp30) REVERT: G 49 GLN cc_start: 0.8890 (pp30) cc_final: 0.8652 (pp30) REVERT: G 61 GLN cc_start: 0.8596 (mt0) cc_final: 0.8360 (mp10) REVERT: G 62 LYS cc_start: 0.9032 (tptm) cc_final: 0.8718 (tppt) REVERT: G 70 GLN cc_start: 0.7442 (tm-30) cc_final: 0.7155 (pp30) REVERT: G 86 ARG cc_start: 0.8651 (ttp-110) cc_final: 0.8360 (ttp80) REVERT: G 87 ASP cc_start: 0.8406 (m-30) cc_final: 0.8058 (m-30) REVERT: G 97 TYR cc_start: 0.8893 (m-10) cc_final: 0.8592 (m-10) REVERT: G 98 CYS cc_start: 0.8175 (p) cc_final: 0.7721 (m) REVERT: G 99 LEU cc_start: 0.9249 (tp) cc_final: 0.8791 (tp) REVERT: G 116 SER cc_start: 0.9302 (p) cc_final: 0.9039 (m) REVERT: G 119 ASN cc_start: 0.9051 (m110) cc_final: 0.8816 (m-40) REVERT: G 122 PHE cc_start: 0.8809 (m-80) cc_final: 0.8513 (m-80) REVERT: G 123 ASP cc_start: 0.7984 (t0) cc_final: 0.7654 (t70) REVERT: G 124 LEU cc_start: 0.9015 (mt) cc_final: 0.8412 (mt) REVERT: G 129 TYR cc_start: 0.8984 (m-80) cc_final: 0.7949 (m-80) REVERT: G 135 TYR cc_start: 0.8759 (t80) cc_final: 0.8449 (t80) REVERT: G 137 LYS cc_start: 0.9062 (ptmt) cc_final: 0.8649 (ttpt) REVERT: G 161 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7818 (mt-10) REVERT: G 163 ASN cc_start: 0.9100 (m-40) cc_final: 0.8500 (m-40) REVERT: G 166 ILE cc_start: 0.9405 (mt) cc_final: 0.8711 (tp) REVERT: G 167 ASP cc_start: 0.8000 (t0) cc_final: 0.7670 (t0) REVERT: H 3 ASP cc_start: 0.8592 (p0) cc_final: 0.8298 (p0) REVERT: H 44 ILE cc_start: 0.9634 (tt) cc_final: 0.9430 (tt) REVERT: H 67 ILE cc_start: 0.9477 (pt) cc_final: 0.9180 (tt) REVERT: H 88 MET cc_start: 0.7836 (mtm) cc_final: 0.7470 (mtm) REVERT: H 145 ASN cc_start: 0.7505 (m-40) cc_final: 0.7060 (m-40) REVERT: I 37 SER cc_start: 0.8990 (p) cc_final: 0.8633 (p) REVERT: I 51 LEU cc_start: 0.8909 (mt) cc_final: 0.8447 (mt) REVERT: I 62 LYS cc_start: 0.9202 (tptm) cc_final: 0.8844 (tptt) REVERT: I 73 GLN cc_start: 0.9281 (pm20) cc_final: 0.8955 (pm20) REVERT: I 94 MET cc_start: 0.8346 (mmm) cc_final: 0.8101 (tpp) REVERT: I 110 TYR cc_start: 0.7922 (m-80) cc_final: 0.7329 (m-10) REVERT: I 119 ASN cc_start: 0.8491 (m110) cc_final: 0.7691 (m110) REVERT: I 166 ILE cc_start: 0.9755 (tt) cc_final: 0.9246 (tt) REVERT: I 173 LEU cc_start: 0.9431 (mt) cc_final: 0.9176 (tp) REVERT: J 17 GLU cc_start: 0.8024 (mp0) cc_final: 0.7800 (mp0) REVERT: J 35 ASN cc_start: 0.8432 (m110) cc_final: 0.7824 (t0) REVERT: J 91 ILE cc_start: 0.9412 (tp) cc_final: 0.9124 (tt) REVERT: J 97 TYR cc_start: 0.8839 (m-10) cc_final: 0.8241 (m-10) REVERT: J 112 LEU cc_start: 0.9500 (mp) cc_final: 0.8800 (mm) REVERT: K 90 TYR cc_start: 0.9105 (m-10) cc_final: 0.8860 (m-80) REVERT: K 129 TYR cc_start: 0.8297 (m-80) cc_final: 0.7852 (m-10) REVERT: K 139 ASN cc_start: 0.7895 (m110) cc_final: 0.7631 (t0) REVERT: K 161 GLU cc_start: 0.8121 (tp30) cc_final: 0.7671 (tp30) REVERT: L 7 LYS cc_start: 0.9059 (ttpp) cc_final: 0.8851 (ptmm) REVERT: L 13 ASP cc_start: 0.8331 (t70) cc_final: 0.8130 (t0) REVERT: L 49 SER cc_start: 0.9205 (t) cc_final: 0.8975 (m) REVERT: L 59 LEU cc_start: 0.9506 (tp) cc_final: 0.9133 (tp) REVERT: L 80 ARG cc_start: 0.8004 (mtm-85) cc_final: 0.7729 (mtt-85) REVERT: L 81 MET cc_start: 0.9022 (tpp) cc_final: 0.8371 (tpp) REVERT: L 88 MET cc_start: 0.7698 (mtm) cc_final: 0.6718 (mtp) REVERT: L 89 GLU cc_start: 0.7787 (pp20) cc_final: 0.7464 (tm-30) REVERT: L 120 GLN cc_start: 0.8837 (tm-30) cc_final: 0.8328 (tm-30) REVERT: L 135 LYS cc_start: 0.8689 (mmtm) cc_final: 0.8453 (mttm) REVERT: L 137 LYS cc_start: 0.9478 (tttt) cc_final: 0.8868 (ttmt) REVERT: L 159 MET cc_start: 0.8642 (mmt) cc_final: 0.8419 (mmt) REVERT: L 161 GLU cc_start: 0.8350 (tt0) cc_final: 0.7786 (tp30) REVERT: M 9 ILE cc_start: 0.9250 (tp) cc_final: 0.8421 (tp) REVERT: M 83 LYS cc_start: 0.8850 (mmtp) cc_final: 0.8284 (mmmm) REVERT: M 115 LEU cc_start: 0.9082 (tt) cc_final: 0.8621 (tp) REVERT: M 118 ILE cc_start: 0.9431 (mm) cc_final: 0.9160 (mm) REVERT: M 129 TYR cc_start: 0.8033 (m-80) cc_final: 0.7772 (m-80) REVERT: M 135 TYR cc_start: 0.8962 (t80) cc_final: 0.8721 (t80) REVERT: M 171 ASN cc_start: 0.7945 (p0) cc_final: 0.7536 (p0) REVERT: N 45 THR cc_start: 0.8399 (t) cc_final: 0.8154 (t) REVERT: N 65 GLN cc_start: 0.7715 (mp10) cc_final: 0.7356 (mp10) REVERT: N 66 LEU cc_start: 0.8828 (mt) cc_final: 0.8517 (mt) REVERT: N 88 MET cc_start: 0.8458 (ttp) cc_final: 0.6677 (tpp) REVERT: N 97 TYR cc_start: 0.8624 (m-10) cc_final: 0.7916 (m-80) REVERT: N 103 ASP cc_start: 0.7227 (t0) cc_final: 0.6888 (t0) REVERT: N 118 THR cc_start: 0.9331 (p) cc_final: 0.9101 (t) REVERT: N 136 MET cc_start: 0.8747 (mtm) cc_final: 0.6648 (mtm) REVERT: N 141 ILE cc_start: 0.9030 (tp) cc_final: 0.8668 (tp) REVERT: O 25 GLN cc_start: 0.7532 (mt0) cc_final: 0.7282 (mt0) REVERT: O 59 VAL cc_start: 0.8688 (p) cc_final: 0.8163 (m) REVERT: O 91 TYR cc_start: 0.9372 (m-80) cc_final: 0.8846 (m-80) REVERT: O 96 THR cc_start: 0.9283 (p) cc_final: 0.9038 (t) REVERT: O 99 LEU cc_start: 0.9275 (mt) cc_final: 0.9024 (tp) REVERT: O 104 THR cc_start: 0.8627 (p) cc_final: 0.8004 (p) REVERT: O 129 TYR cc_start: 0.8534 (m-80) cc_final: 0.7621 (m-80) REVERT: O 134 LYS cc_start: 0.8693 (pptt) cc_final: 0.8261 (pptt) REVERT: P 1 MET cc_start: 0.5978 (ptt) cc_final: 0.5553 (ptt) REVERT: P 29 ASN cc_start: 0.7937 (m-40) cc_final: 0.7649 (m110) REVERT: P 81 MET cc_start: 0.8671 (tpp) cc_final: 0.8408 (tpp) REVERT: P 88 MET cc_start: 0.8409 (mmm) cc_final: 0.8080 (mmm) REVERT: P 97 TYR cc_start: 0.8876 (m-10) cc_final: 0.8482 (m-10) REVERT: P 122 LEU cc_start: 0.8255 (mm) cc_final: 0.7975 (mm) REVERT: P 158 LEU cc_start: 0.9209 (mm) cc_final: 0.8698 (mt) REVERT: P 162 ILE cc_start: 0.9079 (pt) cc_final: 0.8830 (pt) REVERT: Q 7 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7905 (mm-30) REVERT: Q 37 SER cc_start: 0.7830 (m) cc_final: 0.7151 (p) REVERT: Q 69 MET cc_start: 0.7040 (ptm) cc_final: 0.6478 (ptm) REVERT: Q 73 GLN cc_start: 0.8251 (pm20) cc_final: 0.7662 (pm20) REVERT: Q 94 MET cc_start: 0.5911 (tpp) cc_final: 0.5651 (tpp) REVERT: Q 98 CYS cc_start: 0.8262 (m) cc_final: 0.7723 (m) REVERT: Q 107 MET cc_start: 0.7924 (ttm) cc_final: 0.7620 (mtp) REVERT: Q 134 LYS cc_start: 0.7096 (tptt) cc_final: 0.6875 (tptt) REVERT: R 39 ASP cc_start: 0.7927 (m-30) cc_final: 0.7366 (m-30) REVERT: R 49 SER cc_start: 0.9234 (p) cc_final: 0.8858 (t) REVERT: R 80 ARG cc_start: 0.8257 (mtm-85) cc_final: 0.8021 (mtm-85) REVERT: R 85 LEU cc_start: 0.9499 (mt) cc_final: 0.9209 (tp) REVERT: R 90 ILE cc_start: 0.9027 (mm) cc_final: 0.8760 (mt) REVERT: R 93 ARG cc_start: 0.7929 (ttp80) cc_final: 0.7609 (ttp80) REVERT: R 111 CYS cc_start: 0.7096 (t) cc_final: 0.6462 (t) REVERT: R 118 THR cc_start: 0.8647 (p) cc_final: 0.8385 (p) REVERT: R 128 SER cc_start: 0.8628 (m) cc_final: 0.8251 (m) REVERT: R 135 LYS cc_start: 0.7778 (mtmm) cc_final: 0.7562 (ptpp) REVERT: R 136 MET cc_start: 0.8444 (ttp) cc_final: 0.8102 (tmm) REVERT: R 159 MET cc_start: 0.8229 (mmp) cc_final: 0.7634 (ptt) REVERT: R 168 ARG cc_start: 0.8615 (ttt90) cc_final: 0.8274 (tpp80) REVERT: S 18 PHE cc_start: 0.6214 (m-10) cc_final: 0.5951 (m-10) REVERT: S 37 SER cc_start: 0.8318 (p) cc_final: 0.7809 (p) REVERT: S 49 GLN cc_start: 0.8348 (tp-100) cc_final: 0.7556 (pm20) REVERT: S 51 LEU cc_start: 0.8472 (mp) cc_final: 0.8255 (mm) REVERT: S 53 ASP cc_start: 0.8108 (m-30) cc_final: 0.7906 (m-30) REVERT: S 73 GLN cc_start: 0.9019 (pm20) cc_final: 0.8179 (pm20) REVERT: S 79 GLU cc_start: 0.7701 (mp0) cc_final: 0.7452 (tm-30) REVERT: S 90 TYR cc_start: 0.8198 (m-10) cc_final: 0.7611 (m-10) REVERT: S 97 TYR cc_start: 0.9145 (m-80) cc_final: 0.7901 (m-80) REVERT: S 112 ILE cc_start: 0.9563 (mm) cc_final: 0.8980 (tp) REVERT: S 115 LEU cc_start: 0.8480 (tp) cc_final: 0.8172 (tp) REVERT: S 127 SER cc_start: 0.8894 (t) cc_final: 0.8687 (t) REVERT: S 131 GLU cc_start: 0.8295 (tm-30) cc_final: 0.8059 (tm-30) REVERT: S 134 LYS cc_start: 0.9487 (mmpt) cc_final: 0.9264 (mmmm) REVERT: S 137 LYS cc_start: 0.9315 (ttpt) cc_final: 0.8901 (tptt) REVERT: T 13 ASP cc_start: 0.8616 (t70) cc_final: 0.8163 (t0) REVERT: T 15 ARG cc_start: 0.7847 (mtp85) cc_final: 0.7154 (mmp80) REVERT: T 19 LEU cc_start: 0.8126 (mt) cc_final: 0.7531 (mm) REVERT: T 23 GLN cc_start: 0.8408 (mt0) cc_final: 0.8098 (mp10) REVERT: T 25 ASP cc_start: 0.8712 (m-30) cc_final: 0.8401 (m-30) REVERT: T 27 LEU cc_start: 0.8836 (mt) cc_final: 0.8606 (mt) REVERT: T 46 SER cc_start: 0.9155 (p) cc_final: 0.8948 (t) REVERT: T 47 ASN cc_start: 0.7907 (t0) cc_final: 0.7457 (t0) REVERT: T 156 SER cc_start: 0.8392 (m) cc_final: 0.8067 (m) REVERT: U 28 ASP cc_start: 0.7538 (t0) cc_final: 0.7062 (t0) REVERT: U 32 LYS cc_start: 0.9203 (tmmt) cc_final: 0.8991 (tmmt) REVERT: U 69 MET cc_start: 0.7970 (mtt) cc_final: 0.7199 (tpp) REVERT: U 109 GLU cc_start: 0.8396 (tm-30) cc_final: 0.7801 (tm-30) REVERT: U 123 ASP cc_start: 0.8431 (t0) cc_final: 0.7671 (t0) REVERT: U 131 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8285 (mm-30) REVERT: U 134 LYS cc_start: 0.9046 (tppp) cc_final: 0.8791 (tppp) REVERT: U 150 VAL cc_start: 0.9515 (t) cc_final: 0.9286 (p) REVERT: U 163 ASN cc_start: 0.9219 (m-40) cc_final: 0.8974 (m110) REVERT: U 171 ASN cc_start: 0.8728 (t0) cc_final: 0.8251 (t0) REVERT: U 174 SER cc_start: 0.7869 (t) cc_final: 0.7584 (t) REVERT: V 11 GLN cc_start: 0.8598 (tt0) cc_final: 0.7956 (tp40) REVERT: V 13 ASP cc_start: 0.8107 (t0) cc_final: 0.7857 (t0) REVERT: V 60 PHE cc_start: 0.8674 (m-80) cc_final: 0.8270 (m-80) REVERT: V 62 GLU cc_start: 0.7394 (pp20) cc_final: 0.6910 (pp20) REVERT: V 68 GLN cc_start: 0.8564 (pt0) cc_final: 0.8248 (pt0) REVERT: V 78 ASN cc_start: 0.6831 (t0) cc_final: 0.6341 (t0) REVERT: V 81 MET cc_start: 0.8622 (tpp) cc_final: 0.8226 (tpp) REVERT: V 113 ASN cc_start: 0.9075 (t0) cc_final: 0.8156 (t0) REVERT: V 124 THR cc_start: 0.8664 (m) cc_final: 0.8261 (p) REVERT: V 137 LYS cc_start: 0.9240 (tttm) cc_final: 0.8953 (tptp) REVERT: V 162 ILE cc_start: 0.8574 (mt) cc_final: 0.8263 (mt) REVERT: W 42 ARG cc_start: 0.7326 (ttm170) cc_final: 0.6254 (tpp80) REVERT: W 61 GLN cc_start: 0.8254 (mm-40) cc_final: 0.8051 (mm-40) REVERT: W 94 MET cc_start: 0.6993 (mmp) cc_final: 0.6679 (mmp) REVERT: W 97 TYR cc_start: 0.7517 (m-10) cc_final: 0.6929 (m-80) REVERT: W 111 LEU cc_start: 0.7985 (pt) cc_final: 0.7212 (pp) REVERT: W 115 LEU cc_start: 0.7604 (mt) cc_final: 0.7357 (mt) REVERT: W 163 ASN cc_start: 0.7402 (m-40) cc_final: 0.6906 (m-40) REVERT: X 88 MET cc_start: 0.8940 (ttm) cc_final: 0.8701 (ttt) REVERT: X 136 MET cc_start: 0.7701 (mmt) cc_final: 0.7320 (mmm) REVERT: X 166 PHE cc_start: 0.7558 (m-80) cc_final: 0.7355 (m-80) REVERT: Y 20 PHE cc_start: 0.7984 (m-80) cc_final: 0.7698 (m-80) REVERT: Y 24 VAL cc_start: 0.8712 (t) cc_final: 0.8323 (t) REVERT: Y 50 VAL cc_start: 0.9359 (t) cc_final: 0.9095 (p) REVERT: Z 76 VAL cc_start: 0.9605 (t) cc_final: 0.9167 (p) REVERT: Z 93 THR cc_start: 0.8867 (m) cc_final: 0.8591 (p) REVERT: Z 115 ILE cc_start: 0.8775 (mt) cc_final: 0.8531 (mm) REVERT: Z 119 ASP cc_start: 0.7458 (m-30) cc_final: 0.7063 (m-30) REVERT: Z 143 PHE cc_start: 0.8758 (m-10) cc_final: 0.8440 (m-80) REVERT: Z 146 TRP cc_start: 0.8370 (m-90) cc_final: 0.7975 (m-90) REVERT: Z 177 ASN cc_start: 0.9106 (t0) cc_final: 0.8479 (t0) REVERT: Z 179 ASP cc_start: 0.8689 (m-30) cc_final: 0.8407 (m-30) REVERT: Z 182 GLN cc_start: 0.8596 (tt0) cc_final: 0.8241 (tt0) REVERT: Z 196 THR cc_start: 0.9180 (p) cc_final: 0.8825 (t) REVERT: Z 264 TYR cc_start: 0.9198 (t80) cc_final: 0.8632 (t80) REVERT: Z 275 GLN cc_start: 0.8601 (mm110) cc_final: 0.8135 (mm-40) REVERT: a 3 ILE cc_start: 0.7309 (mm) cc_final: 0.7003 (mm) REVERT: a 81 ASP cc_start: 0.8338 (t70) cc_final: 0.7936 (t70) REVERT: a 104 ARG cc_start: 0.8593 (ttt90) cc_final: 0.8152 (ttt90) REVERT: a 119 TYR cc_start: 0.7632 (m-80) cc_final: 0.7007 (m-80) REVERT: a 124 GLU cc_start: 0.7927 (tt0) cc_final: 0.7055 (tt0) REVERT: a 177 TYR cc_start: 0.8500 (p90) cc_final: 0.7621 (p90) outliers start: 5 outliers final: 0 residues processed: 1762 average time/residue: 0.2188 time to fit residues: 627.4302 Evaluate side-chains 1425 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1425 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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: 0.7980 chunk 86 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 chunk 160 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 284 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 351 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN F 11 GLN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 25 GLN G 139 ASN H 47 ASN ** I 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 63 GLN ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 140 HIS ** 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 25 GLN ** S 140 HIS ** 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** V 134 GLN V 145 ASN ** W 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 99 ASN ** Z 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 166 ASN ** Z 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 285 ASN ** a 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.114282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.095820 restraints weight = 123040.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.099708 restraints weight = 59220.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.102310 restraints weight = 33757.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.104025 restraints weight = 21306.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.105135 restraints weight = 14757.248| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3366 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 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 = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3366 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4906 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= 0.161 Angle : 0.757 43.076 49243 Z= 0.354 Chirality : 0.039 0.209 5448 Planarity : 0.005 0.082 6402 Dihedral : 11.466 89.614 5519 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.41 % Favored : 97.53 % 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: 1.22 (0.12), residues: 4448 helix: 1.27 (0.08), residues: 3401 sheet: 2.11 (0.80), residues: 28 loop : -0.62 (0.22), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 15 TYR 0.024 0.002 TYR V 97 PHE 0.028 0.002 PHE X 24 TRP 0.011 0.001 TRP C 128 HIS 0.006 0.002 HIS M 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (36155) covalent geometry : angle 0.75750 / 0.35 (49243) hydrogen bonds : bond 0.04614 / 3.08 ( 2648) hydrogen bonds : angle 4.26911 / 3.11 ( 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 1696 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1690 time to evaluate : 1.336 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 1 MET cc_start: 0.7992 (tpp) cc_final: 0.7270 (tpp) REVERT: A 15 GLN cc_start: 0.8331 (mt0) cc_final: 0.7714 (mt0) REVERT: A 18 PHE cc_start: 0.8071 (m-80) cc_final: 0.7043 (m-80) REVERT: A 30 ARG cc_start: 0.8381 (tpt-90) cc_final: 0.8112 (tmt170) REVERT: A 38 MET cc_start: 0.8588 (mmt) cc_final: 0.7829 (tmm) REVERT: A 62 LYS cc_start: 0.9073 (tmtt) cc_final: 0.8832 (tptt) REVERT: A 90 TYR cc_start: 0.8954 (m-10) cc_final: 0.8403 (m-80) REVERT: A 109 GLU cc_start: 0.8436 (mm-30) cc_final: 0.7899 (mt-10) REVERT: A 115 LEU cc_start: 0.7674 (pp) cc_final: 0.7409 (pp) REVERT: A 131 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7251 (tm-30) REVERT: A 167 ASP cc_start: 0.8241 (t0) cc_final: 0.7450 (t0) REVERT: B 36 LYS cc_start: 0.9555 (mtmm) cc_final: 0.8625 (mppt) REVERT: B 44 ILE cc_start: 0.9363 (mt) cc_final: 0.9160 (tp) REVERT: B 89 GLU cc_start: 0.8597 (pt0) cc_final: 0.8292 (tt0) REVERT: B 120 GLN cc_start: 0.7877 (mt0) cc_final: 0.7399 (tm-30) REVERT: B 136 MET cc_start: 0.7800 (mtt) cc_final: 0.7495 (mtt) REVERT: C 17 ARG cc_start: 0.8459 (ptt90) cc_final: 0.7961 (ptt90) REVERT: C 60 TYR cc_start: 0.5964 (m-80) cc_final: 0.4922 (m-80) REVERT: C 63 PHE cc_start: 0.9031 (m-80) cc_final: 0.8540 (m-10) REVERT: C 69 MET cc_start: 0.7503 (ttm) cc_final: 0.7112 (ttm) REVERT: C 91 TYR cc_start: 0.9126 (m-80) cc_final: 0.8764 (m-80) REVERT: C 94 MET cc_start: 0.9388 (mmt) cc_final: 0.8995 (mmm) REVERT: C 109 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7972 (tp30) REVERT: C 117 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8504 (mm-30) REVERT: D 29 ASN cc_start: 0.9142 (t0) cc_final: 0.8712 (t0) REVERT: D 41 VAL cc_start: 0.9010 (p) cc_final: 0.8702 (p) REVERT: D 49 SER cc_start: 0.8982 (p) cc_final: 0.8692 (p) REVERT: D 88 MET cc_start: 0.8082 (ttm) cc_final: 0.7655 (mmm) REVERT: D 97 TYR cc_start: 0.7922 (m-10) cc_final: 0.6708 (m-80) REVERT: D 113 ASN cc_start: 0.7888 (t0) cc_final: 0.7678 (t0) REVERT: D 128 SER cc_start: 0.9252 (p) cc_final: 0.8838 (m) REVERT: D 134 GLN cc_start: 0.8539 (mt0) cc_final: 0.8263 (mt0) REVERT: D 154 ASP cc_start: 0.6779 (t0) cc_final: 0.6477 (t0) REVERT: E 7 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7841 (mm-30) REVERT: E 15 GLN cc_start: 0.7319 (mt0) cc_final: 0.7036 (mt0) REVERT: E 25 GLN cc_start: 0.8466 (mt0) cc_final: 0.8072 (mm-40) REVERT: E 28 ASP cc_start: 0.8666 (t70) cc_final: 0.8332 (t0) REVERT: E 38 MET cc_start: 0.8131 (mmt) cc_final: 0.7689 (tmm) REVERT: E 47 ASN cc_start: 0.8145 (t0) cc_final: 0.7730 (t0) REVERT: E 62 LYS cc_start: 0.8896 (tptt) cc_final: 0.8647 (tppt) REVERT: E 72 SER cc_start: 0.8894 (m) cc_final: 0.8496 (t) REVERT: E 73 GLN cc_start: 0.8582 (pm20) cc_final: 0.8208 (pm20) REVERT: E 109 GLU cc_start: 0.8501 (tt0) cc_final: 0.8276 (tt0) REVERT: E 121 THR cc_start: 0.9070 (p) cc_final: 0.8650 (t) REVERT: E 129 TYR cc_start: 0.8537 (m-10) cc_final: 0.7969 (m-10) REVERT: E 140 HIS cc_start: 0.8594 (p90) cc_final: 0.8207 (p-80) REVERT: E 163 ASN cc_start: 0.9193 (m-40) cc_final: 0.8971 (m-40) REVERT: E 167 ASP cc_start: 0.8258 (t0) cc_final: 0.7183 (t0) REVERT: E 171 ASN cc_start: 0.8611 (p0) cc_final: 0.8313 (p0) REVERT: E 173 LEU cc_start: 0.9158 (mm) cc_final: 0.8889 (mm) REVERT: F 11 GLN cc_start: 0.8871 (tt0) cc_final: 0.8452 (tt0) REVERT: F 21 ASN cc_start: 0.8080 (m-40) cc_final: 0.6669 (t0) REVERT: F 25 ASP cc_start: 0.8843 (m-30) cc_final: 0.8569 (m-30) REVERT: F 60 PHE cc_start: 0.8634 (m-10) cc_final: 0.8254 (m-10) REVERT: F 65 GLN cc_start: 0.8227 (pt0) cc_final: 0.7942 (pt0) REVERT: F 81 MET cc_start: 0.9122 (tpp) cc_final: 0.8650 (tpt) REVERT: F 93 ARG cc_start: 0.8687 (ttp80) cc_final: 0.8112 (ttp-110) REVERT: F 103 ASP cc_start: 0.8209 (t0) cc_final: 0.7956 (t0) REVERT: F 116 ARG cc_start: 0.8492 (tpt-90) cc_final: 0.8219 (tpt-90) REVERT: F 146 ASP cc_start: 0.8114 (t0) cc_final: 0.7615 (t0) REVERT: F 161 GLU cc_start: 0.8318 (tp30) cc_final: 0.7724 (tp30) REVERT: G 27 VAL cc_start: 0.8921 (t) cc_final: 0.8704 (p) REVERT: G 37 SER cc_start: 0.9383 (p) cc_final: 0.9167 (p) REVERT: G 38 MET cc_start: 0.9052 (mtm) cc_final: 0.8410 (ttm) REVERT: G 49 GLN cc_start: 0.8840 (pp30) cc_final: 0.8557 (pp30) REVERT: G 61 GLN cc_start: 0.8580 (mt0) cc_final: 0.8321 (mp10) REVERT: G 62 LYS cc_start: 0.9017 (tptm) cc_final: 0.8762 (tppt) REVERT: G 86 ARG cc_start: 0.8576 (ttp-170) cc_final: 0.8036 (tmm-80) REVERT: G 97 TYR cc_start: 0.8927 (m-10) cc_final: 0.8637 (m-10) REVERT: G 98 CYS cc_start: 0.8299 (p) cc_final: 0.7707 (m) REVERT: G 116 SER cc_start: 0.9246 (p) cc_final: 0.9018 (m) REVERT: G 117 GLU cc_start: 0.7771 (tt0) cc_final: 0.7426 (tp30) REVERT: G 122 PHE cc_start: 0.8870 (m-80) cc_final: 0.8661 (m-80) REVERT: G 123 ASP cc_start: 0.8041 (t0) cc_final: 0.7838 (t70) REVERT: G 124 LEU cc_start: 0.9034 (mt) cc_final: 0.8506 (mt) REVERT: G 161 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8002 (mt-10) REVERT: G 166 ILE cc_start: 0.9186 (mt) cc_final: 0.8514 (tp) REVERT: H 1 MET cc_start: 0.6164 (mpp) cc_final: 0.5863 (mpp) REVERT: H 67 ILE cc_start: 0.9514 (pt) cc_final: 0.9208 (tt) REVERT: H 145 ASN cc_start: 0.7163 (m-40) cc_final: 0.6293 (m-40) REVERT: H 173 VAL cc_start: 0.8525 (t) cc_final: 0.8319 (t) REVERT: I 15 GLN cc_start: 0.7887 (mt0) cc_final: 0.7648 (mp10) REVERT: I 62 LYS cc_start: 0.9235 (tptm) cc_final: 0.8864 (tptt) REVERT: I 73 GLN cc_start: 0.9238 (pm20) cc_final: 0.8885 (pm20) REVERT: I 94 MET cc_start: 0.8361 (mmm) cc_final: 0.8107 (tpp) REVERT: I 110 TYR cc_start: 0.7972 (m-80) cc_final: 0.7530 (m-10) REVERT: I 115 LEU cc_start: 0.8908 (tp) cc_final: 0.8205 (tp) REVERT: I 119 ASN cc_start: 0.8705 (m110) cc_final: 0.8084 (m110) REVERT: I 127 SER cc_start: 0.9260 (p) cc_final: 0.9032 (p) REVERT: I 129 TYR cc_start: 0.8885 (m-10) cc_final: 0.8578 (m-10) REVERT: I 133 LEU cc_start: 0.9321 (mt) cc_final: 0.8901 (mt) REVERT: J 17 GLU cc_start: 0.8004 (mp0) cc_final: 0.7502 (mp0) REVERT: J 33 GLU cc_start: 0.7385 (mp0) cc_final: 0.7131 (mp0) REVERT: J 88 MET cc_start: 0.9143 (mmm) cc_final: 0.8612 (mmm) REVERT: J 91 ILE cc_start: 0.9460 (tp) cc_final: 0.9163 (tt) REVERT: J 97 TYR cc_start: 0.8787 (m-10) cc_final: 0.8224 (m-10) REVERT: J 112 LEU cc_start: 0.9467 (mp) cc_final: 0.8864 (mm) REVERT: J 136 MET cc_start: 0.9055 (mtp) cc_final: 0.8781 (mtm) REVERT: K 129 TYR cc_start: 0.8567 (m-80) cc_final: 0.8308 (m-80) REVERT: L 2 LEU cc_start: 0.9185 (mt) cc_final: 0.8868 (mt) REVERT: L 7 LYS cc_start: 0.9050 (ttpp) cc_final: 0.8553 (ptmm) REVERT: L 13 ASP cc_start: 0.8306 (t70) cc_final: 0.7988 (t0) REVERT: L 49 SER cc_start: 0.9286 (t) cc_final: 0.9038 (m) REVERT: L 59 LEU cc_start: 0.9571 (tp) cc_final: 0.9334 (tp) REVERT: L 81 MET cc_start: 0.9068 (tpp) cc_final: 0.8363 (tpp) REVERT: L 88 MET cc_start: 0.8089 (mtm) cc_final: 0.7784 (mtp) REVERT: L 89 GLU cc_start: 0.7989 (pp20) cc_final: 0.7559 (tm-30) REVERT: L 103 ASP cc_start: 0.8370 (m-30) cc_final: 0.8064 (m-30) REVERT: L 116 ARG cc_start: 0.8106 (tpp80) cc_final: 0.7727 (tpp80) REVERT: L 120 GLN cc_start: 0.8757 (tm-30) cc_final: 0.8374 (tm-30) REVERT: L 131 VAL cc_start: 0.9611 (t) cc_final: 0.9409 (t) REVERT: L 137 LYS cc_start: 0.9421 (tttt) cc_final: 0.8872 (ttmt) REVERT: L 161 GLU cc_start: 0.8461 (tt0) cc_final: 0.7816 (tp30) REVERT: M 83 LYS cc_start: 0.8812 (mmtp) cc_final: 0.8194 (mmmm) REVERT: M 118 ILE cc_start: 0.9465 (mm) cc_final: 0.9146 (mm) REVERT: M 119 ASN cc_start: 0.8807 (p0) cc_final: 0.8549 (p0) REVERT: M 129 TYR cc_start: 0.7992 (m-80) cc_final: 0.7506 (m-10) REVERT: M 135 TYR cc_start: 0.9043 (t80) cc_final: 0.8835 (t80) REVERT: M 171 ASN cc_start: 0.7976 (p0) cc_final: 0.7510 (p0) REVERT: N 45 THR cc_start: 0.8529 (t) cc_final: 0.8292 (t) REVERT: N 66 LEU cc_start: 0.8881 (mt) cc_final: 0.8498 (mt) REVERT: N 80 ARG cc_start: 0.9044 (mtm-85) cc_final: 0.8739 (mtm-85) REVERT: N 88 MET cc_start: 0.8518 (ttp) cc_final: 0.6729 (tpp) REVERT: N 95 VAL cc_start: 0.9718 (t) cc_final: 0.9354 (p) REVERT: N 97 TYR cc_start: 0.8530 (m-10) cc_final: 0.7953 (m-80) REVERT: N 103 ASP cc_start: 0.7230 (t0) cc_final: 0.6589 (t0) REVERT: N 136 MET cc_start: 0.8696 (mtm) cc_final: 0.6605 (mtm) REVERT: N 165 TYR cc_start: 0.8244 (m-10) cc_final: 0.7898 (m-10) REVERT: O 4 PRO cc_start: 0.8718 (Cg_exo) cc_final: 0.8408 (Cg_endo) REVERT: O 52 ILE cc_start: 0.7966 (pt) cc_final: 0.7704 (pt) REVERT: O 61 GLN cc_start: 0.6866 (mt0) cc_final: 0.6278 (tm-30) REVERT: O 91 TYR cc_start: 0.9357 (m-80) cc_final: 0.8700 (m-80) REVERT: O 96 THR cc_start: 0.9322 (p) cc_final: 0.9069 (t) REVERT: O 104 THR cc_start: 0.9005 (p) cc_final: 0.8190 (p) REVERT: O 111 LEU cc_start: 0.8881 (tt) cc_final: 0.8673 (tp) REVERT: O 129 TYR cc_start: 0.8364 (m-80) cc_final: 0.7557 (m-80) REVERT: P 1 MET cc_start: 0.6070 (ptt) cc_final: 0.5510 (ptt) REVERT: P 29 ASN cc_start: 0.8427 (m-40) cc_final: 0.7995 (m110) REVERT: P 97 TYR cc_start: 0.8901 (m-10) cc_final: 0.8331 (m-10) REVERT: Q 1 MET cc_start: 0.8735 (tpp) cc_final: 0.8529 (tpp) REVERT: Q 7 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7987 (mm-30) REVERT: Q 25 GLN cc_start: 0.8671 (mm-40) cc_final: 0.7966 (mm-40) REVERT: Q 37 SER cc_start: 0.7450 (m) cc_final: 0.6730 (p) REVERT: Q 39 GLU cc_start: 0.7477 (mt-10) cc_final: 0.6735 (pt0) REVERT: Q 94 MET cc_start: 0.5527 (tpp) cc_final: 0.5204 (tpp) REVERT: Q 98 CYS cc_start: 0.8304 (m) cc_final: 0.7862 (m) REVERT: Q 107 MET cc_start: 0.8053 (ttm) cc_final: 0.7797 (mtp) REVERT: Q 134 LYS cc_start: 0.7033 (tptt) cc_final: 0.6832 (tptt) REVERT: R 29 ASN cc_start: 0.7269 (t0) cc_final: 0.6846 (t0) REVERT: R 38 LEU cc_start: 0.8616 (mt) cc_final: 0.8120 (mp) REVERT: R 39 ASP cc_start: 0.7992 (m-30) cc_final: 0.7521 (m-30) REVERT: R 49 SER cc_start: 0.9204 (p) cc_final: 0.8804 (t) REVERT: R 85 LEU cc_start: 0.9602 (mt) cc_final: 0.9274 (tp) REVERT: R 86 ARG cc_start: 0.8224 (tpp80) cc_final: 0.7995 (tpp80) REVERT: R 111 CYS cc_start: 0.8018 (t) cc_final: 0.7563 (t) REVERT: R 118 THR cc_start: 0.8678 (p) cc_final: 0.8453 (p) REVERT: R 128 SER cc_start: 0.8681 (m) cc_final: 0.8329 (m) REVERT: R 135 LYS cc_start: 0.7509 (mtmm) cc_final: 0.7294 (ptpp) REVERT: R 159 MET cc_start: 0.8155 (mmp) cc_final: 0.7485 (ptt) REVERT: S 37 SER cc_start: 0.8477 (p) cc_final: 0.8004 (p) REVERT: S 49 GLN cc_start: 0.8541 (tp-100) cc_final: 0.7846 (pm20) REVERT: S 73 GLN cc_start: 0.8613 (pm20) cc_final: 0.8405 (pm20) REVERT: S 79 GLU cc_start: 0.7794 (mp0) cc_final: 0.7475 (tm-30) REVERT: S 81 LYS cc_start: 0.8585 (mmmt) cc_final: 0.7453 (mtmt) REVERT: S 90 TYR cc_start: 0.8214 (m-10) cc_final: 0.7665 (m-10) REVERT: S 97 TYR cc_start: 0.9106 (m-80) cc_final: 0.8140 (m-80) REVERT: S 112 ILE cc_start: 0.9479 (mm) cc_final: 0.8949 (tp) REVERT: S 115 LEU cc_start: 0.8666 (tp) cc_final: 0.8335 (tp) REVERT: S 134 LYS cc_start: 0.9584 (mmpt) cc_final: 0.9304 (mmmm) REVERT: S 163 ASN cc_start: 0.9404 (m110) cc_final: 0.9047 (m110) REVERT: T 15 ARG cc_start: 0.7658 (mtp85) cc_final: 0.7096 (mmp80) REVERT: T 19 LEU cc_start: 0.8141 (mt) cc_final: 0.7601 (mm) REVERT: T 23 GLN cc_start: 0.8407 (mt0) cc_final: 0.8039 (mp10) REVERT: T 46 SER cc_start: 0.9036 (p) cc_final: 0.8714 (t) REVERT: T 47 ASN cc_start: 0.7877 (t0) cc_final: 0.7379 (t0) REVERT: T 66 LEU cc_start: 0.7922 (pt) cc_final: 0.7592 (pp) REVERT: T 117 GLU cc_start: 0.8913 (tt0) cc_final: 0.8640 (tt0) REVERT: U 28 ASP cc_start: 0.7571 (t0) cc_final: 0.7147 (t0) REVERT: U 33 ARG cc_start: 0.7322 (ttp-170) cc_final: 0.7100 (ttp-170) REVERT: U 98 CYS cc_start: 0.7996 (t) cc_final: 0.7723 (t) REVERT: U 109 GLU cc_start: 0.8393 (tm-30) cc_final: 0.7615 (tm-30) REVERT: U 123 ASP cc_start: 0.8462 (t0) cc_final: 0.7966 (t0) REVERT: U 134 LYS cc_start: 0.8995 (tppp) cc_final: 0.8792 (tppp) REVERT: U 171 ASN cc_start: 0.8834 (t0) cc_final: 0.8531 (t0) REVERT: U 174 SER cc_start: 0.7892 (t) cc_final: 0.7668 (t) REVERT: V 11 GLN cc_start: 0.8533 (tt0) cc_final: 0.8028 (tp40) REVERT: V 29 ASN cc_start: 0.8526 (m-40) cc_final: 0.8226 (t0) REVERT: V 60 PHE cc_start: 0.8860 (m-80) cc_final: 0.8458 (m-80) REVERT: V 62 GLU cc_start: 0.7561 (pp20) cc_final: 0.7125 (pp20) REVERT: V 68 GLN cc_start: 0.8338 (pt0) cc_final: 0.8039 (pt0) REVERT: V 81 MET cc_start: 0.8676 (tpp) cc_final: 0.8442 (tpp) REVERT: V 113 ASN cc_start: 0.9128 (t0) cc_final: 0.8239 (t0) REVERT: V 124 THR cc_start: 0.8701 (m) cc_final: 0.8283 (p) REVERT: V 137 LYS cc_start: 0.9280 (tttm) cc_final: 0.8980 (tttt) REVERT: W 3 THR cc_start: 0.7387 (m) cc_final: 0.7106 (m) REVERT: W 17 ARG cc_start: 0.7628 (ptt-90) cc_final: 0.7418 (ptt90) REVERT: W 42 ARG cc_start: 0.7827 (ttm170) cc_final: 0.6254 (tpt170) REVERT: W 61 GLN cc_start: 0.8276 (mm-40) cc_final: 0.8050 (mm-40) REVERT: W 97 TYR cc_start: 0.7435 (m-10) cc_final: 0.6911 (m-80) REVERT: W 107 MET cc_start: 0.8239 (mmm) cc_final: 0.8034 (mmp) REVERT: X 88 MET cc_start: 0.8983 (ttm) cc_final: 0.8689 (ttt) REVERT: X 89 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7861 (tm-30) REVERT: X 136 MET cc_start: 0.7563 (mmt) cc_final: 0.7283 (mmm) REVERT: X 166 PHE cc_start: 0.7561 (m-80) cc_final: 0.7353 (m-80) REVERT: Y 23 GLU cc_start: 0.6086 (tp30) cc_final: 0.5577 (tp30) REVERT: Y 24 VAL cc_start: 0.9016 (t) cc_final: 0.8774 (t) REVERT: Y 28 ARG cc_start: 0.8679 (tpp80) cc_final: 0.8255 (tpp80) REVERT: Y 50 VAL cc_start: 0.9478 (t) cc_final: 0.9188 (p) REVERT: Z 76 VAL cc_start: 0.9590 (t) cc_final: 0.9346 (p) REVERT: Z 90 ASN cc_start: 0.9088 (m-40) cc_final: 0.8803 (m110) REVERT: Z 93 THR cc_start: 0.8883 (m) cc_final: 0.8534 (p) REVERT: Z 115 ILE cc_start: 0.9042 (mt) cc_final: 0.8712 (mm) REVERT: Z 119 ASP cc_start: 0.7576 (m-30) cc_final: 0.7326 (m-30) REVERT: Z 120 LEU cc_start: 0.9564 (tp) cc_final: 0.9198 (tp) REVERT: Z 124 GLU cc_start: 0.7562 (pm20) cc_final: 0.7345 (pm20) REVERT: Z 129 ASP cc_start: 0.8553 (t0) cc_final: 0.8298 (t0) REVERT: Z 143 PHE cc_start: 0.8866 (m-10) cc_final: 0.8430 (m-10) REVERT: Z 177 ASN cc_start: 0.8721 (t0) cc_final: 0.8474 (t0) REVERT: Z 179 ASP cc_start: 0.8769 (m-30) cc_final: 0.8463 (m-30) REVERT: Z 182 GLN cc_start: 0.8653 (tt0) cc_final: 0.8341 (tt0) REVERT: Z 196 THR cc_start: 0.9127 (p) cc_final: 0.8739 (t) REVERT: Z 264 TYR cc_start: 0.9262 (t80) cc_final: 0.8636 (t80) REVERT: Z 275 GLN cc_start: 0.8534 (mm110) cc_final: 0.8185 (mm-40) REVERT: a 3 ILE cc_start: 0.6988 (mm) cc_final: 0.6732 (mm) REVERT: a 77 ILE cc_start: 0.9065 (pt) cc_final: 0.8850 (pt) REVERT: a 84 ARG cc_start: 0.8738 (ttm110) cc_final: 0.8156 (ttm-80) REVERT: a 104 ARG cc_start: 0.8552 (ttt90) cc_final: 0.8200 (ttt90) REVERT: a 151 GLN cc_start: 0.9075 (mm-40) cc_final: 0.8185 (mt0) REVERT: a 170 PHE cc_start: 0.8267 (m-10) cc_final: 0.7393 (m-80) outliers start: 6 outliers final: 0 residues processed: 1693 average time/residue: 0.2183 time to fit residues: 600.3384 Evaluate side-chains 1393 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1393 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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: 7.9990 chunk 309 optimal weight: 1.9990 chunk 232 optimal weight: 10.0000 chunk 284 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 chunk 391 optimal weight: 9.9990 chunk 174 optimal weight: 2.9990 chunk 333 optimal weight: 1.9990 chunk 314 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 179 optimal weight: 5.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 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 G 21 ASN G 25 GLN H 47 ASN H 78 ASN ** I 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 119 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** S 171 ASN ** U 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 145 ASN ** W 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 23 GLN ** Z 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 141 ASN Z 166 ASN ** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.114710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.096628 restraints weight = 119873.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.100483 restraints weight = 57668.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.102975 restraints weight = 32692.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.104651 restraints weight = 20758.