Starting phenix.real_space_refine on Tue Aug 26 09:16:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7veb_31945/08_2025/7veb_31945.cif Found real_map, /net/cci-nas-00/data/ceres_data/7veb_31945/08_2025/7veb_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7veb_31945/08_2025/7veb_31945.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7veb_31945/08_2025/7veb_31945.map" model { file = "/net/cci-nas-00/data/ceres_data/7veb_31945/08_2025/7veb_31945.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7veb_31945/08_2025/7veb_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 8.77, per 1000 atoms: 0.25 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: 2.84 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 1.2 microseconds 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: 0.71 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: 4.92 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.35: 11941 1.35 - 1.51: 10743 1.51 - 1.67: 13160 1.67 - 1.83: 291 1.83 - 1.99: 20 Bond restraints: 36155 Sorted by residual: bond pdb=" OB CYC T 201 " pdb=" C4B CYC T 201 " ideal model delta sigma weight residual 1.217 1.363 -0.146 2.00e-02 2.50e+03 5.35e+01 bond pdb=" OB CYC Q 201 " pdb=" C4B CYC Q 201 " ideal model delta sigma weight residual 1.217 1.363 -0.146 2.00e-02 2.50e+03 5.34e+01 bond pdb=" OB CYC X 201 " pdb=" C4B CYC X 201 " ideal model delta sigma weight residual 1.217 1.363 -0.146 2.00e-02 2.50e+03 5.33e+01 bond pdb=" OB CYC V 201 " pdb=" C4B CYC V 201 " ideal model delta sigma weight residual 1.217 1.362 -0.145 2.00e-02 2.50e+03 5.28e+01 bond pdb=" OB CYC S 201 " pdb=" C4B CYC S 201 " ideal model delta sigma weight residual 1.217 1.362 -0.145 2.00e-02 2.50e+03 5.26e+01 ... (remaining 36150 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.88: 49017 8.88 - 17.75: 223 17.75 - 26.63: 0 26.63 - 35.50: 0 35.50 - 44.38: 3 Bond angle restraints: 49243 Sorted by residual: angle pdb=" CBA CYC Q 201 " pdb=" CGA CYC Q 201 " pdb=" O2A CYC Q 201 " ideal model delta sigma weight residual 115.71 160.09 -44.38 3.00e+00 1.11e-01 2.19e+02 angle pdb=" CBA CYC Q 201 " pdb=" CGA CYC Q 201 " pdb=" O1A CYC Q 201 " ideal model delta sigma weight residual 117.88 74.34 43.54 3.00e+00 1.11e-01 2.11e+02 angle pdb=" O1A CYC Q 201 " pdb=" CGA CYC Q 201 " pdb=" O2A CYC Q 201 " ideal model delta sigma weight residual 126.41 85.75 40.66 3.00e+00 1.11e-01 1.84e+02 angle pdb=" CA CYS X 155 " pdb=" CB CYS X 155 " pdb=" SG CYS X 155 " ideal model delta sigma weight residual 114.40 131.93 -17.53 2.30e+00 1.89e-01 5.81e+01 angle pdb=" CA CYS H 155 " pdb=" CB CYS H 155 " pdb=" SG CYS H 155 " ideal model delta sigma weight residual 114.40 130.11 -15.71 2.30e+00 1.89e-01 4.66e+01 ... (remaining 49238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 20693 17.99 - 35.99: 1353 35.99 - 53.98: 298 53.98 - 71.97: 92 71.97 - 89.96: 31 Dihedral angle restraints: 22467 sinusoidal: 9272 harmonic: 13195 Sorted by residual: dihedral pdb=" CA PHE Z 15 " pdb=" C PHE Z 15 " pdb=" N SER Z 16 " pdb=" CA SER Z 16 " ideal model delta harmonic sigma weight residual 180.00 -159.35 -20.65 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA TYR Z 250 " pdb=" C TYR Z 250 " pdb=" N PRO Z 251 " pdb=" CA PRO Z 251 " ideal model delta harmonic sigma weight residual 180.00 159.86 20.14 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA LEU E 111 " pdb=" C LEU E 111 " pdb=" N ILE E 112 " pdb=" CA ILE E 112 " ideal model delta harmonic sigma weight residual -180.00 -161.78 -18.22 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 22464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 5397 0.148 - 0.297: 33 0.297 - 0.445: 13 0.445 - 0.594: 3 0.594 - 0.742: 2 Chirality restraints: 5448 Sorted by residual: chirality pdb=" C2C CYC C 201 " pdb=" C1C CYC C 201 " pdb=" C3C CYC C 201 " pdb=" CMC CYC C 201 " both_signs ideal model delta sigma weight residual False -2.52 -1.78 -0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" C2C CYC B 202 " pdb=" C1C CYC B 202 " pdb=" C3C CYC B 202 " pdb=" CMC CYC B 202 " both_signs ideal model delta sigma weight residual False -2.52 -1.90 -0.62 2.00e-01 2.50e+01 9.67e+00 chirality pdb=" C2C CYC I 201 " pdb=" C1C CYC I 201 " pdb=" C3C CYC I 201 " pdb=" CMC CYC I 201 " both_signs ideal model delta sigma weight residual False -2.52 -1.94 -0.58 2.00e-01 2.50e+01 8.46e+00 ... (remaining 5445 not shown) Planarity restraints: 6402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE Z 165 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.68e+00 pdb=" C PHE Z 165 " -0.037 2.00e-02 2.50e+03 pdb=" O PHE Z 165 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN Z 166 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU V 112 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.27e+00 pdb=" C LEU V 112 " 0.036 2.00e-02 2.50e+03 pdb=" O LEU V 112 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN V 113 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET Z 271 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.40e+00 pdb=" C MET Z 271 " -0.032 2.00e-02 2.50e+03 pdb=" O MET Z 271 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN Z 272 " 0.011 2.00e-02 2.50e+03 ... (remaining 6399 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1144 2.71 - 3.26: 39509 3.26 - 3.81: 63189 3.81 - 4.35: 75277 4.35 - 4.90: 122149 Nonbonded interactions: 301268 Sorted by model distance: nonbonded pdb=" OG1 THR Z 156 " pdb=" OB CYC L 201 " model vdw 2.165 3.040 nonbonded pdb=" OH TYR R 76 " pdb=" NH2 ARG S 93 " model vdw 2.229 3.120 nonbonded pdb=" NH1 ARG B 79 " pdb=" O ASN Y 30 " model vdw 2.244 3.120 nonbonded pdb=" O TYR R 76 " pdb=" OG1 THR R 77 " model vdw 2.279 3.040 nonbonded pdb=" O TYR L 76 " pdb=" OG1 THR L 77 " model vdw 2.284 3.040 ... (remaining 301263 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB )) or resid 31 through 52 or (resid 53 and (name N or name \ CA or name C or name O or name CB )) or resid 54 through 56 or resid 58 through \ 107 or (resid 108 through 109 and (name N or name CA or name C or name O or nam \ e CB )) or resid 110 through 122 or (resid 123 and (name N or name CA or name C \ or name O or name CB )) or resid 124 through 201)) selection = (chain 'C' and (resid 1 through 6 or (resid 7 through 8 and (name N or name CA o \ r name C or name O or name CB )) or resid 9 through 27 or (resid 28 and (name N \ or name CA or name C or name O or name CB )) or resid 29 or (resid 30 and (name \ N or name CA or name C or name O or name CB )) or resid 31 through 52 or (resid \ 53 and (name N or name CA or name C or name O or name CB )) or resid 54 through \ 56 or resid 58 through 107 or (resid 108 through 109 and (name N or name CA or n \ ame C or name O or name CB )) or resid 110 through 122 or (resid 123 and (name N \ or name CA or name C or name O or name CB )) or resid 124 through 201)) selection = (chain 'E' and (resid 1 through 6 or (resid 7 through 8 and (name N or name CA o \ r name C or name O or name CB )) or resid 9 through 27 or (resid 28 and (name N \ or name CA or name C or name O or name CB )) or resid 29 or (resid 30 and (name \ N or name CA or name C or name O or name CB )) or resid 31 through 52 or (resid \ 53 and (name N or name CA or name C or name O or name CB )) or resid 54 through \ 56 or resid 58 through 107 or (resid 108 through 109 and (name N or name CA or n \ ame C or name O or name CB )) or resid 110 through 122 or (resid 123 and (name N \ or name CA or name C or name O or name CB )) or resid 124 through 201)) selection = (chain 'G' and (resid 1 through 6 or (resid 7 through 8 and (name N or name CA o \ r name C or name O or name CB )) or resid 9 through 27 or (resid 28 and (name N \ or name CA or name C or name O or name CB )) or resid 29 or (resid 30 and (name \ N or name CA or name C or name O or name CB )) or resid 31 through 52 or (resid \ 53 and (name N or name CA or name C or name O or name CB )) or resid 54 through \ 56 or resid 58 through 107 or (resid 108 through 109 and (name N or name CA or n \ ame C or name O or name CB )) or resid 110 through 122 or (resid 123 and (name N \ or name CA or name C or name O or name CB )) or resid 124 through 201)) selection = (chain 'I' and (resid 1 through 6 or (resid 7 through 8 and (name N or name CA o \ r name C or name O or name CB )) or resid 9 through 27 or (resid 28 and (name N \ or name CA or name C or name O or name CB )) or resid 29 or (resid 30 and (name \ N or name CA or name C or name O or name CB )) or resid 31 through 52 or (resid \ 53 and (name N or name CA or name C or name O or name CB )) or resid 54 through \ 56 or resid 58 through 107 or (resid 108 through 109 and (name N or name CA or n \ ame C or name O or name CB )) or resid 110 through 122 or (resid 123 and (name N \ or name CA or name C or name O or name CB )) or resid 124 through 201)) selection = (chain 'K' and (resid 1 through 6 or (resid 7 through 8 and (name N or name CA o \ r name C or name O or name CB )) or resid 9 through 27 or (resid 28 and (name N \ or name CA or name C or name O or name CB )) or resid 29 or (resid 30 and (name \ N or name CA or name C or name O or name CB )) or resid 31 through 52 or (resid \ 53 and (name N or name CA or name C or name O or name CB )) or resid 54 through \ 56 or resid 58 through 107 or (resid 108 through 109 and (name N or name CA or n \ ame C or name O or name CB )) or resid 110 through 122 or (resid 123 and (name N \ or name CA or name C or name O or name CB )) or resid 124 through 201)) selection = (chain 'M' and (resid 1 through 6 or (resid 7 through 8 and (name N or name CA o \ r name C or name O or name CB )) or resid 9 through 27 or (resid 28 and (name N \ or name CA or name C or name O or name CB )) or resid 29 or (resid 30 and (name \ N or name CA or name C or name O or name CB )) or resid 31 through 52 or (resid \ 53 and (name N or name CA or name C or name O or name CB )) or resid 54 through \ 56 or resid 58 through 107 or (resid 108 through 109 and (name N or name CA or n \ ame C or name O or name CB )) or resid 110 through 122 or (resid 123 and (name N \ or name CA or name C or name O or name CB )) or resid 124 through 201)) selection = (chain 'O' and (resid 1 through 6 or (resid 7 through 8 and (name N or name CA o \ r name C or name O or name CB )) or resid 9 through 27 or (resid 28 and (name N \ or name CA or name C or name O or name CB )) or resid 29 or (resid 30 and (name \ N or name CA or name C or name O or name CB )) or resid 31 through 52 or (resid \ 53 and (name N or name CA or name C or name O or name CB )) or resid 54 through \ 56 or resid 58 through 107 or (resid 108 through 109 and (name N or name CA or n \ ame C or name O or name CB )) or resid 110 through 122 or (resid 123 and (name N \ or name CA or name C or name O or name CB )) or resid 124 through 201)) selection = (chain 'Q' and (resid 1 through 6 or (resid 7 through 8 and (name N or name CA o \ r name C or name O or name CB )) or resid 9 through 27 or (resid 28 and (name N \ or name CA or name C or name O or name CB )) or resid 29 or (resid 30 and (name \ N or name CA or name C or name O or name CB )) or resid 31 through 52 or (resid \ 53 and (name N or name CA or name C or name O or name CB )) or resid 54 through \ 56 or resid 58 through 107 or (resid 108 through 109 and (name N or name CA or n \ ame C or name O or name CB )) or resid 110 through 122 or (resid 123 and (name N \ or name CA or name C or name O or name CB )) or resid 124 through 201)) selection = (chain 'S' and (resid 1 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 52 or (resid 53 and (name N or name \ CA or name C or name O or name CB )) or resid 54 through 56 or resid 58 through \ 201)) selection = (chain 'U' and (resid 1 through 6 or (resid 7 through 8 and (name N or name CA o \ r name C or name O or name CB )) or resid 9 through 27 or (resid 28 and (name N \ or name CA or name C or name O or name CB )) or resid 29 or (resid 30 and (name \ N or name CA or name C or name O or name CB )) or resid 31 through 52 or (resid \ 53 and (name N or name CA or name C or name O or name CB )) or resid 54 through \ 56 or resid 58 through 107 or (resid 108 through 109 and (name N or name CA or n \ ame C or name O or name CB )) or resid 110 through 122 or (resid 123 and (name N \ or name CA or name C or name O or name CB )) or resid 124 through 201)) selection = (chain 'W' and (resid 1 through 6 or (resid 7 through 8 and (name N or name CA o \ r name C or name O or name CB )) or resid 9 through 27 or (resid 28 and (name N \ or name CA or name C or name O or name CB )) or resid 29 or (resid 30 and (name \ N or name CA or name C or name O or name CB )) or resid 31 through 56 or resid 5 \ 8 through 107 or (resid 108 through 109 and (name N or name CA or name C or name \ O or name CB )) or resid 110 through 122 or (resid 123 and (name N or name CA o \ r name C or name O or name CB )) or resid 124 through 201)) } ncs_group { reference = (chain 'B' and (resid 1 through 38 or (resid 39 through 40 and (name N or name C \ A or name C or name O or name CB )) or resid 41 through 102 or (resid 103 and (n \ ame N or name CA or name C or name O or name CB )) or resid 104 through 107 or ( \ resid 108 and (name N or name CA or name C or name O or name CB )) or resid 109 \ through 119 or (resid 120 through 122 and (name N or name CA or name C or name O \ or name CB )) or resid 123 through 133 or (resid 134 and (name N or name CA or \ name C or name O or name CB )) or resid 135 through 136 or (resid 137 and (name \ N or name CA or name C or name O or name CB )) or resid 138 through 202)) selection = (chain 'D' and (resid 1 through 102 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 107 or (resid 108 and (name N or \ name CA or name C or name O or name CB )) or resid 109 through 119 or (resid 12 \ 0 through 122 and (name N or name CA or name C or name O or name CB )) or resid \ 123 through 133 or (resid 134 and (name N or name CA or name C or name O or name \ CB )) or resid 135 through 136 or (resid 137 and (name N or name CA or name C o \ r name O or name CB )) or resid 138 through 202)) selection = (chain 'F' and (resid 1 through 38 or (resid 39 through 40 and (name N or name C \ A or name C or name O or name CB )) or resid 41 through 102 or (resid 103 and (n \ ame N or name CA or name C or name O or name CB )) or resid 104 through 107 or ( \ resid 108 and (name N or name CA or name C or name O or name CB )) or resid 109 \ through 119 or (resid 120 through 122 and (name N or name CA or name C or name O \ or name CB )) or resid 123 through 133 or (resid 134 and (name N or name CA or \ name C or name O or name CB )) or resid 135 through 136 or (resid 137 and (name \ N or name CA or name C or name O or name CB )) or resid 138 through 202)) selection = (chain 'H' and (resid 1 through 38 or (resid 39 through 40 and (name N or name C \ A or name C or name O or name CB )) or resid 41 through 102 or (resid 103 and (n \ ame N or name CA or name C or name O or name CB )) or resid 104 through 107 or ( \ resid 108 and (name N or name CA or name C or name O or name CB )) or resid 109 \ through 119 or (resid 120 through 122 and (name N or name CA or name C or name O \ or name CB )) or resid 123 through 133 or (resid 134 and (name N or name CA or \ name C or name O or name CB )) or resid 135 through 202)) selection = (chain 'J' and (resid 1 through 38 or (resid 39 through 40 and (name N or name C \ A or name C or name O or name CB )) or resid 41 through 102 or (resid 103 and (n \ ame N or name CA or name C or name O or name CB )) or resid 104 through 107 or ( \ resid 108 and (name N or name CA or name C or name O or name CB )) or resid 109 \ through 119 or (resid 120 through 122 and (name N or name CA or name C or name O \ or name CB )) or resid 123 through 133 or (resid 134 and (name N or name CA or \ name C or name O or name CB )) or resid 135 through 136 or (resid 137 and (name \ N or name CA or name C or name O or name CB )) or resid 138 through 202)) selection = (chain 'L' and (resid 1 through 38 or (resid 39 through 40 and (name N or name C \ A or name C or name O or name CB )) or resid 41 through 102 or (resid 103 and (n \ ame N or name CA or name C or name O or name CB )) or resid 104 through 107 or ( \ resid 108 and (name N or name CA or name C or name O or name CB )) or resid 109 \ through 119 or (resid 120 through 122 and (name N or name CA or name C or name O \ or name CB )) or resid 123 through 133 or (resid 134 and (name N or name CA or \ name C or name O or name CB )) or resid 135 through 136 or (resid 137 and (name \ N or name CA or name C or name O or name CB )) or resid 138 through 202)) selection = (chain 'N' and (resid 1 through 38 or (resid 39 through 40 and (name N or name C \ A or name C or name O or name CB )) or resid 41 through 102 or (resid 103 and (n \ ame N or name CA or name C or name O or name CB )) or resid 104 through 107 or ( \ resid 108 and (name N or name CA or name C or name O or name CB )) or resid 109 \ through 119 or (resid 120 through 122 and (name N or name CA or name C or name O \ or name CB )) or resid 123 through 133 or (resid 134 and (name N or name CA or \ name C or name O or name CB )) or resid 135 through 136 or (resid 137 and (name \ N or name CA or name C or name O or name CB )) or resid 138 through 202)) selection = (chain 'P' and (resid 1 through 38 or (resid 39 through 40 and (name N or name C \ A or name C or name O or name CB )) or resid 41 through 102 or (resid 103 and (n \ ame N or name CA or name C or name O or name CB )) or resid 104 through 107 or ( \ resid 108 and (name N or name CA or name C or name O or name CB )) or resid 109 \ through 119 or (resid 120 through 122 and (name N or name CA or name C or name O \ or name CB )) or resid 123 through 133 or (resid 134 and (name N or name CA or \ name C or name O or name CB )) or resid 135 through 136 or (resid 137 and (name \ N or name CA or name C or name O or name CB )) or resid 138 through 202)) selection = (chain 'R' and (resid 1 through 38 or (resid 39 through 40 and (name N or name C \ A or name C or name O or name CB )) or resid 41 through 102 or (resid 103 and (n \ ame N or name CA or name C or name O or name CB )) or resid 104 through 107 or ( \ resid 108 and (name N or name CA or name C or name O or name CB )) or resid 109 \ through 119 or (resid 120 through 122 and (name N or name CA or name C or name O \ or name CB )) or resid 123 through 133 or (resid 134 and (name N or name CA or \ name C or name O or name CB )) or resid 135 through 136 or (resid 137 and (name \ N or name CA or name C or name O or name CB )) or resid 138 through 202)) selection = (chain 'T' and (resid 1 through 38 or (resid 39 through 40 and (name N or name C \ A or name C or name O or name CB )) or resid 41 through 119 or (resid 120 throug \ h 122 and (name N or name CA or name C or name O or name CB )) or resid 123 thro \ ugh 202)) selection = (chain 'V' and (resid 1 through 38 or (resid 39 through 40 and (name N or name C \ A or name C or name O or name CB )) or resid 41 through 102 or (resid 103 and (n \ ame N or name CA or name C or name O or name CB )) or resid 104 through 107 or ( \ resid 108 and (name N or name CA or name C or name O or name CB )) or resid 109 \ through 121 or (resid 122 and (name N or name CA or name C or name O or name CB \ )) or resid 123 through 133 or (resid 134 and (name N or name CA or name C or na \ me O or name CB )) or resid 135 through 136 or (resid 137 and (name N or name CA \ or name C or name O or name CB )) or resid 138 through 202)) selection = (chain 'X' and (resid 1 through 102 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 107 or (resid 108 and (name N or \ name CA or name C or name O or name CB )) or resid 109 through 119 or (resid 12 \ 0 through 122 and (name N or name CA or name C or name O or name CB )) or resid \ 123 through 202)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.160 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: 0.040 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 28.820 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.120 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: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.177 36155 Z= 0.547 Angle : 1.367 44.378 49243 Z= 0.534 Chirality : 0.049 0.742 5448 Planarity : 0.004 0.034 6402 Dihedral : 13.452 89.965 14003 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.61 % Favored : 97.37 % Rotamer: Outliers : 0.74 % Allowed : 4.78 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.12), residues: 4448 helix: 1.02 (0.08), residues: 3365 sheet: 0.83 (0.98), residues: 28 loop : -1.22 (0.20), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 86 TYR 0.021 0.001 TYR D 76 PHE 0.020 0.002 PHE a 82 TRP 0.014 0.002 TRP C 128 HIS 0.005 0.001 HIS G 140 Details of bonding type rmsd covalent geometry : bond 0.01104 (36155) covalent geometry : angle 1.36749 (49243) hydrogen bonds : bond 0.13563 ( 2648) hydrogen bonds : angle 5.56725 ( 7847) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2195 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 2170 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ASP cc_start: 0.9022 (t70) cc_final: 0.8545 (t70) REVERT: A 17 ARG cc_start: 0.8503 (ptp-170) cc_final: 0.7655 (ptp-110) REVERT: A 18 PHE cc_start: 0.8095 (m-80) cc_final: 0.7339 (m-80) REVERT: A 33 ARG cc_start: 0.9176 (mmm160) cc_final: 0.8805 (tpt170) REVERT: A 38 MET cc_start: 0.9117 (mmt) cc_final: 0.8213 (tmm) REVERT: A 39 GLU cc_start: 0.9641 (tp30) cc_final: 0.9100 (mm-30) REVERT: A 49 GLN cc_start: 0.9268 (tp40) cc_final: 0.9023 (tp-100) REVERT: A 63 PHE cc_start: 0.9009 (m-80) cc_final: 0.8635 (m-10) REVERT: A 87 ASP cc_start: 0.9161 (m-30) cc_final: 0.8893 (m-30) REVERT: A 90 TYR cc_start: 0.9265 (m-10) cc_final: 0.8953 (m-80) REVERT: A 119 ASN cc_start: 0.9514 (m-40) cc_final: 0.9305 (p0) REVERT: A 124 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.8940 (mp) REVERT: A 166 ILE cc_start: 0.9772 (mt) cc_final: 0.9449 (mm) REVERT: A 167 ASP cc_start: 0.9188 (t0) cc_final: 0.8569 (t0) REVERT: A 170 ILE cc_start: 0.9391 (mt) cc_final: 0.9035 (mt) REVERT: B 27 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9142 (mm) REVERT: B 29 ASN cc_start: 0.8286 (m-40) cc_final: 0.8056 (t0) REVERT: B 32 LYS cc_start: 0.9038 (ttpp) cc_final: 0.8645 (tppt) REVERT: B 33 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8846 (mm-30) REVERT: B 49 SER cc_start: 0.9630 (m) cc_final: 0.9298 (p) REVERT: B 67 ILE cc_start: 0.9362 (pt) cc_final: 0.9137 (mm) REVERT: B 89 GLU cc_start: 0.9563 (pt0) cc_final: 0.9332 (tt0) REVERT: B 93 ARG cc_start: 0.9481 (ttp80) cc_final: 0.8957 (mtp180) REVERT: B 112 LEU cc_start: 0.9343 (mt) cc_final: 0.8974 (mp) REVERT: B 119 TYR cc_start: 0.9330 (m-80) cc_final: 0.8750 (m-80) REVERT: B 120 GLN cc_start: 0.8762 (mt0) cc_final: 0.8176 (tm-30) REVERT: B 129 VAL cc_start: 0.9721 (t) cc_final: 0.9519 (t) REVERT: B 145 ASN cc_start: 0.9248 (t0) cc_final: 0.8693 (p0) REVERT: C 3 THR cc_start: 0.8823 (m) cc_final: 0.8500 (p) REVERT: C 20 SER cc_start: 0.9369 (p) cc_final: 0.9141 (p) REVERT: C 31 PHE cc_start: 0.9400 (m-80) cc_final: 0.9122 (m-80) REVERT: C 60 TYR cc_start: 0.8042 (m-10) cc_final: 0.7794 (m-80) REVERT: C 65 TYR cc_start: 0.7492 (p90) cc_final: 0.7196 (p90) REVERT: C 69 MET cc_start: 0.7416 (ttm) cc_final: 0.6750 (ttm) REVERT: C 86 ARG cc_start: 0.9472 (ttp-170) cc_final: 0.9271 (ttp-170) REVERT: C 87 ASP cc_start: 0.9692 (m-30) cc_final: 0.9476 (m-30) REVERT: C 94 MET cc_start: 0.9533 (mmt) cc_final: 0.9142 (mmm) REVERT: C 122 PHE cc_start: 0.9067 (m-10) cc_final: 0.8852 (m-10) REVERT: C 125 SER cc_start: 0.9513 (t) cc_final: 0.9133 (p) REVERT: C 128 TRP cc_start: 0.8340 (m-10) cc_final: 0.8075 (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: 0.8067 (m-80) REVERT: D 32 LYS cc_start: 0.9418 (ptmt) cc_final: 0.9142 (pttt) REVERT: D 46 SER cc_start: 0.8931 (m) cc_final: 0.8633 (m) REVERT: D 59 LEU cc_start: 0.9400 (tp) cc_final: 0.9175 (tt) REVERT: D 79 ARG cc_start: 0.7929 (tmt170) cc_final: 0.7682 (tpt170) REVERT: D 97 TYR cc_start: 0.9508 (m-10) cc_final: 0.9273 (m-80) REVERT: D 110 ARG cc_start: 0.9051 (mtt-85) cc_final: 0.8758 (mtm-85) REVERT: D 124 THR cc_start: 0.9076 (m) cc_final: 0.8412 (m) REVERT: D 137 LYS cc_start: 0.8454 (ttpt) cc_final: 0.8153 (tttm) REVERT: D 154 ASP cc_start: 0.7857 (t0) cc_final: 0.7557 (t0) REVERT: D 155 CYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7208 (m) REVERT: D 161 GLU cc_start: 0.8214 (tt0) cc_final: 0.7958 (tt0) REVERT: D 165 TYR cc_start: 0.8487 (m-10) cc_final: 0.8187 (m-80) REVERT: E 9 ILE cc_start: 0.9324 (mt) cc_final: 0.9046 (tt) REVERT: E 25 GLN cc_start: 0.9207 (mt0) cc_final: 0.8828 (mt0) REVERT: E 38 MET cc_start: 0.8751 (mmt) cc_final: 0.8243 (tmm) REVERT: E 62 LYS cc_start: 0.9648 (tptt) cc_final: 0.9393 (tppt) REVERT: E 72 SER cc_start: 0.8976 (m) cc_final: 0.8665 (t) REVERT: E 73 GLN cc_start: 0.9237 (pm20) cc_final: 0.8977 (pm20) REVERT: E 74 TYR cc_start: 0.8855 (m-80) cc_final: 0.8385 (m-10) REVERT: E 109 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8853 (tt0) REVERT: E 115 LEU cc_start: 0.9418 (tp) cc_final: 0.9160 (tt) REVERT: E 122 PHE cc_start: 0.9615 (m-80) cc_final: 0.9216 (m-10) REVERT: E 123 ASP cc_start: 0.9348 (m-30) cc_final: 0.9087 (t70) REVERT: E 167 ASP cc_start: 0.9256 (t0) cc_final: 0.8808 (t0) REVERT: E 173 LEU cc_start: 0.9618 (mm) cc_final: 0.9311 (tp) REVERT: F 21 ASN cc_start: 0.8500 (m-40) cc_final: 0.7989 (t0) REVERT: F 25 ASP cc_start: 0.9214 (m-30) cc_final: 0.8585 (m-30) REVERT: F 27 LEU cc_start: 0.9327 (mt) cc_final: 0.8751 (pp) REVERT: F 29 ASN cc_start: 0.9315 (m-40) cc_final: 0.8957 (m110) REVERT: F 33 GLU cc_start: 0.9238 (mt-10) cc_final: 0.8965 (mp0) REVERT: F 35 ASN cc_start: 0.9283 (m-40) cc_final: 0.8972 (m-40) REVERT: F 62 GLU cc_start: 0.9614 (tt0) cc_final: 0.9359 (tm-30) REVERT: F 65 GLN cc_start: 0.9341 (pm20) cc_final: 0.8972 (mm-40) REVERT: F 76 TYR cc_start: 0.8862 (t80) cc_final: 0.8378 (t80) REVERT: F 93 ARG cc_start: 0.9332 (ttp80) cc_final: 0.8819 (ttp-110) REVERT: F 103 ASP cc_start: 0.9022 (t0) cc_final: 0.8593 (t0) REVERT: F 115 LEU cc_start: 0.9145 (tp) cc_final: 0.8720 (tp) REVERT: F 117 GLU cc_start: 0.9525 (pp20) cc_final: 0.9002 (pp20) REVERT: F 118 THR cc_start: 0.9623 (m) cc_final: 0.9240 (p) REVERT: F 131 VAL cc_start: 0.8606 (t) cc_final: 0.8325 (t) REVERT: F 136 MET cc_start: 0.8922 (mtm) cc_final: 0.8638 (ttp) REVERT: F 138 ASP cc_start: 0.9007 (m-30) cc_final: 0.8697 (t70) REVERT: F 146 ASP cc_start: 0.9001 (t0) cc_final: 0.8783 (t0) REVERT: F 158 LEU cc_start: 0.8763 (tp) cc_final: 0.8264 (tt) REVERT: F 159 MET cc_start: 0.9075 (mmp) cc_final: 0.8791 (mmt) REVERT: F 165 TYR cc_start: 0.9296 (m-80) cc_final: 0.8941 (m-10) REVERT: G 18 PHE cc_start: 0.8366 (m-80) cc_final: 0.6661 (m-80) REVERT: G 42 ARG cc_start: 0.7986 (mtt-85) cc_final: 0.7705 (ttt90) REVERT: G 53 ASP cc_start: 0.9266 (m-30) cc_final: 0.9003 (p0) REVERT: G 62 LYS cc_start: 0.9424 (tptm) cc_final: 0.9130 (tppt) REVERT: G 74 TYR cc_start: 0.8954 (m-80) cc_final: 0.8673 (m-10) REVERT: G 79 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8894 (pp20) REVERT: G 94 MET cc_start: 0.9177 (mmm) cc_final: 0.8927 (mtt) REVERT: G 97 TYR cc_start: 0.9529 (m-10) cc_final: 0.9129 (m-10) REVERT: G 122 PHE cc_start: 0.9312 (m-80) cc_final: 0.8898 (m-10) REVERT: G 124 LEU cc_start: 0.9124 (mt) cc_final: 0.8886 (mt) REVERT: G 129 TYR cc_start: 0.9132 (m-80) cc_final: 0.8473 (m-80) REVERT: G 161 GLU cc_start: 0.9533 (mt-10) cc_final: 0.9303 (mt-10) REVERT: G 166 ILE cc_start: 0.9341 (mt) cc_final: 0.9120 (tt) REVERT: G 167 ASP cc_start: 0.9273 (t0) cc_final: 0.8803 (t0) REVERT: G 170 ILE cc_start: 0.9536 (mt) cc_final: 0.9225 (pt) REVERT: H 15 ARG cc_start: 0.8360 (mmm160) cc_final: 0.7910 (mmt-90) REVERT: H 24 PHE cc_start: 0.8708 (m-80) cc_final: 0.8331 (m-10) REVERT: H 42 ASN cc_start: 0.9105 (t0) cc_final: 0.8881 (t0) REVERT: H 60 PHE cc_start: 0.8763 (m-80) cc_final: 0.8362 (m-10) REVERT: H 63 GLN cc_start: 0.9338 (mt0) cc_final: 0.8847 (mt0) REVERT: H 87 ASP cc_start: 0.9278 (m-30) cc_final: 0.8588 (m-30) REVERT: H 97 TYR cc_start: 0.9368 (m-10) cc_final: 0.8780 (m-10) REVERT: H 107 LEU cc_start: 0.9666 (tp) cc_final: 0.9448 (tt) REVERT: H 117 GLU cc_start: 0.9054 (tp30) cc_final: 0.8334 (tp30) REVERT: H 141 ILE cc_start: 0.9359 (tp) cc_final: 0.8839 (tp) REVERT: H 146 ASP cc_start: 0.8432 (t0) cc_final: 0.8187 (t0) REVERT: H 159 MET cc_start: 0.9024 (mmt) cc_final: 0.8543 (mmt) REVERT: I 51 LEU cc_start: 0.9420 (mt) cc_final: 0.9127 (mt) REVERT: I 60 TYR cc_start: 0.8359 (m-10) cc_final: 0.7923 (m-80) REVERT: I 62 LYS cc_start: 0.9367 (tptm) cc_final: 0.8895 (tptt) REVERT: I 91 TYR cc_start: 0.8929 (m-80) cc_final: 0.8727 (m-80) REVERT: I 107 MET cc_start: 0.9275 (tpp) cc_final: 0.9005 (tpt) REVERT: I 110 TYR cc_start: 0.9249 (m-10) cc_final: 0.8742 (m-10) REVERT: I 111 LEU cc_start: 0.9400 (tp) cc_final: 0.8824 (tp) REVERT: I 115 LEU cc_start: 0.9144 (tp) cc_final: 0.8934 (tp) REVERT: I 118 ILE cc_start: 0.9432 (mm) cc_final: 0.9226 (mm) REVERT: I 167 ASP cc_start: 0.9685 (m-30) cc_final: 0.9441 (m-30) REVERT: J 15 ARG cc_start: 0.8579 (mtm180) cc_final: 0.8267 (mtp-110) REVERT: J 17 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8092 (mp0) REVERT: J 35 ASN cc_start: 0.9114 (m110) cc_final: 0.8403 (t0) REVERT: J 38 LEU cc_start: 0.9411 (mt) cc_final: 0.9035 (mp) REVERT: J 60 PHE cc_start: 0.9212 (m-80) cc_final: 0.8961 (m-80) REVERT: J 97 TYR cc_start: 0.8736 (m-10) cc_final: 0.8273 (m-10) REVERT: J 141 ILE cc_start: 0.8572 (tt) cc_final: 0.7786 (tp) REVERT: K 18 PHE cc_start: 0.8859 (m-80) cc_final: 0.8536 (m-80) REVERT: K 19 LEU cc_start: 0.9293 (mt) cc_final: 0.8903 (tt) REVERT: K 21 ASN cc_start: 0.8925 (p0) cc_final: 0.8664 (t0) REVERT: K 33 ARG cc_start: 0.8774 (mtp85) cc_final: 0.8291 (tpm170) REVERT: K 38 MET cc_start: 0.8981 (mmt) cc_final: 0.8736 (mmp) REVERT: K 61 GLN cc_start: 0.9090 (mt0) cc_final: 0.8662 (mt0) REVERT: K 98 CYS cc_start: 0.8733 (t) cc_final: 0.8440 (t) REVERT: K 107 MET cc_start: 0.9095 (tpp) cc_final: 0.8754 (tpp) REVERT: K 115 LEU cc_start: 0.9005 (tp) cc_final: 0.8522 (tp) REVERT: K 122 PHE cc_start: 0.8509 (m-10) cc_final: 0.8248 (m-10) REVERT: K 125 SER cc_start: 0.9260 (t) cc_final: 0.8920 (p) REVERT: K 133 LEU cc_start: 0.9435 (mt) cc_final: 0.9170 (mt) REVERT: K 140 HIS cc_start: 0.8938 (p-80) cc_final: 0.8618 (p-80) REVERT: K 163 ASN cc_start: 0.9456 (m-40) cc_final: 0.8961 (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: 0.8720 (m-10) REVERT: L 65 GLN cc_start: 0.9305 (pt0) cc_final: 0.8622 (pm20) REVERT: L 68 GLN cc_start: 0.9452 (mt0) cc_final: 0.9225 (pp30) REVERT: L 80 ARG cc_start: 0.9079 (mtm-85) cc_final: 0.8848 (mtt180) REVERT: L 89 GLU cc_start: 0.9053 (pp20) cc_final: 0.8643 (pp20) REVERT: L 90 ILE cc_start: 0.9373 (mt) cc_final: 0.8794 (mm) REVERT: L 93 ARG cc_start: 0.8926 (ttp80) cc_final: 0.8545 (ttp-170) REVERT: L 113 ASN cc_start: 0.9189 (t0) cc_final: 0.8432 (t0) REVERT: L 137 LYS cc_start: 0.9607 (tttt) cc_final: 0.9250 (ttmt) REVERT: L 159 MET cc_start: 0.8953 (mmp) cc_final: 0.8705 (mmt) REVERT: L 165 TYR cc_start: 0.9097 (m-80) cc_final: 0.8870 (m-80) REVERT: M 1 MET cc_start: 0.8127 (mpp) cc_final: 0.7642 (ptp) REVERT: M 2 LYS cc_start: 0.8665 (tttp) cc_final: 0.8456 (ttmm) REVERT: M 17 ARG cc_start: 0.9078 (ptp-110) cc_final: 0.8669 (mtm110) REVERT: M 33 ARG cc_start: 0.9240 (mmt180) cc_final: 0.8494 (tpp-160) REVERT: M 57 GLN cc_start: 0.9602 (mm-40) cc_final: 0.9380 (mm-40) REVERT: M 69 MET cc_start: 0.9518 (tpt) cc_final: 0.9256 (tpp) REVERT: M 74 TYR cc_start: 0.9567 (m-80) cc_final: 0.9365 (m-10) REVERT: M 81 LYS cc_start: 0.8988 (tmtt) cc_final: 0.8736 (mtpp) REVERT: M 91 TYR cc_start: 0.9271 (m-80) cc_final: 0.8927 (m-10) REVERT: M 129 TYR cc_start: 0.8963 (m-80) cc_final: 0.8656 (m-80) REVERT: M 135 TYR cc_start: 0.8994 (t80) cc_final: 0.8699 (t80) REVERT: M 161 GLU cc_start: 0.9461 (tt0) cc_final: 0.9152 (mt-10) REVERT: N 3 ASP cc_start: 0.8751 (p0) cc_final: 0.8536 (p0) REVERT: N 19 LEU cc_start: 0.8470 (mt) cc_final: 0.8224 (mm) REVERT: N 35 ASN cc_start: 0.9352 (m-40) cc_final: 0.9122 (t0) REVERT: N 36 LYS cc_start: 0.8569 (mttt) cc_final: 0.8315 (mmtt) REVERT: N 62 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8509 (tm-30) REVERT: N 67 ILE cc_start: 0.9720 (pt) cc_final: 0.9243 (mt) REVERT: N 80 ARG cc_start: 0.9408 (mtm-85) cc_final: 0.8456 (mtm-85) REVERT: N 88 MET cc_start: 0.9055 (ttp) cc_final: 0.8104 (ttp) REVERT: N 95 VAL cc_start: 0.9780 (t) cc_final: 0.9544 (p) REVERT: N 103 ASP cc_start: 0.8495 (t0) cc_final: 0.8176 (t0) REVERT: N 115 LEU cc_start: 0.9594 (tp) cc_final: 0.9297 (tp) REVERT: N 148 ASN cc_start: 0.9041 (m-40) cc_final: 0.8837 (p0) REVERT: N 165 TYR cc_start: 0.8824 (m-80) cc_final: 0.8363 (m-10) REVERT: N 167 ASP cc_start: 0.9300 (m-30) cc_final: 0.9044 (m-30) REVERT: O 13 ASP cc_start: 0.9286 (t70) cc_final: 0.9068 (t70) REVERT: O 25 GLN cc_start: 0.8456 (mt0) cc_final: 0.8253 (mt0) REVERT: O 32 LYS cc_start: 0.9210 (mmmt) cc_final: 0.8867 (mmmm) REVERT: O 47 ASN cc_start: 0.9300 (m-40) cc_final: 0.9094 (p0) REVERT: O 99 LEU cc_start: 0.9182 (mt) cc_final: 0.8885 (tp) REVERT: O 104 THR cc_start: 0.9207 (p) cc_final: 0.8868 (p) REVERT: O 129 TYR cc_start: 0.8843 (m-80) cc_final: 0.8225 (m-80) REVERT: O 131 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8832 (tm-30) REVERT: O 166 ILE cc_start: 0.9120 (mt) cc_final: 0.8859 (tt) REVERT: P 1 MET cc_start: 0.6960 (ptt) cc_final: 0.6583 (ptt) REVERT: P 9 VAL cc_start: 0.9724 (t) cc_final: 0.9498 (p) REVERT: P 11 GLN cc_start: 0.8735 (mt0) cc_final: 0.8416 (mt0) REVERT: P 23 GLN cc_start: 0.8425 (mt0) cc_final: 0.8142 (mt0) REVERT: P 67 ILE cc_start: 0.9154 (pt) cc_final: 0.8795 (tp) REVERT: P 93 ARG cc_start: 0.9210 (ttp80) cc_final: 0.8425 (ttp-170) REVERT: P 94 TYR cc_start: 0.9219 (m-80) cc_final: 0.8407 (m-80) REVERT: P 97 TYR cc_start: 0.9182 (m-10) cc_final: 0.8571 (m-80) REVERT: P 104 SER cc_start: 0.9362 (p) cc_final: 0.9106 (p) REVERT: P 110 ARG cc_start: 0.8087 (mtt180) cc_final: 0.7785 (mtp85) REVERT: P 156 SER cc_start: 0.8692 (t) cc_final: 0.8362 (m) REVERT: P 159 MET cc_start: 0.9175 (mmm) cc_final: 0.8272 (tmm) REVERT: P 162 ILE cc_start: 0.9528 (pt) cc_final: 0.9280 (pt) REVERT: Q 14 THR cc_start: 0.8687 (p) cc_final: 0.8197 (t) REVERT: Q 15 GLN cc_start: 0.8509 (mm110) cc_final: 0.8226 (mm110) REVERT: Q 24 LEU cc_start: 0.8432 (mt) cc_final: 0.7757 (mt) REVERT: Q 37 SER cc_start: 0.7989 (m) cc_final: 0.7147 (p) REVERT: Q 53 ASP cc_start: 0.7168 (m-30) cc_final: 0.6732 (m-30) REVERT: Q 57 GLN cc_start: 0.6950 (mm110) cc_final: 0.6684 (mm-40) REVERT: Q 73 GLN cc_start: 0.7797 (pm20) cc_final: 0.7101 (pm20) REVERT: Q 86 ARG cc_start: 0.5640 (OUTLIER) cc_final: 0.4756 (mmt90) REVERT: Q 107 MET cc_start: 0.8564 (ttm) cc_final: 0.7980 (mtp) REVERT: Q 108 ASP cc_start: 0.8587 (m-30) cc_final: 0.8284 (m-30) REVERT: Q 168 TYR cc_start: 0.8393 (t80) cc_final: 0.8029 (t80) REVERT: R 38 LEU cc_start: 0.8563 (mt) cc_final: 0.8275 (mp) REVERT: R 39 ASP cc_start: 0.7872 (m-30) cc_final: 0.7649 (m-30) REVERT: R 87 ASP cc_start: 0.7926 (m-30) cc_final: 0.7662 (m-30) REVERT: R 88 MET cc_start: 0.9649 (mmm) cc_final: 0.9078 (mtp) REVERT: R 89 GLU cc_start: 0.9569 (pt0) cc_final: 0.9288 (tm-30) REVERT: R 103 ASP cc_start: 0.7354 (t0) cc_final: 0.6860 (t0) REVERT: R 111 CYS cc_start: 0.8829 (t) cc_final: 0.8617 (t) REVERT: R 115 LEU cc_start: 0.9287 (tt) cc_final: 0.8834 (tt) REVERT: R 136 MET cc_start: 0.9230 (ttp) cc_final: 0.8770 (ttt) REVERT: R 159 MET cc_start: 0.8829 (mmp) cc_final: 0.8063 (ptt) REVERT: S 37 SER cc_start: 0.8987 (t) cc_final: 0.8765 (p) REVERT: S 44 LEU cc_start: 0.9496 (mt) cc_final: 0.8674 (tp) REVERT: S 57 GLN cc_start: 0.9277 (mm-40) cc_final: 0.9064 (mm-40) REVERT: S 73 GLN cc_start: 0.9059 (pt0) cc_final: 0.8829 (pm20) REVERT: S 74 TYR cc_start: 0.9331 (m-80) cc_final: 0.8957 (m-80) REVERT: S 79 GLU cc_start: 0.8643 (mp0) cc_final: 0.8404 (tm-30) REVERT: S 83 LYS cc_start: 0.8721 (mmtp) cc_final: 0.8260 (mmtm) REVERT: S 90 TYR cc_start: 0.8802 (m-10) cc_final: 0.8301 (m-10) REVERT: S 115 LEU cc_start: 0.9076 (tp) cc_final: 0.8868 (tp) REVERT: S 118 ILE cc_start: 0.9581 (OUTLIER) cc_final: 0.9365 (pp) REVERT: T 9 VAL cc_start: 0.9299 (t) cc_final: 0.9054 (p) REVERT: T 13 ASP cc_start: 0.8990 (t70) cc_final: 0.8665 (t0) REVERT: T 15 ARG cc_start: 0.8141 (mtp85) cc_final: 0.7122 (mmt-90) REVERT: T 18 PHE cc_start: 0.8218 (m-80) cc_final: 0.7956 (m-80) REVERT: T 19 LEU cc_start: 0.8129 (mt) cc_final: 0.7754 (mm) REVERT: T 23 GLN cc_start: 0.8537 (mt0) cc_final: 0.8266 (mp10) REVERT: T 35 ASN cc_start: 0.8016 (m-40) cc_final: 0.7763 (p0) REVERT: T 76 TYR cc_start: 0.4893 (t80) cc_final: 0.4620 (t80) REVERT: T 87 ASP cc_start: 0.8707 (m-30) cc_final: 0.8498 (m-30) REVERT: U 18 PHE cc_start: 0.8657 (m-80) cc_final: 0.8431 (m-80) REVERT: U 25 GLN cc_start: 0.9058 (mt0) cc_final: 0.8643 (tt0) REVERT: U 42 ARG cc_start: 0.8035 (ttm-80) cc_final: 0.7518 (mtt180) REVERT: U 61 GLN cc_start: 0.8053 (mt0) cc_final: 0.7606 (pp30) REVERT: U 62 LYS cc_start: 0.9275 (tppp) cc_final: 0.9070 (tptt) REVERT: U 69 MET cc_start: 0.7094 (mtt) cc_final: 0.6480 (tpp) REVERT: U 87 ASP cc_start: 0.7572 (m-30) cc_final: 0.7286 (m-30) REVERT: U 94 MET cc_start: 0.9494 (tpp) cc_final: 0.9209 (tpp) REVERT: U 117 GLU cc_start: 0.9116 (tt0) cc_final: 0.8856 (mp0) REVERT: U 123 ASP cc_start: 0.8995 (t0) cc_final: 0.8741 (t70) REVERT: U 140 HIS cc_start: 0.9408 (p-80) cc_final: 0.9191 (p-80) REVERT: U 173 LEU cc_start: 0.9399 (mt) cc_final: 0.8938 (mt) REVERT: V 5 PHE cc_start: 0.8626 (m-10) cc_final: 0.8301 (m-10) REVERT: V 11 GLN cc_start: 0.8841 (tt0) cc_final: 0.8464 (tp40) REVERT: V 13 ASP cc_start: 0.9198 (t70) cc_final: 0.8701 (t0) REVERT: V 15 ARG cc_start: 0.9393 (mtm110) cc_final: 0.9063 (mtm-85) REVERT: V 17 GLU cc_start: 0.8531 (mp0) cc_final: 0.8283 (mp0) REVERT: V 19 LEU cc_start: 0.9312 (mt) cc_final: 0.9075 (mt) REVERT: V 60 PHE cc_start: 0.8876 (m-80) cc_final: 0.8625 (m-80) REVERT: V 62 GLU cc_start: 0.9214 (tm-30) cc_final: 0.8855 (tm-30) REVERT: V 81 MET cc_start: 0.8779 (tpp) cc_final: 0.8538 (tpp) REVERT: V 93 ARG cc_start: 0.9402 (ttp80) cc_final: 0.8938 (ttp80) REVERT: V 108 ASP cc_start: 0.9303 (m-30) cc_final: 0.9065 (t0) REVERT: V 159 MET cc_start: 0.9029 (mmp) cc_final: 0.8615 (tmm) REVERT: V 168 ARG cc_start: 0.9110 (ttt90) cc_final: 0.8898 (mmm-85) REVERT: W 22 THR cc_start: 0.9502 (p) cc_final: 0.9293 (p) REVERT: W 33 ARG cc_start: 0.8119 (mtp85) cc_final: 0.7875 (tmm160) REVERT: W 42 ARG cc_start: 0.6776 (tpp80) cc_final: 0.6285 (tpp80) REVERT: W 46 ASN cc_start: 0.7349 (m-40) cc_final: 0.6973 (p0) REVERT: W 65 TYR cc_start: 0.8423 (p90) cc_final: 0.7706 (p90) REVERT: W 69 MET cc_start: 0.4555 (mtp) cc_final: 0.4130 (mmm) REVERT: W 97 TYR cc_start: 0.8508 (m-10) cc_final: 0.7985 (m-80) REVERT: W 107 MET cc_start: 0.8741 (mmp) cc_final: 0.8482 (mmm) REVERT: W 111 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7685 (pt) REVERT: W 165 TYR cc_start: 0.8335 (m-80) cc_final: 0.8070 (m-80) REVERT: X 5 PHE cc_start: 0.8067 (m-80) cc_final: 0.7495 (m-80) REVERT: X 38 LEU cc_start: 0.9434 (mt) cc_final: 0.9185 (mt) REVERT: X 79 ARG cc_start: 0.7878 (ttm170) cc_final: 0.7330 (tpm170) REVERT: X 89 GLU cc_start: 0.8940 (tt0) cc_final: 0.8641 (tm-30) REVERT: X 119 TYR cc_start: 0.8045 (m-80) cc_final: 0.7834 (m-80) REVERT: X 136 MET cc_start: 0.7261 (mtm) cc_final: 0.6608 (mtp) REVERT: X 166 PHE cc_start: 0.8073 (m-80) cc_final: 0.7574 (m-80) REVERT: Y 20 PHE cc_start: 0.8967 (m-80) cc_final: 0.8136 (m-10) REVERT: Y 36 MET cc_start: 0.7413 (ttp) cc_final: 0.6907 (mmt) REVERT: Y 37 GLU cc_start: 0.8665 (tp30) cc_final: 0.8386 (tm-30) REVERT: Y 50 VAL cc_start: 0.9558 (t) cc_final: 0.9259 (p) REVERT: Y 55 MET cc_start: 0.9156 (ttp) cc_final: 0.8736 (ttp) REVERT: Z 9 ARG cc_start: 0.7964 (mmt180) cc_final: 0.7696 (mmm160) REVERT: Z 42 GLN cc_start: 0.9071 (tp40) cc_final: 0.8796 (tp40) REVERT: Z 44 LEU cc_start: 0.9176 (mt) cc_final: 0.8939 (mt) REVERT: Z 59 GLU cc_start: 0.8954 (mp0) cc_final: 0.8371 (pt0) REVERT: Z 64 ASN cc_start: 0.9151 (t0) cc_final: 0.8865 (t0) REVERT: Z 78 LYS cc_start: 0.9246 (mttt) cc_final: 0.8672 (ttpt) REVERT: Z 91 PHE cc_start: 0.9165 (t80) cc_final: 0.8103 (t80) REVERT: Z 93 THR cc_start: 0.9479 (m) cc_final: 0.9261 (m) REVERT: Z 101 LYS cc_start: 0.9308 (tttt) cc_final: 0.9033 (ttpp) REVERT: Z 109 TYR cc_start: 0.7807 (m-10) cc_final: 0.7208 (m-10) REVERT: Z 119 ASP cc_start: 0.9445 (m-30) cc_final: 0.8943 (m-30) REVERT: Z 127 ASP cc_start: 0.8993 (m-30) cc_final: 0.8463 (t0) REVERT: Z 150 TYR cc_start: 0.8672 (p90) cc_final: 0.8456 (p90) REVERT: Z 160 GLN cc_start: 0.7988 (pt0) cc_final: 0.7693 (pt0) REVERT: Z 179 ASP cc_start: 0.9431 (m-30) cc_final: 0.8981 (m-30) REVERT: Z 182 GLN cc_start: 0.8526 (tt0) cc_final: 0.8303 (tt0) REVERT: Z 184 GLU cc_start: 0.9131 (pt0) cc_final: 0.8816 (mp0) REVERT: Z 187 MET cc_start: 0.9344 (tmt) cc_final: 0.9007 (mtp) REVERT: Z 196 THR cc_start: 0.9607 (p) cc_final: 0.9359 (t) REVERT: Z 264 TYR cc_start: 0.9255 (t80) cc_final: 0.8861 (t80) REVERT: Z 270 LYS cc_start: 0.9423 (tppt) cc_final: 0.9062 (tptt) REVERT: Z 275 GLN cc_start: 0.9113 (mm-40) cc_final: 0.8436 (mm-40) REVERT: a 3 ILE cc_start: 0.7564 (mm) cc_final: 0.6824 (mm) REVERT: a 21 GLU cc_start: 0.8911 (pt0) cc_final: 0.7828 (tp30) REVERT: a 38 ASP cc_start: 0.7895 (p0) cc_final: 0.7499 (p0) REVERT: a 74 ASN cc_start: 0.9413 (t0) cc_final: 0.8987 (p0) REVERT: a 82 PHE cc_start: 0.9062 (t80) cc_final: 0.8764 (t80) REVERT: a 88 LYS cc_start: 0.9607 (pttt) cc_final: 0.9202 (tptp) REVERT: a 124 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7947 (tt0) REVERT: a 152 ASN cc_start: 0.9214 (m-40) cc_final: 0.9006 (t0) REVERT: a 165 TYR cc_start: 0.5759 (t80) cc_final: 0.5341 (m-10) outliers start: 25 outliers final: 8 residues processed: 2180 average time/residue: 0.2133 time to fit residues: 736.7140 Evaluate side-chains 1570 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 1556 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 432 optimal weight: 0.9980 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 4.9990 chunk 424 optimal weight: 6.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 ASN C 25 GLN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN G 61 GLN G 171 ASN H 145 ASN I 15 GLN ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 49 GLN K 61 GLN K 70 GLN ** K 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 15 GLN M 140 HIS O 73 GLN ** O 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 47 ASN Q 21 ASN R 63 GLN R 134 GLN S 15 GLN ** S 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 21 ASN U 15 GLN U 119 ASN ** U 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 21 ASN ** W 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 ASN ** X 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 92 GLN Z 266 GLN a 13 GLN ** a 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.114341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.096941 restraints weight = 100777.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.100625 restraints weight = 50231.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.103023 restraints weight = 28921.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.104584 restraints weight = 18533.