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.105725 restraints weight = 14438.857| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3379 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3379 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.5307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 36155 Z= 0.150 Angle : 0.744 42.983 49243 Z= 0.351 Chirality : 0.039 0.223 5448 Planarity : 0.005 0.062 6402 Dihedral : 11.499 89.938 5519 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.34 % Favored : 97.59 % Rotamer: Outliers : 0.12 % Allowed : 2.33 % Favored : 97.55 % 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: 1.24 (0.13), residues: 4448 helix: 1.28 (0.08), residues: 3402 sheet: 2.09 (0.80), residues: 28 loop : -0.61 (0.22), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 86 TYR 0.046 0.002 TYR M 97 PHE 0.024 0.002 PHE J 166 TRP 0.015 0.001 TRP C 128 HIS 0.006 0.002 HIS M 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (36155) covalent geometry : angle 0.74365 / 0.35 (49243) hydrogen bonds : bond 0.04413 / 2.95 ( 2648) hydrogen bonds : angle 4.19989 / 3.06 ( 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 1671 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1667 time to evaluate : 1.339 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 18 PHE cc_start: 0.8109 (m-80) cc_final: 0.7163 (m-80) REVERT: A 30 ARG cc_start: 0.8471 (tpt-90) cc_final: 0.8199 (tmt170) REVERT: A 38 MET cc_start: 0.8588 (mmt) cc_final: 0.7880 (tmm) REVERT: A 49 GLN cc_start: 0.8161 (mm-40) cc_final: 0.6800 (mm-40) REVERT: A 59 VAL cc_start: 0.9472 (t) cc_final: 0.9266 (t) REVERT: A 90 TYR cc_start: 0.8646 (m-10) cc_final: 0.7972 (m-80) REVERT: A 98 CYS cc_start: 0.8589 (t) cc_final: 0.7341 (t) REVERT: A 109 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7870 (mt-10) REVERT: A 115 LEU cc_start: 0.7672 (pp) cc_final: 0.7440 (pp) REVERT: A 131 GLU cc_start: 0.7547 (tm-30) cc_final: 0.7220 (tm-30) REVERT: A 165 TYR cc_start: 0.8569 (m-10) cc_final: 0.8293 (m-80) REVERT: A 167 ASP cc_start: 0.8144 (t0) cc_final: 0.7617 (t0) REVERT: A 171 ASN cc_start: 0.8497 (m-40) cc_final: 0.8172 (m-40) REVERT: B 25 ASP cc_start: 0.8273 (p0) cc_final: 0.7686 (p0) REVERT: B 35 ASN cc_start: 0.8556 (m-40) cc_final: 0.7682 (t0) REVERT: B 36 LYS cc_start: 0.9529 (mtmm) cc_final: 0.8619 (mppt) REVERT: B 59 LEU cc_start: 0.8768 (mm) cc_final: 0.8463 (tt) REVERT: B 88 MET cc_start: 0.6959 (tmm) cc_final: 0.6246 (tmm) REVERT: B 120 GLN cc_start: 0.7834 (mt0) cc_final: 0.7396 (tm-30) REVERT: C 60 TYR cc_start: 0.5889 (m-80) cc_final: 0.5120 (m-80) REVERT: C 63 PHE cc_start: 0.8957 (m-80) cc_final: 0.8623 (m-10) REVERT: C 69 MET cc_start: 0.7611 (ttm) cc_final: 0.7201 (ttm) REVERT: C 94 MET cc_start: 0.9367 (mmt) cc_final: 0.9056 (mmm) REVERT: C 117 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8672 (mm-30) REVERT: C 133 LEU cc_start: 0.8583 (mp) cc_final: 0.8298 (mp) REVERT: D 3 ASP cc_start: 0.8365 (p0) cc_final: 0.8002 (p0) REVERT: D 88 MET cc_start: 0.8231 (ttm) cc_final: 0.7822 (mmm) REVERT: D 113 ASN cc_start: 0.7911 (t0) cc_final: 0.7563 (t0) REVERT: D 115 LEU cc_start: 0.8459 (tt) cc_final: 0.8206 (tt) REVERT: D 124 THR cc_start: 0.8981 (m) cc_final: 0.8778 (m) REVERT: D 128 SER cc_start: 0.9241 (p) cc_final: 0.8914 (m) REVERT: D 134 GLN cc_start: 0.8599 (mt0) cc_final: 0.8257 (mt0) REVERT: D 154 ASP cc_start: 0.6952 (t0) cc_final: 0.6484 (t0) REVERT: E 7 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7608 (mm-30) REVERT: E 28 ASP cc_start: 0.8690 (t70) cc_final: 0.8353 (t0) REVERT: E 38 MET cc_start: 0.8271 (mmt) cc_final: 0.7812 (tmm) REVERT: E 69 MET cc_start: 0.8478 (mtp) cc_final: 0.7908 (ttm) REVERT: E 72 SER cc_start: 0.8887 (m) cc_final: 0.8343 (t) REVERT: E 73 GLN cc_start: 0.9149 (pm20) cc_final: 0.7795 (pm20) REVERT: E 109 GLU cc_start: 0.8535 (tt0) cc_final: 0.8273 (tt0) REVERT: E 121 THR cc_start: 0.9165 (p) cc_final: 0.8686 (t) REVERT: E 140 HIS cc_start: 0.8588 (p90) cc_final: 0.8055 (p-80) REVERT: E 167 ASP cc_start: 0.8344 (t0) cc_final: 0.7073 (t0) REVERT: E 168 TYR cc_start: 0.8596 (t80) cc_final: 0.7992 (t80) REVERT: E 171 ASN cc_start: 0.8701 (p0) cc_final: 0.8284 (p0) REVERT: E 173 LEU cc_start: 0.8875 (mm) cc_final: 0.8672 (mm) REVERT: F 11 GLN cc_start: 0.9084 (tt0) cc_final: 0.8409 (tt0) REVERT: F 21 ASN cc_start: 0.8056 (m-40) cc_final: 0.6624 (t0) REVERT: F 25 ASP cc_start: 0.8932 (m-30) cc_final: 0.8657 (m-30) REVERT: F 60 PHE cc_start: 0.8391 (m-10) cc_final: 0.7971 (m-10) REVERT: F 81 MET cc_start: 0.9180 (tpp) cc_final: 0.8711 (tpt) REVERT: F 109 ASP cc_start: 0.8792 (m-30) cc_final: 0.8539 (m-30) REVERT: F 146 ASP cc_start: 0.8221 (t0) cc_final: 0.7919 (t0) REVERT: G 27 VAL cc_start: 0.9027 (t) cc_final: 0.8805 (p) REVERT: G 38 MET cc_start: 0.9125 (mtm) cc_final: 0.8399 (ttm) REVERT: G 61 GLN cc_start: 0.8565 (mt0) cc_final: 0.8319 (mp10) REVERT: G 62 LYS cc_start: 0.9016 (tptm) cc_final: 0.8762 (tppt) REVERT: G 97 TYR cc_start: 0.8961 (m-10) cc_final: 0.8667 (m-10) REVERT: G 98 CYS cc_start: 0.8384 (p) cc_final: 0.7769 (m) REVERT: G 116 SER cc_start: 0.9079 (p) cc_final: 0.8801 (m) REVERT: G 117 GLU cc_start: 0.7731 (tt0) cc_final: 0.6886 (tp30) REVERT: G 124 LEU cc_start: 0.9094 (mt) cc_final: 0.8543 (mt) REVERT: G 135 TYR cc_start: 0.8451 (t80) cc_final: 0.8241 (t80) REVERT: G 161 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8348 (mt-10) REVERT: G 163 ASN cc_start: 0.9201 (m-40) cc_final: 0.7967 (m-40) REVERT: G 166 ILE cc_start: 0.9369 (mt) cc_final: 0.8613 (tp) REVERT: H 1 MET cc_start: 0.6060 (mpp) cc_final: 0.5782 (mpp) REVERT: H 88 MET cc_start: 0.7829 (mtm) cc_final: 0.7490 (mtm) REVERT: H 91 ILE cc_start: 0.9493 (mm) cc_final: 0.9152 (tp) REVERT: H 145 ASN cc_start: 0.7663 (m-40) cc_final: 0.7044 (m-40) REVERT: H 159 MET cc_start: 0.8202 (mmm) cc_final: 0.7760 (mmt) REVERT: I 51 LEU cc_start: 0.8810 (mt) cc_final: 0.8355 (mt) REVERT: I 62 LYS cc_start: 0.9297 (tptm) cc_final: 0.8889 (tptt) REVERT: I 73 GLN cc_start: 0.9233 (pm20) cc_final: 0.8906 (pm20) REVERT: I 110 TYR cc_start: 0.8034 (m-80) cc_final: 0.7548 (m-10) REVERT: I 115 LEU cc_start: 0.8838 (tp) cc_final: 0.8015 (tp) REVERT: I 119 ASN cc_start: 0.8652 (m110) cc_final: 0.8008 (m110) REVERT: I 127 SER cc_start: 0.9115 (p) cc_final: 0.8866 (p) REVERT: J 17 GLU cc_start: 0.8244 (mp0) cc_final: 0.7795 (mp0) REVERT: J 35 ASN cc_start: 0.8755 (m110) cc_final: 0.7880 (t0) REVERT: J 91 ILE cc_start: 0.9382 (tp) cc_final: 0.9143 (tp) REVERT: J 97 TYR cc_start: 0.8700 (m-10) cc_final: 0.8126 (m-10) REVERT: J 107 LEU cc_start: 0.9134 (tp) cc_final: 0.8928 (tp) REVERT: J 112 LEU cc_start: 0.9502 (mp) cc_final: 0.8957 (mm) REVERT: K 33 ARG cc_start: 0.6830 (mmm160) cc_final: 0.6570 (tpt170) REVERT: K 109 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7581 (mm-30) REVERT: K 129 TYR cc_start: 0.8431 (m-80) cc_final: 0.7950 (m-10) REVERT: K 139 ASN cc_start: 0.8864 (t0) cc_final: 0.7935 (t0) REVERT: L 3 ASP cc_start: 0.8777 (p0) cc_final: 0.8481 (p0) REVERT: L 7 LYS cc_start: 0.9080 (ttpp) cc_final: 0.8591 (ptmm) REVERT: L 49 SER cc_start: 0.9322 (t) cc_final: 0.9055 (m) REVERT: L 63 GLN cc_start: 0.9160 (mt0) cc_final: 0.8946 (mt0) REVERT: L 65 GLN cc_start: 0.8476 (pm20) cc_final: 0.8195 (pm20) REVERT: L 81 MET cc_start: 0.9014 (tpp) cc_final: 0.8414 (tpp) REVERT: L 88 MET cc_start: 0.7952 (mtm) cc_final: 0.7588 (mtp) REVERT: L 89 GLU cc_start: 0.7854 (pp20) cc_final: 0.7358 (tm-30) REVERT: L 103 ASP cc_start: 0.8347 (m-30) cc_final: 0.7944 (m-30) REVERT: L 116 ARG cc_start: 0.8082 (tpp80) cc_final: 0.7726 (tpp80) REVERT: L 120 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8138 (tm-30) REVERT: L 135 LYS cc_start: 0.9129 (mttm) cc_final: 0.8923 (mttp) REVERT: L 137 LYS cc_start: 0.9363 (tttt) cc_final: 0.8680 (ttmt) REVERT: L 159 MET cc_start: 0.8966 (mmt) cc_final: 0.8637 (mmt) REVERT: M 9 ILE cc_start: 0.9300 (tp) cc_final: 0.8592 (tp) REVERT: M 81 LYS cc_start: 0.8859 (mtpp) cc_final: 0.8422 (mtmm) REVERT: M 83 LYS cc_start: 0.8731 (mmtp) cc_final: 0.8157 (mmmm) REVERT: M 115 LEU cc_start: 0.8865 (tt) cc_final: 0.8178 (tp) REVERT: M 118 ILE cc_start: 0.9459 (mm) cc_final: 0.9092 (mm) REVERT: M 119 ASN cc_start: 0.8780 (p0) cc_final: 0.8239 (p0) REVERT: M 171 ASN cc_start: 0.7856 (p0) cc_final: 0.7366 (p0) REVERT: N 45 THR cc_start: 0.8545 (t) cc_final: 0.8296 (t) REVERT: N 88 MET cc_start: 0.8476 (ttp) cc_final: 0.6682 (tpp) REVERT: N 89 GLU cc_start: 0.7869 (pp20) cc_final: 0.7270 (pp20) REVERT: N 95 VAL cc_start: 0.9677 (t) cc_final: 0.9385 (p) REVERT: N 97 TYR cc_start: 0.8427 (m-10) cc_final: 0.7857 (m-80) REVERT: N 103 ASP cc_start: 0.7146 (t0) cc_final: 0.6673 (t0) REVERT: N 105 SER cc_start: 0.8310 (t) cc_final: 0.8058 (t) REVERT: N 118 THR cc_start: 0.9319 (p) cc_final: 0.9082 (t) REVERT: N 136 MET cc_start: 0.8733 (mtm) cc_final: 0.6623 (mtm) REVERT: N 162 ILE cc_start: 0.9184 (mt) cc_final: 0.8960 (mt) REVERT: O 4 PRO cc_start: 0.8666 (Cg_exo) cc_final: 0.8324 (Cg_endo) REVERT: O 19 LEU cc_start: 0.8341 (mm) cc_final: 0.7389 (tp) REVERT: O 60 TYR cc_start: 0.5999 (m-10) cc_final: 0.5593 (m-10) REVERT: O 96 THR cc_start: 0.9390 (p) cc_final: 0.9152 (t) REVERT: O 98 CYS cc_start: 0.8280 (m) cc_final: 0.7616 (p) REVERT: O 104 THR cc_start: 0.8960 (p) cc_final: 0.8231 (p) REVERT: O 107 MET cc_start: 0.8796 (tpp) cc_final: 0.7883 (tpp) REVERT: O 111 LEU cc_start: 0.8824 (tt) cc_final: 0.8489 (tt) REVERT: O 129 TYR cc_start: 0.8492 (m-80) cc_final: 0.7806 (m-80) REVERT: O 131 GLU cc_start: 0.8034 (tt0) cc_final: 0.7547 (tt0) REVERT: P 23 GLN cc_start: 0.8588 (mt0) cc_final: 0.8325 (mt0) REVERT: P 39 ASP cc_start: 0.7353 (m-30) cc_final: 0.7124 (m-30) REVERT: P 97 TYR cc_start: 0.8847 (m-10) cc_final: 0.8193 (m-10) REVERT: P 122 LEU cc_start: 0.8324 (mm) cc_final: 0.8057 (mm) REVERT: Q 25 GLN cc_start: 0.8814 (mm-40) cc_final: 0.8211 (mm-40) REVERT: Q 37 SER cc_start: 0.7548 (m) cc_final: 0.6794 (p) REVERT: Q 39 GLU cc_start: 0.7472 (mt-10) cc_final: 0.6721 (pt0) REVERT: Q 63 PHE cc_start: 0.7470 (m-10) cc_final: 0.7043 (m-10) REVERT: Q 69 MET cc_start: 0.7826 (ptm) cc_final: 0.7219 (ptm) REVERT: Q 73 GLN cc_start: 0.7824 (pm20) cc_final: 0.7318 (pm20) REVERT: Q 94 MET cc_start: 0.5339 (tpp) cc_final: 0.4918 (tpp) REVERT: Q 98 CYS cc_start: 0.8155 (m) cc_final: 0.7596 (m) REVERT: Q 107 MET cc_start: 0.8016 (ttm) cc_final: 0.7811 (mtm) REVERT: Q 108 ASP cc_start: 0.8640 (m-30) cc_final: 0.8330 (m-30) REVERT: Q 134 LYS cc_start: 0.8001 (tptt) cc_final: 0.7596 (tptt) REVERT: R 38 LEU cc_start: 0.8637 (mt) cc_final: 0.8233 (mp) REVERT: R 49 SER cc_start: 0.9047 (p) cc_final: 0.8792 (t) REVERT: R 85 LEU cc_start: 0.9621 (mt) cc_final: 0.9288 (tp) REVERT: R 111 CYS cc_start: 0.8145 (t) cc_final: 0.7705 (t) REVERT: R 128 SER cc_start: 0.8736 (m) cc_final: 0.8347 (m) REVERT: R 159 MET cc_start: 0.8124 (mmp) cc_final: 0.7407 (ptt) REVERT: R 160 SER cc_start: 0.9090 (t) cc_final: 0.8759 (p) REVERT: S 37 SER cc_start: 0.8577 (p) cc_final: 0.7915 (t) REVERT: S 44 LEU cc_start: 0.9444 (mt) cc_final: 0.9226 (mt) REVERT: S 49 GLN cc_start: 0.8548 (tp-100) cc_final: 0.7887 (pm20) REVERT: S 73 GLN cc_start: 0.8683 (pm20) cc_final: 0.7879 (pm20) REVERT: S 79 GLU cc_start: 0.7837 (mp0) cc_final: 0.7454 (tm-30) REVERT: S 81 LYS cc_start: 0.8026 (mmmt) cc_final: 0.7477 (mtmt) REVERT: S 90 TYR cc_start: 0.8432 (m-10) cc_final: 0.7954 (m-10) REVERT: S 97 TYR cc_start: 0.9104 (m-80) cc_final: 0.8192 (m-80) REVERT: S 107 MET cc_start: 0.7557 (ptp) cc_final: 0.7307 (ptp) REVERT: S 112 ILE cc_start: 0.9506 (mm) cc_final: 0.8899 (tp) REVERT: S 115 LEU cc_start: 0.8616 (tp) cc_final: 0.8306 (tp) REVERT: S 134 LYS cc_start: 0.9510 (mmpt) cc_final: 0.9251 (mmmm) REVERT: T 15 ARG cc_start: 0.7742 (mtp85) cc_final: 0.7203 (mmp80) REVERT: T 19 LEU cc_start: 0.8107 (mt) cc_final: 0.7490 (mm) REVERT: T 23 GLN cc_start: 0.8425 (mt0) cc_final: 0.8004 (mp10) REVERT: T 47 ASN cc_start: 0.7781 (t0) cc_final: 0.7241 (t0) REVERT: T 104 SER cc_start: 0.9083 (p) cc_final: 0.8723 (p) REVERT: T 162 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8377 (mt) REVERT: T 165 TYR cc_start: 0.8530 (m-80) cc_final: 0.7973 (m-80) REVERT: U 28 ASP cc_start: 0.7559 (t0) cc_final: 0.7261 (t0) REVERT: U 98 CYS cc_start: 0.7906 (t) cc_final: 0.7454 (t) REVERT: U 109 GLU cc_start: 0.8391 (tm-30) cc_final: 0.7642 (tm-30) REVERT: U 123 ASP cc_start: 0.8392 (t0) cc_final: 0.7929 (t0) REVERT: U 131 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8228 (mm-30) REVERT: U 134 LYS cc_start: 0.9047 (tppp) cc_final: 0.8820 (tppp) REVERT: U 171 ASN cc_start: 0.8828 (t0) cc_final: 0.8488 (t0) REVERT: U 174 SER cc_start: 0.7676 (t) cc_final: 0.7375 (t) REVERT: V 11 GLN cc_start: 0.8486 (tt0) cc_final: 0.8116 (tp40) REVERT: V 29 ASN cc_start: 0.8539 (m-40) cc_final: 0.8202 (t0) REVERT: V 35 ASN cc_start: 0.8246 (m110) cc_final: 0.7913 (t0) REVERT: V 60 PHE cc_start: 0.8913 (m-80) cc_final: 0.8557 (m-80) REVERT: V 62 GLU cc_start: 0.7665 (pp20) cc_final: 0.7024 (pp20) REVERT: V 68 GLN cc_start: 0.8311 (pt0) cc_final: 0.7788 (pt0) REVERT: V 78 ASN cc_start: 0.6302 (t0) cc_final: 0.6042 (t0) REVERT: V 81 MET cc_start: 0.8521 (tpp) cc_final: 0.8026 (tpp) REVERT: V 113 ASN cc_start: 0.9141 (t0) cc_final: 0.8311 (t0) REVERT: V 124 THR cc_start: 0.8927 (m) cc_final: 0.8664 (p) REVERT: V 137 LYS cc_start: 0.9323 (tttm) cc_final: 0.8945 (tptp) REVERT: V 162 ILE cc_start: 0.8630 (mt) cc_final: 0.8259 (mt) REVERT: W 3 THR cc_start: 0.7209 (m) cc_final: 0.6605 (m) REVERT: W 42 ARG cc_start: 0.7852 (ttm170) cc_final: 0.6723 (tpt170) REVERT: W 61 GLN cc_start: 0.8261 (mm-40) cc_final: 0.8060 (mm-40) REVERT: W 97 TYR cc_start: 0.7502 (m-10) cc_final: 0.6848 (m-80) REVERT: W 111 LEU cc_start: 0.8405 (pt) cc_final: 0.7692 (pp) REVERT: W 163 ASN cc_start: 0.7432 (m-40) cc_final: 0.7223 (m-40) REVERT: X 2 LEU cc_start: 0.6373 (pp) cc_final: 0.6161 (pp) REVERT: X 3 ASP cc_start: 0.7866 (p0) cc_final: 0.7551 (p0) REVERT: X 18 PHE cc_start: 0.6507 (m-10) cc_final: 0.6192 (m-80) REVERT: X 32 LYS cc_start: 0.8013 (mmtp) cc_final: 0.7279 (mmmm) REVERT: X 88 MET cc_start: 0.8954 (ttm) cc_final: 0.8619 (ttt) REVERT: X 89 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8049 (tm-30) REVERT: Y 50 VAL cc_start: 0.9479 (t) cc_final: 0.9176 (p) REVERT: Z 64 ASN cc_start: 0.9111 (t0) cc_final: 0.8881 (t0) REVERT: Z 76 VAL cc_start: 0.9690 (t) cc_final: 0.9414 (p) REVERT: Z 90 ASN cc_start: 0.9012 (m-40) cc_final: 0.8685 (m110) REVERT: Z 93 THR cc_start: 0.8883 (m) cc_final: 0.8529 (p) REVERT: Z 115 ILE cc_start: 0.9011 (mt) cc_final: 0.8640 (mm) REVERT: Z 119 ASP cc_start: 0.7316 (m-30) cc_final: 0.7097 (m-30) REVERT: Z 120 LEU cc_start: 0.9311 (tp) cc_final: 0.8488 (tp) REVERT: Z 129 ASP cc_start: 0.8636 (t0) cc_final: 0.8267 (t0) REVERT: Z 146 TRP cc_start: 0.8533 (m-90) cc_final: 0.8191 (m-90) REVERT: Z 177 ASN cc_start: 0.8783 (t0) cc_final: 0.8453 (t0) REVERT: Z 179 ASP cc_start: 0.8777 (m-30) cc_final: 0.8412 (m-30) REVERT: Z 182 GLN cc_start: 0.8670 (tt0) cc_final: 0.8417 (tt0) REVERT: Z 196 THR cc_start: 0.9121 (p) cc_final: 0.8680 (m) REVERT: Z 275 GLN cc_start: 0.8412 (mm110) cc_final: 0.8186 (mm-40) REVERT: a 84 ARG cc_start: 0.8845 (ttm110) cc_final: 0.8597 (ttm110) REVERT: a 98 GLU cc_start: 0.8160 (tp30) cc_final: 0.6787 (tp30) REVERT: a 107 GLU cc_start: 0.7832 (pt0) cc_final: 0.7598 (pt0) REVERT: a 151 GLN cc_start: 0.9007 (mm-40) cc_final: 0.8139 (mt0) REVERT: a 165 TYR cc_start: 0.5321 (m-80) cc_final: 0.5075 (m-10) REVERT: a 176 ARG cc_start: 0.7803 (ttp-170) cc_final: 0.7598 (ttt180) outliers start: 4 outliers final: 0 residues processed: 1670 average time/residue: 0.2256 time to fit residues: 613.2803 Evaluate side-chains 1397 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1396 time to evaluate : 1.320 ------------------------------------------------------------------------------- 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: 5.9990 chunk 253 optimal weight: 4.9990 chunk 310 optimal weight: 0.9990 chunk 312 optimal weight: 0.8980 chunk 431 optimal weight: 2.9990 chunk 198 optimal weight: 9.9990 chunk 429 optimal weight: 9.9990 chunk 348 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 227 optimal weight: 0.9990 chunk 334 optimal weight: 6.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 GLN D 29 ASN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN E 119 ASN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN F 134 GLN G 21 ASN G 25 GLN H 47 ASN ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 78 ASN M 140 HIS ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 139 ASN Q 139 ASN ** R 78 ASN ** 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 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 166 ASN ** 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.114938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.096495 restraints weight = 124454.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.100479 restraints weight = 59892.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.103065 restraints weight = 33788.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.104776 restraints weight = 21314.