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.105587 restraints weight = 13083.353| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3372 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 36155 Z= 0.183 Angle : 0.791 43.034 49243 Z= 0.373 Chirality : 0.040 0.247 5448 Planarity : 0.005 0.057 6402 Dihedral : 10.816 89.643 6599 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.82 % Favored : 98.11 % Rotamer: Outliers : 0.24 % Allowed : 3.75 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.12), residues: 4448 helix: 1.30 (0.08), residues: 3390 sheet: 1.78 (1.01), residues: 28 loop : -0.69 (0.21), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 30 TYR 0.041 0.002 TYR M 97 PHE 0.029 0.002 PHE V 166 TRP 0.017 0.002 TRP U 128 HIS 0.005 0.002 HIS K 140 Details of bonding type rmsd covalent geometry : bond 0.00400 (36155) covalent geometry : angle 0.79065 (49243) hydrogen bonds : bond 0.05424 ( 2648) hydrogen bonds : angle 4.47489 ( 7847) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1837 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 1829 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.8406 (ttpt) cc_final: 0.8166 (ttpt) REVERT: A 18 PHE cc_start: 0.7872 (m-80) cc_final: 0.6954 (m-80) REVERT: A 30 ARG cc_start: 0.8450 (tpt-90) cc_final: 0.8017 (tmt170) REVERT: A 33 ARG cc_start: 0.8811 (mmm160) cc_final: 0.8478 (tpt170) REVERT: A 38 MET cc_start: 0.8536 (mmt) cc_final: 0.7874 (tmm) REVERT: A 39 GLU cc_start: 0.8197 (tp30) cc_final: 0.7815 (mm-30) REVERT: A 62 LYS cc_start: 0.8888 (tptt) cc_final: 0.8570 (tptt) REVERT: A 63 PHE cc_start: 0.8774 (m-80) cc_final: 0.8175 (m-80) REVERT: A 90 TYR cc_start: 0.8655 (m-10) cc_final: 0.8265 (m-80) REVERT: A 109 GLU cc_start: 0.7886 (mt-10) cc_final: 0.6791 (mt-10) REVERT: A 129 TYR cc_start: 0.8768 (m-80) cc_final: 0.8518 (m-80) REVERT: A 167 ASP cc_start: 0.7737 (t0) cc_final: 0.7165 (t0) REVERT: A 173 LEU cc_start: 0.8555 (mm) cc_final: 0.8334 (mm) REVERT: B 27 LEU cc_start: 0.8034 (mm) cc_final: 0.7791 (mm) REVERT: B 29 ASN cc_start: 0.8358 (m-40) cc_final: 0.8048 (t0) REVERT: B 44 ILE cc_start: 0.9357 (mt) cc_final: 0.9085 (tp) REVERT: B 89 GLU cc_start: 0.8833 (pt0) cc_final: 0.8197 (tt0) REVERT: B 99 ILE cc_start: 0.9365 (mt) cc_final: 0.9011 (mt) REVERT: B 119 TYR cc_start: 0.9067 (m-80) cc_final: 0.8438 (m-80) REVERT: B 120 GLN cc_start: 0.7570 (mt0) cc_final: 0.7298 (tm-30) REVERT: B 136 MET cc_start: 0.7766 (mtt) cc_final: 0.4171 (mtt) REVERT: B 167 ASP cc_start: 0.8163 (t0) cc_final: 0.7958 (t70) REVERT: C 63 PHE cc_start: 0.9073 (m-80) cc_final: 0.8718 (m-10) REVERT: C 69 MET cc_start: 0.7477 (ttm) cc_final: 0.7055 (ttm) REVERT: C 87 ASP cc_start: 0.9331 (m-30) cc_final: 0.9010 (m-30) REVERT: C 91 TYR cc_start: 0.9039 (m-80) cc_final: 0.8773 (m-80) REVERT: C 94 MET cc_start: 0.9290 (mmt) cc_final: 0.8935 (mmm) REVERT: C 115 LEU cc_start: 0.8018 (pp) cc_final: 0.7503 (pp) REVERT: C 117 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8585 (mm-30) REVERT: C 119 ASN cc_start: 0.7764 (m-40) cc_final: 0.6987 (p0) REVERT: D 3 ASP cc_start: 0.7825 (p0) cc_final: 0.7607 (p0) REVERT: D 37 ARG cc_start: 0.8580 (mtp85) cc_final: 0.8338 (mmm-85) REVERT: D 49 SER cc_start: 0.9196 (p) cc_final: 0.8816 (p) REVERT: D 86 ARG cc_start: 0.8939 (ttp-110) cc_final: 0.8641 (ttp-110) REVERT: D 88 MET cc_start: 0.8119 (ttm) cc_final: 0.7670 (mmm) REVERT: D 97 TYR cc_start: 0.8776 (m-10) cc_final: 0.7590 (m-80) REVERT: D 146 ASP cc_start: 0.8984 (t0) cc_final: 0.8688 (t0) REVERT: D 154 ASP cc_start: 0.6671 (t0) cc_final: 0.6416 (t0) REVERT: E 7 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7825 (mm-30) REVERT: E 15 GLN cc_start: 0.8213 (mt0) cc_final: 0.7832 (mt0) REVERT: E 25 GLN cc_start: 0.8511 (mt0) cc_final: 0.8032 (mm-40) REVERT: E 28 ASP cc_start: 0.8578 (t70) cc_final: 0.8245 (t0) REVERT: E 38 MET cc_start: 0.8226 (mmt) cc_final: 0.7941 (tmm) REVERT: E 62 LYS cc_start: 0.9246 (tptt) cc_final: 0.8854 (tppt) REVERT: E 72 SER cc_start: 0.9038 (m) cc_final: 0.8468 (t) REVERT: E 83 LYS cc_start: 0.9401 (tppt) cc_final: 0.9086 (tppp) REVERT: E 137 LYS cc_start: 0.8807 (tttp) cc_final: 0.8560 (tttp) REVERT: E 140 HIS cc_start: 0.8531 (p90) cc_final: 0.8230 (p-80) REVERT: E 167 ASP cc_start: 0.7988 (t0) cc_final: 0.7070 (t0) REVERT: F 21 ASN cc_start: 0.8061 (m-40) cc_final: 0.7028 (t0) REVERT: F 32 LYS cc_start: 0.8965 (pttm) cc_final: 0.8572 (ptpp) REVERT: F 81 MET cc_start: 0.9236 (tpp) cc_final: 0.8825 (tpp) REVERT: F 129 VAL cc_start: 0.9727 (t) cc_final: 0.9510 (t) REVERT: F 165 TYR cc_start: 0.9212 (m-80) cc_final: 0.8338 (m-10) REVERT: G 9 ILE cc_start: 0.9542 (tp) cc_final: 0.9316 (tp) REVERT: G 49 GLN cc_start: 0.8847 (pp30) cc_final: 0.8583 (pp30) REVERT: G 61 GLN cc_start: 0.8595 (mt0) cc_final: 0.8389 (mp10) REVERT: G 62 LYS cc_start: 0.9155 (tptm) cc_final: 0.8776 (tppt) REVERT: G 65 TYR cc_start: 0.8055 (p90) cc_final: 0.7765 (p90) REVERT: G 70 GLN cc_start: 0.7185 (tm-30) cc_final: 0.6702 (pp30) REVERT: G 95 VAL cc_start: 0.9684 (t) cc_final: 0.8938 (t) REVERT: G 97 TYR cc_start: 0.9063 (m-10) cc_final: 0.8665 (m-10) REVERT: G 99 LEU cc_start: 0.8957 (tp) cc_final: 0.8491 (tp) REVERT: G 117 GLU cc_start: 0.7602 (tp30) cc_final: 0.7284 (tp30) REVERT: G 122 PHE cc_start: 0.8886 (m-80) cc_final: 0.8438 (m-10) REVERT: G 124 LEU cc_start: 0.8933 (mt) cc_final: 0.8479 (mt) REVERT: G 129 TYR cc_start: 0.8863 (m-80) cc_final: 0.7969 (m-80) REVERT: G 137 LYS cc_start: 0.9112 (ptmt) cc_final: 0.8860 (ttpp) REVERT: G 161 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8254 (mt-10) REVERT: H 17 GLU cc_start: 0.8301 (pm20) cc_final: 0.7939 (pm20) REVERT: H 42 ASN cc_start: 0.8713 (t0) cc_final: 0.8460 (t0) REVERT: H 63 GLN cc_start: 0.8910 (mt0) cc_final: 0.8365 (mt0) REVERT: H 67 ILE cc_start: 0.9484 (pt) cc_final: 0.9212 (tt) REVERT: H 91 ILE cc_start: 0.9495 (mm) cc_final: 0.8979 (tp) REVERT: H 145 ASN cc_start: 0.7993 (OUTLIER) cc_final: 0.7692 (m-40) REVERT: I 13 ASP cc_start: 0.8814 (t0) cc_final: 0.8579 (t70) REVERT: I 62 LYS cc_start: 0.9226 (tptm) cc_final: 0.8686 (tptt) REVERT: I 73 GLN cc_start: 0.9236 (pm20) cc_final: 0.8817 (pm20) REVERT: I 90 TYR cc_start: 0.7618 (m-10) cc_final: 0.7031 (m-10) REVERT: I 107 MET cc_start: 0.8846 (tpp) cc_final: 0.8530 (tpt) REVERT: I 110 TYR cc_start: 0.7815 (m-80) cc_final: 0.7445 (m-10) REVERT: I 119 ASN cc_start: 0.8470 (m110) cc_final: 0.7653 (m110) REVERT: I 135 TYR cc_start: 0.8733 (t80) cc_final: 0.8518 (t80) REVERT: I 163 ASN cc_start: 0.9138 (m110) cc_final: 0.8165 (m110) REVERT: I 166 ILE cc_start: 0.9763 (tt) cc_final: 0.9508 (tt) REVERT: J 24 PHE cc_start: 0.7058 (m-80) cc_final: 0.6672 (m-80) REVERT: J 35 ASN cc_start: 0.8458 (m110) cc_final: 0.7917 (t0) REVERT: J 91 ILE cc_start: 0.9418 (tp) cc_final: 0.9077 (tp) REVERT: J 97 TYR cc_start: 0.8973 (m-10) cc_final: 0.8334 (m-10) REVERT: J 141 ILE cc_start: 0.8878 (tt) cc_final: 0.8460 (tp) REVERT: J 145 ASN cc_start: 0.8247 (t0) cc_final: 0.7976 (t0) REVERT: K 49 GLN cc_start: 0.8229 (mm110) cc_final: 0.8023 (tp40) REVERT: K 115 LEU cc_start: 0.8972 (tp) cc_final: 0.8750 (tp) REVERT: K 165 TYR cc_start: 0.9015 (m-10) cc_final: 0.8725 (m-10) REVERT: L 2 LEU cc_start: 0.9213 (mt) cc_final: 0.8580 (mt) REVERT: L 7 LYS cc_start: 0.9069 (ttpp) cc_final: 0.8829 (ptmm) REVERT: L 13 ASP cc_start: 0.8414 (t70) cc_final: 0.8139 (t0) REVERT: L 59 LEU cc_start: 0.9531 (tp) cc_final: 0.9232 (tp) REVERT: L 65 GLN cc_start: 0.8162 (pt0) cc_final: 0.7914 (pm20) REVERT: L 80 ARG cc_start: 0.8060 (mtm-85) cc_final: 0.7834 (mtt180) REVERT: L 81 MET cc_start: 0.9061 (tpp) cc_final: 0.8414 (tpp) REVERT: L 87 ASP cc_start: 0.9084 (m-30) cc_final: 0.8740 (m-30) REVERT: L 89 GLU cc_start: 0.7766 (pp20) cc_final: 0.7368 (tm-30) REVERT: L 90 ILE cc_start: 0.9354 (mt) cc_final: 0.9023 (tt) REVERT: L 93 ARG cc_start: 0.8550 (ttp80) cc_final: 0.8230 (ttp80) REVERT: L 103 ASP cc_start: 0.8368 (m-30) cc_final: 0.7125 (m-30) REVERT: L 120 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8352 (tm-30) REVERT: L 135 LYS cc_start: 0.8669 (mmtm) cc_final: 0.8388 (mttm) REVERT: L 137 LYS cc_start: 0.9443 (tttt) cc_final: 0.8972 (ttmt) REVERT: L 161 GLU cc_start: 0.8247 (tt0) cc_final: 0.7835 (tp30) REVERT: M 9 ILE cc_start: 0.9134 (tp) cc_final: 0.8553 (tp) REVERT: M 33 ARG cc_start: 0.7660 (tpt-90) cc_final: 0.5649 (tpp-160) REVERT: M 98 CYS cc_start: 0.7008 (m) cc_final: 0.6355 (m) REVERT: M 115 LEU cc_start: 0.8876 (tt) cc_final: 0.7798 (tp) REVERT: M 129 TYR cc_start: 0.8415 (m-80) cc_final: 0.8085 (m-80) REVERT: M 135 TYR cc_start: 0.9012 (t80) cc_final: 0.8716 (t80) REVERT: M 171 ASN cc_start: 0.8592 (p0) cc_final: 0.7931 (p0) REVERT: N 3 ASP cc_start: 0.8501 (p0) cc_final: 0.8171 (p0) REVERT: N 36 LYS cc_start: 0.8420 (mttt) cc_final: 0.7666 (mttt) REVERT: N 45 THR cc_start: 0.8285 (t) cc_final: 0.8072 (t) REVERT: N 65 GLN cc_start: 0.7841 (mp10) cc_final: 0.7510 (mp10) REVERT: N 80 ARG cc_start: 0.9155 (mtm-85) cc_final: 0.8812 (mtm-85) REVERT: N 97 TYR cc_start: 0.8684 (m-10) cc_final: 0.7874 (m-80) REVERT: N 103 ASP cc_start: 0.7400 (t0) cc_final: 0.7000 (t0) REVERT: N 105 SER cc_start: 0.8545 (t) cc_final: 0.8220 (t) REVERT: N 136 MET cc_start: 0.8602 (mtm) cc_final: 0.7444 (mtm) REVERT: N 162 ILE cc_start: 0.9495 (mt) cc_final: 0.9092 (mt) REVERT: O 25 GLN cc_start: 0.7266 (mt0) cc_final: 0.6958 (mt0) REVERT: O 59 VAL cc_start: 0.8748 (m) cc_final: 0.8534 (m) REVERT: O 99 LEU cc_start: 0.9240 (mt) cc_final: 0.8954 (tp) REVERT: O 104 THR cc_start: 0.8651 (p) cc_final: 0.8014 (p) REVERT: O 129 TYR cc_start: 0.8516 (m-80) cc_final: 0.7639 (m-80) REVERT: O 150 VAL cc_start: 0.9448 (m) cc_final: 0.9220 (p) REVERT: P 1 MET cc_start: 0.6208 (ptt) cc_final: 0.5936 (ptt) REVERT: P 5 PHE cc_start: 0.8759 (m-10) cc_final: 0.8493 (m-10) REVERT: P 29 ASN cc_start: 0.8139 (m-40) cc_final: 0.7516 (m110) REVERT: P 59 LEU cc_start: 0.9019 (tp) cc_final: 0.8815 (tp) REVERT: P 93 ARG cc_start: 0.8724 (ttp80) cc_final: 0.8325 (ttp-170) REVERT: P 95 VAL cc_start: 0.9145 (t) cc_final: 0.8638 (m) REVERT: P 97 TYR cc_start: 0.8916 (m-10) cc_final: 0.8179 (m-10) REVERT: P 137 LYS cc_start: 0.9012 (tppt) cc_final: 0.8751 (tppt) REVERT: P 158 LEU cc_start: 0.8975 (mm) cc_final: 0.8586 (mt) REVERT: P 159 MET cc_start: 0.8697 (mmm) cc_final: 0.8000 (ppp) REVERT: Q 7 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8060 (mm-30) REVERT: Q 14 THR cc_start: 0.8730 (p) cc_final: 0.8410 (t) REVERT: Q 25 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7717 (mm-40) REVERT: Q 37 SER cc_start: 0.7888 (m) cc_final: 0.7239 (p) REVERT: Q 94 MET cc_start: 0.4795 (tpp) cc_final: 0.4540 (tpp) REVERT: Q 98 CYS cc_start: 0.8110 (m) cc_final: 0.7592 (m) REVERT: Q 107 MET cc_start: 0.8238 (ttm) cc_final: 0.7883 (mtp) REVERT: R 38 LEU cc_start: 0.8584 (mt) cc_final: 0.8271 (mp) REVERT: R 49 SER cc_start: 0.9309 (p) cc_final: 0.9003 (t) REVERT: R 85 LEU cc_start: 0.9433 (mt) cc_final: 0.9130 (tp) REVERT: R 128 SER cc_start: 0.8664 (m) cc_final: 0.8232 (m) REVERT: R 159 MET cc_start: 0.8240 (mmp) cc_final: 0.7879 (ptt) REVERT: S 28 ASP cc_start: 0.7886 (t0) cc_final: 0.7493 (t0) REVERT: S 38 MET cc_start: 0.8381 (mtm) cc_final: 0.8179 (mtt) REVERT: S 49 GLN cc_start: 0.8449 (tp-100) cc_final: 0.7705 (pm20) REVERT: S 79 GLU cc_start: 0.7914 (mp0) cc_final: 0.7657 (tm-30) REVERT: S 90 TYR cc_start: 0.8043 (m-10) cc_final: 0.7462 (m-10) REVERT: S 98 CYS cc_start: 0.8170 (m) cc_final: 0.6633 (m) REVERT: S 115 LEU cc_start: 0.8225 (tp) cc_final: 0.7862 (tp) REVERT: S 133 LEU cc_start: 0.8951 (mt) cc_final: 0.8708 (mt) REVERT: S 134 LYS cc_start: 0.9472 (mmpt) cc_final: 0.9236 (mmmm) REVERT: S 137 LYS cc_start: 0.9295 (ttpt) cc_final: 0.8890 (tptt) REVERT: T 15 ARG cc_start: 0.7719 (mtp85) cc_final: 0.6914 (mmm160) REVERT: T 19 LEU cc_start: 0.8105 (mt) cc_final: 0.7544 (mm) REVERT: T 23 GLN cc_start: 0.8429 (mt0) cc_final: 0.8085 (mp10) REVERT: T 25 ASP cc_start: 0.8569 (m-30) cc_final: 0.8307 (m-30) REVERT: T 47 ASN cc_start: 0.7840 (t0) cc_final: 0.7411 (t0) REVERT: T 136 MET cc_start: 0.7683 (tpt) cc_final: 0.7342 (tpp) REVERT: T 156 SER cc_start: 0.8321 (m) cc_final: 0.8020 (m) REVERT: U 28 ASP cc_start: 0.7810 (t0) cc_final: 0.7163 (t0) REVERT: U 42 ARG cc_start: 0.7770 (ttm-80) cc_final: 0.7376 (ttm170) REVERT: U 61 GLN cc_start: 0.8471 (mt0) cc_final: 0.7595 (tm-30) REVERT: U 69 MET cc_start: 0.6805 (mtt) cc_final: 0.6566 (tpp) REVERT: U 115 LEU cc_start: 0.8224 (tp) cc_final: 0.8013 (tp) REVERT: U 123 ASP cc_start: 0.8122 (t0) cc_final: 0.7862 (t70) REVERT: U 171 ASN cc_start: 0.8751 (t0) cc_final: 0.8297 (t0) REVERT: V 11 GLN cc_start: 0.8500 (tt0) cc_final: 0.8147 (tp40) REVERT: V 68 GLN cc_start: 0.8278 (pt0) cc_final: 0.8003 (pt0) REVERT: V 78 ASN cc_start: 0.6743 (t0) cc_final: 0.6038 (t0) REVERT: V 113 ASN cc_start: 0.8722 (t0) cc_final: 0.8051 (t0) REVERT: V 124 THR cc_start: 0.8847 (m) cc_final: 0.8265 (p) REVERT: V 154 ASP cc_start: 0.8133 (t0) cc_final: 0.7553 (t0) REVERT: V 162 ILE cc_start: 0.8746 (mt) cc_final: 0.8408 (mt) REVERT: W 2 LYS cc_start: 0.7512 (mmtm) cc_final: 0.7137 (mmtm) REVERT: W 7 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7812 (mm-30) REVERT: W 69 MET cc_start: 0.3931 (mtp) cc_final: 0.3726 (mmm) REVERT: W 97 TYR cc_start: 0.7604 (m-10) cc_final: 0.6547 (m-80) REVERT: W 111 LEU cc_start: 0.8074 (pt) cc_final: 0.7635 (pp) REVERT: W 115 LEU cc_start: 0.7912 (mt) cc_final: 0.7556 (mt) REVERT: W 122 PHE cc_start: 0.5928 (m-80) cc_final: 0.5698 (m-80) REVERT: W 163 ASN cc_start: 0.7681 (m-40) cc_final: 0.7317 (m-40) REVERT: X 38 LEU cc_start: 0.9483 (mt) cc_final: 0.9282 (mt) REVERT: X 166 PHE cc_start: 0.7726 (m-80) cc_final: 0.7514 (m-80) REVERT: Y 50 VAL cc_start: 0.9279 (t) cc_final: 0.9031 (p) REVERT: Y 55 MET cc_start: 0.8487 (ttp) cc_final: 0.8225 (ttp) REVERT: Z 64 ASN cc_start: 0.8486 (t0) cc_final: 0.8205 (t0) REVERT: Z 93 THR cc_start: 0.9242 (m) cc_final: 0.8888 (p) REVERT: Z 96 ILE cc_start: 0.9031 (mm) cc_final: 0.8821 (mm) REVERT: Z 98 LEU cc_start: 0.8969 (mt) cc_final: 0.8751 (mm) REVERT: Z 115 ILE cc_start: 0.8857 (mt) cc_final: 0.8581 (mm) REVERT: Z 133 TYR cc_start: 0.8014 (m-80) cc_final: 0.7625 (m-80) REVERT: Z 146 TRP cc_start: 0.8316 (m-90) cc_final: 0.8007 (m-90) REVERT: Z 157 GLN cc_start: 0.7681 (tp40) cc_final: 0.7166 (tp40) REVERT: Z 166 ASN cc_start: 0.8960 (m110) cc_final: 0.8721 (m110) REVERT: Z 175 TYR cc_start: 0.8512 (t80) cc_final: 0.8097 (t80) REVERT: Z 196 THR cc_start: 0.9091 (p) cc_final: 0.8802 (t) REVERT: Z 264 TYR cc_start: 0.8944 (t80) cc_final: 0.8661 (t80) REVERT: a 2 THR cc_start: 0.6974 (p) cc_final: 0.6429 (t) REVERT: a 44 GLU cc_start: 0.7527 (tt0) cc_final: 0.7313 (tt0) REVERT: a 65 GLN cc_start: 0.7987 (tt0) cc_final: 0.7752 (tt0) REVERT: a 74 ASN cc_start: 0.9108 (t0) cc_final: 0.8859 (p0) REVERT: a 77 ILE cc_start: 0.8489 (pt) cc_final: 0.7918 (pt) REVERT: a 104 ARG cc_start: 0.8459 (ttt90) cc_final: 0.7707 (ttp80) REVERT: a 119 TYR cc_start: 0.7825 (m-80) cc_final: 0.6848 (m-10) REVERT: a 152 ASN cc_start: 0.8252 (m-40) cc_final: 0.7766 (m-40) REVERT: a 177 TYR cc_start: 0.8221 (p90) cc_final: 0.7750 (p90) outliers start: 8 outliers final: 1 residues processed: 1832 average time/residue: 0.2014 time to fit residues: 596.4609 Evaluate side-chains 1460 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1458 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 44 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 375 optimal weight: 6.9990 chunk 347 optimal weight: 5.9990 chunk 301 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 341 optimal weight: 0.9990 chunk 328 optimal weight: 6.9990 chunk 377 optimal weight: 9.9990 chunk 400 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 GLN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN E 163 ASN F 11 GLN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 ASN G 25 GLN ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN O 119 ASN ** P 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 171 ASN ** R 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 119 ASN U 139 ASN V 23 GLN ** V 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 61 GLN ** W 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 ASN ** Z 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 200 ASN Z 266 GLN ** Z 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.111707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.094187 restraints weight = 110576.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.097808 restraints weight = 54884.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.100208 restraints weight = 31659.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.101781 restraints weight = 20384.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.102816 restraints weight = 14431.481| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3328 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3328 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 36155 Z= 0.204 Angle : 0.799 43.210 49243 Z= 0.381 Chirality : 0.041 0.271 5448 Planarity : 0.005 0.061 6402 Dihedral : 10.790 88.587 6599 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.52 % Favored : 97.41 % Rotamer: Outliers : 0.15 % Allowed : 4.45 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.12), residues: 4448 helix: 1.13 (0.08), residues: 3397 sheet: 1.86 (0.92), residues: 28 loop : -0.67 (0.22), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 30 TYR 0.053 0.002 TYR M 97 PHE 0.037 0.002 PHE Z 143 TRP 0.016 0.002 TRP C 128 HIS 0.008 0.002 HIS Z 117 Details of bonding type rmsd covalent geometry : bond 0.00448 (36155) covalent geometry : angle 0.79910 (49243) hydrogen bonds : bond 0.05113 ( 2648) hydrogen bonds : angle 4.50621 ( 7847) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1689 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1684 time to evaluate : 1.318 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: A 18 PHE cc_start: 0.7963 (m-80) cc_final: 0.7046 (m-80) REVERT: A 38 MET cc_start: 0.8500 (mmt) cc_final: 0.7636 (tmm) REVERT: A 39 GLU cc_start: 0.8243 (tp30) cc_final: 0.7693 (mm-30) REVERT: A 62 LYS cc_start: 0.8979 (tptt) cc_final: 0.8568 (tptt) REVERT: A 63 PHE cc_start: 0.8771 (m-80) cc_final: 0.8002 (m-80) REVERT: A 109 GLU cc_start: 0.7675 (mt-10) cc_final: 0.6782 (mt-10) REVERT: A 131 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7264 (tm-30) REVERT: A 134 LYS cc_start: 0.8739 (ttmm) cc_final: 0.8081 (mtpp) REVERT: A 136 ILE cc_start: 0.9275 (mm) cc_final: 0.9036 (tp) REVERT: A 165 TYR cc_start: 0.8580 (m-10) cc_final: 0.8378 (m-80) REVERT: A 167 ASP cc_start: 0.8186 (t0) cc_final: 0.7339 (t0) REVERT: A 171 ASN cc_start: 0.8786 (m-40) cc_final: 0.8547 (m-40) REVERT: B 44 ILE cc_start: 0.9406 (mt) cc_final: 0.9149 (tp) REVERT: B 89 GLU cc_start: 0.8825 (pt0) cc_final: 0.8097 (tt0) REVERT: B 99 ILE cc_start: 0.9218 (mt) cc_final: 0.8977 (mt) REVERT: B 120 GLN cc_start: 0.7787 (mt0) cc_final: 0.7392 (tm-30) REVERT: B 136 MET cc_start: 0.7505 (mtt) cc_final: 0.6502 (mtt) REVERT: C 17 ARG cc_start: 0.8464 (ptt90) cc_final: 0.8113 (ptt90) REVERT: C 63 PHE cc_start: 0.9086 (m-80) cc_final: 0.8468 (m-10) REVERT: C 69 MET cc_start: 0.7600 (ttm) cc_final: 0.7127 (ttm) REVERT: C 94 MET cc_start: 0.9433 (mmt) cc_final: 0.8985 (mmm) REVERT: C 117 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8477 (mm-30) REVERT: C 133 LEU cc_start: 0.8641 (mp) cc_final: 0.8369 (tp) REVERT: D 32 LYS cc_start: 0.9391 (pttt) cc_final: 0.9128 (pttm) REVERT: D 49 SER cc_start: 0.9115 (p) cc_final: 0.8818 (p) REVERT: D 81 MET cc_start: 0.7643 (tpp) cc_final: 0.7402 (ttt) REVERT: D 88 MET cc_start: 0.8365 (ttm) cc_final: 0.7996 (mmm) REVERT: D 97 TYR cc_start: 0.8616 (m-10) cc_final: 0.7499 (m-10) REVERT: D 112 LEU cc_start: 0.8797 (pp) cc_final: 0.8525 (pp) REVERT: D 134 GLN cc_start: 0.8200 (mt0) cc_final: 0.7886 (mt0) REVERT: D 146 ASP cc_start: 0.9125 (t0) cc_final: 0.8882 (t0) REVERT: D 154 ASP cc_start: 0.6575 (t0) cc_final: 0.6310 (t0) REVERT: D 162 ILE cc_start: 0.9129 (mm) cc_final: 0.8900 (mm) REVERT: E 25 GLN cc_start: 0.8240 (mt0) cc_final: 0.8024 (mm-40) REVERT: E 28 ASP cc_start: 0.8670 (t70) cc_final: 0.8418 (t0) REVERT: E 38 MET cc_start: 0.8136 (mmt) cc_final: 0.7762 (tmm) REVERT: E 47 ASN cc_start: 0.8136 (t0) cc_final: 0.7535 (t0) REVERT: E 51 LEU cc_start: 0.9548 (mt) cc_final: 0.9332 (mp) REVERT: E 62 LYS cc_start: 0.8958 (tptt) cc_final: 0.8734 (tppt) REVERT: E 72 SER cc_start: 0.9015 (m) cc_final: 0.8590 (t) REVERT: E 73 GLN cc_start: 0.8764 (pm20) cc_final: 0.8123 (pm20) REVERT: E 93 ARG cc_start: 0.8546 (ttp80) cc_final: 0.8216 (ttp-110) REVERT: E 121 THR cc_start: 0.9235 (p) cc_final: 0.8743 (t) REVERT: E 129 TYR cc_start: 0.8532 (m-10) cc_final: 0.8092 (m-10) REVERT: E 140 HIS cc_start: 0.8565 (p90) cc_final: 0.8334 (p-80) REVERT: E 167 ASP cc_start: 0.8004 (t0) cc_final: 0.6996 (t0) REVERT: E 171 ASN cc_start: 0.8719 (p0) cc_final: 0.8469 (p0) REVERT: E 173 LEU cc_start: 0.9179 (mm) cc_final: 0.8971 (mm) REVERT: F 11 GLN cc_start: 0.9102 (tt0) cc_final: 0.8505 (tt0) REVERT: F 25 ASP cc_start: 0.8841 (m-30) cc_final: 0.8547 (m-30) REVERT: F 81 MET cc_start: 0.9270 (tpp) cc_final: 0.8962 (tpp) REVERT: F 117 GLU cc_start: 0.8558 (pp20) cc_final: 0.8247 (pp20) REVERT: F 146 ASP cc_start: 0.8398 (t0) cc_final: 0.8167 (t0) REVERT: F 159 MET cc_start: 0.7003 (mmm) cc_final: 0.6671 (mmt) REVERT: F 161 GLU cc_start: 0.8248 (tp30) cc_final: 0.7577 (tp30) REVERT: G 49 GLN cc_start: 0.8804 (pp30) cc_final: 0.8568 (pp30) REVERT: G 61 GLN cc_start: 0.8606 (mt0) cc_final: 0.8348 (mp10) REVERT: G 62 LYS cc_start: 0.9061 (tptm) cc_final: 0.8730 (tppt) REVERT: G 70 GLN cc_start: 0.7559 (tm-30) cc_final: 0.7289 (pp30) REVERT: G 97 TYR cc_start: 0.8894 (m-10) cc_final: 0.8572 (m-10) REVERT: G 119 ASN cc_start: 0.9368 (m110) cc_final: 0.9118 (m-40) REVERT: G 122 PHE cc_start: 0.8853 (m-80) cc_final: 0.8651 (m-80) REVERT: G 123 ASP cc_start: 0.8073 (t0) cc_final: 0.7775 (t70) REVERT: G 124 LEU cc_start: 0.9022 (mt) cc_final: 0.8410 (mt) REVERT: G 135 TYR cc_start: 0.8754 (t80) cc_final: 0.8480 (t80) REVERT: G 137 LYS cc_start: 0.9058 (ptmt) cc_final: 0.8660 (ttpp) REVERT: G 161 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8077 (mt-10) REVERT: G 163 ASN cc_start: 0.9120 (m-40) cc_final: 0.8737 (m-40) REVERT: H 3 ASP cc_start: 0.8391 (p0) cc_final: 0.7705 (p0) REVERT: H 67 ILE cc_start: 0.9529 (pt) cc_final: 0.9184 (tt) REVERT: H 88 MET cc_start: 0.7964 (mtm) cc_final: 0.7585 (mtm) REVERT: H 159 MET cc_start: 0.8403 (mmm) cc_final: 0.8017 (mmm) REVERT: I 51 LEU cc_start: 0.8935 (mt) cc_final: 0.8670 (mt) REVERT: I 62 LYS cc_start: 0.9226 (tptm) cc_final: 0.8845 (tptt) REVERT: I 90 TYR cc_start: 0.7851 (m-10) cc_final: 0.7354 (m-10) REVERT: I 119 ASN cc_start: 0.8518 (m110) cc_final: 0.7711 (m110) REVERT: I 127 SER cc_start: 0.9274 (p) cc_final: 0.9048 (p) REVERT: I 129 TYR cc_start: 0.8849 (m-10) cc_final: 0.8459 (m-10) REVERT: I 166 ILE cc_start: 0.9802 (tt) cc_final: 0.9293 (tt) REVERT: I 173 LEU cc_start: 0.9516 (mt) cc_final: 0.9111 (tt) REVERT: J 17 GLU cc_start: 0.8127 (mp0) cc_final: 0.7892 (mp0) REVERT: J 35 ASN cc_start: 0.8511 (m110) cc_final: 0.8127 (t0) REVERT: J 91 ILE cc_start: 0.9396 (tp) cc_final: 0.9106 (tt) REVERT: J 97 TYR cc_start: 0.8932 (m-10) cc_final: 0.8327 (m-10) REVERT: J 112 LEU cc_start: 0.9467 (mp) cc_final: 0.8868 (mm) REVERT: K 90 TYR cc_start: 0.9043 (m-10) cc_final: 0.8737 (m-80) REVERT: K 139 ASN cc_start: 0.8049 (m110) cc_final: 0.7846 (t0) REVERT: K 161 GLU cc_start: 0.8433 (tp30) cc_final: 0.8073 (tp30) REVERT: L 2 LEU cc_start: 0.9355 (mt) cc_final: 0.8697 (mt) REVERT: L 13 ASP cc_start: 0.8442 (t70) cc_final: 0.8040 (t0) REVERT: L 59 LEU cc_start: 0.9541 (tp) cc_final: 0.9304 (tp) REVERT: L 80 ARG cc_start: 0.8125 (mtm-85) cc_final: 0.7799 (mtt-85) REVERT: L 81 MET cc_start: 0.8996 (tpp) cc_final: 0.8318 (tpp) REVERT: L 88 MET cc_start: 0.8131 (mtm) cc_final: 0.7848 (mtp) REVERT: L 89 GLU cc_start: 0.7766 (pp20) cc_final: 0.7392 (tm-30) REVERT: L 103 ASP cc_start: 0.8361 (m-30) cc_final: 