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.105862 restraints weight = 14704.142| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 36155 Z= 0.153 Angle : 0.743 42.973 49243 Z= 0.353 Chirality : 0.039 0.233 5448 Planarity : 0.005 0.089 6402 Dihedral : 11.486 89.511 5519 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.56 % Favored : 97.37 % Rotamer: Outliers : 0.06 % Allowed : 2.15 % Favored : 97.79 % 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: 1.25 (0.13), residues: 4448 helix: 1.28 (0.09), residues: 3403 sheet: 1.64 (0.77), residues: 28 loop : -0.57 (0.22), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG T 86 TYR 0.048 0.002 TYR R 97 PHE 0.048 0.002 PHE T 166 TRP 0.016 0.001 TRP C 128 HIS 0.005 0.001 HIS Z 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (36155) covalent geometry : angle 0.74331 / 0.35 (49243) hydrogen bonds : bond 0.04330 / 2.90 ( 2648) hydrogen bonds : angle 4.23209 / 3.08 ( 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 1662 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1660 time to evaluate : 1.340 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 15 GLN cc_start: 0.7928 (mt0) cc_final: 0.6964 (mm110) REVERT: A 18 PHE cc_start: 0.7673 (m-80) cc_final: 0.7419 (m-80) REVERT: A 30 ARG cc_start: 0.8593 (tpt-90) cc_final: 0.8358 (tmt170) REVERT: A 38 MET cc_start: 0.8531 (mmt) cc_final: 0.7845 (tmm) REVERT: A 59 VAL cc_start: 0.9437 (t) cc_final: 0.9214 (t) REVERT: A 66 THR cc_start: 0.9197 (p) cc_final: 0.8985 (p) REVERT: A 90 TYR cc_start: 0.8559 (m-10) cc_final: 0.7982 (m-80) REVERT: A 131 GLU cc_start: 0.7478 (tm-30) cc_final: 0.7041 (tm-30) REVERT: A 165 TYR cc_start: 0.8473 (m-10) cc_final: 0.8159 (m-80) REVERT: A 167 ASP cc_start: 0.8201 (t0) cc_final: 0.7644 (t0) REVERT: A 171 ASN cc_start: 0.8438 (m-40) cc_final: 0.8050 (m-40) REVERT: B 36 LYS cc_start: 0.9490 (mtmm) cc_final: 0.8531 (mppt) REVERT: B 51 ILE cc_start: 0.9513 (mt) cc_final: 0.9005 (mt) REVERT: B 120 GLN cc_start: 0.7891 (mt0) cc_final: 0.7383 (tm-30) REVERT: C 17 ARG cc_start: 0.8413 (ptt90) cc_final: 0.8188 (ptt-90) REVERT: C 63 PHE cc_start: 0.9175 (m-80) cc_final: 0.8561 (m-10) REVERT: C 94 MET cc_start: 0.9454 (mmt) cc_final: 0.9077 (mmm) REVERT: C 111 LEU cc_start: 0.8678 (tp) cc_final: 0.8436 (tp) REVERT: C 117 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8625 (mm-30) REVERT: C 133 LEU cc_start: 0.8528 (mp) cc_final: 0.8230 (tp) REVERT: D 3 ASP cc_start: 0.8382 (p0) cc_final: 0.8107 (p0) REVERT: D 49 SER cc_start: 0.8716 (p) cc_final: 0.8405 (p) REVERT: D 97 TYR cc_start: 0.7891 (m-10) cc_final: 0.6701 (m-80) REVERT: D 113 ASN cc_start: 0.7962 (t0) cc_final: 0.7695 (t0) REVERT: D 128 SER cc_start: 0.9338 (p) cc_final: 0.8944 (m) REVERT: D 134 GLN cc_start: 0.8575 (mt0) cc_final: 0.8373 (mt0) REVERT: D 138 ASP cc_start: 0.8738 (p0) cc_final: 0.8529 (p0) REVERT: D 154 ASP cc_start: 0.6722 (t0) cc_final: 0.6389 (t0) REVERT: D 159 MET cc_start: 0.8401 (mmp) cc_final: 0.8017 (mmt) REVERT: E 28 ASP cc_start: 0.8735 (t70) cc_final: 0.8337 (t0) REVERT: E 38 MET cc_start: 0.8231 (mmt) cc_final: 0.7833 (tmm) REVERT: E 47 ASN cc_start: 0.8402 (m110) cc_final: 0.7680 (m110) REVERT: E 69 MET cc_start: 0.8406 (mtp) cc_final: 0.7907 (ttm) REVERT: E 72 SER cc_start: 0.8911 (m) cc_final: 0.8322 (t) REVERT: E 73 GLN cc_start: 0.8801 (pm20) cc_final: 0.8219 (pm20) REVERT: E 83 LYS cc_start: 0.9378 (tppp) cc_final: 0.8740 (mmmm) REVERT: E 118 ILE cc_start: 0.9468 (mp) cc_final: 0.9175 (tt) REVERT: E 120 SER cc_start: 0.9355 (t) cc_final: 0.9154 (t) REVERT: E 121 THR cc_start: 0.9209 (p) cc_final: 0.8729 (t) REVERT: E 140 HIS cc_start: 0.8554 (p90) cc_final: 0.8084 (p-80) REVERT: E 167 ASP cc_start: 0.8420 (t0) cc_final: 0.7031 (t0) REVERT: E 171 ASN cc_start: 0.8739 (p0) cc_final: 0.8260 (p0) REVERT: E 173 LEU cc_start: 0.8882 (mm) cc_final: 0.8623 (mm) REVERT: F 11 GLN cc_start: 0.9074 (tt0) cc_final: 0.8371 (tt0) REVERT: F 21 ASN cc_start: 0.8108 (m-40) cc_final: 0.6639 (t0) REVERT: F 25 ASP cc_start: 0.8921 (m-30) cc_final: 0.8694 (m-30) REVERT: F 60 PHE cc_start: 0.8207 (m-10) cc_final: 0.7550 (m-10) REVERT: F 81 MET cc_start: 0.9208 (tpp) cc_final: 0.8746 (tpt) REVERT: F 88 MET cc_start: 0.8499 (mmm) cc_final: 0.7606 (mmm) REVERT: F 146 ASP cc_start: 0.8287 (t0) cc_final: 0.7996 (t0) REVERT: G 1 MET cc_start: 0.7638 (tpt) cc_final: 0.7073 (tpt) REVERT: G 20 SER cc_start: 0.8165 (t) cc_final: 0.7027 (p) REVERT: G 38 MET cc_start: 0.9101 (mtm) cc_final: 0.8363 (ttm) REVERT: G 61 GLN cc_start: 0.8480 (mt0) cc_final: 0.8261 (mp10) REVERT: G 62 LYS cc_start: 0.9018 (tptm) cc_final: 0.8750 (tppt) REVERT: G 97 TYR cc_start: 0.8923 (m-10) cc_final: 0.8649 (m-10) REVERT: G 98 CYS cc_start: 0.8383 (p) cc_final: 0.7743 (m) REVERT: G 116 SER cc_start: 0.9009 (p) cc_final: 0.8760 (m) REVERT: G 122 PHE cc_start: 0.8600 (m-80) cc_final: 0.8294 (m-10) REVERT: G 123 ASP cc_start: 0.8090 (t70) cc_final: 0.7870 (t70) REVERT: G 124 LEU cc_start: 0.9186 (mt) cc_final: 0.8533 (mp) REVERT: G 133 LEU cc_start: 0.9573 (mm) cc_final: 0.9373 (mm) REVERT: G 137 LYS cc_start: 0.8676 (ttpt) cc_final: 0.8361 (tttt) REVERT: G 161 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8524 (mt-10) REVERT: G 163 ASN cc_start: 0.9247 (m-40) cc_final: 0.7872 (m110) REVERT: G 166 ILE cc_start: 0.9357 (mt) cc_final: 0.8603 (tp) REVERT: H 3 ASP cc_start: 0.8697 (p0) cc_final: 0.8307 (p0) REVERT: H 17 GLU cc_start: 0.8593 (pm20) cc_final: 0.8331 (pm20) REVERT: H 81 MET cc_start: 0.8738 (mmm) cc_final: 0.8369 (tpp) REVERT: H 91 ILE cc_start: 0.9485 (mm) cc_final: 0.9146 (tp) REVERT: H 145 ASN cc_start: 0.7834 (m-40) cc_final: 0.7086 (m-40) REVERT: H 159 MET cc_start: 0.8292 (mmm) cc_final: 0.7966 (mmt) REVERT: I 19 LEU cc_start: 0.8702 (mt) cc_final: 0.8469 (mt) REVERT: I 51 LEU cc_start: 0.8648 (mt) cc_final: 0.8403 (mt) REVERT: I 62 LYS cc_start: 0.9296 (tptm) cc_final: 0.8905 (tptt) REVERT: I 73 GLN cc_start: 0.9246 (pm20) cc_final: 0.9026 (pm20) REVERT: I 110 TYR cc_start: 0.7990 (m-80) cc_final: 0.7599 (m-10) REVERT: I 111 LEU cc_start: 0.9351 (tp) cc_final: 0.9044 (tp) REVERT: I 115 LEU cc_start: 0.8840 (tp) cc_final: 0.7993 (tp) REVERT: I 119 ASN cc_start: 0.8600 (m110) cc_final: 0.8025 (m110) REVERT: I 129 TYR cc_start: 0.8870 (m-10) cc_final: 0.8665 (m-10) REVERT: J 17 GLU cc_start: 0.8261 (mp0) cc_final: 0.7680 (mp0) REVERT: J 24 PHE cc_start: 0.6652 (m-80) cc_final: 0.6374 (m-10) REVERT: J 28 SER cc_start: 0.9331 (t) cc_final: 0.9073 (p) REVERT: J 35 ASN cc_start: 0.8785 (m110) cc_final: 0.8040 (t0) REVERT: J 91 ILE cc_start: 0.9421 (tp) cc_final: 0.9174 (tt) REVERT: J 97 TYR cc_start: 0.8649 (m-10) cc_final: 0.8106 (m-10) REVERT: J 112 LEU cc_start: 0.9498 (mp) cc_final: 0.8954 (mm) REVERT: K 33 ARG cc_start: 0.6422 (mmm160) cc_final: 0.5953 (tpt170) REVERT: K 129 TYR cc_start: 0.8382 (m-80) cc_final: 0.7820 (m-80) REVERT: K 133 LEU cc_start: 0.8904 (mt) cc_final: 0.8496 (tp) REVERT: K 139 ASN cc_start: 0.8708 (t0) cc_final: 0.8170 (t0) REVERT: L 3 ASP cc_start: 0.8824 (p0) cc_final: 0.8454 (p0) REVERT: L 7 LYS cc_start: 0.9057 (ttpp) cc_final: 0.8582 (ptmm) REVERT: L 49 SER cc_start: 0.9295 (t) cc_final: 0.9029 (m) REVERT: L 65 GLN cc_start: 0.8782 (pm20) cc_final: 0.8560 (pm20) REVERT: L 81 MET cc_start: 0.9013 (tpp) cc_final: 0.8306 (tpp) REVERT: L 88 MET cc_start: 0.7906 (mtm) cc_final: 0.7482 (mtp) REVERT: L 89 GLU cc_start: 0.8024 (pp20) cc_final: 0.7483 (tm-30) REVERT: L 103 ASP cc_start: 0.8256 (m-30) cc_final: 0.7996 (m-30) REVERT: L 116 ARG cc_start: 0.8125 (tpp80) cc_final: 0.7793 (tpp80) REVERT: L 120 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8146 (tm-30) REVERT: L 137 LYS cc_start: 0.9336 (tttt) cc_final: 0.8681 (ttmt) REVERT: L 161 GLU cc_start: 0.8727 (tt0) cc_final: 0.8176 (tp30) REVERT: M 9 ILE cc_start: 0.9209 (tp) cc_final: 0.8492 (tp) REVERT: M 57 GLN cc_start: 0.9442 (mm-40) cc_final: 0.8957 (mm-40) REVERT: M 81 LYS cc_start: 0.8861 (mtpp) cc_final: 0.8443 (mtmm) REVERT: M 83 LYS cc_start: 0.8767 (mmtp) cc_final: 0.8032 (mmmm) REVERT: M 115 LEU cc_start: 0.8847 (tt) cc_final: 0.8209 (tp) REVERT: M 118 ILE cc_start: 0.9395 (mm) cc_final: 0.9082 (mm) REVERT: M 119 ASN cc_start: 0.8769 (p0) cc_final: 0.8171 (p0) REVERT: M 135 TYR cc_start: 0.9124 (t80) cc_final: 0.8865 (t80) REVERT: M 171 ASN cc_start: 0.7814 (p0) cc_final: 0.7324 (p0) REVERT: N 45 THR cc_start: 0.8601 (t) cc_final: 0.8339 (t) REVERT: N 65 GLN cc_start: 0.7469 (pm20) cc_final: 0.6828 (pm20) REVERT: N 88 MET cc_start: 0.8505 (ttp) cc_final: 0.6693 (tpp) REVERT: N 95 VAL cc_start: 0.9654 (t) cc_final: 0.9426 (p) REVERT: N 97 TYR cc_start: 0.8487 (m-10) cc_final: 0.7901 (m-80) REVERT: N 103 ASP cc_start: 0.7391 (t0) cc_final: 0.6843 (t0) REVERT: N 109 ASP cc_start: 0.8393 (t0) cc_final: 0.8190 (t70) REVERT: N 136 MET cc_start: 0.8622 (mtm) cc_final: 0.6622 (mtm) REVERT: O 19 LEU cc_start: 0.8367 (mm) cc_final: 0.7467 (tp) REVERT: O 52 ILE cc_start: 0.7997 (pt) cc_final: 0.7766 (pt) REVERT: O 96 THR cc_start: 0.9413 (p) cc_final: 0.9114 (t) REVERT: O 98 CYS cc_start: 0.8231 (m) cc_final: 0.7554 (p) REVERT: O 104 THR cc_start: 0.8965 (p) cc_final: 0.8054 (p) REVERT: O 107 MET cc_start: 0.8802 (tpp) cc_final: 0.7733 (tpp) REVERT: O 131 GLU cc_start: 0.7592 (tt0) cc_final: 0.7210 (tt0) REVERT: P 23 GLN cc_start: 0.8526 (mt0) cc_final: 0.8149 (mt0) REVERT: P 33 GLU cc_start: 0.8078 (mp0) cc_final: 0.7850 (mp0) REVERT: P 97 TYR cc_start: 0.8877 (m-10) cc_final: 0.8222 (m-10) REVERT: P 122 LEU cc_start: 0.8347 (mm) cc_final: 0.8092 (mm) REVERT: P 159 MET cc_start: 0.8384 (mmp) cc_final: 0.8094 (mmm) REVERT: Q 25 GLN cc_start: 0.8923 (mm-40) cc_final: 0.8291 (mm-40) REVERT: Q 37 SER cc_start: 0.7649 (m) cc_final: 0.6774 (p) REVERT: Q 39 GLU cc_start: 0.7498 (mt-10) cc_final: 0.6719 (pt0) REVERT: Q 62 LYS cc_start: 0.7568 (ttmm) cc_final: 0.7337 (ttmm) REVERT: Q 69 MET cc_start: 0.7883 (ptm) cc_final: 0.7216 (ptm) REVERT: Q 94 MET cc_start: 0.5109 (tpp) cc_final: 0.4696 (tpp) REVERT: Q 98 CYS cc_start: 0.8157 (m) cc_final: 0.7654 (m) REVERT: Q 107 MET cc_start: 0.8030 (ttm) cc_final: 0.7774 (mtp) REVERT: Q 108 ASP cc_start: 0.8717 (m-30) cc_final: 0.8407 (m-30) REVERT: Q 134 LYS cc_start: 0.8292 (tptt) cc_final: 0.7791 (tptt) REVERT: R 1 MET cc_start: 0.7324 (ttm) cc_final: 0.7094 (ttm) REVERT: R 38 LEU cc_start: 0.8608 (mt) cc_final: 0.8171 (mp) REVERT: R 49 SER cc_start: 0.9030 (p) cc_final: 0.8796 (t) REVERT: R 85 LEU cc_start: 0.9645 (mt) cc_final: 0.9261 (tp) REVERT: R 111 CYS cc_start: 0.8197 (t) cc_final: 0.7785 (t) REVERT: R 118 THR cc_start: 0.8977 (p) cc_final: 0.8749 (p) REVERT: R 128 SER cc_start: 0.8748 (m) cc_final: 0.8407 (m) REVERT: R 134 GLN cc_start: 0.7802 (mm-40) cc_final: 0.7258 (mm-40) REVERT: R 141 ILE cc_start: 0.8704 (mm) cc_final: 0.8465 (mm) REVERT: R 160 SER cc_start: 0.9034 (t) cc_final: 0.8709 (p) REVERT: S 32 LYS cc_start: 0.7890 (mmtm) cc_final: 0.7666 (mmpt) REVERT: S 37 SER cc_start: 0.8363 (p) cc_final: 0.7852 (t) REVERT: S 49 GLN cc_start: 0.8462 (tp-100) cc_final: 0.7782 (pm20) REVERT: S 63 PHE cc_start: 0.8216 (m-80) cc_final: 0.7653 (m-80) REVERT: S 73 GLN cc_start: 0.8576 (pm20) cc_final: 0.8286 (pm20) REVERT: S 79 GLU cc_start: 0.7888 (mp0) cc_final: 0.7508 (tm-30) REVERT: S 90 TYR cc_start: 0.8322 (m-10) cc_final: 0.8077 (m-10) REVERT: S 93 ARG cc_start: 0.7759 (ttp80) cc_final: 0.6510 (ttp80) REVERT: S 94 MET cc_start: 0.9414 (mmp) cc_final: 0.9185 (mmt) REVERT: S 97 TYR cc_start: 0.9093 (m-80) cc_final: 0.8239 (m-80) REVERT: S 107 MET cc_start: 0.7506 (ptp) cc_final: 0.7283 (ptp) REVERT: S 112 ILE cc_start: 0.9515 (mm) cc_final: 0.8914 (tp) REVERT: S 115 LEU cc_start: 0.8602 (tp) cc_final: 0.8365 (tp) REVERT: S 134 LYS cc_start: 0.9539 (mmpt) cc_final: 0.9151 (mmmm) REVERT: S 163 ASN cc_start: 0.9410 (m110) cc_final: 0.9181 (m-40) REVERT: T 15 ARG cc_start: 0.7760 (mtp85) cc_final: 0.7185 (mmp80) REVERT: T 19 LEU cc_start: 0.8214 (mt) cc_final: 0.7626 (mm) REVERT: T 23 GLN cc_start: 0.8446 (mt0) cc_final: 0.8021 (mp10) REVERT: T 47 ASN cc_start: 0.7772 (t0) cc_final: 0.6190 (t0) REVERT: T 50 THR cc_start: 0.9277 (m) cc_final: 0.9060 (p) REVERT: T 85 LEU cc_start: 0.8651 (pp) cc_final: 0.8425 (pp) REVERT: T 104 SER cc_start: 0.9049 (p) cc_final: 0.8740 (p) REVERT: T 141 ILE cc_start: 0.8450 (mt) cc_final: 0.8209 (mm) REVERT: T 156 SER cc_start: 0.8538 (m) cc_final: 0.8260 (m) REVERT: T 159 MET cc_start: 0.7913 (mpp) cc_final: 0.6968 (mpp) REVERT: T 165 TYR cc_start: 0.8468 (m-80) cc_final: 0.8172 (m-80) REVERT: U 28 ASP cc_start: 0.7221 (t0) cc_final: 0.6902 (t0) REVERT: U 33 ARG cc_start: 0.7963 (ttp80) cc_final: 0.7663 (ttp80) REVERT: U 98 CYS cc_start: 0.7898 (t) cc_final: 0.7471 (t) REVERT: U 109 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7539 (tm-30) REVERT: U 131 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8226 (mm-30) REVERT: U 171 ASN cc_start: 0.8831 (t0) cc_final: 0.8540 (t0) REVERT: U 174 SER cc_start: 0.7674 (t) cc_final: 0.7461 (t) REVERT: V 11 GLN cc_start: 0.8426 (tt0) cc_final: 0.7657 (tp40) REVERT: V 29 ASN cc_start: 0.8383 (m-40) cc_final: 0.8112 (t0) REVERT: V 35 ASN cc_start: 0.8289 (m110) cc_final: 0.7942 (t0) REVERT: V 60 PHE cc_start: 0.8987 (m-80) cc_final: 0.8559 (m-80) REVERT: V 62 GLU cc_start: 0.7703 (pp20) cc_final: 0.7438 (pp20) REVERT: V 68 GLN cc_start: 0.8284 (pt0) cc_final: 0.7807 (pt0) REVERT: V 78 ASN cc_start: 0.6370 (t0) cc_final: 0.5860 (t0) REVERT: V 81 MET cc_start: 0.8479 (tpp) cc_final: 0.8268 (tpp) REVERT: V 113 ASN cc_start: 0.9132 (t0) cc_final: 0.8309 (t0) REVERT: V 124 THR cc_start: 0.8948 (m) cc_final: 0.8689 (p) REVERT: V 134 GLN cc_start: 0.8232 (mm110) cc_final: 0.8013 (mm110) REVERT: V 137 LYS cc_start: 0.9396 (tttm) cc_final: 0.9115 (tttt) REVERT: V 173 VAL cc_start: 0.8359 (t) cc_final: 0.8151 (t) REVERT: W 1 MET cc_start: 0.5198 (ptp) cc_final: 0.4893 (ptp) REVERT: W 3 THR cc_start: 0.7204 (m) cc_final: 0.6756 (m) REVERT: W 7 GLU cc_start: 0.8202 (mp0) cc_final: 0.7540 (mp0) REVERT: W 9 ILE cc_start: 0.8444 (mm) cc_final: 0.7942 (tt) REVERT: W 42 ARG cc_start: 0.7908 (ttm170) cc_final: 0.6508 (tpt170) REVERT: W 97 TYR cc_start: 0.7323 (m-10) cc_final: 0.6781 (m-80) REVERT: W 111 LEU cc_start: 0.8109 (pt) cc_final: 0.7528 (pp) REVERT: X 3 ASP cc_start: 0.7874 (p0) cc_final: 0.7582 (p0) REVERT: X 18 PHE cc_start: 0.6437 (m-80) cc_final: 0.6097 (m-80) REVERT: X 32 LYS cc_start: 0.8097 (mmtp) cc_final: 0.7382 (mmmm) REVERT: X 52 VAL cc_start: 0.9227 (t) cc_final: 0.8940 (p) REVERT: X 88 MET cc_start: 0.8888 (ttm) cc_final: 0.8379 (ttt) REVERT: X 89 GLU cc_start: 0.8395 (tm-30) cc_final: 0.8075 (tm-30) REVERT: X 93 ARG cc_start: 0.8724 (ttp80) cc_final: 0.7849 (ttt90) REVERT: X 97 TYR cc_start: 0.8420 (m-80) cc_final: 0.7454 (m-80) REVERT: X 110 ARG cc_start: 0.8290 (ttm110) cc_final: 0.8063 (ttm170) REVERT: X 136 MET cc_start: 0.8638 (mmm) cc_final: 0.8204 (mmm) REVERT: Y 23 GLU cc_start: 0.7682 (mp0) cc_final: 0.7317 (mp0) REVERT: Y 50 VAL cc_start: 0.9482 (t) cc_final: 0.9212 (p) REVERT: Y 55 MET cc_start: 0.8313 (ttt) cc_final: 0.8025 (ttt) REVERT: Z 76 VAL cc_start: 0.9702 (t) cc_final: 0.9430 (p) REVERT: Z 90 ASN cc_start: 0.9005 (m-40) cc_final: 0.8676 (m110) REVERT: Z 93 THR cc_start: 0.8861 (m) cc_final: 0.8471 (p) REVERT: Z 101 LYS cc_start: 0.9227 (tmmt) cc_final: 0.8886 (ttpp) REVERT: Z 115 ILE cc_start: 0.8935 (mt) cc_final: 0.8627 (mm) REVERT: Z 119 ASP cc_start: 0.7316 (m-30) cc_final: 0.6457 (m-30) REVERT: Z 120 LEU cc_start: 0.9421 (tp) cc_final: 0.8801 (tt) REVERT: Z 141 ASN cc_start: 0.8829 (m-40) cc_final: 0.8443 (m-40) REVERT: Z 179 ASP cc_start: 0.8786 (m-30) cc_final: 0.8072 (m-30) REVERT: Z 182 GLN cc_start: 0.8674 (tt0) cc_final: 0.8328 (tt0) REVERT: Z 196 THR cc_start: 0.9047 (p) cc_final: 0.8505 (m) REVERT: a 84 ARG cc_start: 0.8987 (ttm110) cc_final: 0.8736 (ttm110) REVERT: a 111 LYS cc_start: 0.8337 (mttm) cc_final: 0.7567 (mttm) REVERT: a 129 ILE cc_start: 0.8881 (tt) cc_final: 0.8461 (tp) REVERT: a 151 GLN cc_start: 0.8981 (mm-40) cc_final: 0.8243 (mt0) REVERT: a 170 PHE cc_start: 0.8163 (m-80) cc_final: 0.7752 (m-80) REVERT: a 176 ARG cc_start: 0.7930 (ttp-170) cc_final: 0.7671 (ttt180) REVERT: a 177 TYR cc_start: 0.8068 (p90) cc_final: 0.7310 (p90) outliers start: 2 outliers final: 1 residues processed: 1662 average time/residue: 0.2172 time to fit residues: 592.7309 Evaluate side-chains 1398 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1397 time to evaluate : 1.333 ------------------------------------------------------------------------------- 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: 8.9990 chunk 210 optimal weight: 3.9990 chunk 276 optimal weight: 1.9990 chunk 314 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 159 optimal weight: 0.8980 chunk 150 optimal weight: 6.9990 chunk 325 optimal weight: 8.9990 chunk 406 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 268 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN ** 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 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 ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 25 GLN ** O 140 HIS ** 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** ** W 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 23 GLN X 78 ASN Z 92 GLN ** Z 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 166 ASN ** Z 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.114423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.097900 restraints weight = 87650.