0.8077 (m-30) REVERT: L 116 ARG cc_start: 0.8109 (tpp80) cc_final: 0.7786 (tpp80) REVERT: L 117 GLU cc_start: 0.8755 (tp30) cc_final: 0.8540 (tp30) REVERT: L 120 GLN cc_start: 0.8888 (tm-30) cc_final: 0.8371 (tm-30) REVERT: L 137 LYS cc_start: 0.9527 (tttt) cc_final: 0.8892 (ttmt) REVERT: L 159 MET cc_start: 0.8679 (mmt) cc_final: 0.8449 (mmt) REVERT: M 9 ILE cc_start: 0.9287 (tp) cc_final: 0.8390 (tp) REVERT: M 107 MET cc_start: 0.8023 (mmm) cc_final: 0.7610 (mmm) REVERT: M 118 ILE cc_start: 0.9539 (tp) cc_final: 0.9128 (tp) REVERT: M 129 TYR cc_start: 0.8145 (m-80) cc_final: 0.7868 (m-80) REVERT: M 135 TYR cc_start: 0.9000 (t80) cc_final: 0.8709 (t80) REVERT: M 171 ASN cc_start: 0.7998 (p0) cc_final: 0.7567 (p0) REVERT: N 36 LYS cc_start: 0.8303 (mttt) cc_final: 0.8095 (mttt) REVERT: N 65 GLN cc_start: 0.7561 (mp10) cc_final: 0.7266 (mp10) REVERT: N 66 LEU cc_start: 0.8948 (mt) cc_final: 0.8698 (mt) REVERT: N 80 ARG cc_start: 0.8954 (mtm-85) cc_final: 0.8480 (mtm-85) REVERT: N 97 TYR cc_start: 0.8621 (m-10) cc_final: 0.7924 (m-80) REVERT: N 103 ASP cc_start: 0.6788 (t0) cc_final: 0.6311 (t0) REVERT: N 105 SER cc_start: 0.8347 (t) cc_final: 0.8117 (t) REVERT: N 136 MET cc_start: 0.8741 (mtm) cc_final: 0.8458 (mtm) REVERT: N 141 ILE cc_start: 0.9176 (tp) cc_final: 0.8867 (tp) REVERT: O 3 THR cc_start: 0.8153 (m) cc_final: 0.7908 (m) REVERT: O 25 GLN cc_start: 0.7555 (mt0) cc_final: 0.7317 (mt0) REVERT: O 52 ILE cc_start: 0.7956 (pt) cc_final: 0.7721 (pt) REVERT: O 96 THR cc_start: 0.9282 (p) cc_final: 0.9048 (t) REVERT: O 99 LEU cc_start: 0.9294 (mt) cc_final: 0.9047 (tp) REVERT: O 104 THR cc_start: 0.8677 (p) cc_final: 0.7913 (p) REVERT: O 112 ILE cc_start: 0.9347 (mp) cc_final: 0.8960 (mp) REVERT: O 129 TYR cc_start: 0.8520 (m-80) cc_final: 0.7905 (m-80) REVERT: O 130 ILE cc_start: 0.9105 (mm) cc_final: 0.8896 (mm) REVERT: O 131 GLU cc_start: 0.8724 (pt0) cc_final: 0.8515 (pt0) REVERT: O 163 ASN cc_start: 0.8413 (m-40) cc_final: 0.7902 (m-40) REVERT: P 1 MET cc_start: 0.5823 (ptt) cc_final: 0.5203 (ptt) REVERT: P 39 ASP cc_start: 0.7121 (m-30) cc_final: 0.6918 (m-30) REVERT: P 81 MET cc_start: 0.8391 (tpp) cc_final: 0.8189 (tpp) REVERT: P 97 TYR cc_start: 0.8751 (m-10) cc_final: 0.8259 (m-10) REVERT: P 159 MET cc_start: 0.9041 (mmm) cc_final: 0.8389 (mmm) REVERT: Q 14 THR cc_start: 0.8720 (p) cc_final: 0.8439 (t) REVERT: Q 37 SER cc_start: 0.7896 (m) cc_final: 0.7224 (p) REVERT: Q 53 ASP cc_start: 0.5643 (m-30) cc_final: 0.5287 (m-30) REVERT: Q 62 LYS cc_start: 0.7410 (ttmt) cc_final: 0.7132 (tttm) REVERT: Q 73 GLN cc_start: 0.8305 (pm20) cc_final: 0.7773 (pm20) REVERT: Q 94 MET cc_start: 0.5525 (tpp) cc_final: 0.5114 (tpp) REVERT: Q 98 CYS cc_start: 0.8384 (m) cc_final: 0.7783 (m) REVERT: Q 107 MET cc_start: 0.7989 (ttm) cc_final: 0.7732 (mtp) REVERT: Q 108 ASP cc_start: 0.8371 (m-30) cc_final: 0.7958 (m-30) REVERT: R 39 ASP cc_start: 0.8036 (m-30) cc_final: 0.7468 (m-30) REVERT: R 49 SER cc_start: 0.9147 (p) cc_final: 0.8919 (t) REVERT: R 59 LEU cc_start: 0.9031 (tt) cc_final: 0.8789 (tt) REVERT: R 80 ARG cc_start: 0.8492 (mtm-85) cc_final: 0.8165 (mtm-85) REVERT: R 85 LEU cc_start: 0.9587 (mt) cc_final: 0.9274 (tp) REVERT: R 93 ARG cc_start: 0.8293 (ttp80) cc_final: 0.8060 (ttp80) REVERT: R 111 CYS cc_start: 0.7283 (t) cc_final: 0.6708 (t) REVERT: R 118 THR cc_start: 0.8636 (p) cc_final: 0.7443 (p) REVERT: R 128 SER cc_start: 0.8656 (m) cc_final: 0.8275 (m) REVERT: R 134 GLN cc_start: 0.7671 (mm110) cc_final: 0.7099 (mm110) REVERT: R 135 LYS cc_start: 0.7716 (mtmm) cc_final: 0.7465 (ptpp) REVERT: R 159 MET cc_start: 0.8251 (mmp) cc_final: 0.7552 (ptt) REVERT: R 168 ARG cc_start: 0.8653 (ttt90) cc_final: 0.8303 (tpp80) REVERT: S 37 SER cc_start: 0.8376 (p) cc_final: 0.7646 (t) REVERT: S 49 GLN cc_start: 0.8361 (tp-100) cc_final: 0.7619 (pm20) REVERT: S 51 LEU cc_start: 0.8545 (mp) cc_final: 0.8322 (mm) REVERT: S 52 ILE cc_start: 0.8994 (tt) cc_final: 0.8775 (tp) REVERT: S 79 GLU cc_start: 0.7751 (mp0) cc_final: 0.7481 (tm-30) REVERT: S 90 TYR cc_start: 0.8239 (m-10) cc_final: 0.7604 (m-10) REVERT: S 94 MET cc_start: 0.9512 (mmt) cc_final: 0.8613 (mmm) REVERT: S 97 TYR cc_start: 0.9090 (m-80) cc_final: 0.7717 (m-80) REVERT: S 112 ILE cc_start: 0.9537 (mm) cc_final: 0.9036 (tp) REVERT: S 115 LEU cc_start: 0.8430 (tp) cc_final: 0.8065 (tp) REVERT: S 131 GLU cc_start: 0.8295 (tm-30) cc_final: 0.8091 (tm-30) REVERT: S 133 LEU cc_start: 0.9114 (mt) cc_final: 0.8904 (mt) REVERT: S 134 LYS cc_start: 0.9513 (mmpt) cc_final: 0.9284 (mmmm) REVERT: S 137 LYS cc_start: 0.9334 (ttpt) cc_final: 0.8782 (tptt) REVERT: S 161 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7049 (mm-30) REVERT: S 165 TYR cc_start: 0.8578 (m-80) cc_final: 0.8311 (m-80) REVERT: T 13 ASP cc_start: 0.8511 (t70) cc_final: 0.7902 (t0) REVERT: T 15 ARG cc_start: 0.7925 (mtp85) cc_final: 0.7184 (mmp80) REVERT: T 19 LEU cc_start: 0.8283 (mt) cc_final: 0.7745 (mm) REVERT: T 23 GLN cc_start: 0.8390 (mt0) cc_final: 0.8046 (mp10) REVERT: T 25 ASP cc_start: 0.8628 (m-30) cc_final: 0.8320 (m-30) REVERT: T 27 LEU cc_start: 0.8849 (mt) cc_final: 0.8612 (mt) REVERT: T 47 ASN cc_start: 0.7971 (t0) cc_final: 0.7507 (t0) REVERT: T 59 LEU cc_start: 0.8950 (mt) cc_final: 0.8288 (mt) REVERT: T 76 TYR cc_start: 0.3390 (t80) cc_final: 0.3173 (t80) REVERT: T 97 TYR cc_start: 0.8839 (m-10) cc_final: 0.8378 (m-10) REVERT: T 104 SER cc_start: 0.9120 (p) cc_final: 0.8819 (p) REVERT: T 156 SER cc_start: 0.8495 (m) cc_final: 0.8072 (m) REVERT: T 162 ILE cc_start: 0.9170 (mt) cc_final: 0.8901 (mt) REVERT: T 165 TYR cc_start: 0.8655 (m-80) cc_final: 0.8081 (m-80) REVERT: U 7 GLU cc_start: 0.8384 (pm20) cc_final: 0.8153 (pm20) REVERT: U 24 LEU cc_start: 0.9296 (mt) cc_final: 0.9059 (mt) REVERT: U 28 ASP cc_start: 0.7528 (t0) cc_final: 0.7078 (t0) REVERT: U 32 LYS cc_start: 0.9230 (tmmt) cc_final: 0.8991 (tmmt) REVERT: U 42 ARG cc_start: 0.7350 (ttm-80) cc_final: 0.6748 (mtt180) REVERT: U 109 GLU cc_start: 0.8477 (tm-30) cc_final: 0.7852 (tm-30) REVERT: U 115 LEU cc_start: 0.8675 (tp) cc_final: 0.8254 (tp) REVERT: U 119 ASN cc_start: 0.8781 (m110) cc_final: 0.8581 (m110) REVERT: U 123 ASP cc_start: 0.8534 (t0) cc_final: 0.7820 (t0) REVERT: U 131 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8296 (mm-30) REVERT: U 134 LYS cc_start: 0.9069 (tppp) cc_final: 0.8854 (tppp) REVERT: U 137 LYS cc_start: 0.9547 (tttp) cc_final: 0.9245 (tttp) REVERT: U 150 VAL cc_start: 0.9540 (t) cc_final: 0.9314 (p) REVERT: U 163 ASN cc_start: 0.9227 (m-40) cc_final: 0.8924 (m-40) REVERT: U 171 ASN cc_start: 0.8782 (t0) cc_final: 0.8235 (t0) REVERT: U 174 SER cc_start: 0.7913 (t) cc_final: 0.7636 (t) REVERT: V 11 GLN cc_start: 0.8415 (tt0) cc_final: 0.7751 (tp40) REVERT: V 13 ASP cc_start: 0.8155 (t0) cc_final: 0.7906 (t0) REVERT: V 62 GLU cc_start: 0.7509 (pp20) cc_final: 0.5419 (pp20) REVERT: V 63 GLN cc_start: 0.8851 (mt0) cc_final: 0.8514 (mp10) REVERT: V 68 GLN cc_start: 0.8553 (pt0) cc_final: 0.8262 (pt0) REVERT: V 113 ASN cc_start: 0.9082 (t0) cc_final: 0.8222 (t0) REVERT: V 124 THR cc_start: 0.8658 (m) cc_final: 0.8100 (p) REVERT: V 162 ILE cc_start: 0.8655 (mt) cc_final: 0.8386 (mt) REVERT: W 42 ARG cc_start: 0.7527 (ttm170) cc_final: 0.6252 (tpt170) REVERT: W 69 MET cc_start: 0.3782 (mtp) cc_final: 0.3326 (mmm) REVERT: W 107 MET cc_start: 0.8020 (mmp) cc_final: 0.7379 (mmp) REVERT: W 163 ASN cc_start: 0.7578 (m-40) cc_final: 0.6984 (m-40) REVERT: X 44 ILE cc_start: 0.8056 (mm) cc_final: 0.7617 (tp) REVERT: X 88 MET cc_start: 0.8954 (ttm) cc_final: 0.8710 (ttt) REVERT: X 109 ASP cc_start: 0.8093 (t70) cc_final: 0.7820 (t70) REVERT: X 166 PHE cc_start: 0.7581 (m-80) cc_final: 0.7357 (m-80) REVERT: Y 20 PHE cc_start: 0.8041 (m-80) cc_final: 0.7677 (m-80) REVERT: Y 24 VAL cc_start: 0.8718 (t) cc_final: 0.8295 (t) REVERT: Y 28 ARG cc_start: 0.8925 (ttp-170) cc_final: 0.8676 (ttm170) REVERT: Y 50 VAL cc_start: 0.9416 (t) cc_final: 0.9170 (p) REVERT: Z 42 GLN cc_start: 0.8855 (tp40) cc_final: 0.8544 (tp40) REVERT: Z 93 THR cc_start: 0.8922 (m) cc_final: 0.8661 (p) REVERT: Z 115 ILE cc_start: 0.8795 (mt) cc_final: 0.8569 (mm) REVERT: Z 119 ASP cc_start: 0.7524 (m-30) cc_final: 0.7072 (m-30) REVERT: Z 133 TYR cc_start: 0.8595 (m-80) cc_final: 0.8263 (m-80) REVERT: Z 146 TRP cc_start: 0.8431 (m-90) cc_final: 0.8196 (m-90) REVERT: Z 179 ASP cc_start: 0.8692 (m-30) cc_final: 0.8313 (m-30) REVERT: Z 192 ARG cc_start: 0.8127 (ttp-110) cc_final: 0.7593 (ttp-110) REVERT: Z 196 THR cc_start: 0.9238 (p) cc_final: 0.8842 (t) REVERT: Z 264 TYR cc_start: 0.9246 (t80) cc_final: 0.8637 (t80) REVERT: Z 275 GLN cc_start: 0.8622 (mm110) cc_final: 0.8224 (mm-40) REVERT: a 3 ILE cc_start: 0.7269 (mm) cc_final: 0.6897 (mm) REVERT: a 74 ASN cc_start: 0.9045 (t0) cc_final: 0.8727 (p0) REVERT: a 81 ASP cc_start: 0.8300 (t70) cc_final: 0.8032 (t70) REVERT: a 119 TYR cc_start: 0.7180 (m-80) cc_final: 0.6875 (m-80) REVERT: a 151 GLN cc_start: 0.8976 (mm-40) cc_final: 0.8160 (mt0) REVERT: a 170 PHE cc_start: 0.8337 (m-10) cc_final: 0.7446 (m-80) outliers start: 5 outliers final: 0 residues processed: 1686 average time/residue: 0.2072 time to fit residues: 566.7948 Evaluate side-chains 1387 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1387 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 226 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 106 optimal weight: 0.0050 chunk 160 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 284 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 351 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 GLN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 25 GLN G 139 ASN H 47 ASN H 78 ASN ** I 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 29 ASN ** P 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 70 GLN ** R 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 ASN ** U 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 92 GLN Z 117 HIS Z 166 ASN ** Z 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.115434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.097292 restraints weight = 122319.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.101260 restraints weight = 57963.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.103880 restraints weight = 32473.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.105589 restraints weight = 20356.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.106674 restraints weight = 14016.908| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3394 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3394 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4990 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= 0.146 Angle : 0.758 42.916 49243 Z= 0.354 Chirality : 0.039 0.198 5448 Planarity : 0.005 0.064 6402 Dihedral : 10.754 87.491 6599 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.23 % Favored : 97.71 % Rotamer: Outliers : 0.18 % Allowed : 2.65 % Favored : 97.17 % 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 aren not related in a simple way. whole: 1.15 (0.12), residues: 4448 helix: 1.22 (0.08), residues: 3394 sheet: 1.85 (0.80), residues: 28 loop : -0.64 (0.22), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 30 TYR 0.055 0.002 TYR M 97 PHE 0.050 0.002 PHE T 166 TRP 0.013 0.001 TRP U 128 HIS 0.006 0.002 HIS M 140 Details of bonding type rmsd covalent geometry : bond 0.00319 (36155) covalent geometry : angle 0.75788 (49243) hydrogen bonds : bond 0.04552 ( 2648) hydrogen bonds : angle 4.24382 ( 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 1747 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1741 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ILE cc_start: 0.9031 (mp) cc_final: 0.8809 (mm) REVERT: A 18 PHE cc_start: 0.8064 (m-80) cc_final: 0.7050 (m-80) REVERT: A 38 MET cc_start: 0.8502 (mmt) cc_final: 0.7844 (tmm) REVERT: A 39 GLU cc_start: 0.8319 (tp30) cc_final: 0.7733 (mm-30) REVERT: A 62 LYS cc_start: 0.9191 (tptt) cc_final: 0.8967 (tptt) REVERT: A 63 PHE cc_start: 0.8730 (m-80) cc_final: 0.8141 (m-80) REVERT: A 90 TYR cc_start: 0.8901 (m-10) cc_final: 0.8553 (m-80) REVERT: A 93 ARG cc_start: 0.8338 (ttp80) cc_final: 0.8075 (tpp80) REVERT: A 109 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7792 (mt-10) REVERT: A 115 LEU cc_start: 0.7556 (pp) cc_final: 0.7244 (pp) REVERT: A 131 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7145 (tm-30) REVERT: A 136 ILE cc_start: 0.9300 (mm) cc_final: 0.9085 (tp) REVERT: A 167 ASP cc_start: 0.8226 (t0) cc_final: 0.7552 (t0) REVERT: A 171 ASN cc_start: 0.8682 (m-40) cc_final: 0.8238 (m-40) REVERT: B 25 ASP cc_start: 0.8190 (p0) cc_final: 0.7768 (p0) REVERT: B 36 LYS cc_start: 0.9557 (mtmm) cc_final: 0.8597 (mppt) REVERT: B 89 GLU cc_start: 0.8601 (pt0) cc_final: 0.8301 (tt0) REVERT: B 120 GLN cc_start: 0.7794 (mt0) cc_final: 0.7289 (tm-30) REVERT: B 136 MET cc_start: 0.7439 (mtt) cc_final: 0.6053 (mtt) REVERT: B 141 ILE cc_start: 0.9162 (tt) cc_final: 0.8939 (tt) REVERT: C 17 ARG cc_start: 0.8507 (ptt90) cc_final: 0.8061 (ptt90) REVERT: C 69 MET cc_start: 0.7561 (ttm) cc_final: 0.7210 (ttm) REVERT: C 94 MET cc_start: 0.9381 (mmt) cc_final: 0.9099 (mmm) REVERT: C 109 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7785 (tp30) REVERT: C 117 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8671 (mm-30) REVERT: C 131 GLU cc_start: 0.8480 (tp30) cc_final: 0.8211 (mm-30) REVERT: D 29 ASN cc_start: 0.8976 (t0) cc_final: 0.8591 (t0) REVERT: D 32 LYS cc_start: 0.9336 (pttt) cc_final: 0.9101 (pttm) REVERT: D 49 SER cc_start: 0.8888 (p) cc_final: 0.8673 (p) REVERT: D 65 GLN cc_start: 0.8655 (tp40) cc_final: 0.8453 (tp40) REVERT: D 85 LEU cc_start: 0.9497 (mm) cc_final: 0.9284 (mm) REVERT: D 88 MET cc_start: 0.8371 (ttm) cc_final: 0.8131 (mmm) REVERT: D 97 TYR cc_start: 0.8609 (m-10) cc_final: 0.7361 (m-10) REVERT: D 113 ASN cc_start: 0.7847 (t0) cc_final: 0.7528 (t0) REVERT: D 115 LEU cc_start: 0.8464 (tt) cc_final: 0.8252 (tt) REVERT: D 128 SER cc_start: 0.9318 (p) cc_final: 0.8903 (m) REVERT: D 134 GLN cc_start: 0.8513 (mt0) cc_final: 0.8220 (mt0) REVERT: D 136 MET cc_start: 0.8070 (ttm) cc_final: 0.7848 (ttm) REVERT: D 146 ASP cc_start: 0.9203 (t0) cc_final: 0.8896 (t0) REVERT: D 154 ASP cc_start: 0.6794 (t0) cc_final: 0.6512 (t0) REVERT: E 7 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7574 (mm-30) REVERT: E 15 GLN cc_start: 0.7261 (mt0) cc_final: 0.6985 (mt0) REVERT: E 25 GLN cc_start: 0.8388 (mt0) cc_final: 0.8156 (mm-40) REVERT: E 28 ASP cc_start: 0.8651 (t70) cc_final: 0.8287 (t0) REVERT: E 38 MET cc_start: 0.8248 (mmt) cc_final: 0.7898 (tmm) REVERT: E 47 ASN cc_start: 0.8176 (t0) cc_final: 0.7795 (t0) REVERT: E 62 LYS cc_start: 0.8914 (tptt) cc_final: 0.8650 (tppt) REVERT: E 72 SER cc_start: 0.8846 (m) cc_final: 0.8491 (t) REVERT: E 73 GLN cc_start: 0.8565 (pm20) cc_final: 0.8280 (pm20) REVERT: E 83 LYS cc_start: 0.9233 (mmmm) cc_final: 0.8777 (mmmm) REVERT: E 109 GLU cc_start: 0.8506 (tt0) cc_final: 0.8285 (tt0) REVERT: E 121 THR cc_start: 0.9022 (p) cc_final: 0.8625 (t) REVERT: E 129 TYR cc_start: 0.8616 (m-10) cc_final: 0.7916 (m-10) REVERT: E 140 HIS cc_start: 0.8550 (p90) cc_final: 0.8051 (p-80) REVERT: E 167 ASP cc_start: 0.8291 (t0) cc_final: 0.7057 (t0) REVERT: E 168 TYR cc_start: 0.8589 (t80) cc_final: 0.7937 (t80) REVERT: E 171 ASN cc_start: 0.8550 (p0) cc_final: 0.8249 (p0) REVERT: E 173 LEU cc_start: 0.9113 (mm) cc_final: 0.8846 (mm) REVERT: F 11 GLN cc_start: 0.9109 (tt0) cc_final: 0.8447 (tt0) REVERT: F 25 ASP cc_start: 0.8782 (m-30) cc_final: 0.8450 (m-30) REVERT: F 60 PHE cc_start: 0.8650 (m-10) cc_final: 0.8021 (m-10) REVERT: F 81 MET cc_start: 0.9092 (tpp) cc_final: 0.8680 (tpt) REVERT: F 146 ASP cc_start: 0.8026 (t0) cc_final: 0.7823 (t0) REVERT: F 161 GLU cc_start: 0.8240 (tp30) cc_final: 0.7971 (tp30) REVERT: G 20 SER cc_start: 0.7848 (t) cc_final: 0.7315 (m) REVERT: G 25 GLN cc_start: 0.8867 (mt0) cc_final: 0.8247 (mt0) REVERT: G 28 ASP cc_start: 0.8401 (t0) cc_final: 0.8145 (t70) REVERT: G 38 MET cc_start: 0.9338 (mtm) cc_final: 0.8468 (ttm) REVERT: G 49 GLN cc_start: 0.8863 (pp30) cc_final: 0.8595 (pp30) REVERT: G 61 GLN cc_start: 0.8562 (mt0) cc_final: 0.8333 (mp10) REVERT: G 62 LYS cc_start: 0.9042 (tptm) cc_final: 0.8775 (tppt) REVERT: G 97 TYR cc_start: 0.8968 (m-10) cc_final: 0.8727 (m-10) REVERT: G 98 CYS cc_start: 0.8499 (p) cc_final: 0.7884 (m) REVERT: G 123 ASP cc_start: 0.8024 (t0) cc_final: 0.7800 (t70) REVERT: G 124 LEU cc_start: 0.9034 (mt) cc_final: 0.8498 (mt) REVERT: G 135 TYR cc_start: 0.8417 (t80) cc_final: 0.8128 (t80) REVERT: G 161 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8147 (mt-10) REVERT: H 1 MET cc_start: 0.6246 (mpp) cc_final: 0.5861 (mpp) REVERT: H 67 ILE cc_start: 0.9517 (pt) cc_final: 0.9195 (tt) REVERT: H 87 ASP cc_start: 0.8758 (m-30) cc_final: 0.7826 (m-30) REVERT: H 103 ASP cc_start: 0.7560 (t70) cc_final: 0.7311 (t70) REVERT: I 19 LEU cc_start: 0.8654 (mt) cc_final: 0.8401 (mt) REVERT: I 51 LEU cc_start: 0.8873 (mt) cc_final: 0.8561 (mt) REVERT: I 62 LYS cc_start: 0.9240 (tptm) cc_final: 0.8913 (tptt) REVERT: I 73 GLN cc_start: 0.9226 (pm20) cc_final: 0.8877 (pm20) REVERT: I 111 LEU cc_start: 0.9101 (tp) cc_final: 0.8808 (tp) REVERT: I 115 LEU cc_start: 0.8803 (tp) cc_final: 0.8091 (tp) REVERT: I 119 ASN cc_start: 0.8590 (m110) cc_final: 0.7740 (m110) REVERT: I 129 TYR cc_start: 0.8795 (m-10) cc_final: 0.8341 (m-10) REVERT: I 173 LEU cc_start: 0.9392 (mt) cc_final: 0.9097 (tt) REVERT: J 17 GLU cc_start: 0.7978 (mp0) cc_final: 0.7758 (mp0) REVERT: J 91 ILE cc_start: 0.9407 (tp) cc_final: 0.9062 (tt) REVERT: J 97 TYR cc_start: 0.8703 (m-10) cc_final: 0.8248 (m-10) REVERT: J 112 LEU cc_start: 0.9453 (mp) cc_final: 0.8856 (mm) REVERT: K 5 ILE cc_start: 0.9221 (mm) cc_final: 0.8948 (mm) REVERT: K 30 ARG cc_start: 0.8382 (tpt-90) cc_final: 0.8166 (tpt-90) REVERT: K 90 TYR cc_start: 0.8965 (m-10) cc_final: 0.8603 (m-80) REVERT: K 111 LEU cc_start: 0.9192 (tp) cc_final: 0.8848 (tp) REVERT: K 129 TYR cc_start: 0.8614 (m-80) cc_final: 0.8171 (m-10) REVERT: K 139 ASN cc_start: 0.8321 (m110) cc_final: 0.7892 (t0) REVERT: L 2 LEU cc_start: 0.9378 (mt) cc_final: 0.9004 (mt) REVERT: L 7 LYS cc_start: 0.8754 (ptmm) cc_final: 0.8381 (ptmm) REVERT: L 13 ASP cc_start: 0.8456 (t70) cc_final: 0.8193 (t0) REVERT: L 81 MET cc_start: 0.9013 (tpp) cc_final: 0.8340 (tpp) REVERT: L 88 MET cc_start: 0.8024 (mtm) cc_final: 0.7216 (mtp) REVERT: L 89 GLU cc_start: 0.8066 (pp20) cc_final: 0.7533 (tm-30) REVERT: L 103 ASP cc_start: 0.8023 (m-30) cc_final: 0.7663 (m-30) REVERT: L 108 ASP cc_start: 0.8140 (m-30) cc_final: 0.7889 (m-30) REVERT: L 116 ARG cc_start: 0.8047 (tpp80) cc_final: 0.7692 (tpp80) REVERT: L 120 GLN cc_start: 0.8832 (tm-30) cc_final: 0.8323 (tm-30) REVERT: L 137 LYS cc_start: 0.9404 (tttt) cc_final: 0.8916 (ttmt) REVERT: L 161 GLU cc_start: 0.8555 (tt0) cc_final: 0.7795 (tp30) REVERT: M 107 MET cc_start: 0.7954 (mmm) cc_final: 0.7505 (mmm) REVERT: M 110 TYR cc_start: 0.8998 (m-10) cc_final: 0.8679 (m-10) REVERT: M 115 LEU cc_start: 0.8798 (tt) cc_final: 0.8322 (tp) REVERT: M 118 ILE cc_start: 0.9613 (tp) cc_final: 0.9216 (tp) REVERT: M 129 TYR cc_start: 0.7980 (m-80) cc_final: 0.7399 (m-10) REVERT: M 135 TYR cc_start: 0.8833 (t80) cc_final: 0.8629 (t80) REVERT: M 171 ASN cc_start: 0.7842 (p0) cc_final: 0.7343 (p0) REVERT: N 66 LEU cc_start: 0.8823 (mt) cc_final: 0.8386 (mt) REVERT: N 80 ARG cc_start: 0.8817 (mtm-85) cc_final: 0.8036 (mtm-85) REVERT: N 87 ASP cc_start: 0.8569 (m-30) cc_final: 0.8262 (m-30) REVERT: N 88 MET cc_start: 0.8286 (ttm) cc_final: 0.7909 (tpp) REVERT: N 95 VAL cc_start: 0.9609 (t) cc_final: 0.9369 (p) REVERT: N 97 TYR cc_start: 0.8554 (m-10) cc_final: 0.7997 (m-80) REVERT: N 103 ASP cc_start: 0.7006 (t0) cc_final: 0.6221 (t0) REVERT: N 118 THR cc_start: 0.9299 (p) cc_final: 0.8991 (t) REVERT: N 136 MET cc_start: 0.8861 (mtm) cc_final: 0.7718 (mtm) REVERT: O 4 PRO cc_start: 0.8697 (Cg_exo) cc_final: 0.8338 (Cg_endo) REVERT: O 19 LEU cc_start: 0.8322 (mm) cc_final: 0.7368 (tp) REVERT: O 52 ILE cc_start: 0.7992 (pt) cc_final: 0.7775 (pt) REVERT: O 61 GLN cc_start: 0.8127 (mt0) cc_final: 0.7910 (mt0) REVERT: O 96 THR cc_start: 0.9318 (p) cc_final: 0.9052 (t) REVERT: O 104 THR cc_start: 0.9024 (p) cc_final: 0.8345 (p) REVERT: O 115 LEU cc_start: 0.8370 (tp) cc_final: 0.8080 (tp) REVERT: O 130 ILE cc_start: 0.9141 (mm) cc_final: 0.8912 (mm) REVERT: P 97 TYR cc_start: 0.8780 (m-10) cc_final: 0.8444 (m-10) REVERT: P 122 LEU cc_start: 0.8299 (mm) cc_final: 0.8022 (mm) REVERT: P 158 LEU cc_start: 0.9206 (mm) cc_final: 0.8847 (mm) REVERT: Q 13 ASP cc_start: 0.8838 (t0) cc_final: 0.8625 (t0) REVERT: Q 25 GLN cc_start: 0.8722 (mm-40) cc_final: 0.7970 (mm-40) REVERT: Q 37 SER cc_start: 0.7305 (m) cc_final: 0.6593 (p) REVERT: Q 39 GLU cc_start: 0.7470 (mt-10) cc_final: 0.6765 (pt0) REVERT: Q 53 ASP cc_start: 0.5783 (m-30) cc_final: 0.5536 (m-30) REVERT: Q 69 MET cc_start: 0.7400 (ptm) cc_final: 0.6700 (ptm) REVERT: Q 74 TYR cc_start: 0.7239 (m-80) cc_final: 0.6366 (m-80) REVERT: Q 94 MET cc_start: 0.6104 (tpp) cc_final: 0.5707 (tpp) REVERT: Q 98 CYS cc_start: 0.8307 (m) cc_final: 0.7810 (m) REVERT: Q 139 ASN cc_start: 0.7576 (m-40) cc_final: 0.7286 (m-40) REVERT: R 21 ASN cc_start: 0.6066 (p0) cc_final: 0.5847 (p0) REVERT: R 29 ASN cc_start: 0.7210 (t0) cc_final: 0.6741 (t0) REVERT: R 38 LEU cc_start: 0.8618 (mt) cc_final: 0.8084 (mp) REVERT: R 39 ASP cc_start: 0.8044 (m-30) cc_final: 0.7488 (m-30) REVERT: R 49 SER cc_start: 0.8979 (p) cc_final: 0.8779 (t) REVERT: R 111 CYS cc_start: 0.8085 (t) cc_final: 0.7584 (t) REVERT: R 118 THR cc_start: 0.8674 (p) cc_final: 0.8455 (p) REVERT: R 128 SER cc_start: 0.8627 (m) cc_final: 0.8300 (m) REVERT: R 159 MET cc_start: 0.8231 (mmp) cc_final: 0.7623 (ptt) REVERT: S 37 SER cc_start: 0.8461 (p) cc_final: 0.7727 (t) REVERT: S 49 GLN cc_start: 0.8522 (tp-100) cc_final: 0.7826 (pm20) REVERT: S 79 GLU cc_start: 0.7798 (mp0) cc_final: 0.7459 (tm-30) REVERT: S 90 TYR cc_start: 0.8239 (m-10) cc_final: 0.7601 (m-10) REVERT: S 94 MET cc_start: 0.9478 (mmt) cc_final: 0.8634 (mmm) REVERT: S 97 TYR cc_start: 0.9085 (m-80) cc_final: 0.8067 (m-80) REVERT: S 112 ILE cc_start: 0.9485 (mm) cc_final: 0.8936 (tp) REVERT: S 115 LEU cc_start: 0.8611 (tp) cc_final: 0.8309 (tp) REVERT: S 133 LEU cc_start: 0.9072 (mt) cc_final: 0.8843 (mt) REVERT: S 134 LYS cc_start: 0.9555 (mmpt) cc_final: 0.9136 (mmmm) REVERT: S 161 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7252 (mm-30) REVERT: T 15 ARG cc_start: 0.7614 (mtp85) cc_final: 0.7092 (mmp80) REVERT: T 19 LEU cc_start: 0.8125 (mt) cc_final: 0.7545 (mm) REVERT: T 23 GLN cc_start: 0.8402 (mt0) cc_final: 0.8043 (mp10) REVERT: T 47 ASN cc_start: 0.7817 (t0) cc_final: 0.7300 (t0) REVERT: T 59 LEU cc_start: 0.9374 (mt) cc_final: 0.9065 (mt) REVERT: T 62 GLU cc_start: 0.7096 (pt0) cc_final: 0.6815 (mm-30) REVERT: T 66 LEU cc_start: 0.7915 (pt) cc_final: 0.7627 (pp) REVERT: T 104 SER cc_start: 0.9124 (p) cc_final: 0.8741 (p) REVERT: T 162 ILE cc_start: 0.8958 (mt) cc_final: 0.8732 (mt) REVERT: T 165 TYR cc_start: 0.8238 (m-80) cc_final: 0.8026 (m-80) REVERT: U 28 ASP cc_start: 0.7523 (t0) cc_final: 0.7019 (t0) REVERT: U 42 ARG cc_start: 0.7307 (ttm-80) cc_final: 0.7097 (mtt90) REVERT: U 98 CYS cc_start: 0.7989 (t) cc_final: 0.7517 (t) REVERT: U 109 GLU cc_start: 0.8340 (tm-30) cc_final: 0.7508 (tm-30) REVERT: U 115 LEU cc_start: 0.8594 (tp) cc_final: 0.8185 (tp) REVERT: U 119 ASN cc_start: 0.8968 (m110) cc_final: 0.8753 (m110) REVERT: U 123 ASP cc_start: 0.8392 (t0) cc_final: 0.7934 (t0) REVERT: U 137 LYS cc_start: 0.9586 (tttp) cc_final: 0.9189 (tptp) REVERT: U 140 HIS cc_start: 0.8698 (p-80) cc_final: 0.8431 (p-80) REVERT: U 171 ASN cc_start: 0.8817 (t0) cc_final: 0.8484 (t0) REVERT: U 174 SER cc_start: 0.7889 (t) cc_final: 0.7646 (t) REVERT: V 11 GLN cc_start: 0.8512 (tt0) cc_final: 0.7570 (tp40) REVERT: V 17 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7147 (mp0) REVERT: V 62 GLU cc_start: 0.7591 (pp20) cc_final: 0.7154 (pp20) REVERT: V 68 GLN cc_start: 0.8523 (pt0) cc_final: 0.8250 (pt0) REVERT: V 81 MET cc_start: 0.8668 (tpp) cc_final: 0.8149 (tpp) REVERT: V 90 ILE cc_start: 0.9499 (mm) cc_final: 0.9289 (mm) REVERT: V 103 ASP cc_start: 0.8085 (t70) cc_final: 0.7861 (p0) REVERT: V 113 ASN cc_start: 0.9132 (t0) cc_final: 0.8235 (t0) REVERT: V 124 THR cc_start: 0.8888 (m) cc_final: 0.8518 (p) REVERT: V 136 MET cc_start: 0.9198 (mtm) cc_final: 0.8929 (mtp) REVERT: V 162 ILE cc_start: 0.8640 (mt) cc_final: 0.8429 (mt) REVERT: W 42 ARG cc_start: 0.7430 (ttm170) cc_final: 0.6031 (tpt170) REVERT: W 111 LEU cc_start: 0.8468 (pt) cc_final: 0.8048 (pp) REVERT: W 163 ASN cc_start: 0.7325 (m-40) cc_final: 0.7114 (m-40) REVERT: X 32 LYS cc_start: 0.7570 (mmtp) cc_final: 0.7006 (mmmm) REVERT: X 44 ILE cc_start: 0.8062 (mm) cc_final: 0.7664 (tp) REVERT: X 52 VAL cc_start: 0.9156 (t) cc_final: 0.8873 (p) REVERT: X 88 MET cc_start: 0.8927 (ttm) cc_final: 0.8632 (ttt) REVERT: X 89 GLU cc_start: 0.8372 (tm-30) cc_final: 0.7912 (tm-30) REVERT: X 109 ASP cc_start: 0.8235 (t70) cc_final: 0.7665 (m-30) REVERT: Y 55 MET cc_start: 0.8937 (tpt) cc_final: 0.8584 (tpt) REVERT: Z 64 ASN cc_start: 0.8964 (t0) cc_final: 0.8684 (t0) REVERT: Z 115 ILE cc_start: 0.9095 (mt) cc_final: 0.8727 (mm) REVERT: Z 120 LEU cc_start: 0.9190 (tp) cc_final: 0.7999 (tp) REVERT: Z 124 GLU cc_start: 0.7497 (pm20) cc_final: 0.6761 (pm20) REVERT: Z 196 THR cc_start: 0.9301 (p) cc_final: 0.8881 (t) REVERT: Z 264 TYR cc_start: 0.9258 (t80) cc_final: 0.8616 (t80) REVERT: Z 275 GLN cc_start: 0.8417 (mm110) cc_final: 0.8190 (mm-40) REVERT: a 5 LEU cc_start: 0.6789 (pt) cc_final: 0.6587 (pp) REVERT: a 44 GLU cc_start: 0.7724 (tt0) cc_final: 0.7506 (tt0) REVERT: a 74 ASN cc_start: 0.9026 (t0) cc_final: 0.8629 (p0) REVERT: a 84 ARG cc_start: 0.8676 (ttm110) cc_final: 0.8218 (ttm-80) REVERT: a 138 LYS cc_start: 0.9307 (mttt) cc_final: 0.8763 (mtmt) REVERT: a 151 GLN cc_start: 0.8942 (mm-40) cc_final: 0.8109 (mt0) outliers start: 6 outliers final: 0 residues processed: 1744 average time/residue: 0.1948 time to fit residues: 555.1207 Evaluate side-chains 1427 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1427 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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: 3.9990 chunk 309 optimal weight: 10.0000 chunk 232 optimal weight: 4.9990 chunk 284 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 391 optimal weight: 9.9990 chunk 174 optimal weight: 4.9990 chunk 333 optimal weight: 9.9990 chunk 314 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 179 optimal weight: 0.0030 overall best weight: 2.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 GLN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN G 139 ASN ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 ASN ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 HIS ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN O 73 GLN O 119 ASN ** P 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 57 GLN Q 139 ASN ** R 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 92 GLN Z 141 ASN ** Z 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.112513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.094399 restraints weight = 121278.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.098256 restraints weight = 59258.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.100770 restraints weight = 33746.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.102413 restraints weight = 21497.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.103565 restraints weight = 15025.012| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.5315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 36155 Z= 0.185 Angle : 0.772 43.108 49243 Z= 0.369 Chirality : 0.040 0.225 5448 Planarity : 0.005 0.064 6402 Dihedral : 10.858 88.998 6599 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.74 % Favored : 97.19 % Rotamer: Outliers : 0.06 % Allowed : 2.45 % Favored : 97.49 % 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 aren not related in a simple way. whole: 1.14 (0.13), residues: 4448 helix: 1.22 (0.09), residues: 3372 sheet: 1.72 (0.81), residues: 28 loop : -0.60 (0.22), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG T 86 TYR 0.043 0.002 TYR M 97 PHE 0.020 0.002 PHE a 139 TRP 0.014 0.001 TRP C 128 HIS 0.006 0.002 HIS Z 117 Details of bonding type rmsd covalent geometry : bond 0.00413 (36155) covalent geometry : angle 0.77208 (49243) hydrogen bonds : bond 0.04670 ( 2648) hydrogen bonds : angle 4.34508 ( 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 1638 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1636 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7399 (tpp) cc_final: 0.7167 (tpp) REVERT: A 15 GLN cc_start: 0.8291 (mt0) cc_final: 0.8081 (mt0) REVERT: A 18 PHE cc_start: 0.7931 (m-80) cc_final: 0.7303 (m-80) REVERT: A 38 MET cc_start: 0.8469 (mmt) cc_final: 0.7588 (tmm) REVERT: A 39 GLU cc_start: 0.8228 (tp30) cc_final: 0.7680 (mm-30) REVERT: A 49 GLN cc_start: 0.7959 (mp-120) cc_final: 0.6949 (mm-40) REVERT: A 62 LYS cc_start: 0.9192 (tptt) cc_final: 0.8906 (tptt) REVERT: A 63 PHE cc_start: 0.8824 (m-80) cc_final: 0.8254 (m-80) REVERT: A 90 TYR cc_start: 0.8924 (m-10) cc_final: 0.8512 (m-80) REVERT: A 109 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7634 (mt-10) REVERT: A 131 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7296 (tm-30) REVERT: A 167 ASP cc_start: 0.8362 (t0) cc_final: 0.7604 (t0) REVERT: A 171 ASN cc_start: 0.8614 (m-40) cc_final: 0.8374 (m-40) REVERT: B 35 ASN cc_start: 0.8603 (m-40) cc_final: 0.7782 (t0) REVERT: B 36 LYS cc_start: 0.9565 (mtmm) cc_final: 0.8653 (mppt) REVERT: B 88 MET cc_start: 0.6923 (tmm) cc_final: 0.6292 (tmm) REVERT: B 120 GLN cc_start: 0.7957 (mt0) cc_final: 0.7410 (tm-30) REVERT: C 17 ARG cc_start: 0.8666 (ptt90) cc_final: 0.8440 (ptt90) REVERT: C 69 MET cc_start: 0.7430 (ttm) cc_final: 0.7014 (ttm) REVERT: C 94 MET cc_start: 0.9440 (mmt) cc_final: 0.9004 (mmm) REVERT: C 109 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8077 (tp30) REVERT: C 117 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8642 (mm-30) REVERT: C 133 LEU cc_start: 0.8522 (mp) cc_final: 0.8221 (mp) REVERT: D 49 SER cc_start: 0.8693 (p) cc_final: 0.8467 (p) REVERT: D 88 MET cc_start: 0.8366 (ttm) cc_final: 0.7951 (mmm) REVERT: D 111 CYS cc_start: 0.7589 (t) cc_final: 0.7337 (t) REVERT: D 113 ASN cc_start: 0.8101 (t0) cc_final: 0.7783 (t0) REVERT: D 134 GLN cc_start: 0.8612 (mt0) cc_final: 0.8311 (mt0) REVERT: D 154 ASP cc_start: 0.6809 (t0) cc_final: 0.6336 (t0) REVERT: D 159 MET cc_start: 0.8589 (mmp) cc_final: 0.8346 (mmp) REVERT: D 162 ILE cc_start: 0.8793 (mm) cc_final: 0.8489 (mm) REVERT: E 7 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7605 (mm-30) REVERT: E 28 ASP cc_start: 0.8774 (t70) cc_final: 0.8425 (t0) REVERT: E 38 MET cc_start: 0.8274 (mmt) cc_final: 0.7890 (tmm) REVERT: E 47 ASN cc_start: 0.8191 (t0) cc_final: 0.7771 (t0) REVERT: E 69 MET cc_start: 0.8461 (mtp) cc_final: 0.7911 (ttm) REVERT: E 72 SER cc_start: 0.8964 (m) cc_final: 0.8531 (t) REVERT: E 73 GLN cc_start: 0.9032 (pm20) cc_final: 0.7743 (pm20) REVERT: E 83 LYS cc_start: 0.9194 (mmmm) cc_final: 0.8774 (mmmm) REVERT: E 121 THR cc_start: 0.9189 (p) cc_final: 0.8718 (t) REVERT: E 140 HIS cc_start: 0.8642 (p90) cc_final: 0.8156 (p-80) REVERT: E 167 ASP cc_start: 0.8339 (t0) cc_final: 0.7176 (t0) REVERT: E 171 ASN cc_start: 0.8705 (p0) cc_final: 0.8329 (p0) REVERT: E 173 LEU cc_start: 0.8911 (mm) cc_final: 0.8676 (mm) REVERT: F 11 GLN cc_start: 0.8963 (tt0) cc_final: 0.8538 (tt0) REVERT: F 25 ASP cc_start: 0.8854 (m-30) cc_final: 0.8561 (m-30) REVERT: F 60 PHE cc_start: 0.8374 (m-10) cc_final: 0.7827 (m-10) REVERT: F 81 MET cc_start: 0.9235 (tpp) cc_final: 0.8843 (tpt) REVERT: F 88 MET cc_start: 0.8507 (tpt) cc_final: 0.8136 (mmm) REVERT: F 136 MET cc_start: 0.8283 (ttt) cc_final: 0.8064 (ttt) REVERT: G 20 SER cc_start: 0.7861 (t) cc_final: 0.7086 (m) REVERT: G 25 GLN cc_start: 0.8755 (mt0) cc_final: 0.8197 (mt0) REVERT: G 61 GLN cc_start: 0.8604 (mt0) cc_final: 0.8319 (mp10) REVERT: G 62 LYS cc_start: 0.9041 (tptm) cc_final: 0.8764 (tppt) REVERT: G 97 TYR cc_start: 0.8988 (m-10) cc_final: 0.8743 (m-10) REVERT: G 98 CYS cc_start: 0.8464 (p) cc_final: 0.7958 (m) REVERT: G 107 MET cc_start: 0.8511 (tpp) cc_final: 0.7989 (tpp) REVERT: G 117 GLU cc_start: 0.7436 (tp30) cc_final: 0.6845 (tp30) REVERT: G 122 PHE cc_start: 0.8635 (m-80) cc_final: 0.8328 (m-10) REVERT: G 123 ASP cc_start: 0.8073 (t0) cc_final: 0.7801 (t0) REVERT: G 124 LEU cc_start: 0.9245 (mt) cc_final: 0.8528 (mp) REVERT: G 135 TYR cc_start: 0.8742 (t80) cc_final: 0.8274 (t80) REVERT: H 1 MET cc_start: 0.6446 (mpp) cc_final: 0.6229 (mpp) REVERT: H 88 MET cc_start: 0.7768 (mtm) cc_final: 0.7385 (mtm) REVERT: H 91 ILE cc_start: 0.9526 (mm) cc_final: 0.9140 (tp) REVERT: H 129 VAL cc_start: 0.9233 (t) cc_final: 0.8979 (t) REVERT: H 161 GLU cc_start: 0.7568 (pm20) cc_final: 0.7289 (pm20) REVERT: I 51 LEU cc_start: 0.8922 (mt) cc_final: 0.8694 (mt) REVERT: I 62 LYS cc_start: 0.9319 (tptm) cc_final: 0.8967 (tptt) REVERT: I 115 LEU cc_start: 0.8826 (tp) cc_final: 0.8241 (tt) REVERT: I 119 ASN cc_start: 0.8682 (m110) cc_final: 0.7651 (m110) REVERT: I 144 LEU cc_start: 0.8802 (mt) cc_final: 0.8199 (mt) REVERT: I 173 LEU cc_start: 0.9384 (mt) cc_final: 0.9098 (tt) REVERT: J 17 GLU cc_start: 0.8013 (mp0) cc_final: 0.7470 (mp0) REVERT: J 24 PHE cc_start: 0.6587 (m-80) cc_final: 0.6188 (m-80) REVERT: J 28 SER cc_start: 0.9337 (t) cc_final: 0.9093 (p) REVERT: J 35 ASN cc_start: 0.8762 (m110) cc_final: 0.7941 (t0) REVERT: J 50 THR cc_start: 0.9167 (m) cc_final: 0.8855 (t) REVERT: J 51 ILE cc_start: 0.8807 (mm) cc_final: 0.8595 (mm) REVERT: J 91 ILE cc_start: 0.9406 (tp) cc_final: 0.9135 (tt) REVERT: J 97 TYR cc_start: 0.8817 (m-10) cc_final: 0.8295 (m-10) REVERT: J 112 LEU cc_start: 0.9502 (mp) cc_final: 0.8979 (mm) REVERT: K 30 ARG cc_start: 0.8539 (tpt-90) cc_final: 0.8041 (tpt-90) REVERT: K 97 TYR cc_start: 0.8057 (m-10) cc_final: 0.7735 (m-80) REVERT: L 2 LEU cc_start: 0.9461 (mt) cc_final: 0.8747 (mt) REVERT: L 3 ASP cc_start: 0.8832 (p0) cc_final: 0.8620 (p0) REVERT: L 7 LYS cc_start: 0.8777 (ptmm) cc_final: 0.8562 (ptmm) REVERT: L 13 ASP cc_start: 0.8368 (t70) cc_final: 0.8031 (t0) REVERT: L 81 MET cc_start: 0.9066 (tpp) cc_final: 0.8376 (tpp) REVERT: L 88 MET cc_start: 0.8293 (mtm) cc_final: 0.7910 (mtp) REVERT: L 89 GLU cc_start: 0.8030 (pp20) cc_final: 0.7514 (tm-30) REVERT: L 103 ASP cc_start: 0.8025 (m-30) cc_final: 0.7799 (m-30) REVERT: L 116 ARG cc_start: 0.8167 (tpp80) cc_final: 0.7887 (tpp80) REVERT: L 120 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8440 (tm-30) REVERT: L 135 LYS cc_start: 0.8985 (mttp) cc_final: 0.8769 (mttp) REVERT: L 137 LYS cc_start: 0.9529 (tttt) cc_final: 0.8828 (ttmt) REVERT: L 146 ASP cc_start: 0.9205 (t0) cc_final: 0.8993 (t0) REVERT: L 159 MET cc_start: 0.9036 (mmt) cc_final: 0.8526 (mtp) REVERT: L 161 GLU cc_start: 0.8612 (tt0) cc_final: 0.7792 (tp30) REVERT: M 9 ILE cc_start: 0.9309 (tp) cc_final: 0.8582 (tp) REVERT: M 107 MET cc_start: 0.8043 (mmm) cc_final: 0.7547 (mmm) REVERT: M 115 LEU cc_start: 0.8897 (tt) cc_final: 0.8270 (tp) REVERT: M 118 ILE cc_start: 0.9633 (tp) cc_final: 0.9212 (tp) REVERT: M 129 TYR cc_start: 0.8180 (m-80) cc_final: 0.7872 (m-80) REVERT: M 171 ASN cc_start: 0.7862 (p0) cc_final: 0.7385 (p0) REVERT: N 45 THR cc_start: 0.8518 (t) cc_final: 0.8295 (t) REVERT: N 66 LEU cc_start: 0.8900 (mt) cc_final: 0.8660 (mt) REVERT: N 87 ASP cc_start: 0.8624 (m-30) cc_final: 0.8273 (m-30) REVERT: N 88 MET cc_start: 0.8737 (ttm) cc_final: 0.8098 (tpp) REVERT: N 97 TYR cc_start: 0.8545 (m-10) cc_final: 0.7889 (m-80) REVERT: N 103 ASP cc_start: 0.7199 (t0) cc_final: 0.6845 (t0) REVERT: N 136 MET cc_start: 0.8933 (mtm) cc_final: 0.7992 (mtm) REVERT: O 4 PRO cc_start: 0.8754 (Cg_exo) cc_final: 0.8393 (Cg_endo) REVERT: O 19 LEU cc_start: 0.8405 (mm) cc_final: 0.7534 (tp) REVERT: O 52 ILE cc_start: 0.8249 (pt) cc_final: 0.8042 (pt) REVERT: O 61 GLN cc_start: 0.7563 (mt0) cc_final: 0.7343 (mt0) REVERT: O 96 THR cc_start: 0.9365 (p) cc_final: 0.9136 (t) REVERT: O 104 THR cc_start: 0.8708 (p) cc_final: 0.7962 (p) REVERT: O 130 ILE cc_start: 0.9170 (mm) cc_final: 0.8329 (mt) REVERT: O 131 GLU cc_start: 0.8102 (tt0) cc_final: 0.7831 (tt0) REVERT: O 133 LEU cc_start: 0.9271 (mt) cc_final: 0.8866 (pp) REVERT: P 29 ASN cc_start: 0.8023 (t0) cc_final: 0.7582 (t0) REVERT: P 59 LEU cc_start: 0.8742 (tt) cc_final: 0.8305 (tt) REVERT: P 97 TYR cc_start: 0.8700 (m-10) cc_final: 0.8197 (m-10) REVERT: P 158 LEU cc_start: 0.9322 (mm) cc_final: 0.8719 (mm) REVERT: P 159 MET cc_start: 0.8825 (mmp) cc_final: 0.8521 (mmm) REVERT: Q 25 GLN cc_start: 0.8724 (mm-40) cc_final: 0.7996 (mm110) REVERT: Q 39 GLU cc_start: 0.7495 (mt-10) cc_final: 0.6732 (pt0) REVERT: Q 69 MET cc_start: 0.7097 (ptm) cc_final: 0.6330 (ptm) REVERT: Q 73 GLN cc_start: 0.8253 (pm20) cc_final: 0.7587 (pm20) REVERT: Q 94 MET cc_start: 0.5776 (tpp) cc_final: 0.5437 (tpp) REVERT: Q 108 ASP cc_start: 0.8760 (m-30) cc_final: 0.8319 (m-30) REVERT: R 38 LEU cc_start: 0.8676 (mt) cc_final: 0.8277 (mp) REVERT: R 85 LEU cc_start: 0.9621 (mt) cc_final: 0.9187 (tp) REVERT: R 111 CYS cc_start: 0.8256 (t) cc_final: 0.7774 (t) REVERT: R 118 THR cc_start: 0.8826 (p) cc_final: 0.8566 (p) REVERT: R 128 SER cc_start: 0.8725 (m) cc_final: 0.8359 (m) REVERT: R 134 GLN cc_start: 0.7842 (mm110) cc_final: 0.7287 (mm-40) REVERT: R 159 MET cc_start: 0.8234 (mmp) cc_final: 0.7436 (ptt) REVERT: R 160 SER cc_start: 0.9014 (t) cc_final: 0.8722 (p) REVERT: S 37 SER cc_start: 0.8632 (p) cc_final: 0.7768 (t) REVERT: S 49 GLN cc_start: 0.8552 (tp-100) cc_final: 0.7722 (pm20) REVERT: S 74 TYR cc_start: 0.8698 (m-80) cc_final: 0.7970 (m-80) REVERT: S 79 GLU cc_start: 0.7833 (mp0) cc_final: 0.7459 (tm-30) REVERT: S 90 TYR cc_start: 0.8445 (m-10) cc_final: 0.7925 (m-10) REVERT: S 94 MET cc_start: 0.9523 (mmt) cc_final: 0.8691 (mmm) REVERT: S 97 TYR cc_start: 0.9099 (m-80) cc_final: 0.8124 (m-80) REVERT: S 112 ILE cc_start: 0.9520 (mm) cc_final: 0.8917 (tp) REVERT: S 115 LEU cc_start: 0.8639 (tp) cc_final: 0.8349 (tp) REVERT: S 134 LYS cc_start: 0.9438 (mmpt) cc_final: 0.9217 (mmmm) REVERT: S 140 HIS cc_start: 0.6854 (p-80) cc_final: 0.6613 (p-80) REVERT: T 15 ARG cc_start: 0.7696 (mtp85) cc_final: 0.7116 (mmp80) REVERT: T 19 LEU cc_start: 0.8121 (mt) cc_final: 0.7510 (mm) REVERT: T 23 GLN cc_start: 0.8472 (mt0) cc_final: 0.7987 (mp10) REVERT: T 47 ASN cc_start: 0.7445 (t0) cc_final: 0.6248 (t0) REVERT: T 50 THR cc_start: 0.9242 (m) cc_final: 0.8997 (p) REVERT: U 28 ASP cc_start: 0.7443 (t0) cc_final: 0.7053 (t0) REVERT: U 63 PHE cc_start: 0.7805 (m-80) cc_final: 0.7566 (m-80) REVERT: U 109 GLU cc_start: 0.8481 (tm-30) cc_final: 0.7564 (tm-30) REVERT: U 115 LEU cc_start: 0.8510 (tp) cc_final: 0.8031 (tp) REVERT: U 119 ASN cc_start: 0.9074 (m110) cc_final: 0.8863 (m110) REVERT: U 123 ASP cc_start: 0.8519 (t0) cc_final: 0.8053 (t0) REVERT: U 137 LYS cc_start: 0.9598 (tttp) cc_final: 0.9178 (tptp) REVERT: U 171 ASN cc_start: 0.8844 (t0) cc_final: 0.8521 (t0) REVERT: U 174 SER cc_start: 0.7725 (t) cc_final: 0.7425 (t) REVERT: V 11 GLN cc_start: 0.8435 (tt0) cc_final: 0.7817 (tp40) REVERT: V 60 PHE cc_start: 0.8633 (m-80) cc_final: 0.8310 (m-80) REVERT: V 62 GLU cc_start: 0.7892 (pp20) cc_final: 0.7673 (pp20) REVERT: V 68 GLN cc_start: 0.8386 (pt0) cc_final: 0.7873 (pt0) REVERT: V 78 ASN cc_start: 0.6534 (t0) cc_final: 0.6250 (t0) REVERT: V 81 MET cc_start: 0.8564 (tpp) cc_final: 0.7827 (tpp) REVERT: V 103 ASP cc_start: 0.8163 (t70) cc_final: 0.7958 (p0) REVERT: V 113 ASN cc_start: 0.8989 (t0) cc_final: 0.8382 (t0) REVERT: V 124 THR cc_start: 0.8945 (m) cc_final: 0.8569 (p) REVERT: V 134 GLN cc_start: 0.8313 (mm110) cc_final: 0.8076 (mm110) REVERT: W 7 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8104 (mm-30) REVERT: W 24 LEU cc_start: 0.8854 (mt) cc_final: 0.8639 (mt) REVERT: W 42 ARG cc_start: 0.7561 (ttm170) cc_final: 0.6210 (tpt170) REVERT: W 111 LEU cc_start: 0.8190 (pt) cc_final: 0.7715 (pp) REVERT: W 163 ASN cc_start: 0.7503 (m-40) cc_final: 0.7228 (m-40) REVERT: X 3 ASP cc_start: 0.7770 (p0) cc_final: 0.7420 (p0) REVERT: X 32 LYS cc_start: 0.7887 (mmtp) cc_final: 0.7124 (mmmm) REVERT: X 44 ILE cc_start: 0.8099 (mm) cc_final: 0.7751 (tp) REVERT: X 52 VAL cc_start: 0.9236 (t) cc_final: 0.8859 (p) REVERT: X 86 ARG cc_start: 0.7616 (ttp80) cc_final: 0.7322 (ttp80) REVERT: X 88 MET cc_start: 0.8787 (ttm) cc_final: 0.8349 (ttt) REVERT: X 89 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8121 (tm-30) REVERT: X 109 ASP cc_start: 0.7897 (t70) cc_final: 0.7621 (t70) REVERT: Y 20 PHE cc_start: 0.8476 (m-10) cc_final: 0.8012 (m-10) REVERT: Y 23 GLU cc_start: 0.8053 (mp0) cc_final: 0.7825 (mp0) REVERT: Y 50 VAL cc_start: 0.9544 (t) cc_final: 0.9340 (p) REVERT: Z 47 ASP cc_start: 0.7804 (t0) cc_final: 0.7556 (t0) REVERT: Z 59 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7798 (pm20) REVERT: Z 120 LEU cc_start: 0.9294 (tp) cc_final: 0.8544 (tp) REVERT: Z 196 THR cc_start: 0.9084 (p) cc_final: 0.8605 (m) REVERT: Z 264 TYR cc_start: 0.9254 (t80) cc_final: 0.8493 (t80) REVERT: Z 275 GLN cc_start: 0.8489 (mm110) cc_final: 0.8225 (mm-40) REVERT: a 68 LEU cc_start: 0.8162 (mp) cc_final: 0.7564 (mp) REVERT: a 74 ASN cc_start: 0.9158 (t0) cc_final: 0.8840 (p0) REVERT: a 84 ARG cc_start: 0.8811 (ttm110) cc_final: 0.8095 (ttm-80) REVERT: a 119 TYR cc_start: 0.7448 (m-10) cc_final: 0.7179 (m-80) REVERT: a 134 ASP cc_start: 0.8619 (m-30) cc_final: 0.8069 (m-30) REVERT: a 138 LYS cc_start: 0.9341 (mttt) cc_final: 0.8833 (mtmt) REVERT: a 151 GLN cc_start: 0.9018 (mm-40) cc_final: 0.8138 (mt0) outliers start: 2 outliers final: 0 residues processed: 1638 average time/residue: 0.2113 time to fit residues: 565.0266 Evaluate side-chains 1370 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1369 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 96 optimal weight: 0.1980 chunk 253 optimal weight: 6.9990 chunk 310 optimal weight: 6.9990 chunk 312 optimal weight: 4.9990 chunk 431 optimal weight: 1.9990 chunk 198 optimal weight: 9.9990 chunk 429 optimal weight: 0.0980 chunk 348 optimal weight: 0.9980 chunk 165 optimal weight: 0.8980 chunk 227 optimal weight: 0.9980 chunk 334 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 GLN D 23 GLN ** D 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN H 78 ASN ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 147 GLN L 63 GLN M 140 HIS ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 119 ASN Q 139 ASN ** R 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 92 GLN ** Z 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.115825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.097801 restraints weight = 123181.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.101703 restraints weight = 59703.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.104212 restraints weight = 33839.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.105846 restraints weight = 21454.