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.101158 restraints weight = 45932.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.103275 restraints weight = 27426.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.104734 restraints weight = 18100.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.105606 restraints weight = 12977.430| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3379 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3379 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.5787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 36155 Z= 0.161 Angle : 0.762 42.989 49243 Z= 0.363 Chirality : 0.040 0.225 5448 Planarity : 0.005 0.090 6402 Dihedral : 11.529 89.721 5519 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.56 % Favored : 97.35 % Rotamer: Outliers : 0.03 % Allowed : 1.50 % Favored : 98.47 % 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: 1.20 (0.09), residues: 3415 sheet: 1.46 (0.79), residues: 28 loop : -0.56 (0.22), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG T 86 TYR 0.057 0.002 TYR R 97 PHE 0.031 0.002 PHE T 166 TRP 0.020 0.001 TRP C 128 HIS 0.006 0.002 HIS M 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (36155) covalent geometry : angle 0.76229 / 0.36 (49243) hydrogen bonds : bond 0.04385 / 2.93 ( 2648) hydrogen bonds : angle 4.28218 / 3.13 ( 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 1629 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1628 time to evaluate : 1.389 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: A 15 GLN cc_start: 0.7790 (mt0) cc_final: 0.6860 (mm110) REVERT: A 30 ARG cc_start: 0.8512 (tpt-90) cc_final: 0.8126 (tmt170) REVERT: A 38 MET cc_start: 0.8518 (mmt) cc_final: 0.7863 (tmm) REVERT: A 39 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7726 (mm-30) REVERT: A 49 GLN cc_start: 0.8376 (mm-40) cc_final: 0.7090 (mm-40) REVERT: A 59 VAL cc_start: 0.9489 (t) cc_final: 0.9215 (t) REVERT: A 90 TYR cc_start: 0.8566 (m-10) cc_final: 0.8056 (m-80) REVERT: A 118 ILE cc_start: 0.8927 (mm) cc_final: 0.8632 (mm) REVERT: A 131 GLU cc_start: 0.7449 (tm-30) cc_final: 0.6978 (tm-30) REVERT: A 167 ASP cc_start: 0.8194 (t0) cc_final: 0.7593 (t0) REVERT: A 171 ASN cc_start: 0.8328 (m-40) cc_final: 0.8022 (m-40) REVERT: B 1 MET cc_start: 0.7013 (ppp) cc_final: 0.6776 (tmm) REVERT: B 120 GLN cc_start: 0.7964 (mt0) cc_final: 0.7469 (tm-30) REVERT: B 137 LYS cc_start: 0.9209 (ttpp) cc_final: 0.8345 (pttp) REVERT: B 141 ILE cc_start: 0.9243 (tt) cc_final: 0.9026 (tt) REVERT: C 17 ARG cc_start: 0.8437 (ptt90) cc_final: 0.8225 (ptt-90) REVERT: C 94 MET cc_start: 0.9439 (mmt) cc_final: 0.9008 (mmm) REVERT: C 117 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8611 (mm-30) REVERT: D 3 ASP cc_start: 0.8356 (p0) cc_final: 0.8043 (p0) REVERT: D 29 ASN cc_start: 0.9085 (t0) cc_final: 0.7792 (t0) REVERT: D 49 SER cc_start: 0.8712 (p) cc_final: 0.8468 (p) REVERT: D 97 TYR cc_start: 0.7875 (m-10) cc_final: 0.6671 (m-80) REVERT: D 113 ASN cc_start: 0.8034 (t0) cc_final: 0.7777 (t0) REVERT: D 128 SER cc_start: 0.9380 (p) cc_final: 0.8828 (m) REVERT: D 134 GLN cc_start: 0.8623 (mt0) cc_final: 0.8117 (mt0) REVERT: D 138 ASP cc_start: 0.8683 (p0) cc_final: 0.8431 (p0) REVERT: D 154 ASP cc_start: 0.6881 (t0) cc_final: 0.6433 (t0) REVERT: E 7 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7922 (mm-30) REVERT: E 28 ASP cc_start: 0.8597 (t70) cc_final: 0.8320 (t0) REVERT: E 38 MET cc_start: 0.8155 (mmt) cc_final: 0.7842 (tmm) REVERT: E 47 ASN cc_start: 0.8398 (m110) cc_final: 0.8004 (m110) REVERT: E 72 SER cc_start: 0.8991 (m) cc_final: 0.8366 (t) REVERT: E 73 GLN cc_start: 0.8761 (pm20) cc_final: 0.8215 (pm20) REVERT: E 118 ILE cc_start: 0.9414 (mp) cc_final: 0.9186 (tt) REVERT: E 120 SER cc_start: 0.9222 (t) cc_final: 0.9006 (t) REVERT: E 121 THR cc_start: 0.9266 (p) cc_final: 0.8755 (t) REVERT: E 140 HIS cc_start: 0.8561 (p90) cc_final: 0.8106 (p-80) REVERT: E 167 ASP cc_start: 0.8422 (t0) cc_final: 0.6999 (t0) REVERT: E 171 ASN cc_start: 0.8787 (p0) cc_final: 0.8312 (p0) REVERT: F 11 GLN cc_start: 0.8942 (tt0) cc_final: 0.8458 (tt0) REVERT: F 21 ASN cc_start: 0.8093 (m-40) cc_final: 0.6619 (t0) REVERT: F 25 ASP cc_start: 0.8847 (m-30) cc_final: 0.8593 (m-30) REVERT: F 60 PHE cc_start: 0.8112 (m-10) cc_final: 0.7477 (m-10) REVERT: F 81 MET cc_start: 0.9233 (tpp) cc_final: 0.8798 (tpt) REVERT: F 117 GLU cc_start: 0.8567 (pp20) cc_final: 0.8342 (pp20) REVERT: F 146 ASP cc_start: 0.8317 (t0) cc_final: 0.8052 (t0) REVERT: G 1 MET cc_start: 0.7701 (tpt) cc_final: 0.7304 (tpt) REVERT: G 25 GLN cc_start: 0.8629 (mt0) cc_final: 0.7955 (mt0) REVERT: G 30 ARG cc_start: 0.9219 (tmt-80) cc_final: 0.8846 (tmt-80) REVERT: G 38 MET cc_start: 0.9075 (mtm) cc_final: 0.8395 (ttm) REVERT: G 57 GLN cc_start: 0.8717 (mp10) cc_final: 0.8405 (mp10) REVERT: G 62 LYS cc_start: 0.9044 (tptm) cc_final: 0.8789 (tppt) REVERT: G 70 GLN cc_start: 0.7778 (pp30) cc_final: 0.7536 (pp30) REVERT: G 97 TYR cc_start: 0.8906 (m-10) cc_final: 0.8634 (m-10) REVERT: G 98 CYS cc_start: 0.8425 (p) cc_final: 0.7762 (m) REVERT: G 107 MET cc_start: 0.8780 (tpp) cc_final: 0.8453 (tpp) REVERT: G 116 SER cc_start: 0.9026 (p) cc_final: 0.8747 (m) REVERT: G 122 PHE cc_start: 0.8702 (m-80) cc_final: 0.8098 (m-10) REVERT: G 124 LEU cc_start: 0.9222 (mt) cc_final: 0.8547 (mp) REVERT: G 133 LEU cc_start: 0.9562 (mm) cc_final: 0.9100 (mm) REVERT: G 135 TYR cc_start: 0.8582 (t80) cc_final: 0.8372 (t80) REVERT: G 137 LYS cc_start: 0.8837 (ttpt) cc_final: 0.8407 (ttpt) REVERT: G 161 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8618 (mt-10) REVERT: G 163 ASN cc_start: 0.9259 (m-40) cc_final: 0.8214 (m-40) REVERT: H 3 ASP cc_start: 0.8702 (p0) cc_final: 0.8480 (p0) REVERT: H 59 LEU cc_start: 0.8357 (tp) cc_final: 0.8094 (tt) REVERT: H 81 MET cc_start: 0.8744 (mmm) cc_final: 0.8527 (tpp) REVERT: H 91 ILE cc_start: 0.9432 (mm) cc_final: 0.9121 (tp) REVERT: H 145 ASN cc_start: 0.7935 (m-40) cc_final: 0.7384 (m-40) REVERT: I 51 LEU cc_start: 0.8720 (mt) cc_final: 0.8368 (mt) REVERT: I 60 TYR cc_start: 0.7308 (m-80) cc_final: 0.7066 (m-80) REVERT: I 62 LYS cc_start: 0.9277 (tptm) cc_final: 0.8919 (tptt) REVERT: I 73 GLN cc_start: 0.9214 (pm20) cc_final: 0.8912 (pm20) REVERT: I 94 MET cc_start: 0.8595 (mmm) cc_final: 0.8044 (tpp) REVERT: I 110 TYR cc_start: 0.7962 (m-80) cc_final: 0.7618 (m-10) REVERT: I 115 LEU cc_start: 0.8857 (tp) cc_final: 0.8165 (tp) REVERT: I 119 ASN cc_start: 0.8500 (m110) cc_final: 0.7940 (m110) REVERT: I 127 SER cc_start: 0.8929 (p) cc_final: 0.8728 (p) REVERT: J 17 GLU cc_start: 0.8278 (mp0) cc_final: 0.7665 (mp0) REVERT: J 24 PHE cc_start: 0.6717 (m-80) cc_final: 0.6453 (m-80) REVERT: J 35 ASN cc_start: 0.8758 (m110) cc_final: 0.7996 (t0) REVERT: J 88 MET cc_start: 0.8977 (mmt) cc_final: 0.8394 (mmm) REVERT: J 91 ILE cc_start: 0.9438 (tp) cc_final: 0.9230 (tt) REVERT: J 97 TYR cc_start: 0.8634 (m-10) cc_final: 0.8071 (m-10) REVERT: J 112 LEU cc_start: 0.9542 (mp) cc_final: 0.8949 (mm) REVERT: K 33 ARG cc_start: 0.6431 (mmm160) cc_final: 0.5924 (tpt170) REVERT: K 94 MET cc_start: 0.9000 (tpp) cc_final: 0.8708 (mmt) REVERT: K 133 LEU cc_start: 0.8784 (mt) cc_final: 0.8529 (tp) REVERT: K 139 ASN cc_start: 0.8694 (t0) cc_final: 0.8245 (t0) REVERT: L 3 ASP cc_start: 0.8862 (p0) cc_final: 0.8462 (p0) REVERT: L 7 LYS cc_start: 0.9056 (ttpp) cc_final: 0.8604 (ptmm) REVERT: L 49 SER cc_start: 0.9231 (t) cc_final: 0.8970 (m) REVERT: L 81 MET cc_start: 0.8975 (tpp) cc_final: 0.8281 (tpp) REVERT: L 88 MET cc_start: 0.7551 (mtm) cc_final: 0.7213 (mtp) REVERT: L 89 GLU cc_start: 0.7766 (pp20) cc_final: 0.7461 (tm-30) REVERT: L 103 ASP cc_start: 0.8220 (m-30) cc_final: 0.7843 (m-30) REVERT: L 116 ARG cc_start: 0.8126 (tpp80) cc_final: 0.7784 (tpp80) REVERT: L 120 GLN cc_start: 0.8807 (tm-30) cc_final: 0.8161 (tm-30) REVERT: L 137 LYS cc_start: 0.9396 (tttt) cc_final: 0.8735 (ttmt) REVERT: L 161 GLU cc_start: 0.8761 (tt0) cc_final: 0.8221 (tp30) REVERT: L 165 TYR cc_start: 0.8110 (m-80) cc_final: 0.7730 (m-80) REVERT: M 57 GLN cc_start: 0.9409 (mm-40) cc_final: 0.8975 (mm-40) REVERT: M 115 LEU cc_start: 0.9029 (tt) cc_final: 0.8533 (tp) REVERT: M 118 ILE cc_start: 0.9390 (mm) cc_final: 0.9120 (mm) REVERT: M 119 ASN cc_start: 0.8805 (p0) cc_final: 0.8442 (p0) REVERT: M 171 ASN cc_start: 0.7801 (p0) cc_final: 0.7335 (p0) REVERT: N 20 THR cc_start: 0.8115 (t) cc_final: 0.7744 (p) REVERT: N 42 ASN cc_start: 0.9512 (t0) cc_final: 0.8809 (t0) REVERT: N 45 THR cc_start: 0.8618 (t) cc_final: 0.8312 (t) REVERT: N 87 ASP cc_start: 0.8982 (m-30) cc_final: 0.8573 (m-30) REVERT: N 88 MET cc_start: 0.8409 (ttp) cc_final: 0.6707 (tpp) REVERT: N 89 GLU cc_start: 0.7871 (pp20) cc_final: 0.7285 (pp20) REVERT: N 95 VAL cc_start: 0.9681 (t) cc_final: 0.9423 (p) REVERT: N 97 TYR cc_start: 0.8565 (m-10) cc_final: 0.7949 (m-80) REVERT: N 103 ASP cc_start: 0.7043 (t0) cc_final: 0.6642 (t0) REVERT: N 136 MET cc_start: 0.8669 (mtm) cc_final: 0.6658 (mtm) REVERT: N 162 ILE cc_start: 0.9109 (mt) cc_final: 0.8862 (mt) REVERT: O 52 ILE cc_start: 0.8065 (pt) cc_final: 0.7838 (pt) REVERT: O 61 GLN cc_start: 0.7649 (mt0) cc_final: 0.6910 (tm-30) REVERT: O 96 THR cc_start: 0.9406 (p) cc_final: 0.9148 (t) REVERT: O 104 THR cc_start: 0.8942 (p) cc_final: 0.7855 (p) REVERT: O 170 ILE cc_start: 0.9031 (tt) cc_final: 0.8675 (tp) REVERT: P 23 GLN cc_start: 0.8529 (mt0) cc_final: 0.8061 (mt0) REVERT: P 29 ASN cc_start: 0.8730 (t0) cc_final: 0.8235 (t0) REVERT: P 33 GLU cc_start: 0.8176 (mp0) cc_final: 0.7849 (mp0) REVERT: P 97 TYR cc_start: 0.8846 (m-10) cc_final: 0.8227 (m-10) REVERT: P 122 LEU cc_start: 0.8441 (mm) cc_final: 0.8168 (mm) REVERT: Q 25 GLN cc_start: 0.8946 (mm-40) cc_final: 0.8293 (mm-40) REVERT: Q 39 GLU cc_start: 0.7512 (mt-10) cc_final: 0.6634 (pt0) REVERT: Q 62 LYS cc_start: 0.7606 (ttmm) cc_final: 0.7345 (ttmm) REVERT: Q 94 MET cc_start: 0.5144 (tpp) cc_final: 0.4800 (tpp) REVERT: Q 108 ASP cc_start: 0.8773 (m-30) cc_final: 0.8409 (m-30) REVERT: Q 134 LYS cc_start: 0.8324 (tptt) cc_final: 0.7806 (tptt) REVERT: R 49 SER cc_start: 0.8960 (p) cc_final: 0.8712 (t) REVERT: R 85 LEU cc_start: 0.9600 (mt) cc_final: 0.9223 (tp) REVERT: R 111 CYS cc_start: 0.8224 (t) cc_final: 0.7770 (t) REVERT: R 128 SER cc_start: 0.8842 (m) cc_final: 0.8468 (m) REVERT: R 134 GLN cc_start: 0.7791 (mm-40) cc_final: 0.7273 (mm-40) REVERT: R 136 MET cc_start: 0.8323 (tmm) cc_final: 0.7814 (tmm) REVERT: R 141 ILE cc_start: 0.8411 (mm) cc_final: 0.7872 (pt) REVERT: S 1 MET cc_start: 0.7323 (mmp) cc_final: 0.6976 (mmm) REVERT: S 32 LYS cc_start: 0.7962 (mmtm) cc_final: 0.7692 (mmpt) REVERT: S 37 SER cc_start: 0.8341 (p) cc_final: 0.7867 (t) REVERT: S 49 GLN cc_start: 0.8407 (tp-100) cc_final: 0.7764 (pm20) REVERT: S 73 GLN cc_start: 0.8542 (pm20) cc_final: 0.8228 (pm20) REVERT: S 79 GLU cc_start: 0.7934 (mp0) cc_final: 0.7533 (tm-30) REVERT: S 93 ARG cc_start: 0.7763 (ttp80) cc_final: 0.6729 (ttp80) REVERT: S 97 TYR cc_start: 0.9110 (m-10) cc_final: 0.8201 (m-80) REVERT: S 107 MET cc_start: 0.7516 (ptp) cc_final: 0.7284 (ptp) REVERT: S 112 ILE cc_start: 0.9525 (mm) cc_final: 0.8921 (tp) REVERT: S 115 LEU cc_start: 0.8606 (tp) cc_final: 0.8331 (tp) REVERT: S 134 LYS cc_start: 0.9495 (mmpt) cc_final: 0.9264 (mmmm) REVERT: T 13 ASP cc_start: 0.8729 (t70) cc_final: 0.8432 (t0) REVERT: T 15 ARG cc_start: 0.7756 (mtp85) cc_final: 0.7187 (mmp80) REVERT: T 19 LEU cc_start: 0.8220 (mt) cc_final: 0.7640 (mm) REVERT: T 23 GLN cc_start: 0.8418 (mt0) cc_final: 0.8088 (mp10) REVERT: T 25 ASP cc_start: 0.8704 (m-30) cc_final: 0.8373 (m-30) REVERT: T 47 ASN cc_start: 0.7794 (t0) cc_final: 0.6300 (t0) REVERT: T 66 LEU cc_start: 0.7639 (pt) cc_final: 0.7251 (pp) REVERT: T 156 SER cc_start: 0.8496 (m) cc_final: 0.8234 (m) REVERT: T 158 LEU cc_start: 0.8292 (tt) cc_final: 0.8071 (tt) REVERT: T 159 MET cc_start: 0.8086 (mpp) cc_final: 0.6949 (mpp) REVERT: U 28 ASP cc_start: 0.7172 (t0) cc_final: 0.6855 (t0) REVERT: U 33 ARG cc_start: 0.8012 (ttp80) cc_final: 0.7683 (ttp80) REVERT: U 98 CYS cc_start: 0.7876 (t) cc_final: 0.7588 (t) REVERT: U 109 GLU cc_start: 0.8436 (tm-30) cc_final: 0.7560 (tm-30) REVERT: U 123 ASP cc_start: 0.8482 (t70) cc_final: 0.8183 (t0) REVERT: U 137 LYS cc_start: 0.9367 (tttp) cc_final: 0.9067 (tptp) REVERT: U 171 ASN cc_start: 0.8985 (t0) cc_final: 0.8662 (t0) REVERT: U 174 SER cc_start: 0.7890 (t) cc_final: 0.7607 (t) REVERT: V 11 GLN cc_start: 0.8480 (tt0) cc_final: 0.8075 (tp40) REVERT: V 29 ASN cc_start: 0.8479 (m-40) cc_final: 0.8183 (t0) REVERT: V 35 ASN cc_start: 0.8191 (m110) cc_final: 0.7947 (t0) REVERT: V 60 PHE cc_start: 0.9012 (m-80) cc_final: 0.8629 (m-80) REVERT: V 62 GLU cc_start: 0.7748 (pp20) cc_final: 0.7424 (pp20) REVERT: V 68 GLN cc_start: 0.8212 (pt0) cc_final: 0.7651 (pt0) REVERT: V 81 MET cc_start: 0.8557 (tpp) cc_final: 0.8308 (tpp) REVERT: V 90 ILE cc_start: 0.9456 (mm) cc_final: 0.9211 (mm) REVERT: V 113 ASN cc_start: 0.9257 (t0) cc_final: 0.8448 (t0) REVERT: V 124 THR cc_start: 0.8919 (m) cc_final: 0.8661 (p) REVERT: V 137 LYS cc_start: 0.9349 (tttm) cc_final: 0.9042 (tttt) REVERT: W 1 MET cc_start: 0.5156 (ptp) cc_final: 0.4787 (ptp) REVERT: W 3 THR cc_start: 0.7434 (m) cc_final: 0.6739 (m) REVERT: W 9 ILE cc_start: 0.8508 (mm) cc_final: 0.8259 (mm) REVERT: W 42 ARG cc_start: 0.7392 (ttm170) cc_final: 0.6807 (tpt170) REVERT: W 61 GLN cc_start: 0.8154 (mm-40) cc_final: 0.7870 (mm-40) REVERT: W 69 MET cc_start: 0.3975 (mmm) cc_final: 0.3500 (tpt) REVERT: W 97 TYR cc_start: 0.7321 (m-10) cc_final: 0.6832 (m-80) REVERT: W 111 LEU cc_start: 0.7706 (pt) cc_final: 0.7251 (pp) REVERT: X 3 ASP cc_start: 0.7884 (p0) cc_final: 0.7622 (p0) REVERT: X 18 PHE cc_start: 0.6280 (m-80) cc_final: 0.6045 (m-80) REVERT: X 32 LYS cc_start: 0.8109 (mmtp) cc_final: 0.7446 (mmmm) REVERT: X 52 VAL cc_start: 0.9258 (t) cc_final: 0.8968 (p) REVERT: X 88 MET cc_start: 0.8845 (ttm) cc_final: 0.8372 (ttt) REVERT: X 89 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8041 (tm-30) REVERT: X 93 ARG cc_start: 0.8774 (ttp80) cc_final: 0.8332 (ttp80) REVERT: X 97 TYR cc_start: 0.8359 (m-80) cc_final: 0.8071 (m-80) REVERT: X 110 ARG cc_start: 0.8473 (ttm110) cc_final: 0.8158 (ttm170) REVERT: X 117 GLU cc_start: 0.7727 (pm20) cc_final: 0.7496 (pm20) REVERT: X 136 MET cc_start: 0.8756 (mmm) cc_final: 0.8379 (mmm) REVERT: Y 20 PHE cc_start: 0.8373 (m-10) cc_final: 0.7984 (m-10) REVERT: Y 23 GLU cc_start: 0.7813 (mp0) cc_final: 0.7402 (mp0) REVERT: Y 50 VAL cc_start: 0.9494 (t) cc_final: 0.9216 (p) REVERT: Y 55 MET cc_start: 0.8285 (ttt) cc_final: 0.8047 (ttt) REVERT: Z 59 GLU cc_start: 0.8294 (pt0) cc_final: 0.8026 (pt0) REVERT: Z 90 ASN cc_start: 0.9011 (m-40) cc_final: 0.8684 (m110) REVERT: Z 101 LYS cc_start: 0.9255 (tmmt) cc_final: 0.8938 (ttpp) REVERT: Z 119 ASP cc_start: 0.8085 (m-30) cc_final: 0.7884 (m-30) REVERT: Z 124 GLU cc_start: 0.8182 (pm20) cc_final: 0.7958 (pm20) REVERT: Z 141 ASN cc_start: 0.8768 (m-40) cc_final: 0.8545 (m-40) REVERT: Z 179 ASP cc_start: 0.8800 (m-30) cc_final: 0.8404 (m-30) REVERT: Z 196 THR cc_start: 0.9068 (p) cc_final: 0.8632 (m) REVERT: a 44 GLU cc_start: 0.7773 (tt0) cc_final: 0.7518 (tt0) REVERT: a 84 ARG cc_start: 0.8948 (ttm110) cc_final: 0.8553 (ttm-80) REVERT: a 88 LYS cc_start: 0.8993 (pttm) cc_final: 0.8163 (tppt) REVERT: a 127 TRP cc_start: 0.8156 (m100) cc_final: 0.7905 (m100) REVERT: a 129 ILE cc_start: 0.8881 (tt) cc_final: 0.8489 (tp) REVERT: a 137 GLN cc_start: 0.7954 (tp40) cc_final: 0.7263 (tp40) REVERT: a 151 GLN cc_start: 0.8868 (mm-40) cc_final: 0.8021 (mt0) REVERT: a 177 TYR cc_start: 0.8080 (p90) cc_final: 0.7319 (p90) outliers start: 1 outliers final: 0 residues processed: 1629 average time/residue: 0.2192 time to fit residues: 587.3211 Evaluate side-chains 1393 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1393 time to evaluate : 1.225 ------------------------------------------------------------------------------- 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: 5.9990 chunk 43 optimal weight: 0.9990 chunk 437 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 407 optimal weight: 8.9990 chunk 177 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 287 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 199 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 GLN H 78 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** ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 139 ASN ** R 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 139 ASN ** S 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 ASN ** V 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 92 GLN ** Z 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 161 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.115052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.097852 restraints weight = 100266.