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.106969 restraints weight = 14960.257| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3406 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.5710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 36155 Z= 0.141 Angle : 0.751 42.900 49243 Z= 0.357 Chirality : 0.039 0.226 5448 Planarity : 0.005 0.058 6402 Dihedral : 10.772 88.559 6599 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.61 % Favored : 97.30 % Rotamer: Outliers : 0.06 % Allowed : 2.27 % Favored : 97.67 % 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 aren not related in a simple way. whole: 1.17 (0.13), residues: 4448 helix: 1.26 (0.09), residues: 3354 sheet: 1.53 (0.81), residues: 28 loop : -0.62 (0.21), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG T 86 TYR 0.035 0.002 TYR M 97 PHE 0.044 0.002 PHE T 166 TRP 0.010 0.001 TRP C 128 HIS 0.004 0.001 HIS E 140 Details of bonding type rmsd covalent geometry : bond 0.00311 (36155) covalent geometry : angle 0.75114 (49243) hydrogen bonds : bond 0.04296 ( 2648) hydrogen bonds : angle 4.22836 ( 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 1676 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1674 time to evaluate : 1.375 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: 0.8203 (mt0) cc_final: 0.7713 (mt0) REVERT: A 38 MET cc_start: 0.8525 (mmt) cc_final: 0.7634 (tmm) REVERT: A 63 PHE cc_start: 0.8990 (m-80) cc_final: 0.8295 (m-80) REVERT: A 90 TYR cc_start: 0.8867 (m-10) cc_final: 0.8424 (m-80) REVERT: A 109 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7687 (mt-10) REVERT: A 131 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7239 (tm-30) REVERT: A 167 ASP cc_start: 0.8389 (t0) cc_final: 0.7606 (t0) REVERT: B 25 ASP cc_start: 0.8211 (p0) cc_final: 0.7590 (p0) REVERT: B 35 ASN cc_start: 0.8528 (m-40) cc_final: 0.7590 (t0) REVERT: B 36 LYS cc_start: 0.9509 (mtmm) cc_final: 0.8437 (mppt) REVERT: B 120 GLN cc_start: 0.7909 (mt0) cc_final: 0.7420 (tm-30) REVERT: C 17 ARG cc_start: 0.8663 (ptt90) cc_final: 0.8145 (ptt90) REVERT: C 94 MET cc_start: 0.9393 (mmt) cc_final: 0.9056 (mmm) REVERT: C 117 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8641 (mm-30) REVERT: C 133 LEU cc_start: 0.8509 (mp) cc_final: 0.8302 (mp) REVERT: D 49 SER cc_start: 0.8751 (p) cc_final: 0.8438 (p) REVERT: D 97 TYR cc_start: 0.8399 (m-10) cc_final: 0.7323 (m-10) REVERT: D 113 ASN cc_start: 0.8101 (t0) cc_final: 0.7788 (t0) REVERT: D 128 SER cc_start: 0.9381 (p) cc_final: 0.9041 (m) REVERT: D 134 GLN cc_start: 0.8563 (mt0) cc_final: 0.8168 (mt0) REVERT: D 136 MET cc_start: 0.7801 (ttm) cc_final: 0.7506 (ttm) REVERT: D 154 ASP cc_start: 0.6673 (t0) cc_final: 0.6370 (t0) REVERT: D 162 ILE cc_start: 0.8777 (mm) cc_final: 0.8528 (mt) REVERT: E 7 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7791 (mm-30) REVERT: E 28 ASP cc_start: 0.8748 (t70) cc_final: 0.8344 (t0) REVERT: E 38 MET cc_start: 0.8282 (mmt) cc_final: 0.7997 (tmm) REVERT: E 69 MET cc_start: 0.8380 (mtp) cc_final: 0.7805 (ttm) REVERT: E 72 SER cc_start: 0.8813 (m) cc_final: 0.8218 (t) REVERT: E 83 LYS cc_start: 0.9187 (mmmm) cc_final: 0.8741 (mmmm) REVERT: E 94 MET cc_start: 0.8426 (tpp) cc_final: 0.7718 (ttm) REVERT: E 109 GLU cc_start: 0.8535 (tt0) cc_final: 0.8235 (tt0) REVERT: E 121 THR cc_start: 0.9181 (p) cc_final: 0.8676 (t) REVERT: E 140 HIS cc_start: 0.8461 (p90) cc_final: 0.7996 (p-80) REVERT: E 167 ASP cc_start: 0.8418 (t0) cc_final: 0.6936 (t0) REVERT: E 171 ASN cc_start: 0.8687 (p0) cc_final: 0.8280 (p0) REVERT: F 11 GLN cc_start: 0.9017 (tt0) cc_final: 0.8207 (tt0) REVERT: F 25 ASP cc_start: 0.8916 (m-30) cc_final: 0.8370 (m-30) REVERT: F 29 ASN cc_start: 0.9118 (m-40) cc_final: 0.8802 (m110) REVERT: F 62 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7584 (tm-30) REVERT: F 81 MET cc_start: 0.9136 (tpp) cc_final: 0.8763 (tpp) REVERT: G 20 SER cc_start: 0.7987 (t) cc_final: 0.6772 (m) REVERT: G 25 GLN cc_start: 0.8591 (mt0) cc_final: 0.8176 (mt0) REVERT: G 38 MET cc_start: 0.9304 (mtm) cc_final: 0.8488 (ttm) REVERT: G 62 LYS cc_start: 0.9039 (tptm) cc_final: 0.8769 (tppt) REVERT: G 97 TYR cc_start: 0.8918 (m-10) cc_final: 0.8706 (m-10) REVERT: G 98 CYS cc_start: 0.8535 (p) cc_final: 0.7860 (m) REVERT: G 122 PHE cc_start: 0.8638 (m-80) cc_final: 0.7989 (m-10) REVERT: G 124 LEU cc_start: 0.9229 (mt) cc_final: 0.8458 (mp) REVERT: G 135 TYR cc_start: 0.8737 (t80) cc_final: 0.8452 (t80) REVERT: G 137 LYS cc_start: 0.9267 (ttmt) cc_final: 0.8807 (ttpp) REVERT: H 3 ASP cc_start: 0.8414 (p0) cc_final: 0.8056 (p0) REVERT: H 17 GLU cc_start: 0.8410 (pm20) cc_final: 0.7484 (pm20) REVERT: H 81 MET cc_start: 0.8724 (mmm) cc_final: 0.8327 (tpp) REVERT: H 91 ILE cc_start: 0.9473 (mm) cc_final: 0.9097 (tp) REVERT: H 112 LEU cc_start: 0.9404 (mt) cc_final: 0.9096 (mt) REVERT: H 159 MET cc_start: 0.8221 (mmm) cc_final: 0.7361 (mmt) REVERT: I 51 LEU cc_start: 0.9108 (mt) cc_final: 0.8865 (mt) REVERT: I 62 LYS cc_start: 0.9299 (tptm) cc_final: 0.8916 (tptt) REVERT: I 115 LEU cc_start: 0.8885 (tp) cc_final: 0.8303 (tt) REVERT: I 119 ASN cc_start: 0.8666 (m110) cc_final: 0.7698 (m110) REVERT: I 127 SER cc_start: 0.9179 (p) cc_final: 0.8945 (p) REVERT: I 129 TYR cc_start: 0.8876 (m-10) cc_final: 0.8268 (m-10) REVERT: I 144 LEU cc_start: 0.8750 (mt) cc_final: 0.8273 (mt) REVERT: I 173 LEU cc_start: 0.9318 (mt) cc_final: 0.9102 (tt) REVERT: J 17 GLU cc_start: 0.8101 (mp0) cc_final: 0.7579 (mp0) REVERT: J 24 PHE cc_start: 0.6520 (m-80) cc_final: 0.6256 (m-80) REVERT: J 28 SER cc_start: 0.9355 (t) cc_final: 0.9079 (p) REVERT: J 35 ASN cc_start: 0.8774 (m110) cc_final: 0.8028 (t0) REVERT: J 88 MET cc_start: 0.8823 (mmt) cc_final: 0.8438 (mmm) REVERT: J 91 ILE cc_start: 0.9374 (tp) cc_final: 0.9160 (tt) REVERT: J 97 TYR cc_start: 0.8548 (m-10) cc_final: 0.8059 (m-10) REVERT: J 112 LEU cc_start: 0.9534 (mp) cc_final: 0.8909 (mm) REVERT: K 30 ARG cc_start: 0.8564 (tpt-90) cc_final: 0.8239 (tpt-90) REVERT: K 90 TYR cc_start: 0.8671 (m-10) cc_final: 0.8412 (m-80) REVERT: K 111 LEU cc_start: 0.9268 (tp) cc_final: 0.9010 (tp) REVERT: K 133 LEU cc_start: 0.8733 (mt) cc_final: 0.8472 (tp) REVERT: K 139 ASN cc_start: 0.8966 (t0) cc_final: 0.8306 (t0) REVERT: K 163 ASN cc_start: 0.9093 (m-40) cc_final: 0.8889 (m110) REVERT: L 2 LEU cc_start: 0.9307 (mt) cc_final: 0.8575 (mt) REVERT: L 3 ASP cc_start: 0.8802 (p0) cc_final: 0.8491 (p0) REVERT: L 81 MET cc_start: 0.8995 (tpp) cc_final: 0.8340 (tpp) REVERT: L 88 MET cc_start: 0.7638 (mtm) cc_final: 0.6967 (mtp) REVERT: L 89 GLU cc_start: 0.7667 (pp20) cc_final: 0.7412 (tm-30) REVERT: L 103 ASP cc_start: 0.8006 (m-30) cc_final: 0.7700 (m-30) REVERT: L 116 ARG cc_start: 0.8171 (tpp80) cc_final: 0.7906 (tpp80) REVERT: L 120 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8060 (tm-30) REVERT: L 137 LYS cc_start: 0.9476 (tttt) cc_final: 0.8752 (ttmt) REVERT: L 146 ASP cc_start: 0.9234 (t0) cc_final: 0.9005 (t0) REVERT: L 159 MET cc_start: 0.9018 (mmt) cc_final: 0.8722 (mtp) REVERT: L 161 GLU cc_start: 0.8717 (tt0) cc_final: 0.7825 (tp30) REVERT: M 9 ILE cc_start: 0.9169 (tp) cc_final: 0.8419 (tp) REVERT: M 57 GLN cc_start: 0.9463 (mm-40) cc_final: 0.9069 (mm-40) REVERT: M 107 MET cc_start: 0.8056 (mmm) cc_final: 0.7396 (mmm) REVERT: M 115 LEU cc_start: 0.8797 (tt) cc_final: 0.8316 (tp) REVERT: M 118 ILE cc_start: 0.9644 (tp) cc_final: 0.9035 (tp) REVERT: M 122 PHE cc_start: 0.9271 (m-80) cc_final: 0.8868 (m-10) REVERT: M 129 TYR cc_start: 0.8058 (m-80) cc_final: 0.7692 (m-80) REVERT: M 135 TYR cc_start: 0.9200 (t80) cc_final: 0.8859 (t80) REVERT: M 161 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8130 (mt-10) REVERT: M 171 ASN cc_start: 0.7578 (p0) cc_final: 0.7261 (p0) REVERT: N 17 GLU cc_start: 0.7546 (pm20) cc_final: 0.7222 (pm20) REVERT: N 20 THR cc_start: 0.7799 (t) cc_final: 0.7544 (p) REVERT: N 42 ASN cc_start: 0.9534 (t0) cc_final: 0.8946 (t0) REVERT: N 65 GLN cc_start: 0.7375 (pm20) cc_final: 0.7003 (pm20) REVERT: N 87 ASP cc_start: 0.8934 (m-30) cc_final: 0.8624 (m-30) REVERT: N 88 MET cc_start: 0.8354 (ttm) cc_final: 0.7725 (tpp) REVERT: N 89 GLU cc_start: 0.7858 (pp20) cc_final: 0.7328 (pp20) REVERT: N 97 TYR cc_start: 0.8363 (m-10) cc_final: 0.7811 (m-80) REVERT: N 103 ASP cc_start: 0.6969 (t0) cc_final: 0.6268 (t0) REVERT: N 118 THR cc_start: 0.9014 (p) cc_final: 0.8809 (t) REVERT: N 136 MET cc_start: 0.8825 (mtm) cc_final: 0.7741 (mtm) REVERT: O 19 LEU cc_start: 0.8422 (mm) cc_final: 0.7590 (tp) REVERT: O 60 TYR cc_start: 0.6044 (m-10) cc_final: 0.5730 (m-10) REVERT: O 61 GLN cc_start: 0.7598 (mt0) cc_final: 0.6907 (tm-30) REVERT: O 96 THR cc_start: 0.9393 (p) cc_final: 0.9144 (t) REVERT: O 98 CYS cc_start: 0.8316 (m) cc_final: 0.7336 (p) REVERT: O 104 THR cc_start: 0.8885 (p) cc_final: 0.8093 (p) REVERT: O 107 MET cc_start: 0.8412 (tpp) cc_final: 0.7974 (mmp) REVERT: O 131 GLU cc_start: 0.8197 (tt0) cc_final: 0.7872 (tt0) REVERT: O 163 ASN cc_start: 0.8542 (m-40) cc_final: 0.8195 (m110) REVERT: O 170 ILE cc_start: 0.9012 (tt) cc_final: 0.8690 (tp) REVERT: P 97 TYR cc_start: 0.8621 (m-10) cc_final: 0.8118 (m-80) REVERT: P 122 LEU cc_start: 0.8355 (mm) cc_final: 0.8102 (mm) REVERT: Q 25 GLN cc_start: 0.8920 (mm-40) cc_final: 0.8311 (mm-40) REVERT: Q 37 SER cc_start: 0.7485 (m) cc_final: 0.6706 (p) REVERT: Q 39 GLU cc_start: 0.7477 (mt-10) cc_final: 0.6726 (pt0) REVERT: Q 53 ASP cc_start: 0.6353 (m-30) cc_final: 0.6090 (m-30) REVERT: Q 62 LYS cc_start: 0.7599 (ttmm) cc_final: 0.7353 (ttmm) REVERT: Q 63 PHE cc_start: 0.7471 (m-10) cc_final: 0.7265 (m-10) REVERT: Q 69 MET cc_start: 0.7105 (ptm) cc_final: 0.6492 (ptm) REVERT: Q 73 GLN cc_start: 0.8375 (pm20) cc_final: 0.7905 (pt0) REVERT: Q 94 MET cc_start: 0.5393 (tpp) cc_final: 0.4968 (tpp) REVERT: Q 108 ASP cc_start: 0.8817 (m-30) cc_final: 0.8417 (m-30) REVERT: R 38 LEU cc_start: 0.8552 (mt) cc_final: 0.8129 (mp) REVERT: R 85 LEU cc_start: 0.9654 (mt) cc_final: 0.9159 (tp) REVERT: R 111 CYS cc_start: 0.8169 (t) cc_final: 0.7716 (t) REVERT: R 118 THR cc_start: 0.8935 (p) cc_final: 0.7513 (p) REVERT: R 124 THR cc_start: 0.7498 (p) cc_final: 0.7293 (p) REVERT: R 128 SER cc_start: 0.8715 (m) cc_final: 0.8381 (m) REVERT: R 160 SER cc_start: 0.9013 (t) cc_final: 0.8509 (p) REVERT: R 161 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7651 (mm-30) REVERT: S 37 SER cc_start: 0.8501 (p) cc_final: 0.8074 (p) REVERT: S 49 GLN cc_start: 0.8326 (tp-100) cc_final: 0.7758 (pm20) REVERT: S 74 TYR cc_start: 0.8696 (m-80) cc_final: 0.8019 (m-10) REVERT: S 79 GLU cc_start: 0.7851 (mp0) cc_final: 0.7484 (tm-30) REVERT: S 93 ARG cc_start: 0.7795 (ttp80) cc_final: 0.6625 (ttp80) REVERT: S 97 TYR cc_start: 0.9006 (m-80) cc_final: 0.8164 (m-80) REVERT: S 112 ILE cc_start: 0.9498 (mm) cc_final: 0.8907 (tp) REVERT: S 115 LEU cc_start: 0.8614 (tp) cc_final: 0.8301 (tp) REVERT: S 134 LYS cc_start: 0.9467 (mmpt) cc_final: 0.9069 (mmmm) REVERT: S 163 ASN cc_start: 0.9365 (m110) cc_final: 0.9082 (m-40) REVERT: T 19 LEU cc_start: 0.8114 (mt) cc_final: 0.7612 (mm) REVERT: T 23 GLN cc_start: 0.8358 (mt0) cc_final: 0.8090 (mp10) REVERT: T 47 ASN cc_start: 0.7722 (t0) cc_final: 0.6108 (t0) REVERT: T 50 THR cc_start: 0.9221 (m) cc_final: 0.8861 (p) REVERT: T 66 LEU cc_start: 0.7453 (pt) cc_final: 0.7013 (pp) REVERT: T 162 ILE cc_start: 0.8883 (mt) cc_final: 0.8630 (mm) REVERT: T 165 TYR cc_start: 0.8445 (m-80) cc_final: 0.7856 (m-80) REVERT: U 23 GLU cc_start: 0.8710 (pm20) cc_final: 0.8510 (pm20) REVERT: U 28 ASP cc_start: 0.7460 (t0) cc_final: 0.7156 (t0) REVERT: U 32 LYS cc_start: 0.9274 (tmmt) cc_final: 0.9033 (tmmt) REVERT: U 63 PHE cc_start: 0.7937 (m-80) cc_final: 0.7576 (m-80) REVERT: U 98 CYS cc_start: 0.8059 (t) cc_final: 0.7534 (t) REVERT: U 109 GLU cc_start: 0.8402 (tm-30) cc_final: 0.7441 (tm-30) REVERT: U 115 LEU cc_start: 0.8359 (tp) cc_final: 0.7936 (tp) REVERT: U 119 ASN cc_start: 0.9117 (m110) cc_final: 0.8889 (m110) REVERT: U 123 ASP cc_start: 0.8139 (t0) cc_final: 0.7717 (t70) REVERT: U 137 LYS cc_start: 0.9449 (tttp) cc_final: 0.9016 (tptp) REVERT: U 171 ASN cc_start: 0.8913 (t0) cc_final: 0.8592 (t0) REVERT: U 174 SER cc_start: 0.7652 (t) cc_final: 0.7346 (t) REVERT: V 29 ASN cc_start: 0.8316 (m-40) cc_final: 0.8066 (t0) REVERT: V 35 ASN cc_start: 0.8379 (m110) cc_final: 0.8062 (t0) REVERT: V 60 PHE cc_start: 0.8842 (m-80) cc_final: 0.8397 (m-80) REVERT: V 62 GLU cc_start: 0.7651 (pp20) cc_final: 0.7346 (pp20) REVERT: V 68 GLN cc_start: 0.8290 (pt0) cc_final: 0.7759 (pt0) REVERT: V 78 ASN cc_start: 0.6283 (t0) cc_final: 0.6015 (t0) REVERT: V 81 MET cc_start: 0.8534 (tpp) cc_final: 0.7847 (tpp) REVERT: V 90 ILE cc_start: 0.9458 (mm) cc_final: 0.9236 (mm) REVERT: V 103 ASP cc_start: 0.8102 (t70) cc_final: 0.7842 (p0) REVERT: V 113 ASN cc_start: 0.9144 (t0) cc_final: 0.8298 (t0) REVERT: V 124 THR cc_start: 0.9007 (m) cc_final: 0.8734 (p) REVERT: V 134 GLN cc_start: 0.8432 (mm110) cc_final: 0.8185 (mm110) REVERT: V 162 ILE cc_start: 0.8562 (mt) cc_final: 0.8260 (mt) REVERT: W 42 ARG cc_start: 0.7352 (ttm170) cc_final: 0.6036 (tpt170) REVERT: W 61 GLN cc_start: 0.8325 (mm110) cc_final: 0.8115 (mm-40) REVERT: W 69 MET cc_start: 0.3845 (mmm) cc_final: 0.3424 (tpt) REVERT: W 94 MET cc_start: 0.8147 (ptt) cc_final: 0.7883 (ppp) REVERT: W 111 LEU cc_start: 0.8451 (pt) cc_final: 0.8010 (pp) REVERT: W 165 TYR cc_start: 0.7843 (m-80) cc_final: 0.7612 (m-80) REVERT: X 3 ASP cc_start: 0.7823 (p0) cc_final: 0.7483 (p0) REVERT: X 44 ILE cc_start: 0.8143 (mm) cc_final: 0.7762 (tp) REVERT: X 52 VAL cc_start: 0.9279 (t) cc_final: 0.8995 (p) REVERT: X 88 MET cc_start: 0.8853 (ttm) cc_final: 0.8411 (ttt) REVERT: X 89 GLU cc_start: 0.8352 (tm-30) cc_final: 0.8057 (tm-30) REVERT: Y 20 PHE cc_start: 0.8415 (m-10) cc_final: 0.7908 (m-10) REVERT: Y 23 GLU cc_start: 0.7819 (mp0) cc_final: 0.7352 (mp0) REVERT: Y 33 THR cc_start: 0.9110 (p) cc_final: 0.8747 (t) REVERT: Y 50 VAL cc_start: 0.9478 (t) cc_final: 0.9257 (p) REVERT: Y 55 MET cc_start: 0.8622 (tpt) cc_final: 0.8362 (tpt) REVERT: Z 59 GLU cc_start: 0.8458 (pm20) cc_final: 0.7919 (pm20) REVERT: Z 120 LEU cc_start: 0.9417 (tp) cc_final: 0.8840 (tp) REVERT: Z 196 THR cc_start: 0.9069 (p) cc_final: 0.8538 (m) REVERT: Z 272 GLN cc_start: 0.8353 (mm-40) cc_final: 0.8103 (mm-40) REVERT: a 51 ARG cc_start: 0.8876 (ttp80) cc_final: 0.8415 (mtp-110) REVERT: a 68 LEU cc_start: 0.8181 (mp) cc_final: 0.7657 (mp) REVERT: a 74 ASN cc_start: 0.9113 (t0) cc_final: 0.8639 (p0) REVERT: a 84 ARG cc_start: 0.8935 (ttm110) cc_final: 0.8563 (ttm110) REVERT: a 98 GLU cc_start: 0.8156 (pt0) cc_final: 0.7558 (pt0) outliers start: 2 outliers final: 1 residues processed: 1675 average time/residue: 0.2286 time to fit residues: 623.7835 Evaluate side-chains 1384 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1383 time to evaluate : 1.382 ------------------------------------------------------------------------------- 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: 3.9990 chunk 210 optimal weight: 2.9990 chunk 276 optimal weight: 6.9990 chunk 314 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 325 optimal weight: 10.0000 chunk 406 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 268 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 ASN D 23 GLN D 29 ASN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 ASN H 47 ASN ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 ASN ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 HIS N 47 ASN ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 139 ASN ** R 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 139 ASN ** S 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 ASN V 68 GLN ** V 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 23 GLN Z 64 ASN ** Z 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 156 ASN a 161 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.110034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.093918 restraints weight = 90040.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.096994 restraints weight = 47545.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.098994 restraints weight = 28670.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.100430 restraints weight = 19257.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.101375 restraints weight = 13859.351| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3308 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3308 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.5874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 36155 Z= 0.253 Angle : 0.846 43.072 49243 Z= 0.413 Chirality : 0.043 0.254 5448 Planarity : 0.006 0.075 6402 Dihedral : 10.961 88.741 6599 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.24 % Favored : 96.67 % Rotamer: Outliers : 0.03 % Allowed : 2.24 % Favored : 97.73 % 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 aren not related in a simple way. whole: 0.86 (0.12), residues: 4448 helix: 1.01 (0.08), residues: 3394 sheet: 0.98 (0.76), residues: 28 loop : -0.71 (0.22), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 33 TYR 0.046 0.003 TYR R 97 PHE 0.023 0.003 PHE P 60 TRP 0.007 0.001 TRP C 128 HIS 0.004 0.002 HIS I 140 Details of bonding type rmsd covalent geometry : bond 0.00558 (36155) covalent geometry : angle 0.84554 (49243) hydrogen bonds : bond 0.04882 ( 2648) hydrogen bonds : angle 4.56320 ( 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 1550 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1549 time to evaluate : 1.493 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 2 LYS cc_start: 0.7835 (ttpt) cc_final: 0.6803 (ttpt) REVERT: A 15 GLN cc_start: 0.8363 (mt0) cc_final: 0.7496 (mm110) REVERT: A 90 TYR cc_start: 0.8528 (m-10) cc_final: 0.7980 (m-80) REVERT: A 109 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7625 (mt-10) REVERT: A 131 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7381 (tm-30) REVERT: A 167 ASP cc_start: 0.8292 (t0) cc_final: 0.7652 (t0) REVERT: B 35 ASN cc_start: 0.8767 (m-40) cc_final: 0.7706 (t0) REVERT: B 36 LYS cc_start: 0.9526 (mtmm) cc_final: 0.8580 (mppt) REVERT: B 37 ARG cc_start: 0.9069 (ttm170) cc_final: 0.8836 (tpp80) REVERT: B 59 LEU cc_start: 0.8823 (mm) cc_final: 0.8620 (tt) REVERT: B 120 GLN cc_start: 0.8034 (mt0) cc_final: 0.7500 (tm-30) REVERT: B 122 LEU cc_start: 0.9220 (mm) cc_final: 0.8853 (mm) REVERT: C 17 ARG cc_start: 0.8798 (ptt90) cc_final: 0.8553 (ptt90) REVERT: C 51 LEU cc_start: 0.8612 (mp) cc_final: 0.8251 (tp) REVERT: C 69 MET cc_start: 0.7637 (ttm) cc_final: 0.7200 (ttm) REVERT: C 74 TYR cc_start: 0.7173 (m-80) cc_final: 0.6787 (m-80) REVERT: C 94 MET cc_start: 0.9321 (mmt) cc_final: 0.8919 (mmm) REVERT: C 115 LEU cc_start: 0.8074 (pp) cc_final: 0.7551 (pp) REVERT: C 131 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8253 (tp30) REVERT: C 133 LEU cc_start: 0.8515 (mp) cc_final: 0.8263 (mm) REVERT: D 49 SER cc_start: 0.8809 (p) cc_final: 0.8580 (p) REVERT: D 113 ASN cc_start: 0.7645 (t0) cc_final: 0.7426 (t0) REVERT: D 120 GLN cc_start: 0.8007 (tp40) cc_final: 0.7780 (tm-30) REVERT: D 128 SER cc_start: 0.9509 (p) cc_final: 0.8882 (m) REVERT: D 134 GLN cc_start: 0.8679 (mt0) cc_final: 0.8441 (mt0) REVERT: D 146 ASP cc_start: 0.9166 (t0) cc_final: 0.8891 (t0) REVERT: D 154 ASP cc_start: 0.6832 (t0) cc_final: 0.6363 (t0) REVERT: E 1 MET cc_start: 0.8171 (mpp) cc_final: 0.7482 (mpp) REVERT: E 7 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7821 (mm-30) REVERT: E 38 MET cc_start: 0.8223 (mmt) cc_final: 0.7778 (tmm) REVERT: E 47 ASN cc_start: 0.8632 (m110) cc_final: 0.7918 (m110) REVERT: E 69 MET cc_start: 0.8389 (mtp) cc_final: 0.8122 (ttm) REVERT: E 72 SER cc_start: 0.9097 (m) cc_final: 0.8682 (t) REVERT: E 83 LYS cc_start: 0.9202 (mmmm) cc_final: 0.8961 (mmmm) REVERT: E 163 ASN cc_start: 0.9089 (m-40) cc_final: 0.8814 (m-40) REVERT: E 167 ASP cc_start: 0.8495 (t0) cc_final: 0.7283 (t0) REVERT: E 171 ASN cc_start: 0.8858 (p0) cc_final: 0.8466 (p0) REVERT: F 1 MET cc_start: 0.6786 (pmm) cc_final: 0.6521 (pmm) REVERT: F 11 GLN cc_start: 0.9121 (tt0) cc_final: 0.8420 (tt0) REVERT: F 25 ASP cc_start: 0.8719 (m-30) cc_final: 0.8252 (m-30) REVERT: F 29 ASN cc_start: 0.9026 (m-40) cc_final: 0.8791 (m110) REVERT: F 68 GLN cc_start: 0.8516 (tp-100) cc_final: 0.8315 (mm-40) REVERT: F 81 MET cc_start: 0.9185 (tpp) cc_final: 0.8879 (tpt) REVERT: F 117 GLU cc_start: 0.8784 (pp20) cc_final: 0.8429 (pp20) REVERT: F 146 ASP cc_start: 0.8274 (t70) cc_final: 0.7908 (t0) REVERT: F 161 GLU cc_start: 0.8247 (tp30) cc_final: 0.7939 (tp30) REVERT: F 162 ILE cc_start: 0.9339 (mt) cc_final: 0.9093 (mm) REVERT: G 1 MET cc_start: 0.8070 (tpp) cc_final: 0.7725 (tpp) REVERT: G 25 GLN cc_start: 0.8545 (mt0) cc_final: 0.8318 (mt0) REVERT: G 62 LYS cc_start: 0.9065 (tptm) cc_final: 0.8800 (tppt) REVERT: G 95 VAL cc_start: 0.9416 (t) cc_final: 0.9099 (t) REVERT: G 97 TYR cc_start: 0.8944 (m-10) cc_final: 0.8644 (m-10) REVERT: G 123 ASP cc_start: 0.8309 (t0) cc_final: 0.7964 (t0) REVERT: G 124 LEU cc_start: 0.9301 (mt) cc_final: 0.8699 (mt) REVERT: G 133 LEU cc_start: 0.9482 (mm) cc_final: 0.9253 (mm) REVERT: G 135 TYR cc_start: 0.8691 (t80) cc_final: 0.8448 (t80) REVERT: G 173 LEU cc_start: 0.8568 (mm) cc_final: 0.8338 (tp) REVERT: H 38 LEU cc_start: 0.9090 (mt) cc_final: 0.8546 (tt) REVERT: H 88 MET cc_start: 0.7612 (mtm) cc_final: 0.7361 (mtm) REVERT: H 91 ILE cc_start: 0.9523 (mm) cc_final: 0.9125 (tp) REVERT: H 145 ASN cc_start: 0.8148 (m-40) cc_final: 0.7368 (m-40) REVERT: H 159 MET cc_start: 0.8333 (mmm) cc_final: 0.7968 (mmt) REVERT: I 62 LYS cc_start: 0.9323 (tptm) cc_final: 0.8909 (tptt) REVERT: I 73 GLN cc_start: 0.9351 (pm20) cc_final: 0.8905 (pm20) REVERT: I 115 LEU cc_start: 0.8895 (tp) cc_final: 0.7962 (tp) REVERT: I 119 ASN cc_start: 0.8560 (m110) cc_final: 0.7901 (m110) REVERT: J 17 GLU cc_start: 0.8298 (mp0) cc_final: 0.7745 (mp0) REVERT: J 35 ASN cc_start: 0.8787 (m110) cc_final: 0.7994 (t0) REVERT: J 91 ILE cc_start: 0.9445 (tp) cc_final: 0.9186 (tt) REVERT: J 107 LEU cc_start: 0.9216 (tp) cc_final: 0.8843 (tt) REVERT: J 112 LEU cc_start: 0.9544 (mp) cc_final: 0.9081 (mm) REVERT: K 2 LYS cc_start: 0.7565 (tmtt) cc_final: 0.7209 (tttm) REVERT: K 30 ARG cc_start: 0.8683 (tpt-90) cc_final: 0.8065 (tpt-90) REVERT: K 69 MET cc_start: 0.7133 (tpt) cc_final: 0.6597 (mtp) REVERT: K 94 MET cc_start: 0.8767 (mmt) cc_final: 0.8379 (mmt) REVERT: K 130 ILE cc_start: 0.9266 (pt) cc_final: 0.8897 (pt) REVERT: K 139 ASN cc_start: 0.9023 (t0) cc_final: 0.8523 (t0) REVERT: K 163 ASN cc_start: 0.9460 (m-40) cc_final: 0.9205 (m110) REVERT: L 2 LEU cc_start: 0.9481 (mt) cc_final: 0.8666 (mt) REVERT: L 3 ASP cc_start: 0.8827 (p0) cc_final: 0.8569 (p0) REVERT: L 7 LYS cc_start: 0.8927 (ptmm) cc_final: 0.8680 (ptmm) REVERT: L 62 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7879 (tm-30) REVERT: L 63 GLN cc_start: 0.8504 (tt0) cc_final: 0.8296 (tt0) REVERT: L 81 MET cc_start: 0.8919 (tpp) cc_final: 0.8170 (tpp) REVERT: L 88 MET cc_start: 0.8010 (mtm) cc_final: 0.7733 (mtp) REVERT: L 89 GLU cc_start: 0.7974 (pp20) cc_final: 0.7591 (tm-30) REVERT: L 120 GLN cc_start: 0.8893 (tm-30) cc_final: 0.8251 (tm-30) REVERT: L 137 LYS cc_start: 0.9567 (tttt) cc_final: 0.9323 (tttt) REVERT: L 146 ASP cc_start: 0.9252 (t0) cc_final: 0.8984 (t0) REVERT: L 161 GLU cc_start: 0.8703 (tt0) cc_final: 0.7761 (tp30) REVERT: M 57 GLN cc_start: 0.9291 (mm-40) cc_final: 0.9014 (mm-40) REVERT: M 115 LEU cc_start: 0.8966 (tt) cc_final: 0.8336 (tt) REVERT: M 118 ILE cc_start: 0.9693 (tp) cc_final: 0.9241 (tp) REVERT: M 122 PHE cc_start: 0.9371 (m-80) cc_final: 0.9145 (m-10) REVERT: M 129 TYR cc_start: 0.8361 (m-80) cc_final: 0.7709 (m-10) REVERT: M 171 ASN cc_start: 0.7620 (p0) cc_final: 0.7357 (p0) REVERT: N 67 ILE cc_start: 0.9614 (pt) cc_final: 0.9164 (tp) REVERT: N 80 ARG cc_start: 0.9010 (mtm-85) cc_final: 0.8393 (mtm-85) REVERT: N 87 ASP cc_start: 0.8628 (m-30) cc_final: 0.8256 (m-30) REVERT: N 88 MET cc_start: 0.8935 (ttm) cc_final: 0.8081 (tpp) REVERT: N 97 TYR cc_start: 0.8561 (m-10) cc_final: 0.7942 (m-80) REVERT: N 103 ASP cc_start: 0.7349 (t0) cc_final: 0.6971 (t0) REVERT: N 117 GLU cc_start: 0.7599 (pt0) cc_final: 0.7376 (pt0) REVERT: N 136 MET cc_start: 0.8704 (mtm) cc_final: 0.7894 (mtm) REVERT: N 173 VAL cc_start: 0.6279 (p) cc_final: 0.5722 (t) REVERT: O 19 LEU cc_start: 0.8222 (mm) cc_final: 0.7485 (tp) REVERT: O 60 TYR cc_start: 0.6169 (m-10) cc_final: 0.5922 (m-10) REVERT: O 61 GLN cc_start: 0.7686 (mt0) cc_final: 0.6859 (tm-30) REVERT: O 96 THR cc_start: 0.9414 (p) cc_final: 0.9152 (t) REVERT: O 104 THR cc_start: 0.8743 (p) cc_final: 0.8123 (p) REVERT: P 2 LEU cc_start: 0.9067 (mp) cc_final: 0.8416 (mp) REVERT: P 97 TYR cc_start: 0.8788 (m-10) cc_final: 0.8030 (m-80) REVERT: P 122 LEU cc_start: 0.8519 (mm) cc_final: 0.8020 (mm) REVERT: P 134 GLN cc_start: 0.8584 (mm110) cc_final: 0.8283 (mp10) REVERT: Q 25 GLN cc_start: 0.9020 (mm-40) cc_final: 0.8386 (mm110) REVERT: Q 39 GLU cc_start: 0.7625 (mt-10) cc_final: 0.6730 (pt0) REVERT: Q 62 LYS cc_start: 0.7872 (ttmm) cc_final: 0.7620 (ttmm) REVERT: Q 74 TYR cc_start: 0.7801 (m-80) cc_final: 0.7400 (m-80) REVERT: Q 94 MET cc_start: 0.5467 (tpp) cc_final: 0.5007 (tpp) REVERT: Q 108 ASP cc_start: 0.8728 (m-30) cc_final: 0.8506 (m-30) REVERT: R 1 MET cc_start: 0.7216 (ttm) cc_final: 0.6762 (ttp) REVERT: R 85 LEU cc_start: 0.9626 (mt) cc_final: 0.9181 (tp) REVERT: R 111 CYS cc_start: 0.8501 (t) cc_final: 0.7985 (t) REVERT: R 118 THR cc_start: 0.8969 (p) cc_final: 0.7633 (p) REVERT: R 128 SER cc_start: 0.8914 (m) cc_final: 0.8591 (m) REVERT: R 136 MET cc_start: 0.8582 (tmm) cc_final: 0.8029 (tmm) REVERT: R 141 ILE cc_start: 0.8452 (mm) cc_final: 0.7842 (pt) REVERT: R 161 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7670 (mm-30) REVERT: S 49 GLN cc_start: 0.8292 (tp-100) cc_final: 0.7486 (pm20) REVERT: S 63 PHE cc_start: 0.8255 (m-10) cc_final: 0.7816 (m-10) REVERT: S 74 TYR cc_start: 0.8879 (m-80) cc_final: 0.7815 (m-80) REVERT: S 79 GLU cc_start: 0.7904 (mp0) cc_final: 0.7477 (tm-30) REVERT: S 94 MET cc_start: 0.9486 (mmt) cc_final: 0.8690 (mmm) REVERT: S 97 TYR cc_start: 0.8966 (m-10) cc_final: 0.8261 (m-80) REVERT: S 99 LEU cc_start: 0.8470 (tp) cc_final: 0.7636 (tp) REVERT: S 112 ILE cc_start: 0.9480 (mm) cc_final: 0.8990 (tp) REVERT: S 115 LEU cc_start: 0.8706 (tp) cc_final: 0.8405 (tp) REVERT: S 134 LYS cc_start: 0.9626 (mmpt) cc_final: 0.9203 (mmmm) REVERT: S 139 ASN cc_start: 0.8889 (OUTLIER) cc_final: 0.8516 (t0) REVERT: T 1 MET cc_start: 0.7750 (mmp) cc_final: 0.7459 (mmp) REVERT: T 15 ARG cc_start: 0.7875 (mtp85) cc_final: 0.7255 (mmp80) REVERT: T 19 LEU cc_start: 0.8111 (mt) cc_final: 0.7464 (mm) REVERT: T 23 GLN cc_start: 0.7976 (mt0) cc_final: 0.7771 (mp10) REVERT: T 47 ASN cc_start: 0.7896 (t0) cc_final: 0.6263 (t0) REVERT: T 62 GLU cc_start: 0.8128 (pt0) cc_final: 0.7919 (pp20) REVERT: T 104 SER cc_start: 0.9124 (p) cc_final: 0.8756 (p) REVERT: T 156 SER cc_start: 0.8594 (m) cc_final: 0.8270 (m) REVERT: T 159 MET cc_start: 0.7975 (mpp) cc_final: 0.7292 (mpp) REVERT: T 162 ILE cc_start: 0.8768 (mt) cc_final: 0.8471 (mt) REVERT: T 165 TYR cc_start: 0.8637 (m-80) cc_final: 0.7812 (m-80) REVERT: U 28 ASP cc_start: 0.7074 (t0) cc_final: 0.6825 (t0) REVERT: U 98 CYS cc_start: 0.8256 (t) cc_final: 0.7773 (t) REVERT: U 109 GLU cc_start: 0.8608 (tm-30) cc_final: 0.7861 (tm-30) REVERT: U 115 LEU cc_start: 0.8546 (tp) cc_final: 0.8106 (tp) REVERT: U 119 ASN cc_start: 0.9208 (m110) cc_final: 0.8938 (m110) REVERT: U 123 ASP cc_start: 0.8292 (t0) cc_final: 0.7928 (t70) REVERT: U 134 LYS cc_start: 0.9163 (tppp) cc_final: 0.8808 (tppt) REVERT: U 171 ASN cc_start: 0.8881 (t0) cc_final: 0.8589 (t0) REVERT: U 174 SER cc_start: 0.7934 (t) cc_final: 0.7591 (t) REVERT: V 11 GLN cc_start: 0.8206 (tt0) cc_final: 0.7814 (tp40) REVERT: V 25 ASP cc_start: 0.8085 (p0) cc_final: 0.7801 (p0) REVERT: V 68 GLN cc_start: 0.8302 (pt0) cc_final: 0.7671 (pt0) REVERT: V 81 MET cc_start: 0.8489 (tpp) cc_final: 0.8077 (tpp) REVERT: V 117 GLU cc_start: 0.8502 (mm-30) cc_final: 0.7902 (mm-30) REVERT: V 124 THR cc_start: 0.8956 (m) cc_final: 0.8655 (p) REVERT: V 162 ILE cc_start: 0.8570 (mt) cc_final: 0.8356 (mt) REVERT: W 24 LEU cc_start: 0.9049 (mt) cc_final: 0.8834 (mt) REVERT: W 42 ARG cc_start: 0.7972 (ttm170) cc_final: 0.6630 (tpt170) REVERT: W 69 MET cc_start: 0.4223 (mmm) cc_final: 0.3682 (tpt) REVERT: W 94 MET cc_start: 0.8322 (ptt) cc_final: 0.7943 (ppp) REVERT: W 111 LEU cc_start: 0.8496 (pt) cc_final: 0.7885 (pp) REVERT: X 3 ASP cc_start: 0.7832 (p0) cc_final: 0.7378 (p0) REVERT: X 44 ILE cc_start: 0.8174 (mm) cc_final: 0.7878 (tp) REVERT: X 52 VAL cc_start: 0.9371 (t) cc_final: 0.9027 (p) REVERT: X 88 MET cc_start: 0.8681 (ttm) cc_final: 0.8124 (ttt) REVERT: X 89 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8071 (tm-30) REVERT: X 117 GLU cc_start: 0.7853 (pm20) cc_final: 0.7485 (pm20) REVERT: X 119 TYR cc_start: 0.7884 (m-80) cc_final: 0.7533 (m-80) REVERT: X 133 ILE cc_start: 0.8898 (mm) cc_final: 0.8015 (tp) REVERT: Y 20 PHE cc_start: 0.8579 (m-10) cc_final: 0.8005 (m-10) REVERT: Z 42 GLN cc_start: 0.8872 (tp-100) cc_final: 0.7830 (tm-30) REVERT: Z 59 GLU cc_start: 0.8468 (pm20) cc_final: 0.7903 (pm20) REVERT: Z 101 LYS cc_start: 0.9162 (tmmt) cc_final: 0.8914 (tmmt) REVERT: Z 103 LEU cc_start: 0.9002 (mt) cc_final: 0.8652 (mt) REVERT: Z 196 THR cc_start: 0.9142 (p) cc_final: 0.8726 (m) REVERT: a 69 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7963 (mt-10) REVERT: a 84 ARG cc_start: 0.9024 (ttm110) cc_final: 0.8181 (ttm-80) REVERT: a 98 GLU cc_start: 0.8313 (pt0) cc_final: 0.7879 (pt0) REVERT: a 151 GLN cc_start: 0.8898 (mm-40) cc_final: 0.8039 (mt0) REVERT: a 156 ASN cc_start: 0.8470 (m-40) cc_final: 0.8180 (m-40) REVERT: a 170 PHE cc_start: 0.8428 (m-80) cc_final: 0.7758 (m-80) outliers start: 1 outliers final: 0 residues processed: 1550 average time/residue: 0.2253 time to fit residues: 571.4269 Evaluate side-chains 1284 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1283 time to evaluate : 1.379 ------------------------------------------------------------------------------- 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: 6.9990 chunk 43 optimal weight: 3.9990 chunk 437 optimal weight: 0.8980 chunk 152 optimal weight: 9.9990 chunk 174 optimal weight: 0.8980 chunk 407 optimal weight: 8.9990 chunk 177 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 287 optimal weight: 6.9990 chunk 14 optimal weight: 0.5980 chunk 199 optimal weight: 7.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 GLN C 119 ASN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 GLN ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 ASN ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 78 ASN ** K 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 147 GLN M 140 HIS ** M 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 139 ASN ** R 78 ASN ** 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 63 GLN ** W 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 61 GLN ** W 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 23 GLN X 47 ASN Z 42 GLN ** Z 177 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.114908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.098101 restraints weight = 100034.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.101486 restraints weight = 51241.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.103698 restraints weight = 30249.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.105182 restraints weight = 19796.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.106224 restraints weight = 14194.700| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3394 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3394 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.6161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 36155 Z= 0.150 Angle : 0.782 42.899 49243 Z= 0.376 Chirality : 0.040 0.269 5448 Planarity : 0.005 0.060 6402 Dihedral : 10.881 87.683 6599 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.61 % Favored : 97.30 % Rotamer: Outliers : 0.03 % Allowed : 1.12 % Favored : 98.85 % 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 aren not related in a simple way. whole: 0.99 (0.13), residues: 4448 helix: 1.10 (0.09), residues: 3393 sheet: 0.97 (0.83), residues: 28 loop : -0.64 (0.22), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG a 30 TYR 0.053 0.002 TYR R 97 PHE 0.032 0.002 PHE T 166 TRP 0.010 0.001 TRP C 128 HIS 0.006 0.002 HIS K 140 Details of bonding type rmsd covalent geometry : bond 0.00334 (36155) covalent geometry : angle 0.78213 (49243) hydrogen bonds : bond 0.04425 ( 2648) hydrogen bonds : angle 4.31834 ( 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 1605 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1604 time to evaluate : 1.391 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 2 LYS cc_start: 0.8119 (ttpt) cc_final: 0.6716 (ttpt) REVERT: A 15 GLN cc_start: 0.8152 (mt0) cc_final: 0.7359 (mm110) REVERT: A 38 MET cc_start: 0.8646 (mmt) cc_final: 0.7921 (tpt) REVERT: A 62 LYS cc_start: 0.9122 (tmtt) cc_final: 0.8909 (tptp) REVERT: A 90 TYR cc_start: 0.8482 (m-10) cc_final: 0.8077 (m-80) REVERT: A 131 GLU cc_start: 0.7145 (tm-30) cc_final: 0.6700 (tm-30) REVERT: B 25 ASP cc_start: 0.8006 (p0) cc_final: 0.7261 (p0) REVERT: B 120 GLN cc_start: 0.8104 (mt0) cc_final: 0.7573 (tm-30) REVERT: B 122 LEU cc_start: 0.9005 (mm) cc_final: 0.8794 (mm) REVERT: B 159 MET cc_start: 0.8370 (mpp) cc_final: 0.7918 (mpp) REVERT: C 17 ARG cc_start: 0.8787 (ptt90) cc_final: 0.8465 (ptt90) REVERT: C 69 MET cc_start: 0.7498 (ttm) cc_final: 0.7048 (ttm) REVERT: C 74 TYR cc_start: 0.7215 (m-80) cc_final: 0.6890 (m-80) REVERT: C 94 MET cc_start: 0.9407 (mmt) cc_final: 0.9022 (mmm) REVERT: C 119 ASN cc_start: 0.7282 (m110) cc_final: 0.6937 (p0) REVERT: D 29 ASN cc_start: 0.9069 (t0) cc_final: 0.7712 (t0) REVERT: D 49 SER cc_start: 0.8774 (p) cc_final: 0.8443 (p) REVERT: D 97 TYR cc_start: 0.8180 (m-10) cc_final: 0.7962 (m-10) REVERT: D 128 SER cc_start: 0.9421 (p) cc_final: 0.8908 (m) REVERT: D 134 GLN cc_start: 0.8635 (mt0) cc_final: 0.8279 (mt0) REVERT: D 138 ASP cc_start: 0.8706 (p0) cc_final: 0.8504 (p0) REVERT: D 146 ASP cc_start: 0.9125 (t0) cc_final: 0.8861 (t0) REVERT: D 154 ASP cc_start: 0.6673 (t0) cc_final: 0.6325 (t0) REVERT: E 28 ASP cc_start: 0.8889 (t0) cc_final: 0.8656 (t0) REVERT: E 38 MET cc_start: 0.8218 (mmt) cc_final: 0.7774 (tmm) REVERT: E 47 ASN cc_start: 0.8581 (m110) cc_final: 0.7802 (m110) REVERT: E 72 SER cc_start: 0.8926 (m) cc_final: 0.8450 (t) REVERT: E 83 LYS cc_start: 0.9180 (mmmm) cc_final: 0.8909 (mmmm) REVERT: E 94 MET cc_start: 0.8225 (tpp) cc_final: 0.7753 (ttm) REVERT: E 109 GLU cc_start: 0.8580 (tt0) cc_final: 0.8186 (tt0) REVERT: E 111 LEU cc_start: 0.8861 (mt) cc_final: 0.7933 (mt) REVERT: E 121 THR cc_start: 0.9270 (p) cc_final: 0.8712 (t) REVERT: E 167 ASP cc_start: 0.8505 (t0) cc_final: 0.6990 (t0) REVERT: E 171 ASN cc_start: 0.8829 (p0) cc_final: 0.8273 (p0) REVERT: F 1 MET cc_start: 0.6672 (pmm) cc_final: 0.6461 (pmm) REVERT: F 11 GLN cc_start: 0.9081 (tt0) cc_final: 0.8364 (tt0) REVERT: F 25 ASP cc_start: 0.8836 (m-30) cc_final: 0.8389 (m-30) REVERT: F 117 GLU cc_start: 0.8535 (pp20) cc_final: 0.8188 (pp20) REVERT: F 120 GLN cc_start: 0.8927 (tt0) cc_final: 0.8508 (tt0) REVERT: F 131 VAL cc_start: 0.8209 (t) cc_final: 0.7752 (t) REVERT: F 136 MET cc_start: 0.7931 (ttt) cc_final: 0.7552 (ttt) REVERT: F 146 ASP cc_start: 0.7839 (t70) cc_final: 0.7563 (t0) REVERT: F 161 GLU cc_start: 0.8215 (tp30) cc_final: 0.7882 (tp30) REVERT: G 1 MET cc_start: 0.8168 (tpp) cc_final: 0.7644 (tpp) REVERT: G 20 SER cc_start: 0.8333 (t) cc_final: 0.7537 (m) REVERT: G 25 GLN cc_start: 0.8703 (mt0) cc_final: 0.8452 (mt0) REVERT: G 28 ASP cc_start: 0.8433 (t0) cc_final: 0.8025 (t70) REVERT: G 57 GLN cc_start: 0.8517 (mp10) cc_final: 0.8292 (mp10) REVERT: G 97 TYR cc_start: 0.8967 (m-10) cc_final: 0.8695 (m-10) REVERT: G 98 CYS cc_start: 0.8531 (p) cc_final: 0.8180 (p) REVERT: G 123 ASP cc_start: 0.8020 (t0) cc_final: 0.7612 (t0) REVERT: G 124 LEU cc_start: 0.9176 (mt) cc_final: 0.8587 (mt) REVERT: H 3 ASP cc_start: 0.8379 (p0) cc_final: 0.8063 (p0) REVERT: H 38 LEU cc_start: 0.9132 (mt) cc_final: 0.8619 (tt) REVERT: H 91 ILE cc_start: 0.9493 (mm) cc_final: 0.9143 (tp) REVERT: H 107 LEU cc_start: 0.9430 (tp) cc_final: 0.9204 (tt) REVERT: H 133 ILE cc_start: 0.9654 (mm) cc_final: 0.9443 (mm) REVERT: H 159 MET cc_start: 0.8190 (mmm) cc_final: 0.7494 (mmt) REVERT: H 161 GLU cc_start: 0.7620 (pm20) cc_final: 0.7415 (pm20) REVERT: I 62 LYS cc_start: 0.9310 (tptm) cc_final: 0.8932 (tptt) REVERT: I 73 GLN cc_start: 0.9335 (pm20) cc_final: 0.8909 (pm20) REVERT: I 115 LEU cc_start: 0.8949 (tp) cc_final: 0.8377 (tt) REVERT: I 119 ASN cc_start: 0.8543 (m110) cc_final: 0.7695 (m110) REVERT: I 127 SER cc_start: 0.9144 (p) cc_final: 0.8871 (p) REVERT: I 129 TYR cc_start: 0.8950 (m-10) cc_final: 0.8744 (m-10) REVERT: I 167 ASP cc_start: 0.7809 (m-30) cc_final: 0.7583 (m-30) REVERT: J 17 GLU cc_start: 0.8154 (mp0) cc_final: 0.7602 (mp0) REVERT: J 28 SER cc_start: 0.9415 (t) cc_final: 0.9173 (p) REVERT: J 35 ASN cc_start: 0.8814 (m110) cc_final: 0.7946 (t0) REVERT: J 88 MET cc_start: 0.9158 (mmm) cc_final: 0.8631 (mmm) REVERT: J 91 ILE cc_start: 0.9391 (tp) cc_final: 0.9111 (tt) REVERT: J 97 TYR cc_start: 0.8967 (m-10) cc_final: 0.8650 (m-10) REVERT: J 112 LEU cc_start: 0.9528 (mp) cc_final: 0.8917 (mm) REVERT: K 30 ARG cc_start: 0.8462 (tpt-90) cc_final: 0.8115 (tpt-90) REVERT: K 69 MET cc_start: 0.6854 (tpt) cc_final: 0.6644 (mtp) REVERT: K 90 TYR cc_start: 0.8661 (m-10) cc_final: 0.8381 (m-80) REVERT: K 133 LEU cc_start: 0.8710 (mt) cc_final: 0.8447 (tp) REVERT: K 135 TYR cc_start: 0.7825 (t80) cc_final: 0.7533 (t80) REVERT: K 137 LYS cc_start: 0.9000 (ttpp) cc_final: 0.8735 (ttpp) REVERT: K 139 ASN cc_start: 0.9023 (t0) cc_final: 0.8312 (t0) REVERT: K 166 ILE cc_start: 0.9409 (mm) cc_final: 0.9191 (mm) REVERT: L 2 LEU cc_start: 0.9466 (mt) cc_final: 0.8671 (mt) REVERT: L 3 ASP cc_start: 0.8820 (p0) cc_final: 0.8610 (p0) REVERT: L 62 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8035 (tm-30) REVERT: L 81 MET cc_start: 0.8979 (tpp) cc_final: 0.8357 (tpp) REVERT: L 88 MET cc_start: 0.7476 (mtm) cc_final: 0.6884 (mtp) REVERT: L 89 GLU cc_start: 0.7689 (pp20) cc_final: 0.7465 (tm-30) REVERT: L 103 ASP cc_start: 0.7831 (m-30) cc_final: 0.7608 (m-30) REVERT: L 120 GLN cc_start: 0.8701 (tm-30) cc_final: 0.8021 (tm-30) REVERT: L 137 LYS cc_start: 0.9438 (tttt) cc_final: 0.8697 (ttmt) REVERT: L 146 ASP cc_start: 0.9467 (t0) cc_final: 0.9231 (t0) REVERT: L 161 GLU cc_start: 0.8788 (tt0) cc_final: 0.8403 (tt0) REVERT: M 57 GLN cc_start: 0.9168 (mm-40) cc_final: 0.8903 (mm-40) REVERT: M 94 MET cc_start: 0.8025 (mtp) cc_final: 0.7546 (mtp) REVERT: M 115 LEU cc_start: 0.8947 (tt) cc_final: 0.8373 (tp) REVERT: M 118 ILE cc_start: 0.9670 (tp) cc_final: 0.9255 (tp) REVERT: M 129 TYR cc_start: 0.8102 (m-80) cc_final: 0.7545 (m-10) REVERT: M 163 ASN cc_start: 0.7761 (t0) cc_final: 0.7454 (t0) REVERT: M 171 ASN cc_start: 0.7428 (p0) cc_final: 0.7166 (p0) REVERT: N 17 GLU cc_start: 0.7759 (pm20) cc_final: 0.7448 (pm20) REVERT: N 20 THR cc_start: 0.8064 (t) cc_final: 0.7757 (p) REVERT: N 42 ASN cc_start: 0.9536 (t0) cc_final: 0.9014 (t0) REVERT: N 65 GLN cc_start: 0.7537 (pm20) cc_final: 0.7029 (pm20) REVERT: N 67 ILE cc_start: 0.9592 (pt) cc_final: 0.9186 (tp) REVERT: N 87 ASP cc_start: 0.8458 (m-30) cc_final: 0.8079 (m-30) REVERT: N 88 MET cc_start: 0.8620 (ttm) cc_final: 0.7707 (tpp) REVERT: N 89 GLU cc_start: 0.7868 (pp20) cc_final: 0.7428 (pp20) REVERT: N 97 TYR cc_start: 0.8457 (m-10) cc_final: 0.7919 (m-80) REVERT: N 103 ASP cc_start: 0.7057 (t0) cc_final: 0.6443 (t0) REVERT: N 116 ARG cc_start: 0.7733 (ttm170) cc_final: 0.7424 (ttm170) REVERT: N 135 LYS cc_start: 0.8157 (mmmm) cc_final: 0.7439 (mmmm) REVERT: N 136 MET cc_start: 0.8641 (mtm) cc_final: 0.7797 (mtm) REVERT: N 137 LYS cc_start: 0.8383 (ttmm) cc_final: 0.7922 (ttmt) REVERT: N 165 TYR cc_start: 0.8244 (m-10) cc_final: 0.7923 (m-10) REVERT: N 173 VAL cc_start: 0.6207 (p) cc_final: 0.5770 (t) REVERT: O 60 TYR cc_start: 0.6039 (m-10) cc_final: 0.5824 (m-10) REVERT: O 61 GLN cc_start: 0.7605 (mt0) cc_final: 0.6880 (tm-30) REVERT: O 68 THR cc_start: 0.7239 (t) cc_final: 0.7032 (m) REVERT: O 94 MET cc_start: 0.9022 (mmp) cc_final: 0.8809 (mmp) REVERT: O 96 THR cc_start: 0.9385 (p) cc_final: 0.9079 (t) REVERT: O 104 THR cc_start: 0.9004 (p) cc_final: 0.8054 (p) REVERT: P 97 TYR cc_start: 0.8664 (m-10) cc_final: 0.8010 (m-10) REVERT: P 122 LEU cc_start: 0.8417 (mm) cc_final: 0.8019 (mm) REVERT: Q 25 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8320 (mm-40) REVERT: Q 39 GLU cc_start: 0.7365 (mt-10) cc_final: 0.6651 (pt0) REVERT: Q 57 GLN cc_start: 0.8461 (mm110) cc_final: 0.7696 (mm-40) REVERT: Q 62 LYS cc_start: 0.7432 (ttmm) cc_final: 0.7162 (ttmm) REVERT: Q 69 MET cc_start: 0.7340 (ptm) cc_final: 0.6776 (ptm) REVERT: Q 73 GLN cc_start: 0.8199 (pm20) cc_final: 0.7958 (pt0) REVERT: Q 94 MET cc_start: 0.5464 (tpp) cc_final: 0.5013 (tpp) REVERT: Q 108 ASP cc_start: 0.8974 (m-30) cc_final: 0.8488 (m-30) REVERT: R 1 MET cc_start: 0.7023 (ttm) cc_final: 0.6551 (ttp) REVERT: R 111 CYS cc_start: 0.8352 (t) cc_final: 0.7813 (t) REVERT: R 118 THR cc_start: 0.8924 (p) cc_final: 0.7563 (p) REVERT: R 128 SER cc_start: 0.8982 (m) cc_final: 0.8693 (m) REVERT: R 136 MET cc_start: 0.8720 (tmm) cc_final: 0.8208 (tmm) REVERT: R 141 ILE cc_start: 0.8406 (mm) cc_final: 0.7882 (pt) REVERT: R 160 SER cc_start: 0.8969 (t) cc_final: 0.8593 (p) REVERT: S 49 GLN cc_start: 0.8391 (tp-100) cc_final: 0.7872 (pm20) REVERT: S 74 TYR cc_start: 0.8739 (m-80) cc_final: 0.7848 (m-10) REVERT: S 79 GLU cc_start: 0.7943 (mp0) cc_final: 0.7521 (tm-30) REVERT: S 93 ARG cc_start: 0.7618 (ttp80) cc_final: 0.6835 (ttp80) REVERT: S 94 MET cc_start: 0.9431 (mmt) cc_final: 0.8802 (mmm) REVERT: S 97 TYR cc_start: 0.8837 (m-10) cc_final: 0.8238 (m-80) REVERT: S 112 ILE cc_start: 0.9508 (mm) cc_final: 0.8906 (tp) REVERT: S 115 LEU cc_start: 0.8690 (tp) cc_final: 0.8301 (tp) REVERT: S 134 LYS cc_start: 0.9516 (mmpt) cc_final: 0.9097 (mmmm) REVERT: S 139 ASN cc_start: 0.9115 (t0) cc_final: 0.8766 (t0) REVERT: T 1 MET cc_start: 0.7820 (mmp) cc_final: 0.6947 (ptt) REVERT: T 15 ARG cc_start: 0.7716 (mtp85) cc_final: 0.7136 (mmp80) REVERT: T 19 LEU cc_start: 0.8261 (mt) cc_final: 0.7657 (mm) REVERT: T 23 GLN cc_start: 0.8335 (mt0) cc_final: 0.8064 (mp10) REVERT: T 141 ILE cc_start: 0.8585 (mt) cc_final: 0.8384 (mm) REVERT: T 156 SER cc_start: 0.8674 (m) cc_final: 0.8386 (m) REVERT: T 159 MET cc_start: 0.7995 (mpp) cc_final: 0.7297 (mpp) REVERT: T 162 ILE cc_start: 0.8921 (mt) cc_final: 0.8519 (mt) REVERT: T 165 TYR cc_start: 0.8541 (m-80) cc_final: 0.8118 (m-80) REVERT: U 28 ASP cc_start: 0.7101 (t0) cc_final: 0.6802 (t0) REVERT: U 32 LYS cc_start: 0.9293 (tmmt) cc_final: 0.9027 (tmmt) REVERT: U 63 PHE cc_start: 0.7646 (m-80) cc_final: 0.7274 (m-80) REVERT: U 97 TYR cc_start: 0.8457 (m-10) cc_final: 0.7860 (m-80) REVERT: U 98 CYS cc_start: 0.8013 (t) cc_final: 0.7482 (t) REVERT: U 109 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7480 (tm-30) REVERT: U 115 LEU cc_start: 0.8522 (tp) cc_final: 0.8184 (tp) REVERT: U 119 ASN cc_start: 0.9115 (m110) cc_final: 0.8890 (m110) REVERT: U 123 ASP cc_start: 0.8150 (t0) cc_final: 0.7746 (t0) REVERT: U 134 LYS cc_start: 0.9111 (tppp) cc_final: 0.8764 (tppt) REVERT: U 171 ASN cc_start: 0.8914 (t0) cc_final: 0.8619 (t0) REVERT: U 174 SER cc_start: 0.7760 (t) cc_final: 0.7404 (t) REVERT: V 29 ASN cc_start: 0.8082 (m-40) cc_final: 0.7582 (t0) REVERT: V 113 ASN cc_start: 0.9233 (t0) cc_final: 0.8437 (t0) REVERT: V 124 THR cc_start: 0.8894 (m) cc_final: 0.8544 (p) REVERT: V 162 ILE cc_start: 0.8540 (mt) cc_final: 0.8325 (mt) REVERT: W 42 ARG cc_start: 0.7444 (ttm170) cc_final: 0.5983 (tpt170) REVERT: W 69 MET cc_start: 0.4107 (mmm) cc_final: 0.3704 (tpt) REVERT: W 72 SER cc_start: 0.8717 (m) cc_final: 0.8427 (p) REVERT: W 88 ILE cc_start: 0.8577 (mm) cc_final: 0.8345 (mm) REVERT: W 94 MET cc_start: 0.8394 (ptt) cc_final: 0.7868 (ppp) REVERT: W 111 LEU cc_start: 0.8402 (pt) cc_final: 0.7867 (pp) REVERT: X 3 ASP cc_start: 0.7759 (p0) cc_final: 0.7379 (p0) REVERT: X 44 ILE cc_start: 0.8146 (mm) cc_final: 0.7835 (tp) REVERT: X 52 VAL cc_start: 0.9376 (t) cc_final: 0.9062 (p) REVERT: X 88 MET cc_start: 0.8599 (ttm) cc_final: 0.8342 (ttm) REVERT: X 89 GLU cc_start: 0.8431 (tm-30) cc_final: 0.8057 (tm-30) REVERT: X 93 ARG cc_start: 0.8554 (ttp80) cc_final: 0.7961 (ttt90) REVERT: X 117 GLU cc_start: 0.7830 (pm20) cc_final: 0.7577 (pm20) REVERT: X 119 TYR cc_start: 0.8015 (m-80) cc_final: 0.7730 (m-80) REVERT: X 136 MET cc_start: 0.8034 (mmm) cc_final: 0.7500 (mmm) REVERT: Y 36 MET cc_start: 0.7903 (mmp) cc_final: 0.7202 (mmt) REVERT: Y 64 ARG cc_start: 0.8772 (mtp-110) cc_final: 0.8471 (ttm110) REVERT: Z 42 GLN cc_start: 0.9048 (tp40) cc_final: 0.8711 (tp40) REVERT: Z 59 GLU cc_start: 0.8606 (pm20) cc_final: 0.7938 (pm20) REVERT: Z 76 VAL cc_start: 0.9613 (t) cc_final: 0.9407 (p) REVERT: Z 120 LEU cc_start: 0.9584 (tp) cc_final: 0.8940 (tt) REVERT: Z 141 ASN cc_start: 0.8517 (m-40) cc_final: 0.7983 (m-40) REVERT: Z 196 THR cc_start: 0.9123 (p) cc_final: 0.8727 (m) REVERT: a 51 ARG cc_start: 0.8913 (ttp80) cc_final: 0.8571 (mtp-110) REVERT: a 68 LEU cc_start: 0.8767 (mm) cc_final: 0.8473 (mm) REVERT: a 84 ARG cc_start: 0.8912 (ttm110) cc_final: 0.8594 (ttm-80) REVERT: a 88 LYS cc_start: 0.8882 (pttm) cc_final: 0.8284 (tppt) REVERT: a 98 GLU cc_start: 0.8029 (pt0) cc_final: 0.7237 (pt0) REVERT: a 129 ILE cc_start: 0.8782 (tt) cc_final: 0.8463 (tp) REVERT: a 137 GLN cc_start: 0.7811 (tp40) cc_final: 0.7138 (tp40) REVERT: a 151 GLN cc_start: 0.8866 (mm-40) cc_final: 0.7913 (mt0) REVERT: a 156 ASN cc_start: 0.8453 (m-40) cc_final: 0.8187 (m-40) outliers start: 1 outliers final: 0 residues processed: 1605 average time/residue: 0.2330 time to fit residues: 609.0601 Evaluate side-chains 1346 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1346 time to evaluate : 1.341 ------------------------------------------------------------------------------- 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: 0.9990 chunk 56 optimal weight: 7.9990 chunk 412 optimal weight: 6.9990 chunk 362 optimal weight: 10.0000 chunk 287 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 chunk 348 optimal weight: 2.9990 chunk 365 optimal weight: 5.9990 chunk 330 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 427 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 29 ASN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 GLN G 139 ASN ** G 163 ASN ** 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** I 171 ASN ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 139 ASN ** R 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 ASN ** U 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 78 ASN X 42 ASN Z 64 ASN ** Z 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.110143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.094889 restraints weight = 81475.