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.101327 restraints weight = 51457.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.103615 restraints weight = 30291.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.105178 restraints weight = 19782.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.106181 restraints weight = 13968.698| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3385 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3385 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.5972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 36155 Z= 0.154 Angle : 0.769 42.964 49243 Z= 0.366 Chirality : 0.040 0.216 5448 Planarity : 0.005 0.084 6402 Dihedral : 11.534 89.751 5519 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.72 % Favored : 97.21 % Rotamer: Outliers : 0.06 % Allowed : 1.12 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.12 (0.13), residues: 4448 helix: 1.17 (0.09), residues: 3408 sheet: 1.24 (0.78), residues: 28 loop : -0.55 (0.22), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG T 86 TYR 0.051 0.002 TYR Q 90 PHE 0.037 0.002 PHE Z 165 TRP 0.038 0.002 TRP a 29 HIS 0.005 0.002 HIS M 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (36155) covalent geometry : angle 0.76908 / 0.37 (49243) hydrogen bonds : bond 0.04351 / 2.90 ( 2648) hydrogen bonds : angle 4.28218 / 3.12 ( 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 1633 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1631 time to evaluate : 1.284 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 15 GLN cc_start: 0.7601 (mt0) cc_final: 0.6976 (mm110) REVERT: A 18 PHE cc_start: 0.7644 (m-80) cc_final: 0.7437 (m-80) REVERT: A 30 ARG cc_start: 0.8475 (tpt-90) cc_final: 0.8114 (tmt170) REVERT: A 37 SER cc_start: 0.9065 (p) cc_final: 0.8620 (p) REVERT: A 38 MET cc_start: 0.8611 (mmt) cc_final: 0.7966 (tmm) REVERT: A 39 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7113 (mm-30) REVERT: A 90 TYR cc_start: 0.8523 (m-10) cc_final: 0.8106 (m-80) REVERT: A 94 MET cc_start: 0.8364 (tpp) cc_final: 0.7192 (tpt) REVERT: A 131 GLU cc_start: 0.7341 (tm-30) cc_final: 0.6965 (tm-30) REVERT: A 167 ASP cc_start: 0.8163 (t0) cc_final: 0.7603 (t0) REVERT: A 171 ASN cc_start: 0.8332 (m-40) cc_final: 0.7922 (m-40) REVERT: B 35 ASN cc_start: 0.8692 (m-40) cc_final: 0.7856 (t0) REVERT: B 36 LYS cc_start: 0.9429 (mtmm) cc_final: 0.8715 (mppt) REVERT: B 120 GLN cc_start: 0.7942 (mt0) cc_final: 0.7423 (tm-30) REVERT: B 137 LYS cc_start: 0.9261 (ttpp) cc_final: 0.8318 (pttp) REVERT: C 60 TYR cc_start: 0.6174 (m-80) cc_final: 0.5726 (m-80) REVERT: C 94 MET cc_start: 0.9407 (mmt) cc_final: 0.9033 (mmm) REVERT: C 117 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8612 (mm-30) REVERT: D 29 ASN cc_start: 0.9023 (t0) cc_final: 0.7723 (t0) REVERT: D 49 SER cc_start: 0.8710 (p) cc_final: 0.8454 (p) REVERT: D 97 TYR cc_start: 0.7831 (m-10) cc_final: 0.7355 (m-10) REVERT: D 113 ASN cc_start: 0.8068 (t0) cc_final: 0.7713 (t0) REVERT: D 128 SER cc_start: 0.9352 (p) cc_final: 0.8882 (m) REVERT: D 136 MET cc_start: 0.8280 (mmm) cc_final: 0.8054 (tpp) REVERT: D 154 ASP cc_start: 0.6566 (t0) cc_final: 0.6346 (t0) REVERT: E 7 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7642 (mm-30) REVERT: E 28 ASP cc_start: 0.8586 (t70) cc_final: 0.8231 (t0) REVERT: E 38 MET cc_start: 0.8127 (mmt) cc_final: 0.7897 (tmm) REVERT: E 47 ASN cc_start: 0.8348 (m110) cc_final: 0.7974 (m110) REVERT: E 72 SER cc_start: 0.8970 (m) cc_final: 0.8337 (t) REVERT: E 94 MET cc_start: 0.7820 (tpp) cc_final: 0.7540 (ttm) REVERT: E 98 CYS cc_start: 0.8141 (m) cc_final: 0.7917 (m) REVERT: E 109 GLU cc_start: 0.8521 (tt0) cc_final: 0.8126 (tt0) REVERT: E 111 LEU cc_start: 0.8790 (mt) cc_final: 0.7481 (mt) REVERT: E 120 SER cc_start: 0.9186 (t) cc_final: 0.8978 (t) REVERT: E 121 THR cc_start: 0.9328 (p) cc_final: 0.8693 (t) REVERT: E 140 HIS cc_start: 0.8390 (p90) cc_final: 0.8050 (p90) REVERT: E 167 ASP cc_start: 0.8323 (t0) cc_final: 0.6920 (t0) REVERT: E 171 ASN cc_start: 0.8791 (p0) cc_final: 0.8264 (p0) REVERT: F 11 GLN cc_start: 0.8970 (tt0) cc_final: 0.8097 (tt0) REVERT: F 21 ASN cc_start: 0.8049 (m-40) cc_final: 0.6585 (t0) REVERT: F 25 ASP cc_start: 0.8732 (m-30) cc_final: 0.8241 (m-30) REVERT: F 29 ASN cc_start: 0.9170 (m-40) cc_final: 0.8949 (m-40) REVERT: F 60 PHE cc_start: 0.8031 (m-10) cc_final: 0.7300 (m-10) REVERT: F 81 MET cc_start: 0.9136 (tpp) cc_final: 0.8730 (tpt) REVERT: F 146 ASP cc_start: 0.7992 (t0) cc_final: 0.7605 (t0) REVERT: G 20 SER cc_start: 0.8149 (t) cc_final: 0.7249 (m) REVERT: G 25 GLN cc_start: 0.8630 (mt0) cc_final: 0.8009 (mt0) REVERT: G 30 ARG cc_start: 0.9168 (tmt-80) cc_final: 0.8806 (tmt-80) REVERT: G 38 MET cc_start: 0.8980 (mtm) cc_final: 0.8228 (ttm) REVERT: G 62 LYS cc_start: 0.9040 (tptm) cc_final: 0.8803 (tppt) REVERT: G 70 GLN cc_start: 0.7860 (pp30) cc_final: 0.7604 (pp30) REVERT: G 97 TYR cc_start: 0.8941 (m-10) cc_final: 0.8610 (m-10) REVERT: G 98 CYS cc_start: 0.8349 (p) cc_final: 0.7797 (m) REVERT: G 107 MET cc_start: 0.8574 (tpp) cc_final: 0.8182 (tpp) REVERT: G 116 SER cc_start: 0.9021 (p) cc_final: 0.8660 (m) REVERT: G 124 LEU cc_start: 0.9160 (mt) cc_final: 0.8662 (mt) REVERT: G 133 LEU cc_start: 0.9620 (mm) cc_final: 0.9190 (mm) REVERT: G 161 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8555 (mt-10) REVERT: G 163 ASN cc_start: 0.9215 (m-40) cc_final: 0.8356 (m-40) REVERT: H 3 ASP cc_start: 0.8689 (p0) cc_final: 0.8383 (p0) REVERT: H 38 LEU cc_start: 0.9036 (mt) cc_final: 0.8665 (tt) REVERT: H 91 ILE cc_start: 0.9450 (mm) cc_final: 0.9067 (tp) REVERT: H 136 MET cc_start: 0.8587 (mtm) cc_final: 0.7512 (mtm) REVERT: H 156 SER cc_start: 0.8832 (m) cc_final: 0.8599 (p) REVERT: H 159 MET cc_start: 0.8121 (mmm) cc_final: 0.7605 (mmt) REVERT: I 51 LEU cc_start: 0.8696 (mt) cc_final: 0.8297 (mt) REVERT: I 60 TYR cc_start: 0.7291 (m-80) cc_final: 0.7068 (m-80) REVERT: I 62 LYS cc_start: 0.9193 (tptm) cc_final: 0.8901 (tptt) REVERT: I 73 GLN cc_start: 0.9152 (pm20) cc_final: 0.8949 (pm20) REVERT: I 83 LYS cc_start: 0.8950 (mmtm) cc_final: 0.8696 (mmmm) REVERT: I 94 MET cc_start: 0.8505 (mmm) cc_final: 0.7989 (tpp) REVERT: I 107 MET cc_start: 0.8401 (tpp) cc_final: 0.7878 (tpt) REVERT: I 110 TYR cc_start: 0.7638 (m-80) cc_final: 0.7345 (m-10) REVERT: I 115 LEU cc_start: 0.8999 (tp) cc_final: 0.8365 (tp) REVERT: I 119 ASN cc_start: 0.8390 (m110) cc_final: 0.7930 (m-40) REVERT: I 127 SER cc_start: 0.8722 (p) cc_final: 0.8421 (p) REVERT: J 17 GLU cc_start: 0.8242 (mp0) cc_final: 0.7648 (mp0) REVERT: J 35 ASN cc_start: 0.8676 (m110) cc_final: 0.8025 (t0) REVERT: J 88 MET cc_start: 0.8882 (mmt) cc_final: 0.8445 (mmm) REVERT: J 91 ILE cc_start: 0.9465 (tp) cc_final: 0.9246 (tt) REVERT: J 97 TYR cc_start: 0.8582 (m-10) cc_final: 0.8001 (m-10) REVERT: J 112 LEU cc_start: 0.9542 (mp) cc_final: 0.8933 (mm) REVERT: K 33 ARG cc_start: 0.6342 (mmm160) cc_final: 0.6040 (tpt170) REVERT: K 94 MET cc_start: 0.8901 (tpp) cc_final: 0.8631 (tpp) REVERT: K 133 LEU cc_start: 0.8726 (mt) cc_final: 0.8487 (tp) REVERT: K 139 ASN cc_start: 0.8770 (t0) cc_final: 0.8055 (t0) REVERT: L 2 LEU cc_start: 0.9331 (mt) cc_final: 0.8971 (mt) REVERT: L 3 ASP cc_start: 0.8868 (p0) cc_final: 0.8441 (p0) REVERT: L 7 LYS cc_start: 0.8739 (ttpp) cc_final: 0.8218 (ptmm) REVERT: L 81 MET cc_start: 0.8648 (tpp) cc_final: 0.8041 (tpp) REVERT: L 88 MET cc_start: 0.7220 (mtm) cc_final: 0.6447 (mtp) REVERT: L 89 GLU cc_start: 0.7570 (pp20) cc_final: 0.7316 (tm-30) REVERT: L 103 ASP cc_start: 0.8145 (m-30) cc_final: 0.7761 (m-30) REVERT: L 116 ARG cc_start: 0.8058 (tpp80) cc_final: 0.7771 (tpp80) REVERT: L 120 GLN cc_start: 0.8613 (tm-30) cc_final: 0.8066 (tm-30) REVERT: L 137 LYS cc_start: 0.9334 (tttt) cc_final: 0.8789 (ttmt) REVERT: L 161 GLU cc_start: 0.8750 (tt0) cc_final: 0.8219 (tp30) REVERT: L 165 TYR cc_start: 0.8153 (m-80) cc_final: 0.7724 (m-80) REVERT: M 33 ARG cc_start: 0.8093 (ttt180) cc_final: 0.7762 (ttt180) REVERT: M 38 MET cc_start: 0.7794 (tpt) cc_final: 0.7477 (tpt) REVERT: M 57 GLN cc_start: 0.9453 (mm-40) cc_final: 0.9091 (mm-40) REVERT: M 94 MET cc_start: 0.8548 (ttm) cc_final: 0.8171 (mtt) REVERT: M 111 LEU cc_start: 0.8954 (tp) cc_final: 0.8700 (tp) REVERT: M 115 LEU cc_start: 0.8986 (tt) cc_final: 0.8462 (tt) REVERT: M 118 ILE cc_start: 0.9269 (mm) cc_final: 0.9066 (mm) REVERT: M 119 ASN cc_start: 0.8732 (p0) cc_final: 0.8258 (p0) REVERT: M 171 ASN cc_start: 0.8048 (p0) cc_final: 0.7664 (p0) REVERT: N 20 THR cc_start: 0.8097 (t) cc_final: 0.7776 (p) REVERT: N 42 ASN cc_start: 0.9507 (t0) cc_final: 0.8805 (t0) REVERT: N 45 THR cc_start: 0.8558 (t) cc_final: 0.8288 (t) REVERT: N 65 GLN cc_start: 0.7607 (pm20) cc_final: 0.6928 (pm20) REVERT: N 88 MET cc_start: 0.8344 (ttp) cc_final: 0.6704 (tpp) REVERT: N 89 GLU cc_start: 0.7777 (pp20) cc_final: 0.7180 (pp20) REVERT: N 95 VAL cc_start: 0.9678 (t) cc_final: 0.9455 (p) REVERT: N 97 TYR cc_start: 0.8502 (m-10) cc_final: 0.7907 (m-80) REVERT: N 103 ASP cc_start: 0.7188 (t0) cc_final: 0.6737 (t0) REVERT: N 136 MET cc_start: 0.8654 (mtm) cc_final: 0.6666 (mtm) REVERT: N 156 SER cc_start: 0.8747 (m) cc_final: 0.8489 (m) REVERT: O 19 LEU cc_start: 0.8582 (mm) cc_final: 0.7718 (tp) REVERT: O 61 GLN cc_start: 0.7467 (mt0) cc_final: 0.6687 (tm-30) REVERT: O 91 TYR cc_start: 0.9126 (m-10) cc_final: 0.8786 (m-80) REVERT: O 96 THR cc_start: 0.9388 (p) cc_final: 0.9091 (t) REVERT: O 98 CYS cc_start: 0.8369 (m) cc_final: 0.7323 (p) REVERT: O 104 THR cc_start: 0.8893 (p) cc_final: 0.8072 (p) REVERT: O 107 MET cc_start: 0.8706 (tpp) cc_final: 0.7739 (tpp) REVERT: P 2 LEU cc_start: 0.9045 (mp) cc_final: 0.8225 (mp) REVERT: P 19 LEU cc_start: 0.8519 (mt) cc_final: 0.8266 (tp) REVERT: P 23 GLN cc_start: 0.8437 (mt0) cc_final: 0.8052 (mt0) REVERT: P 29 ASN cc_start: 0.8644 (t0) cc_final: 0.8213 (t0) REVERT: P 33 GLU cc_start: 0.7986 (mp0) cc_final: 0.7605 (mp0) REVERT: P 97 TYR cc_start: 0.8884 (m-10) cc_final: 0.8157 (m-10) REVERT: P 122 LEU cc_start: 0.8415 (mm) cc_final: 0.8106 (mm) REVERT: Q 25 GLN cc_start: 0.9041 (mm-40) cc_final: 0.8457 (mm-40) REVERT: Q 39 GLU cc_start: 0.7525 (mt-10) cc_final: 0.6728 (pt0) REVERT: Q 53 ASP cc_start: 0.7106 (m-30) cc_final: 0.6846 (m-30) REVERT: Q 62 LYS cc_start: 0.7458 (ttmm) cc_final: 0.7233 (ttmm) REVERT: Q 90 TYR cc_start: 0.7243 (m-80) cc_final: 0.7021 (m-10) REVERT: Q 94 MET cc_start: 0.5502 (tpp) cc_final: 0.5206 (tpp) REVERT: Q 108 ASP cc_start: 0.8832 (m-30) cc_final: 0.8492 (m-30) REVERT: Q 134 LYS cc_start: 0.8381 (tptt) cc_final: 0.7902 (tptt) REVERT: R 49 SER cc_start: 0.8860 (p) cc_final: 0.8652 (t) REVERT: R 85 LEU cc_start: 0.9533 (mt) cc_final: 0.9163 (tp) REVERT: R 111 CYS cc_start: 0.8241 (t) cc_final: 0.7766 (t) REVERT: R 128 SER cc_start: 0.8970 (m) cc_final: 0.8638 (m) REVERT: R 136 MET cc_start: 0.8506 (tmm) cc_final: 0.7845 (tmm) REVERT: S 32 LYS cc_start: 0.8232 (mmtm) cc_final: 0.7783 (mmpt) REVERT: S 37 SER cc_start: 0.8363 (p) cc_final: 0.8025 (t) REVERT: S 49 GLN cc_start: 0.8228 (tp-100) cc_final: 0.7560 (pm20) REVERT: S 73 GLN cc_start: 0.8562 (pm20) cc_final: 0.7713 (pm20) REVERT: S 79 GLU cc_start: 0.7919 (mp0) cc_final: 0.7565 (tm-30) REVERT: S 93 ARG cc_start: 0.7803 (ttp80) cc_final: 0.7096 (ttp80) REVERT: S 97 TYR cc_start: 0.9099 (m-10) cc_final: 0.8339 (m-80) REVERT: S 107 MET cc_start: 0.7419 (ptp) cc_final: 0.7209 (ptp) REVERT: S 112 ILE cc_start: 0.9478 (mm) cc_final: 0.8950 (tp) REVERT: S 134 LYS cc_start: 0.9458 (mmpt) cc_final: 0.9110 (mmmm) REVERT: S 139 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.8280 (t0) REVERT: S 163 ASN cc_start: 0.9284 (m110) cc_final: 0.9037 (m-40) REVERT: T 13 ASP cc_start: 0.8719 (t70) cc_final: 0.8381 (t0) REVERT: T 15 ARG cc_start: 0.7681 (mtp85) cc_final: 0.7158 (mmp80) REVERT: T 19 LEU cc_start: 0.8156 (mt) cc_final: 0.7631 (mm) REVERT: T 23 GLN cc_start: 0.8370 (mt0) cc_final: 0.8061 (mp10) REVERT: T 25 ASP cc_start: 0.8698 (m-30) cc_final: 0.8297 (m-30) REVERT: T 156 SER cc_start: 0.8467 (m) cc_final: 0.8215 (m) REVERT: T 159 MET cc_start: 0.8391 (mpp) cc_final: 0.7543 (mpp) REVERT: U 28 ASP cc_start: 0.7077 (t0) cc_final: 0.6761 (t0) REVERT: U 33 ARG cc_start: 0.7471 (mtp180) cc_final: 0.6618 (mtp180) REVERT: U 98 CYS cc_start: 0.7945 (t) cc_final: 0.7394 (t) REVERT: U 109 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7546 (tm-30) REVERT: U 123 ASP cc_start: 0.8068 (t70) cc_final: 0.7807 (t0) REVERT: U 171 ASN cc_start: 0.8728 (t0) cc_final: 0.8360 (t0) REVERT: U 174 SER cc_start: 0.7900 (t) cc_final: 0.7532 (t) REVERT: V 11 GLN cc_start: 0.8417 (tt0) cc_final: 0.8148 (tp40) REVERT: V 35 ASN cc_start: 0.8249 (m110) cc_final: 0.7898 (t0) REVERT: V 60 PHE cc_start: 0.8986 (m-80) cc_final: 0.8582 (m-80) REVERT: V 62 GLU cc_start: 0.7792 (pp20) cc_final: 0.7586 (pp20) REVERT: V 68 GLN cc_start: 0.8122 (pt0) cc_final: 0.7639 (pt0) REVERT: V 81 MET cc_start: 0.8489 (tpp) cc_final: 0.7858 (tpp) REVERT: V 90 ILE cc_start: 0.9424 (mm) cc_final: 0.9173 (mm) REVERT: V 94 TYR cc_start: 0.8853 (m-80) cc_final: 0.8463 (m-80) REVERT: V 113 ASN cc_start: 0.9207 (t0) cc_final: 0.8416 (t0) REVERT: V 124 THR cc_start: 0.8888 (m) cc_final: 0.8618 (p) REVERT: V 131 VAL cc_start: 0.9002 (t) cc_final: 0.8793 (t) REVERT: V 137 LYS cc_start: 0.9441 (tttm) cc_final: 0.9191 (tptm) REVERT: W 9 ILE cc_start: 0.8510 (mm) cc_final: 0.8271 (mm) REVERT: W 42 ARG cc_start: 0.7934 (ttm170) cc_final: 0.6584 (tpt170) REVERT: W 69 MET cc_start: 0.3953 (mmm) cc_final: 0.3538 (tpt) REVERT: W 72 SER cc_start: 0.8688 (m) cc_final: 0.8410 (p) REVERT: W 97 TYR cc_start: 0.7237 (m-10) cc_final: 0.6925 (m-80) REVERT: W 111 LEU cc_start: 0.7756 (pt) cc_final: 0.7293 (pp) REVERT: X 3 ASP cc_start: 0.7848 (p0) cc_final: 0.7621 (p0) REVERT: X 18 PHE cc_start: 0.6259 (m-80) cc_final: 0.5939 (m-80) REVERT: X 32 LYS cc_start: 0.8112 (mmtp) cc_final: 0.7829 (tptm) REVERT: X 52 VAL cc_start: 0.9259 (t) cc_final: 0.8917 (p) REVERT: X 88 MET cc_start: 0.8646 (ttm) cc_final: 0.8427 (ttm) REVERT: X 89 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7770 (tm-30) REVERT: X 93 ARG cc_start: 0.8752 (ttp80) cc_final: 0.8186 (ttp80) REVERT: X 97 TYR cc_start: 0.8231 (m-80) cc_final: 0.7615 (m-80) REVERT: X 110 ARG cc_start: 0.8529 (ttm110) cc_final: 0.7932 (ttm170) REVERT: X 136 MET cc_start: 0.8733 (mmm) cc_final: 0.8418 (mmm) REVERT: Y 20 PHE cc_start: 0.8449 (m-10) cc_final: 0.7996 (m-10) REVERT: Y 23 GLU cc_start: 0.7692 (mp0) cc_final: 0.7297 (mp0) REVERT: Z 76 VAL cc_start: 0.9730 (t) cc_final: 0.9430 (p) REVERT: Z 90 ASN cc_start: 0.8810 (m-40) cc_final: 0.8469 (m110) REVERT: Z 101 LYS cc_start: 0.9227 (tmmt) cc_final: 0.8831 (ttpp) REVERT: Z 141 ASN cc_start: 0.8714 (m-40) cc_final: 0.8363 (m-40) REVERT: Z 179 ASP cc_start: 0.8615 (m-30) cc_final: 0.8231 (m-30) REVERT: Z 196 THR cc_start: 0.9030 (p) cc_final: 0.8544 (m) REVERT: a 84 ARG cc_start: 0.9002 (ttm110) cc_final: 0.8561 (ttm-80) REVERT: a 88 LYS cc_start: 0.9024 (pttm) cc_final: 0.8170 (tppt) REVERT: a 98 GLU cc_start: 0.8311 (tp30) cc_final: 0.8076 (tp30) REVERT: a 127 TRP cc_start: 0.8183 (m100) cc_final: 0.7967 (m100) REVERT: a 129 ILE cc_start: 0.8891 (tt) cc_final: 0.8455 (tp) REVERT: a 137 GLN cc_start: 0.7935 (tp40) cc_final: 0.7249 (tp40) REVERT: a 151 GLN cc_start: 0.8811 (mm-40) cc_final: 0.7958 (mt0) REVERT: a 170 PHE cc_start: 0.8199 (m-80) cc_final: 0.7756 (m-80) REVERT: a 177 TYR cc_start: 0.7978 (p90) cc_final: 0.7239 (p90) outliers start: 2 outliers final: 0 residues processed: 1631 average time/residue: 0.2162 time to fit residues: 579.6312 Evaluate side-chains 1372 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1371 time to evaluate : 1.309 ------------------------------------------------------------------------------- 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: 0.9990 chunk 412 optimal weight: 0.9990 chunk 362 optimal weight: 6.9990 chunk 287 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 348 optimal weight: 3.9990 chunk 365 optimal weight: 8.9990 chunk 330 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 427 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 139 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** ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 140 HIS ** 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** ** X 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 92 GLN ** Z 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 161 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.114592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.098670 restraints weight = 80677.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.101725 restraints weight = 43711.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.103768 restraints weight = 26684.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.105129 restraints weight = 17837.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.105970 restraints weight = 12949.271| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.6150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 36155 Z= 0.168 Angle : 0.803 42.982 49243 Z= 0.384 Chirality : 0.041 0.205 5448 Planarity : 0.005 0.067 6402 Dihedral : 11.548 89.948 5519 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.86 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: 1.13 (0.13), residues: 4448 helix: 1.20 (0.09), residues: 3390 sheet: 1.18 (0.77), residues: 28 loop : -0.59 (0.22), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 17 TYR 0.061 0.002 TYR R 97 PHE 0.037 0.002 PHE T 166 TRP 0.031 0.002 TRP K 128 HIS 0.007 0.002 HIS M 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (36155) covalent geometry : angle 0.80283 / 0.38 (49243) hydrogen bonds : bond 0.04404 / 2.93 ( 2648) hydrogen bonds : angle 4.33609 / 3.17 ( 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 1603 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1603 time to evaluate : 1.474 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: A 15 GLN cc_start: 0.7548 (mt0) cc_final: 0.6909 (mm110) REVERT: A 30 ARG cc_start: 0.8465 (tpt-90) cc_final: 0.8044 (tmt170) REVERT: A 38 MET cc_start: 0.8425 (mmt) cc_final: 0.7553 (tmm) REVERT: A 39 GLU cc_start: 0.7756 (mt-10) cc_final: 0.6931 (mt-10) REVERT: A 59 VAL cc_start: 0.9364 (t) cc_final: 0.9085 (t) REVERT: A 60 TYR cc_start: 0.8433 (m-80) cc_final: 0.8199 (m-80) REVERT: A 90 TYR cc_start: 0.8554 (m-10) cc_final: 0.8181 (m-80) REVERT: A 98 CYS cc_start: 0.8553 (t) cc_final: 0.7991 (t) REVERT: A 131 GLU cc_start: 0.7416 (tm-30) cc_final: 0.7041 (tm-30) REVERT: A 163 ASN cc_start: 0.8507 (t0) cc_final: 0.8245 (t0) REVERT: A 167 ASP cc_start: 0.8092 (t0) cc_final: 0.7522 (t0) REVERT: A 171 ASN cc_start: 0.8271 (m-40) cc_final: 0.7906 (m-40) REVERT: B 35 ASN cc_start: 0.8741 (m-40) cc_final: 0.7873 (t0) REVERT: B 36 LYS cc_start: 0.9462 (mtmm) cc_final: 0.8735 (mppt) REVERT: B 120 GLN cc_start: 0.7959 (mt0) cc_final: 0.7468 (tm-30) REVERT: B 137 LYS cc_start: 0.9273 (ttpp) cc_final: 0.8702 (ttpp) REVERT: C 94 MET cc_start: 0.9361 (mmt) cc_final: 0.9032 (mmm) REVERT: D 3 ASP cc_start: 0.8295 (p0) cc_final: 0.7894 (p0) REVERT: D 29 ASN cc_start: 0.9030 (t0) cc_final: 0.7672 (t0) REVERT: D 97 TYR cc_start: 0.7711 (m-10) cc_final: 0.7289 (m-10) REVERT: D 113 ASN cc_start: 0.8080 (t0) cc_final: 0.7767 (t0) REVERT: D 128 SER cc_start: 0.9365 (p) cc_final: 0.8905 (m) REVERT: D 136 MET cc_start: 0.8376 (mmm) cc_final: 0.8142 (tpp) REVERT: D 154 ASP cc_start: 0.6715 (t0) cc_final: 0.6323 (t0) REVERT: E 7 GLU cc_start: 0.8362 (mm-30) cc_final: 0.7944 (mm-30) REVERT: E 17 ARG cc_start: 0.7964 (ptt90) cc_final: 0.7739 (ptt-90) REVERT: E 28 ASP cc_start: 0.8519 (t70) cc_final: 0.8234 (t0) REVERT: E 38 MET cc_start: 0.8121 (mmt) cc_final: 0.7883 (tmm) REVERT: E 47 ASN cc_start: 0.8354 (m110) cc_final: 0.8007 (m110) REVERT: E 72 SER cc_start: 0.9010 (m) cc_final: 0.8414 (t) REVERT: E 107 MET cc_start: 0.7508 (mmp) cc_final: 0.6571 (mmm) REVERT: E 109 GLU cc_start: 0.8566 (tt0) cc_final: 0.8066 (tt0) REVERT: E 111 LEU cc_start: 0.8581 (mt) cc_final: 0.8070 (mt) REVERT: E 120 SER cc_start: 0.9188 (t) cc_final: 0.8972 (t) REVERT: E 121 THR cc_start: 0.9294 (p) cc_final: 0.8706 (t) REVERT: E 131 GLU cc_start: 0.8090 (pp20) cc_final: 0.7834 (pp20) REVERT: E 167 ASP cc_start: 0.8365 (t0) cc_final: 0.6976 (t0) REVERT: E 171 ASN cc_start: 0.8770 (p0) cc_final: 0.8390 (p0) REVERT: F 11 GLN cc_start: 0.9003 (tt0) cc_final: 0.8254 (tt0) REVERT: F 21 ASN cc_start: 0.8027 (m-40) cc_final: 0.6592 (t0) REVERT: F 25 ASP cc_start: 0.8733 (m-30) cc_final: 0.8230 (m-30) REVERT: F 29 ASN cc_start: 0.9095 (m-40) cc_final: 0.8833 (m110) REVERT: F 81 MET cc_start: 0.9188 (tpp) cc_final: 0.8872 (tpp) REVERT: F 117 GLU cc_start: 0.8448 (pp20) cc_final: 0.8179 (pp20) REVERT: F 146 ASP cc_start: 0.7828 (t0) cc_final: 0.7534 (t0) REVERT: G 20 SER cc_start: 0.8207 (t) cc_final: 0.7323 (m) REVERT: G 25 GLN cc_start: 0.8570 (mt0) cc_final: 0.8105 (mt0) REVERT: G 62 LYS cc_start: 0.8993 (tptm) cc_final: 0.8747 (tppt) REVERT: G 95 VAL cc_start: 0.9421 (t) cc_final: 0.9062 (t) REVERT: G 97 TYR cc_start: 0.8871 (m-10) cc_final: 0.8534 (m-10) REVERT: G 116 SER cc_start: 0.9020 (p) cc_final: 0.8700 (m) REVERT: G 122 PHE cc_start: 0.8051 (m-10) cc_final: 0.7706 (m-10) REVERT: G 124 LEU cc_start: 0.9167 (mt) cc_final: 0.8707 (mt) REVERT: G 133 LEU cc_start: 0.9580 (mm) cc_final: 0.9004 (mm) REVERT: G 134 LYS cc_start: 0.8964 (mmmm) cc_final: 0.8592 (ttmm) REVERT: G 161 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8593 (mt-10) REVERT: G 163 ASN cc_start: 0.9191 (m-40) cc_final: 0.8363 (m110) REVERT: H 38 LEU cc_start: 0.8943 (mt) cc_final: 0.8698 (tt) REVERT: H 91 ILE cc_start: 0.9332 (mm) cc_final: 0.9101 (tp) REVERT: I 15 GLN cc_start: 0.8104 (mt0) cc_final: 0.7672 (mp10) REVERT: I 51 LEU cc_start: 0.8596 (mt) cc_final: 0.8284 (mt) REVERT: I 60 TYR cc_start: 0.7346 (m-80) cc_final: 0.7034 (m-80) REVERT: I 62 LYS cc_start: 0.9301 (tptm) cc_final: 0.8954 (tptt) REVERT: I 83 LYS cc_start: 0.8927 (mmtm) cc_final: 0.8679 (mmmm) REVERT: I 94 MET cc_start: 0.8489 (mmm) cc_final: 0.8052 (tpp) REVERT: I 107 MET cc_start: 0.8467 (tpp) cc_final: 0.7931 (tpt) REVERT: I 115 LEU cc_start: 0.9013 (tp) cc_final: 0.8321 (tp) REVERT: I 119 ASN cc_start: 0.8338 (m110) cc_final: 0.7978 (m110) REVERT: I 127 SER cc_start: 0.8728 (p) cc_final: 0.8507 (p) REVERT: J 17 GLU cc_start: 0.8234 (mp0) cc_final: 0.7685 (mp0) REVERT: J 35 ASN cc_start: 0.8699 (m110) cc_final: 0.8013 (t0) REVERT: J 76 TYR cc_start: 0.8514 (t80) cc_final: 0.8216 (t80) REVERT: J 88 MET cc_start: 0.8803 (mmt) cc_final: 0.8588 (mmm) REVERT: J 91 ILE cc_start: 0.9453 (tp) cc_final: 0.9205 (tt) REVERT: J 97 TYR cc_start: 0.8591 (m-10) cc_final: 0.8033 (m-10) REVERT: J 112 LEU cc_start: 0.9531 (mp) cc_final: 0.8906 (mm) REVERT: J 133 ILE cc_start: 0.8807 (tt) cc_final: 0.8549 (tt) REVERT: J 136 MET cc_start: 0.8397 (mtp) cc_final: 0.8127 (mtm) REVERT: K 33 ARG cc_start: 0.6341 (mmm160) cc_final: 0.6003 (tpt170) REVERT: K 90 TYR cc_start: 0.8740 (m-10) cc_final: 0.8534 (m-80) REVERT: K 129 TYR cc_start: 0.8520 (m-80) cc_final: 0.8167 (m-80) REVERT: K 130 ILE cc_start: 0.9283 (pt) cc_final: 0.8910 (pt) REVERT: K 133 LEU cc_start: 0.8743 (mt) cc_final: 0.8525 (tp) REVERT: K 139 ASN cc_start: 0.8637 (t0) cc_final: 0.8181 (t0) REVERT: L 3 ASP cc_start: 0.8535 (p0) cc_final: 0.8172 (p0) REVERT: L 7 LYS cc_start: 0.8716 (ttpp) cc_final: 0.8220 (ptmm) REVERT: L 81 MET cc_start: 0.8634 (tpp) cc_final: 0.8092 (tpp) REVERT: L 88 MET cc_start: 0.7181 (mtm) cc_final: 0.6412 (mtp) REVERT: L 89 GLU cc_start: 0.7728 (pp20) cc_final: 0.7419 (tm-30) REVERT: L 103 ASP cc_start: 0.8127 (m-30) cc_final: 0.7668 (m-30) REVERT: L 120 GLN cc_start: 0.8799 (tm-30) cc_final: 0.8120 (tm-30) REVERT: L 137 LYS cc_start: 0.9320 (tttt) cc_final: 0.9117 (tttt) REVERT: L 159 MET cc_start: 0.8254 (mmt) cc_final: 0.7869 (mmt) REVERT: L 161 GLU cc_start: 0.8740 (tt0) cc_final: 0.8498 (tt0) REVERT: M 2 LYS cc_start: 0.9053 (mmmt) cc_final: 0.8779 (mmmt) REVERT: M 33 ARG cc_start: 0.8163 (ttt180) cc_final: 0.7739 (ttt90) REVERT: M 38 MET cc_start: 0.7884 (tpt) cc_final: 0.7579 (tpt) REVERT: M 57 GLN cc_start: 0.9431 (mm-40) cc_final: 0.9083 (mm-40) REVERT: M 94 MET cc_start: 0.8973 (ttm) cc_final: 0.8091 (mtp) REVERT: M 115 LEU cc_start: 0.8942 (tt) cc_final: 0.8492 (tt) REVERT: M 119 ASN cc_start: 0.8739 (p0) cc_final: 0.8329 (p0) REVERT: M 171 ASN cc_start: 0.8046 (p0) cc_final: 0.7679 (p0) REVERT: N 20 THR cc_start: 0.8099 (t) cc_final: 0.7782 (p) REVERT: N 42 ASN cc_start: 0.9531 (t0) cc_final: 0.8827 (t0) REVERT: N 45 THR cc_start: 0.8655 (t) cc_final: 0.8339 (t) REVERT: N 50 THR cc_start: 0.8653 (t) cc_final: 0.8428 (t) REVERT: N 87 ASP cc_start: 0.8958 (m-30) cc_final: 0.8738 (m-30) REVERT: N 88 MET cc_start: 0.8789 (ttm) cc_final: 0.7276 (tpp) REVERT: N 89 GLU cc_start: 0.7809 (pp20) cc_final: 0.7202 (pp20) REVERT: N 97 TYR cc_start: 0.8511 (m-10) cc_final: 0.7924 (m-80) REVERT: N 103 ASP cc_start: 0.7065 (t0) cc_final: 0.6591 (t0) REVERT: N 136 MET cc_start: 0.8620 (mtm) cc_final: 0.6772 (mtm) REVERT: O 61 GLN cc_start: 0.7655 (mt0) cc_final: 0.6936 (tm-30) REVERT: O 96 THR cc_start: 0.9403 (p) cc_final: 0.9113 (t) REVERT: O 104 THR cc_start: 0.8902 (p) cc_final: 0.7948 (p) REVERT: O 108 ASP cc_start: 0.7900 (m-30) cc_final: 0.7596 (m-30) REVERT: O 111 LEU cc_start: 0.8679 (tp) cc_final: 0.8425 (tp) REVERT: P 19 LEU cc_start: 0.8537 (mt) cc_final: 0.8288 (tp) REVERT: P 23 GLN cc_start: 0.8494 (mt0) cc_final: 0.8054 (mt0) REVERT: P 29 ASN cc_start: 0.8659 (t0) cc_final: 0.8214 (t0) REVERT: P 33 GLU cc_start: 0.7989 (mp0) cc_final: 0.7581 (mp0) REVERT: P 67 ILE cc_start: 0.8428 (mm) cc_final: 0.8199 (mm) REVERT: P 79 ARG cc_start: 0.8146 (ptm-80) cc_final: 0.7767 (ttp80) REVERT: P 97 TYR cc_start: 0.8766 (m-10) cc_final: 0.8210 (m-10) REVERT: P 122 LEU cc_start: 0.8665 (mm) cc_final: 0.8303 (mm) REVERT: P 134 GLN cc_start: 0.8573 (mm110) cc_final: 0.8298 (mp10) REVERT: Q 25 GLN cc_start: 0.8682 (mm-40) cc_final: 0.8468 (mm-40) REVERT: Q 39 GLU cc_start: 0.7529 (mt-10) cc_final: 0.6726 (pt0) REVERT: Q 90 TYR cc_start: 0.7349 (m-80) cc_final: 0.6855 (m-10) REVERT: Q 94 MET cc_start: 0.5521 (tpp) cc_final: 0.5163 (tpp) REVERT: Q 108 ASP cc_start: 0.8830 (m-30) cc_final: 0.8452 (m-30) REVERT: Q 134 LYS cc_start: 0.8429 (tptt) cc_final: 0.7801 (tptt) REVERT: R 29 ASN cc_start: 0.8210 (t0) cc_final: 0.7974 (t0) REVERT: R 38 LEU cc_start: 0.8531 (mt) cc_final: 0.8100 (mp) REVERT: R 49 SER cc_start: 0.8868 (p) cc_final: 0.8623 (t) REVERT: R 85 LEU cc_start: 0.9550 (mt) cc_final: 0.9142 (tp) REVERT: R 111 CYS cc_start: 0.8309 (t) cc_final: 0.7869 (t) REVERT: R 118 THR cc_start: 0.9015 (p) cc_final: 0.8804 (p) REVERT: R 128 SER cc_start: 0.8984 (m) cc_final: 0.8692 (m) REVERT: R 136 MET cc_start: 0.8511 (tmm) cc_final: 0.7967 (tmm) REVERT: S 1 MET cc_start: 0.6955 (mmm) cc_final: 0.6323 (mmm) REVERT: S 32 LYS cc_start: 0.8239 (mmtm) cc_final: 0.7791 (mmpt) REVERT: S 37 SER cc_start: 0.8321 (p) cc_final: 0.7835 (t) REVERT: S 49 GLN cc_start: 0.8331 (tp-100) cc_final: 0.7550 (pm20) REVERT: S 73 GLN cc_start: 0.8602 (pm20) cc_final: 0.8259 (pm20) REVERT: S 79 GLU cc_start: 0.7965 (mp0) cc_final: 0.7340 (tp30) REVERT: S 81 LYS cc_start: 0.9168 (tppt) cc_final: 0.8863 (mmmt) REVERT: S 83 LYS cc_start: 0.8356 (mmtp) cc_final: 0.7544 (tppt) REVERT: S 93 ARG cc_start: 0.7771 (ttp80) cc_final: 0.7073 (ttp80) REVERT: S 97 TYR cc_start: 0.9037 (m-10) cc_final: 0.8357 (m-80) REVERT: S 112 ILE cc_start: 0.9457 (mm) cc_final: 0.8966 (tp) REVERT: S 134 LYS cc_start: 0.9457 (mmpt) cc_final: 0.9167 (mmmm) REVERT: S 163 ASN cc_start: 0.9307 (m110) cc_final: 0.8851 (m-40) REVERT: T 13 ASP cc_start: 0.8725 (t70) cc_final: 0.8373 (t0) REVERT: T 15 ARG cc_start: 0.7713 (mtp85) cc_final: 0.6977 (mmm160) REVERT: T 19 LEU cc_start: 0.8150 (mt) cc_final: 0.7626 (mm) REVERT: T 23 GLN cc_start: 0.8383 (mt0) cc_final: 0.8081 (mp10) REVERT: T 25 ASP cc_start: 0.8555 (m-30) cc_final: 0.8139 (m-30) REVERT: T 110 ARG cc_start: 0.7397 (mmm-85) cc_final: 0.6747 (mmm160) REVERT: U 28 ASP cc_start: 0.7064 (t0) cc_final: 0.6776 (t0) REVERT: U 33 ARG cc_start: 0.7480 (mtp180) cc_final: 0.6617 (mtp180) REVERT: U 98 CYS cc_start: 0.7791 (t) cc_final: 0.7389 (t) REVERT: U 131 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8323 (mm-30) REVERT: U 137 LYS cc_start: 0.9392 (tttp) cc_final: 0.9128 (tptp) REVERT: U 171 ASN cc_start: 0.8752 (t0) cc_final: 0.8381 (t0) REVERT: U 174 SER cc_start: 0.7870 (t) cc_final: 0.7530 (t) REVERT: V 11 GLN cc_start: 0.8414 (tt0) cc_final: 0.8158 (tp40) REVERT: V 60 PHE cc_start: 0.8941 (m-80) cc_final: 0.8550 (m-80) REVERT: V 81 MET cc_start: 0.8466 (tpp) cc_final: 0.8008 (tpp) REVERT: V 113 ASN cc_start: 0.9156 (t0) cc_final: 0.8402 (t0) REVERT: W 9 ILE cc_start: 0.8485 (mm) cc_final: 0.8080 (tt) REVERT: W 32 LYS cc_start: 0.8938 (mttm) cc_final: 0.8516 (tppt) REVERT: W 42 ARG cc_start: 0.7734 (ttm170) cc_final: 0.6608 (tpt170) REVERT: W 69 MET cc_start: 0.4058 (mmm) cc_final: 0.3630 (tpt) REVERT: W 72 SER cc_start: 0.8675 (m) cc_final: 0.8400 (p) REVERT: W 94 MET cc_start: 0.8756 (ppp) cc_final: 0.8475 (ppp) REVERT: W 97 TYR cc_start: 0.7249 (m-10) cc_final: 0.6928 (m-80) REVERT: W 111 LEU cc_start: 0.7780 (pt) cc_final: 0.7392 (pp) REVERT: W 165 TYR cc_start: 0.7668 (m-80) cc_final: 0.7433 (m-80) REVERT: X 3 ASP cc_start: 0.7938 (p0) cc_final: 0.7644 (p0) REVERT: X 18 PHE cc_start: 0.6004 (m-80) cc_final: 0.5616 (m-80) REVERT: X 32 LYS cc_start: 0.8084 (mmtp) cc_final: 0.7763 (tptm) REVERT: X 52 VAL cc_start: 0.9291 (t) cc_final: 0.8952 (p) REVERT: X 89 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7779 (tm-30) REVERT: X 93 ARG cc_start: 0.8757 (ttp80) cc_final: 0.8145 (ttp80) REVERT: X 97 TYR cc_start: 0.8189 (m-80) cc_final: 0.7537 (m-80) REVERT: X 117 GLU cc_start: 0.7864 (pm20) cc_final: 0.7615 (pm20) REVERT: Y 23 GLU cc_start: 0.7751 (mp0) cc_final: 0.7314 (mp0) REVERT: Z 34 THR cc_start: 0.8906 (p) cc_final: 0.8673 (p) REVERT: Z 59 GLU cc_start: 0.8290 (pt0) cc_final: 0.8088 (pt0) REVERT: Z 76 VAL cc_start: 0.9722 (t) cc_final: 0.9485 (p) REVERT: Z 90 ASN cc_start: 0.8775 (m-40) cc_final: 0.8429 (m110) REVERT: Z 98 LEU cc_start: 0.9027 (mm) cc_final: 0.8039 (mm) REVERT: Z 127 ASP cc_start: 0.7659 (m-30) cc_final: 0.7304 (t0) REVERT: Z 196 THR cc_start: 0.8983 (p) cc_final: 0.8518 (m) REVERT: a 31 TYR cc_start: 0.7774 (m-80) cc_final: 0.7528 (m-10) REVERT: a 84 ARG cc_start: 0.8959 (ttm110) cc_final: 0.8601 (ttm-80) REVERT: a 88 LYS cc_start: 0.8996 (pttm) cc_final: 0.7989 (tppt) REVERT: a 127 TRP cc_start: 0.8249 (m100) cc_final: 0.7961 (m100) REVERT: a 129 ILE cc_start: 0.8888 (tt) cc_final: 0.8474 (tp) REVERT: a 137 GLN cc_start: 0.7874 (tp40) cc_final: 0.7299 (tp40) REVERT: a 151 GLN cc_start: 0.8763 (mm-40) cc_final: 0.7869 (mt0) REVERT: a 165 TYR cc_start: 0.5812 (m-80) cc_final: 0.5360 (m-80) REVERT: a 177 TYR cc_start: 0.8051 (p90) cc_final: 0.7267 (p90) outliers start: 0 outliers final: 0 residues processed: 1603 average time/residue: 0.2229 time to fit residues: 588.0316 Evaluate side-chains 1357 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1357 time to evaluate : 1.325 ------------------------------------------------------------------------------- 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: 4.9990 chunk 398 optimal weight: 20.0000 chunk 327 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 366 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 170 optimal weight: 9.9990 chunk 221 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 GLN ** 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** ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 119 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 T 47 ASN ** V 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 78 ASN Z 92 GLN ** Z 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3495 r_free = 0.3495 target = 0.113648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.096167 restraints weight = 110923.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.099789 restraints weight = 56306.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.102115 restraints weight = 32810.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.103712 restraints weight = 21292.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.104772 restraints weight = 14995.402| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3361 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 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 = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3361 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 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 0.062 36155 Z= 0.187 Angle : 0.819 43.008 49243 Z= 0.394 Chirality : 0.042 0.255 5448 Planarity : 0.005 0.065 6402 Dihedral : 11.612 89.932 5519 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.01 % Favored : 96.92 % Rotamer: Outliers : 0.03 % Allowed : 0.47 % Favored : 99.50 % 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: 1.06 (0.13), residues: 4448 helix: 1.14 (0.09), residues: 3384 sheet: 0.89 (0.78), residues: 28 loop : -0.56 (0.22), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 15 TYR 0.048 0.002 TYR R 97 PHE 0.050 0.002 PHE T 166 TRP 0.022 0.002 TRP K 128 HIS 0.007 0.002 HIS M 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (36155) covalent geometry : angle 0.81923 / 0.39 (49243) hydrogen bonds : bond 0.04486 / 2.99 ( 2648) hydrogen bonds : angle 4.42596 / 3.22 ( 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 1577 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1576 time to evaluate : 1.392 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: A 15 GLN cc_start: 0.7588 (mt0) cc_final: 0.7052 (mm110) REVERT: A 30 ARG cc_start: 0.8503 (tpt-90) cc_final: 0.8039 (tmt170) REVERT: A 38 MET cc_start: 0.8387 (mmt) cc_final: 0.7527 (tmm) REVERT: A 59 VAL cc_start: 0.9370 (t) cc_final: 0.9144 (t) REVERT: A 90 TYR cc_start: 0.8520 (m-10) cc_final: 0.8187 (m-80) REVERT: A 98 CYS cc_start: 0.8462 (t) cc_final: 0.7682 (t) REVERT: A 131 GLU cc_start: 0.7386 (tm-30) cc_final: 0.7037 (tm-30) REVERT: A 163 ASN cc_start: 0.8467 (t0) cc_final: 0.8211 (t0) REVERT: A 167 ASP cc_start: 0.8169 (t0) cc_final: 0.7641 (t0) REVERT: A 171 ASN cc_start: 0.8239 (m-40) cc_final: 0.7913 (m-40) REVERT: B 35 ASN cc_start: 0.8811 (m-40) cc_final: 0.7957 (t0) REVERT: B 36 LYS cc_start: 0.9453 (mtmm) cc_final: 0.8746 (mppt) REVERT: B 120 GLN cc_start: 0.8064 (mt0) cc_final: 0.7551 (tm-30) REVERT: B 137 LYS cc_start: 0.9288 (ttpp) cc_final: 0.8644 (ttpp) REVERT: B 159 MET cc_start: 0.8778 (mpp) cc_final: 0.8545 (mpp) REVERT: C 23 GLU cc_start: 0.6996 (mp0) cc_final: 0.6693 (mp0) REVERT: C 33 ARG cc_start: 0.8360 (mtt90) cc_final: 0.8086 (mtp180) REVERT: C 69 MET cc_start: 0.4511 (ptp) cc_final: 0.4239 (ptp) REVERT: C 94 MET cc_start: 0.9360 (mmt) cc_final: 0.9026 (mmm) REVERT: D 3 ASP cc_start: 0.8276 (p0) cc_final: 0.7902 (p0) REVERT: D 29 ASN cc_start: 0.9082 (t0) cc_final: 0.8635 (t0) REVERT: D 49 SER cc_start: 0.8770 (p) cc_final: 0.8506 (p) REVERT: D 97 TYR cc_start: 0.7884 (m-10) cc_final: 0.6899 (m-80) REVERT: D 128 SER cc_start: 0.9404 (p) cc_final: 0.8908 (m) REVERT: D 154 ASP cc_start: 0.6771 (t0) cc_final: 0.6375 (t0) REVERT: E 7 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7610 (mm-30) REVERT: E 28 ASP cc_start: 0.8539 (t70) cc_final: 0.8262 (t0) REVERT: E 38 MET cc_start: 0.8116 (mmt) cc_final: 0.7812 (tmm) REVERT: E 47 ASN cc_start: 0.8380 (m110) cc_final: 0.7953 (m110) REVERT: E 120 SER cc_start: 0.9227 (t) cc_final: 0.8990 (t) REVERT: E 121 THR cc_start: 0.9322 (p) cc_final: 0.8780 (t) REVERT: E 131 GLU cc_start: 0.8072 (pp20) cc_final: 0.7741 (pp20) REVERT: E 167 ASP cc_start: 0.8427 (t0) cc_final: 0.7096 (t0) REVERT: E 171 ASN cc_start: 0.8774 (p0) cc_final: 0.8391 (p0) REVERT: F 11 GLN cc_start: 0.9036 (tt0) cc_final: 0.8279 (tt0) REVERT: F 25 ASP cc_start: 0.8612 (m-30) cc_final: 0.8151 (m-30) REVERT: F 146 ASP cc_start: 0.7814 (t0) cc_final: 0.7611 (t0) REVERT: G 33 ARG cc_start: 0.7847 (mtp-110) cc_final: 0.7632 (mtp85) REVERT: G 97 TYR cc_start: 0.8893 (m-10) cc_final: 0.8619 (m-10) REVERT: G 98 CYS cc_start: 0.8469 (p) cc_final: 0.7777 (m) REVERT: G 116 SER cc_start: 0.8951 (p) cc_final: 0.8626 (m) REVERT: G 124 LEU cc_start: 0.9162 (mt) cc_final: 0.8665 (mt) REVERT: G 133 LEU cc_start: 0.9610 (mm) cc_final: 0.9295 (mm) REVERT: G 137 LYS cc_start: 0.8860 (ttmt) cc_final: 0.8658 (ttmt) REVERT: G 163 ASN cc_start: 0.9178 (m-40) cc_final: 0.8428 (m110) REVERT: H 38 LEU cc_start: 0.9086 (mt) cc_final: 0.8677 (tt) REVERT: H 59 LEU cc_start: 0.8263 (tp) cc_final: 0.8031 (tt) REVERT: H 81 MET cc_start: 0.8956 (mmp) cc_final: 0.8348 (mmp) REVERT: H 91 ILE cc_start: 0.9261 (mm) cc_final: 0.9051 (tp) REVERT: H 161 GLU cc_start: 0.7824 (pm20) cc_final: 0.7413 (pm20) REVERT: I 15 GLN cc_start: 0.8482 (mt0) cc_final: 0.7692 (mp10) REVERT: I 60 TYR cc_start: 0.7347 (m-80) cc_final: 0.7065 (m-80) REVERT: I 62 LYS cc_start: 0.9280 (tptm) cc_final: 0.8940 (tptt) REVERT: I 73 GLN cc_start: 0.9289 (pm20) cc_final: 0.8829 (pm20) REVERT: I 83 LYS cc_start: 0.8933 (mmtm) cc_final: 0.8708 (mmmm) REVERT: I 94 MET cc_start: 0.8473 (mmm) cc_final: 0.7916 (tpp) REVERT: I 107 MET cc_start: 0.8551 (tpp) cc_final: 0.7944 (tpt) REVERT: I 115 LEU cc_start: 0.9032 (tp) cc_final: 0.8363 (tp) REVERT: I 119 ASN cc_start: 0.8340 (m110) cc_final: 0.7766 (m110) REVERT: I 127 SER cc_start: 0.8798 (p) cc_final: 0.8592 (p) REVERT: I 144 LEU cc_start: 0.8963 (mt) cc_final: 0.8736 (mt) REVERT: J 5 PHE cc_start: 0.7891 (m-10) cc_final: 0.7683 (m-10) REVERT: J 17 GLU cc_start: 0.8280 (mp0) cc_final: 0.7691 (mp0) REVERT: J 35 ASN cc_start: 0.8679 (m110) cc_final: 0.8030 (t0) REVERT: J 76 TYR cc_start: 0.8544 (t80) cc_final: 0.8255 (t80) REVERT: J 91 ILE cc_start: 0.9489 (tp) cc_final: 0.9203 (tt) REVERT: J 97 TYR cc_start: 0.8626 (m-10) cc_final: 0.8068 (m-10) REVERT: J 112 LEU cc_start: 0.9531 (mp) cc_final: 0.8904 (mm) REVERT: J 133 ILE cc_start: 0.8629 (tt) cc_final: 0.8342 (tt) REVERT: J 136 MET cc_start: 0.8358 (mtp) cc_final: 0.8087 (mtm) REVERT: K 2 LYS cc_start: 0.8061 (tmtt) cc_final: 0.7819 (mmmt) REVERT: K 33 ARG cc_start: 0.6369 (mmm160) cc_final: 0.6083 (tpt170) REVERT: K 109 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7605 (mt-10) REVERT: K 129 TYR cc_start: 0.8556 (m-80) cc_final: 0.8280 (m-80) REVERT: K 139 ASN cc_start: 0.8902 (t0) cc_final: 0.8193 (t0) REVERT: L 3 ASP cc_start: 0.8553 (p0) cc_final: 0.8222 (p0) REVERT: L 7 LYS cc_start: 0.8748 (ttpp) cc_final: 0.8222 (ptmm) REVERT: L 81 MET cc_start: 0.8650 (tpp) cc_final: 0.8029 (tpp) REVERT: L 88 MET cc_start: 0.8012 (mtm) cc_final: 0.7591 (mtp) REVERT: L 89 GLU cc_start: 0.7750 (pp20) cc_final: 0.7413 (tm-30) REVERT: L 103 ASP cc_start: 0.8212 (m-30) cc_final: 0.7820 (m-30) REVERT: L 120 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8089 (tm-30) REVERT: L 161 GLU cc_start: 0.8733 (tt0) cc_final: 0.8511 (tt0) REVERT: M 2 LYS cc_start: 0.9077 (mmmt) cc_final: 0.8757 (mmmt) REVERT: M 33 ARG cc_start: 0.8116 (ttt180) cc_final: 0.7715 (ttt90) REVERT: M 38 MET cc_start: 0.7705 (tpt) cc_final: 0.7480 (tpt) REVERT: M 94 MET cc_start: 0.8491 (ttm) cc_final: 0.7918 (mtp) REVERT: M 115 LEU cc_start: 0.9022 (tt) cc_final: 0.8429 (tp) REVERT: M 118 ILE cc_start: 0.9281 (mm) cc_final: 0.8968 (mm) REVERT: M 119 ASN cc_start: 0.8743 (p0) cc_final: 0.8373 (p0) REVERT: M 171 ASN cc_start: 0.8082 (p0) cc_final: 0.7726 (p0) REVERT: N 20 THR cc_start: 0.8165 (t) cc_final: 0.7964 (p) REVERT: N 42 ASN cc_start: 0.9541 (t0) cc_final: 0.8859 (t0) REVERT: N 45 THR cc_start: 0.8548 (t) cc_final: 0.8281 (t) REVERT: N 50 THR cc_start: 0.8659 (t) cc_final: 0.8459 (t) REVERT: N 65 GLN cc_start: 0.7831 (pm20) cc_final: 0.6890 (pm20) REVERT: N 67 ILE cc_start: 0.9579 (pt) cc_final: 0.9178 (tp) REVERT: N 87 ASP cc_start: 0.9014 (m-30) cc_final: 0.8695 (m-30) REVERT: N 88 MET cc_start: 0.8806 (ttm) cc_final: 0.7812 (mtp) REVERT: N 89 GLU cc_start: 0.7798 (pp20) cc_final: 0.7301 (pp20) REVERT: N 97 TYR cc_start: 0.8511 (m-10) cc_final: 0.7908 (m-80) REVERT: N 103 ASP cc_start: 0.7294 (t0) cc_final: 0.6835 (t0) REVERT: N 162 ILE cc_start: 0.9160 (mt) cc_final: 0.8915 (mt) REVERT: O 1 MET cc_start: 0.7755 (mmm) cc_final: 0.7535 (tpt) REVERT: O 61 GLN cc_start: 0.7678 (mt0) cc_final: 0.6927 (tm-30) REVERT: O 96 THR cc_start: 0.9406 (p) cc_final: 0.9078 (t) REVERT: O 104 THR cc_start: 0.8993 (p) cc_final: 0.8178 (p) REVERT: O 108 ASP cc_start: 0.7936 (m-30) cc_final: 0.7564 (m-30) REVERT: O 111 LEU cc_start: 0.8625 (tp) cc_final: 0.8132 (tt) REVERT: P 23 GLN cc_start: 0.8562 (mt0) cc_final: 0.8194 (mt0) REVERT: P 29 ASN cc_start: 0.8747 (t0) cc_final: 0.8206 (t0) REVERT: P 33 GLU cc_start: 0.8230 (mp0) cc_final: 0.7889 (mp0) REVERT: P 79 ARG cc_start: 0.8140 (ptm-80) cc_final: 0.7870 (ttp80) REVERT: P 97 TYR cc_start: 0.8844 (m-10) cc_final: 0.7852 (m-80) REVERT: P 122 LEU cc_start: 0.8640 (mm) cc_final: 0.8328 (mm) REVERT: P 158 LEU cc_start: 0.9347 (mm) cc_final: 0.9103 (mm) REVERT: Q 25 GLN cc_start: 0.9068 (mm-40) cc_final: 0.8509 (mm-40) REVERT: Q 39 GLU cc_start: 0.7304 (mt-10) cc_final: 0.6451 (pt0) REVERT: Q 62 LYS cc_start: 0.7695 (tttp) cc_final: 0.7479 (ttmm) REVERT: Q 94 MET cc_start: 0.5569 (tpp) cc_final: 0.5217 (tpp) REVERT: Q 108 ASP cc_start: 0.8795 (m-30) cc_final: 0.8442 (m-30) REVERT: Q 134 LYS cc_start: 0.8471 (tptt) cc_final: 0.7845 (tptt) REVERT: R 1 MET cc_start: 0.7058 (ttm) cc_final: 0.6797 (ttp) REVERT: R 38 LEU cc_start: 0.8499 (mt) cc_final: 0.8218 (mp) REVERT: R 49 SER cc_start: 0.8897 (p) cc_final: 0.8634 (t) REVERT: R 85 LEU cc_start: 0.9554 (mt) cc_final: 0.9145 (tp) REVERT: R 111 CYS cc_start: 0.8210 (t) cc_final: 0.7843 (t) REVERT: R 118 THR cc_start: 0.9039 (p) cc_final: 0.8311 (p) REVERT: R 128 SER cc_start: 0.9079 (m) cc_final: 0.8734 (m) REVERT: R 136 MET cc_start: 0.8484 (tmm) cc_final: 0.7910 (tmm) REVERT: S 32 LYS cc_start: 0.8264 (mmtm) cc_final: 0.7823 (mmpt) REVERT: S 37 SER cc_start: 0.8340 (p) cc_final: 0.7841 (t) REVERT: S 44 LEU cc_start: 0.9499 (mt) cc_final: 0.9089 (tp) REVERT: S 49 GLN cc_start: 0.8360 (tp-100) cc_final: 0.7573 (pm20) REVERT: S 73 GLN cc_start: 0.8820 (pm20) cc_final: 0.7854 (pm20) REVERT: S 74 TYR cc_start: 0.8433 (m-10) cc_final: 0.8224 (m-10) REVERT: S 79 GLU cc_start: 0.7990 (mp0) cc_final: 0.7339 (tp30) REVERT: S 81 LYS cc_start: 0.9186 (tppt) cc_final: 0.8720 (mmtp) REVERT: S 83 LYS cc_start: 0.8433 (mmtp) cc_final: 0.7706 (tppt) REVERT: S 93 ARG cc_start: 0.7823 (ttp80) cc_final: 0.6924 (ttp80) REVERT: S 97 TYR cc_start: 0.9165 (m-10) cc_final: 0.8358 (m-80) REVERT: S 112 ILE cc_start: 0.9488 (mm) cc_final: 0.8980 (tp) REVERT: S 134 LYS cc_start: 0.9595 (mmpt) cc_final: 0.9091 (mmmm) REVERT: T 13 ASP cc_start: 0.8713 (t70) cc_final: 0.8417 (t0) REVERT: T 15 ARG cc_start: 0.7723 (mtp85) cc_final: 0.6992 (mmm160) REVERT: T 19 LEU cc_start: 0.8068 (mt) cc_final: 0.7729 (mm) REVERT: T 47 ASN cc_start: 0.7970 (t0) cc_final: 0.7015 (t0) REVERT: U 28 ASP cc_start: 0.7086 (t0) cc_final: 0.6785 (t0) REVERT: U 33 ARG cc_start: 0.7467 (mtp180) cc_final: 0.6570 (mtp180) REVERT: U 98 CYS cc_start: 0.7901 (t) cc_final: 0.7399 (t) REVERT: U 131 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8356 (mm-30) REVERT: U 134 LYS cc_start: 0.8890 (tppp) cc_final: 0.8686 (tppp) REVERT: U 137 LYS cc_start: 0.9329 (tttp) cc_final: 0.8964 (tptp) REVERT: U 171 ASN cc_start: 0.8763 (t0) cc_final: 0.8415 (t0) REVERT: U 174 SER cc_start: 0.7884 (t) cc_final: 0.7482 (t) REVERT: V 11 GLN cc_start: 0.8414 (tt0) cc_final: 0.8160 (tp40) REVERT: V 81 MET cc_start: 0.8437 (tpp) cc_final: 0.8128 (tpp) REVERT: V 90 ILE cc_start: 0.9419 (mm) cc_final: 0.9188 (mm) REVERT: V 113 ASN cc_start: 0.9217 (t0) cc_final: 0.8428 (t0) REVERT: V 131 VAL cc_start: 0.8995 (t) cc_final: 0.8759 (t) REVERT: V 137 LYS cc_start: 0.9386 (tttm) cc_final: 0.9116 (tttt) REVERT: W 9 ILE cc_start: 0.8331 (mm) cc_final: 0.7980 (tt) REVERT: W 32 LYS cc_start: 0.8964 (mttm) cc_final: 0.8612 (tptp) REVERT: W 42 ARG cc_start: 0.7804 (ttm170) cc_final: 0.6652 (tpt170) REVERT: W 63 PHE cc_start: 0.5725 (m-80) cc_final: 0.5383 (m-80) REVERT: W 69 MET cc_start: 0.5115 (mmm) cc_final: 0.4686 (tpt) REVERT: W 72 SER cc_start: 0.8629 (m) cc_final: 0.8361 (p) REVERT: W 94 MET cc_start: 0.8782 (ppp) cc_final: 0.8520 (ppp) REVERT: W 97 TYR cc_start: 0.7293 (m-10) cc_final: 0.6944 (m-80) REVERT: W 111 LEU cc_start: 0.7842 (pt) cc_final: 0.7454 (pp) REVERT: X 3 ASP cc_start: 0.7981 (p0) cc_final: 0.7686 (p0) REVERT: X 18 PHE cc_start: 0.6052 (m-80) cc_final: 0.5755 (m-80) REVERT: X 32 LYS cc_start: 0.8100 (mmtp) cc_final: 0.7767 (tptm) REVERT: X 52 VAL cc_start: 0.9319 (t) cc_final: 0.9008 (p) REVERT: X 89 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7923 (tm-30) REVERT: X 93 ARG cc_start: 0.8045 (ttp80) cc_final: 0.7425 (ttp80) REVERT: X 97 TYR cc_start: 0.8127 (m-80) cc_final: 0.7778 (m-80) REVERT: X 110 ARG cc_start: 0.8278 (ttm110) cc_final: 0.7798 (ttm170) REVERT: X 117 GLU cc_start: 0.7921 (pm20) cc_final: 0.7675 (pm20) REVERT: Y 23 GLU cc_start: 0.7735 (mp0) cc_final: 0.7289 (mp0) REVERT: Y 61 ARG cc_start: 0.8656 (ttp80) cc_final: 0.7683 (ttp80) REVERT: Z 76 VAL cc_start: 0.9723 (t) cc_final: 0.9519 (p) REVERT: Z 90 ASN cc_start: 0.8775 (m-40) cc_final: 0.8421 (m110) REVERT: Z 127 ASP cc_start: 0.7645 (m-30) cc_final: 0.7293 (t0) REVERT: Z 196 THR cc_start: 0.9055 (p) cc_final: 0.8542 (m) REVERT: a 31 TYR cc_start: 0.7728 (m-80) cc_final: 0.7525 (m-10) REVERT: a 44 GLU cc_start: 0.7321 (tt0) cc_final: 0.7069 (tt0) REVERT: a 45 LEU cc_start: 0.9254 (tt) cc_final: 0.9022 (tp) REVERT: a 84 ARG cc_start: 0.8951 (ttm110) cc_final: 0.8331 (ttm-80) REVERT: a 88 LYS cc_start: 0.9024 (pttm) cc_final: 0.7989 (tppt) REVERT: a 129 ILE cc_start: 0.8664 (tt) cc_final: 0.8314 (tp) REVERT: a 137 GLN cc_start: 0.7938 (tp40) cc_final: 0.7324 (tp40) REVERT: a 151 GLN cc_start: 0.8908 (mm-40) cc_final: 0.8074 (mt0) REVERT: a 165 TYR cc_start: 0.5929 (m-80) cc_final: 0.5421 (m-80) outliers start: 1 outliers final: 0 residues processed: 1576 average time/residue: 0.2236 time to fit residues: 579.6646 Evaluate side-chains 1338 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1338 time to evaluate : 1.305 ------------------------------------------------------------------------------- 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: 1.9990 chunk 430 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 160 optimal weight: 0.9990 chunk 337 optimal weight: 0.9990 chunk 420 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 438 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN F 29 ASN F 42 ASN ** F 65 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** M 163 ASN ** N 68 GLN ** 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 63 GLN ** V 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 GLN X 47 ASN X 78 ASN Z 92 GLN ** Z 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 285 ASN ** a 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.114484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.096938 restraints weight = 113689.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.100630 restraints weight = 57464.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.103007 restraints weight = 33383.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.104613 restraints weight = 21489.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.105622 restraints weight = 15057.046| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3374 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3374 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.6410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 36155 Z= 0.171 Angle : 0.815 42.975 49243 Z= 0.393 Chirality : 0.042 0.261 5448 Planarity : 0.005 0.063 6402 Dihedral : 11.597 89.372 5519 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.01 % Favored : 96.92 % Rotamer: Outliers : 0.03 % Allowed : 0.35 % Favored : 99.62 % 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: 1.12 (0.09), residues: 3384 sheet: 0.88 (0.78), residues: 28 loop : -0.58 (0.22), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Y 35 TYR 0.060 0.002 TYR R 97 PHE 0.018 0.002 PHE D 166 TRP 0.019 0.002 TRP K 128 HIS 0.005 0.002 HIS M 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (36155) covalent geometry : angle 0.81459 / 0.39 (49243) hydrogen bonds : bond 0.04459 / 2.96 ( 2648) hydrogen bonds : angle 4.42515 / 3.23 ( 7847) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10075.53 seconds wall clock time: 173 minutes 24.37 seconds (10404.37 seconds total)