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.097698 restraints weight = 44651.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.099554 restraints weight = 27556.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.100840 restraints weight = 18741.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.101651 restraints weight = 13811.129| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3320 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3320 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.6233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 36155 Z= 0.234 Angle : 0.850 42.958 49243 Z= 0.418 Chirality : 0.043 0.230 5448 Planarity : 0.006 0.083 6402 Dihedral : 10.999 87.290 6599 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.58 % Favored : 96.36 % Rotamer: Outliers : 0.06 % Allowed : 1.00 % Favored : 98.94 % 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 aren not related in a simple way. whole: 0.75 (0.12), residues: 4448 helix: 0.91 (0.09), residues: 3393 sheet: 0.87 (0.78), residues: 28 loop : -0.64 (0.22), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 17 TYR 0.059 0.003 TYR M 97 PHE 0.037 0.002 PHE a 139 TRP 0.049 0.002 TRP a 29 HIS 0.007 0.002 HIS K 140 Details of bonding type rmsd covalent geometry : bond 0.00522 (36155) covalent geometry : angle 0.85008 (49243) hydrogen bonds : bond 0.04819 ( 2648) hydrogen bonds : angle 4.59858 ( 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 1542 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1540 time to evaluate : 1.884 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: A 15 GLN cc_start: 0.8261 (mt0) cc_final: 0.7674 (mm110) REVERT: A 17 ARG cc_start: 0.7807 (ptp-170) cc_final: 0.7192 (ptp90) REVERT: A 38 MET cc_start: 0.8753 (mmt) cc_final: 0.8382 (mmm) REVERT: A 60 TYR cc_start: 0.8604 (m-80) cc_final: 0.8301 (m-80) REVERT: A 62 LYS cc_start: 0.9203 (tmtt) cc_final: 0.8953 (tptp) REVERT: A 94 MET cc_start: 0.8721 (tpp) cc_final: 0.7861 (tpt) REVERT: A 98 CYS cc_start: 0.8185 (t) cc_final: 0.7650 (t) REVERT: A 109 GLU cc_start: 0.7978 (pm20) cc_final: 0.7520 (mp0) REVERT: A 131 GLU cc_start: 0.7268 (tm-30) cc_final: 0.6975 (tm-30) REVERT: A 165 TYR cc_start: 0.8600 (m-80) cc_final: 0.8151 (m-80) REVERT: B 25 ASP cc_start: 0.7574 (p0) cc_final: 0.7252 (p0) REVERT: B 29 ASN cc_start: 0.8121 (m110) cc_final: 0.7900 (m110) REVERT: B 35 ASN cc_start: 0.9005 (m-40) cc_final: 0.8033 (t0) REVERT: B 36 LYS cc_start: 0.9553 (mtmm) cc_final: 0.8740 (mppt) REVERT: B 120 GLN cc_start: 0.8311 (mt0) cc_final: 0.7782 (tm-30) REVERT: B 141 ILE cc_start: 0.9350 (tt) cc_final: 0.9148 (tt) REVERT: C 69 MET cc_start: 0.7685 (ttm) cc_final: 0.7244 (ttm) REVERT: C 74 TYR cc_start: 0.7493 (m-80) cc_final: 0.7099 (m-80) REVERT: C 94 MET cc_start: 0.9309 (mmt) cc_final: 0.8940 (mmm) REVERT: C 119 ASN cc_start: 0.7361 (m110) cc_final: 0.6624 (p0) REVERT: C 131 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8276 (tp30) REVERT: D 19 LEU cc_start: 0.9256 (mt) cc_final: 0.8648 (tp) REVERT: D 29 ASN cc_start: 0.9114 (t0) cc_final: 0.8585 (t0) REVERT: D 127 SER cc_start: 0.8954 (p) cc_final: 0.8586 (t) REVERT: D 128 SER cc_start: 0.9469 (p) cc_final: 0.8802 (m) REVERT: D 134 GLN cc_start: 0.8539 (mt0) cc_final: 0.8239 (mt0) REVERT: D 154 ASP cc_start: 0.6703 (t0) cc_final: 0.6323 (t0) REVERT: E 38 MET cc_start: 0.8448 (mmt) cc_final: 0.7948 (tmm) REVERT: E 47 ASN cc_start: 0.8712 (m110) cc_final: 0.7974 (m110) REVERT: E 69 MET cc_start: 0.7791 (ttm) cc_final: 0.7509 (ttm) REVERT: E 83 LYS cc_start: 0.9155 (mmmm) cc_final: 0.8746 (mmmm) REVERT: E 109 GLU cc_start: 0.8730 (tt0) cc_final: 0.8492 (tt0) REVERT: E 111 LEU cc_start: 0.9008 (mt) cc_final: 0.8717 (mt) REVERT: E 163 ASN cc_start: 0.9069 (m-40) cc_final: 0.8861 (m-40) REVERT: E 167 ASP cc_start: 0.8529 (t0) cc_final: 0.7216 (t0) REVERT: E 171 ASN cc_start: 0.8837 (p0) cc_final: 0.8449 (p0) REVERT: F 11 GLN cc_start: 0.9228 (tt0) cc_final: 0.8530 (tt0) REVERT: F 117 GLU cc_start: 0.8688 (pp20) cc_final: 0.8181 (pp20) REVERT: F 120 GLN cc_start: 0.8883 (tt0) cc_final: 0.8360 (tt0) REVERT: F 136 MET cc_start: 0.7993 (ttt) cc_final: 0.7520 (ttt) REVERT: F 146 ASP cc_start: 0.8176 (t70) cc_final: 0.7894 (t0) REVERT: F 161 GLU cc_start: 0.8144 (tp30) cc_final: 0.7878 (tp30) REVERT: G 1 MET cc_start: 0.8304 (tpp) cc_final: 0.8080 (tpp) REVERT: G 28 ASP cc_start: 0.8692 (t0) cc_final: 0.8488 (t70) REVERT: G 98 CYS cc_start: 0.8545 (p) cc_final: 0.7821 (m) REVERT: G 107 MET cc_start: 0.9383 (tpp) cc_final: 0.8766 (tpp) REVERT: G 123 ASP cc_start: 0.8083 (t0) cc_final: 0.7789 (t0) REVERT: G 124 LEU cc_start: 0.9241 (mt) cc_final: 0.8630 (mt) REVERT: G 129 TYR cc_start: 0.9031 (m-80) cc_final: 0.8798 (m-10) REVERT: G 133 LEU cc_start: 0.9471 (mm) cc_final: 0.9116 (mm) REVERT: H 5 PHE cc_start: 0.9286 (m-80) cc_final: 0.9062 (m-80) REVERT: H 38 LEU cc_start: 0.9125 (mt) cc_final: 0.8464 (tt) REVERT: H 76 TYR cc_start: 0.8845 (t80) cc_final: 0.8461 (t80) REVERT: H 81 MET cc_start: 0.8987 (mmp) cc_final: 0.8592 (mmm) REVERT: H 91 ILE cc_start: 0.9561 (mm) cc_final: 0.9171 (tp) REVERT: H 145 ASN cc_start: 0.8323 (m-40) cc_final: 0.7558 (m-40) REVERT: H 159 MET cc_start: 0.8252 (mmm) cc_final: 0.8042 (mmt) REVERT: I 62 LYS cc_start: 0.9297 (tptm) cc_final: 0.8925 (tptt) REVERT: I 73 GLN cc_start: 0.9347 (pm20) cc_final: 0.8948 (pm20) REVERT: I 98 CYS cc_start: 0.7807 (m) cc_final: 0.7497 (m) REVERT: I 119 ASN cc_start: 0.8413 (m110) cc_final: 0.7843 (m110) REVERT: I 127 SER cc_start: 0.9211 (p) cc_final: 0.9004 (p) REVERT: I 133 LEU cc_start: 0.9545 (mt) cc_final: 0.9315 (mt) REVERT: J 17 GLU cc_start: 0.8239 (mp0) cc_final: 0.7689 (mp0) REVERT: J 24 PHE cc_start: 0.7299 (m-80) cc_final: 0.6906 (m-80) REVERT: J 35 ASN cc_start: 0.8854 (m110) cc_final: 0.8084 (t0) REVERT: J 88 MET cc_start: 0.9149 (mmm) cc_final: 0.8624 (mmm) REVERT: J 91 ILE cc_start: 0.9441 (tp) cc_final: 0.9150 (tt) REVERT: J 112 LEU cc_start: 0.9551 (mp) cc_final: 0.8966 (mm) REVERT: K 30 ARG cc_start: 0.8711 (tpt-90) cc_final: 0.8198 (tpt-90) REVERT: K 62 LYS cc_start: 0.9161 (tptp) cc_final: 0.8729 (tptm) REVERT: K 87 ASP cc_start: 0.8550 (t0) cc_final: 0.7546 (t70) REVERT: K 90 TYR cc_start: 0.8778 (m-10) cc_final: 0.8333 (m-80) REVERT: K 135 TYR cc_start: 0.7987 (t80) cc_final: 0.7675 (t80) REVERT: K 137 LYS cc_start: 0.9135 (ttpp) cc_final: 0.8753 (ttpp) REVERT: K 139 ASN cc_start: 0.8627 (t0) cc_final: 0.8305 (t0) REVERT: L 2 LEU cc_start: 0.9514 (mt) cc_final: 0.8725 (mt) REVERT: L 3 ASP cc_start: 0.8806 (p0) cc_final: 0.8603 (p0) REVERT: L 63 GLN cc_start: 0.8626 (tt0) cc_final: 0.8383 (tt0) REVERT: L 81 MET cc_start: 0.8867 (tpp) cc_final: 0.8165 (tpp) REVERT: L 88 MET cc_start: 0.8254 (mtm) cc_final: 0.7882 (mtp) REVERT: L 89 GLU cc_start: 0.7822 (pp20) cc_final: 0.7582 (tm-30) REVERT: L 120 GLN cc_start: 0.8887 (tm-30) cc_final: 0.8283 (tm-30) REVERT: L 137 LYS cc_start: 0.9544 (tttt) cc_final: 0.9281 (tttt) REVERT: L 146 ASP cc_start: 0.9486 (t0) cc_final: 0.9178 (t0) REVERT: L 161 GLU cc_start: 0.8832 (tt0) cc_final: 0.7708 (tp30) REVERT: M 2 LYS cc_start: 0.8309 (mmmt) cc_final: 0.8085 (mmtp) REVERT: M 33 ARG cc_start: 0.8140 (ttt180) cc_final: 0.7800 (ttt180) REVERT: M 57 GLN cc_start: 0.9254 (mm-40) cc_final: 0.8944 (mm-40) REVERT: M 115 LEU cc_start: 0.9049 (tt) cc_final: 0.8389 (tt) REVERT: M 118 ILE cc_start: 0.9736 (tp) cc_final: 0.9376 (tp) REVERT: M 129 TYR cc_start: 0.8295 (m-80) cc_final: 0.7858 (m-10) REVERT: M 135 TYR cc_start: 0.9014 (t80) cc_final: 0.8786 (t80) REVERT: N 3 ASP cc_start: 0.8563 (p0) cc_final: 0.8343 (p0) REVERT: N 17 GLU cc_start: 0.7945 (pm20) cc_final: 0.7542 (pm20) REVERT: N 20 THR cc_start: 0.8282 (t) cc_final: 0.8066 (p) REVERT: N 65 GLN cc_start: 0.7759 (pm20) cc_final: 0.7329 (pm20) REVERT: N 67 ILE cc_start: 0.9635 (pt) cc_final: 0.9241 (tp) REVERT: N 80 ARG cc_start: 0.8965 (mtm-85) cc_final: 0.8356 (mtm-85) REVERT: N 87 ASP cc_start: 0.8566 (m-30) cc_final: 0.8193 (m-30) REVERT: N 88 MET cc_start: 0.8649 (ttm) cc_final: 0.7612 (tpp) REVERT: N 97 TYR cc_start: 0.8474 (m-10) cc_final: 0.8020 (m-80) REVERT: N 103 ASP cc_start: 0.7256 (t0) cc_final: 0.6752 (t0) REVERT: N 117 GLU cc_start: 0.7464 (pt0) cc_final: 0.7243 (pt0) REVERT: N 135 LYS cc_start: 0.7899 (mmmm) cc_final: 0.7604 (mmmm) REVERT: O 18 PHE cc_start: 0.8533 (m-80) cc_final: 0.8109 (m-80) REVERT: O 60 TYR cc_start: 0.6416 (m-10) cc_final: 0.6212 (m-10) REVERT: O 61 GLN cc_start: 0.7763 (mt0) cc_final: 0.7010 (tm-30) REVERT: O 94 MET cc_start: 0.9086 (mmp) cc_final: 0.8878 (mmp) REVERT: O 96 THR cc_start: 0.9433 (p) cc_final: 0.9208 (t) REVERT: O 98 CYS cc_start: 0.8518 (m) cc_final: 0.7571 (p) REVERT: O 104 THR cc_start: 0.8661 (p) cc_final: 0.7836 (p) REVERT: O 131 GLU cc_start: 0.8206 (tt0) cc_final: 0.7984 (tt0) REVERT: P 38 LEU cc_start: 0.8622 (pp) cc_final: 0.8292 (tt) REVERT: P 97 TYR cc_start: 0.8940 (m-10) cc_final: 0.7854 (m-80) REVERT: P 122 LEU cc_start: 0.8474 (mm) cc_final: 0.8090 (mm) REVERT: P 167 ASP cc_start: 0.8412 (t70) cc_final: 0.8211 (t0) REVERT: Q 1 MET cc_start: 0.7244 (tpt) cc_final: 0.6706 (tpt) REVERT: Q 25 GLN cc_start: 0.9033 (mm-40) cc_final: 0.8359 (mm-40) REVERT: Q 39 GLU cc_start: 0.7508 (mt-10) cc_final: 0.6690 (pt0) REVERT: Q 57 GLN cc_start: 0.8444 (mm110) cc_final: 0.7716 (mm-40) REVERT: Q 69 MET cc_start: 0.7406 (ptm) cc_final: 0.6762 (ptm) REVERT: Q 73 GLN cc_start: 0.8293 (pm20) cc_final: 0.8017 (pt0) REVERT: Q 94 MET cc_start: 0.5543 (tpp) cc_final: 0.5067 (tpp) REVERT: Q 108 ASP cc_start: 0.9008 (m-30) cc_final: 0.8414 (m-30) REVERT: R 1 MET cc_start: 0.7158 (ttm) cc_final: 0.6647 (ttp) REVERT: R 85 LEU cc_start: 0.9618 (mt) cc_final: 0.9136 (tp) REVERT: R 111 CYS cc_start: 0.8518 (t) cc_final: 0.8007 (t) REVERT: R 118 THR cc_start: 0.8987 (p) cc_final: 0.7607 (p) REVERT: R 128 SER cc_start: 0.9097 (m) cc_final: 0.8737 (m) REVERT: R 136 MET cc_start: 0.8636 (tmm) cc_final: 0.8113 (tmm) REVERT: R 160 SER cc_start: 0.8650 (t) cc_final: 0.8416 (p) REVERT: S 1 MET cc_start: 0.7698 (mmp) cc_final: 0.7349 (mmm) REVERT: S 39 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7797 (mm-30) REVERT: S 44 LEU cc_start: 0.9514 (mt) cc_final: 0.8772 (tp) REVERT: S 74 TYR cc_start: 0.8715 (m-80) cc_final: 0.8053 (m-10) REVERT: S 79 GLU cc_start: 0.7963 (mp0) cc_final: 0.7533 (tm-30) REVERT: S 94 MET cc_start: 0.9423 (mmt) cc_final: 0.8677 (mmm) REVERT: S 97 TYR cc_start: 0.8964 (m-10) cc_final: 0.8392 (m-80) REVERT: S 112 ILE cc_start: 0.9492 (mm) cc_final: 0.8998 (tp) REVERT: S 134 LYS cc_start: 0.9644 (mmpt) cc_final: 0.9091 (mmmm) REVERT: S 139 ASN cc_start: 0.9013 (t0) cc_final: 0.8784 (t0) REVERT: T 15 ARG cc_start: 0.7844 (mtp85) cc_final: 0.7235 (mmp80) REVERT: T 19 LEU cc_start: 0.7675 (mt) cc_final: 0.7137 (mm) REVERT: T 23 GLN cc_start: 0.8137 (mt0) cc_final: 0.7880 (mt0) REVERT: T 25 ASP cc_start: 0.8722 (m-30) cc_final: 0.8371 (m-30) REVERT: T 104 SER cc_start: 0.8877 (p) cc_final: 0.8534 (p) REVERT: T 124 THR cc_start: 0.8219 (m) cc_final: 0.7687 (p) REVERT: T 156 SER cc_start: 0.8712 (m) cc_final: 0.8440 (m) REVERT: T 159 MET cc_start: 0.8082 (mpp) cc_final: 0.7312 (mpp) REVERT: T 162 ILE cc_start: 0.8882 (mt) cc_final: 0.8566 (mt) REVERT: T 165 TYR cc_start: 0.8498 (m-80) cc_final: 0.8121 (m-80) REVERT: U 28 ASP cc_start: 0.7133 (t0) cc_final: 0.6828 (t0) REVERT: U 32 LYS cc_start: 0.9244 (tmmt) cc_final: 0.8975 (tmmt) REVERT: U 98 CYS cc_start: 0.8148 (t) cc_final: 0.7603 (t) REVERT: U 109 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8024 (tm-30) REVERT: U 123 ASP cc_start: 0.8152 (t0) cc_final: 0.7515 (t0) REVERT: U 134 LYS cc_start: 0.9157 (tppp) cc_final: 0.8796 (tppt) REVERT: U 171 ASN cc_start: 0.8818 (t0) cc_final: 0.8588 (t0) REVERT: U 174 SER cc_start: 0.7832 (t) cc_final: 0.7495 (t) REVERT: V 11 GLN cc_start: 0.8397 (tt0) cc_final: 0.7561 (tp40) REVERT: V 124 THR cc_start: 0.8948 (m) cc_final: 0.8610 (p) REVERT: V 162 ILE cc_start: 0.8569 (mt) cc_final: 0.8352 (mt) REVERT: W 1 MET cc_start: 0.6074 (pmm) cc_final: 0.5373 (pmm) REVERT: W 42 ARG cc_start: 0.8057 (ttm170) cc_final: 0.6630 (tpt170) REVERT: W 49 GLN cc_start: 0.8982 (mp10) cc_final: 0.8696 (mp10) REVERT: W 63 PHE cc_start: 0.6003 (m-80) cc_final: 0.5767 (m-80) REVERT: W 69 MET cc_start: 0.5610 (mmm) cc_final: 0.5363 (tpt) REVERT: W 94 MET cc_start: 0.8429 (ptt) cc_final: 0.7964 (ppp) REVERT: W 111 LEU cc_start: 0.8493 (pt) cc_final: 0.7928 (pp) REVERT: X 3 ASP cc_start: 0.7754 (p0) cc_final: 0.7367 (p0) REVERT: X 44 ILE cc_start: 0.8093 (mm) cc_final: 0.7832 (tp) REVERT: X 52 VAL cc_start: 0.9343 (t) cc_final: 0.9054 (p) REVERT: X 89 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8058 (tm-30) REVERT: X 117 GLU cc_start: 0.7936 (pm20) cc_final: 0.7612 (pm20) REVERT: X 133 ILE cc_start: 0.8894 (mm) cc_final: 0.8228 (tp) REVERT: Y 20 PHE cc_start: 0.8338 (m-10) cc_final: 0.8040 (m-10) REVERT: Y 23 GLU cc_start: 0.7813 (mp0) cc_final: 0.7516 (mp0) REVERT: Y 64 ARG cc_start: 0.8782 (mtp-110) cc_final: 0.8541 (ttm110) REVERT: Z 42 GLN cc_start: 0.9287 (tp40) cc_final: 0.8149 (tm-30) REVERT: Z 59 GLU cc_start: 0.8428 (pm20) cc_final: 0.8074 (pm20) REVERT: Z 85 LYS cc_start: 0.8610 (tppt) cc_final: 0.8308 (tppt) REVERT: Z 86 PHE cc_start: 0.8791 (m-80) cc_final: 0.8543 (m-80) REVERT: Z 196 THR cc_start: 0.9106 (p) cc_final: 0.8656 (m) REVERT: a 65 GLN cc_start: 0.8094 (tt0) cc_final: 0.7881 (tt0) REVERT: a 68 LEU cc_start: 0.9006 (mm) cc_final: 0.8714 (mm) REVERT: a 69 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7722 (mt-10) REVERT: a 84 ARG cc_start: 0.8900 (ttm110) cc_final: 0.8301 (ttm-80) REVERT: a 88 LYS cc_start: 0.8897 (pttm) cc_final: 0.8510 (tppt) REVERT: a 97 VAL cc_start: 0.9266 (t) cc_final: 0.8992 (t) REVERT: a 98 GLU cc_start: 0.8319 (pt0) cc_final: 0.7929 (pt0) REVERT: a 151 GLN cc_start: 0.8829 (mm-40) cc_final: 0.8068 (mt0) REVERT: a 156 ASN cc_start: 0.8397 (m-40) cc_final: 0.8149 (m-40) outliers start: 2 outliers final: 0 residues processed: 1540 average time/residue: 0.2362 time to fit residues: 596.2324 Evaluate side-chains 1293 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1293 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 310 optimal weight: 0.9980 chunk 398 optimal weight: 4.9990 chunk 327 optimal weight: 0.0570 chunk 119 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 366 optimal weight: 0.1980 chunk 168 optimal weight: 3.9990 chunk 170 optimal weight: 10.0000 chunk 221 optimal weight: 2.9990 overall best weight: 0.6502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 GLN C 119 ASN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 ASN ** 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 147 GLN ** K 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN P 42 ASN ** P 78 ASN ** 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 49 GLN ** S 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 ASN ** U 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 78 ASN X 42 ASN Z 64 ASN Z 92 GLN ** 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 = 0.3511 r_free = 0.3511 target = 0.114564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.097222 restraints weight = 108898.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.100840 restraints weight = 54602.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.103191 restraints weight = 31679.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.104817 restraints weight = 20383.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.105904 restraints weight = 14245.216| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3386 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3386 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.6490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 36155 Z= 0.154 Angle : 0.815 42.956 49243 Z= 0.395 Chirality : 0.041 0.231 5448 Planarity : 0.005 0.067 6402 Dihedral : 10.929 89.773 6599 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.88 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.13), residues: 4448 helix: 1.01 (0.09), residues: 3381 sheet: 0.91 (0.85), residues: 28 loop : -0.58 (0.22), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG M 17 TYR 0.058 0.002 TYR S 90 PHE 0.038 0.002 PHE X 24 TRP 0.022 0.001 TRP a 29 HIS 0.007 0.002 HIS Z 117 Details of bonding type rmsd covalent geometry : bond 0.00341 (36155) covalent geometry : angle 0.81540 (49243) hydrogen bonds : bond 0.04470 ( 2648) hydrogen bonds : angle 4.41977 ( 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 1562 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1562 time to evaluate : 1.423 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: A 15 GLN cc_start: 0.8252 (mt0) cc_final: 0.7483 (mm110) REVERT: A 17 ARG cc_start: 0.7860 (ptp-170) cc_final: 0.7184 (ptp90) REVERT: A 37 SER cc_start: 0.8942 (p) cc_final: 0.8533 (p) REVERT: A 38 MET cc_start: 0.8736 (mmt) cc_final: 0.8216 (mmm) REVERT: A 60 TYR cc_start: 0.8436 (m-80) cc_final: 0.8182 (m-80) REVERT: A 62 LYS cc_start: 0.9115 (tmtt) cc_final: 0.8915 (tptp) REVERT: A 73 GLN cc_start: 0.8778 (pt0) cc_final: 0.8418 (pt0) REVERT: A 90 TYR cc_start: 0.8784 (m-80) cc_final: 0.8446 (m-80) REVERT: A 98 CYS cc_start: 0.8665 (t) cc_final: 0.8150 (m) REVERT: A 99 LEU cc_start: 0.8737 (mt) cc_final: 0.8410 (mt) REVERT: A 131 GLU cc_start: 0.7229 (tm-30) cc_final: 0.6960 (tm-30) REVERT: A 161 GLU cc_start: 0.8897 (pp20) cc_final: 0.8635 (pp20) REVERT: A 163 ASN cc_start: 0.8603 (t0) cc_final: 0.8309 (t0) REVERT: A 167 ASP cc_start: 0.8189 (t70) cc_final: 0.7932 (t0) REVERT: B 25 ASP cc_start: 0.7472 (p0) cc_final: 0.7166 (p0) REVERT: B 35 ASN cc_start: 0.8483 (m-40) cc_final: 0.7315 (t0) REVERT: B 36 LYS cc_start: 0.9367 (mtmm) cc_final: 0.8178 (mppt) REVERT: B 59 LEU cc_start: 0.9188 (tp) cc_final: 0.8469 (tt) REVERT: B 120 GLN cc_start: 0.8280 (mt0) cc_final: 0.7842 (tm-30) REVERT: C 69 MET cc_start: 0.7502 (ttm) cc_final: 0.7181 (ttm) REVERT: C 74 TYR cc_start: 0.7465 (m-80) cc_final: 0.7144 (m-80) REVERT: C 94 MET cc_start: 0.9385 (mmt) cc_final: 0.9132 (mmm) REVERT: C 119 ASN cc_start: 0.7637 (m-40) cc_final: 0.6724 (p0) REVERT: C 128 TRP cc_start: 0.7418 (m-10) cc_final: 0.7205 (m-10) REVERT: C 131 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8267 (tp30) REVERT: C 165 TYR cc_start: 0.8744 (m-10) cc_final: 0.8538 (m-10) REVERT: D 3 ASP cc_start: 0.8685 (p0) cc_final: 0.8423 (p0) REVERT: D 15 ARG cc_start: 0.7441 (tmm-80) cc_final: 0.7233 (ttp80) REVERT: D 49 SER cc_start: 0.8665 (p) cc_final: 0.8462 (p) REVERT: D 51 ILE cc_start: 0.9346 (mm) cc_final: 0.9083 (mt) REVERT: D 97 TYR cc_start: 0.8224 (m-10) cc_final: 0.7052 (m-80) REVERT: D 120 GLN cc_start: 0.8378 (tp40) cc_final: 0.8168 (tm-30) REVERT: D 127 SER cc_start: 0.8882 (p) cc_final: 0.8579 (t) REVERT: D 128 SER cc_start: 0.9442 (p) cc_final: 0.8766 (m) REVERT: D 134 GLN cc_start: 0.8536 (mt0) cc_final: 0.8210 (mt0) REVERT: D 136 MET cc_start: 0.8236 (mmm) cc_final: 0.7843 (tpp) REVERT: D 146 ASP cc_start: 0.9227 (t0) cc_final: 0.8974 (t0) REVERT: D 154 ASP cc_start: 0.6787 (t0) cc_final: 0.6325 (t0) REVERT: E 38 MET cc_start: 0.8221 (mmt) cc_final: 0.7755 (tmm) REVERT: E 47 ASN cc_start: 0.8682 (m110) cc_final: 0.7868 (m110) REVERT: E 69 MET cc_start: 0.7900 (ttm) cc_final: 0.7658 (ttm) REVERT: E 83 LYS cc_start: 0.9000 (mmmm) cc_final: 0.8674 (mmmm) REVERT: E 94 MET cc_start: 0.8310 (tpp) cc_final: 0.7724 (ttm) REVERT: E 109 GLU cc_start: 0.8618 (tt0) cc_final: 0.8138 (tt0) REVERT: E 167 ASP cc_start: 0.8552 (t0) cc_final: 0.7000 (t0) REVERT: E 171 ASN cc_start: 0.8774 (p0) cc_final: 0.8334 (p0) REVERT: F 1 MET cc_start: 0.6885 (pmm) cc_final: 0.6552 (pmm) REVERT: F 11 GLN cc_start: 0.9081 (tt0) cc_final: 0.8349 (tt0) REVERT: F 117 GLU cc_start: 0.8557 (pp20) cc_final: 0.8153 (pp20) REVERT: F 120 GLN cc_start: 0.8884 (tt0) cc_final: 0.8395 (tt0) REVERT: F 146 ASP cc_start: 0.7658 (t70) cc_final: 0.7386 (t0) REVERT: G 1 MET cc_start: 0.8817 (tpp) cc_final: 0.8245 (tpp) REVERT: G 28 ASP cc_start: 0.8343 (t0) cc_final: 0.7955 (t70) REVERT: G 33 ARG cc_start: 0.8037 (mtp-110) cc_final: 0.7494 (mtp85) REVERT: G 98 CYS cc_start: 0.8453 (p) cc_final: 0.7815 (p) REVERT: G 107 MET cc_start: 0.9384 (tpp) cc_final: 0.8901 (tpp) REVERT: G 123 ASP cc_start: 0.8040 (t0) cc_final: 0.7809 (t0) REVERT: G 124 LEU cc_start: 0.9119 (mt) cc_final: 0.8458 (mt) REVERT: G 133 LEU cc_start: 0.9402 (mm) cc_final: 0.9136 (mm) REVERT: H 3 ASP cc_start: 0.8383 (p0) cc_final: 0.8090 (p0) REVERT: H 38 LEU cc_start: 0.9099 (mt) cc_final: 0.8572 (tt) REVERT: H 76 TYR cc_start: 0.8495 (t80) cc_final: 0.8103 (t80) REVERT: H 91 ILE cc_start: 0.9507 (mm) cc_final: 0.9136 (tp) REVERT: H 145 ASN cc_start: 0.8115 (m-40) cc_final: 0.7396 (m-40) REVERT: H 159 MET cc_start: 0.8210 (mmm) cc_final: 0.7872 (mmt) REVERT: H 161 GLU cc_start: 0.7750 (pm20) cc_final: 0.7403 (pm20) REVERT: I 62 LYS cc_start: 0.9257 (tptm) cc_final: 0.8877 (tptt) REVERT: I 73 GLN cc_start: 0.9342 (pm20) cc_final: 0.8913 (pm20) REVERT: I 83 LYS cc_start: 0.9115 (mmtm) cc_final: 0.8858 (mmmm) REVERT: I 115 LEU cc_start: 0.9037 (tp) cc_final: 0.8339 (tp) REVERT: I 119 ASN cc_start: 0.8446 (m110) cc_final: 0.8002 (m110) REVERT: I 127 SER cc_start: 0.9053 (p) cc_final: 0.8806 (p) REVERT: I 135 TYR cc_start: 0.8437 (t80) cc_final: 0.8067 (t80) REVERT: I 167 ASP cc_start: 0.7880 (m-30) cc_final: 0.7625 (m-30) REVERT: J 17 GLU cc_start: 0.8121 (mp0) cc_final: 0.7543 (mp0) REVERT: J 33 GLU cc_start: 0.7289 (pm20) cc_final: 0.7034 (pm20) REVERT: J 35 ASN cc_start: 0.8956 (m110) cc_final: 0.8025 (t0) REVERT: J 76 TYR cc_start: 0.8701 (t80) cc_final: 0.8109 (t80) REVERT: J 88 MET cc_start: 0.9110 (mmm) cc_final: 0.8666 (mmm) REVERT: J 91 ILE cc_start: 0.9412 (tp) cc_final: 0.9069 (tt) REVERT: J 112 LEU cc_start: 0.9523 (mp) cc_final: 0.8931 (mm) REVERT: K 18 PHE cc_start: 0.8134 (m-80) cc_final: 0.7807 (m-80) REVERT: K 30 ARG cc_start: 0.8437 (tpt-90) cc_final: 0.8078 (tpt-90) REVERT: K 62 LYS cc_start: 0.9200 (tptp) cc_final: 0.8778 (tptm) REVERT: K 87 ASP cc_start: 0.8063 (t0) cc_final: 0.7707 (t0) REVERT: K 90 TYR cc_start: 0.8660 (m-10) cc_final: 0.8216 (m-80) REVERT: K 133 LEU cc_start: 0.8775 (mt) cc_final: 0.8457 (tp) REVERT: K 135 TYR cc_start: 0.7823 (t80) cc_final: 0.7547 (t80) REVERT: K 137 LYS cc_start: 0.9147 (ttpp) cc_final: 0.8783 (ttpp) REVERT: K 139 ASN cc_start: 0.9035 (t0) cc_final: 0.8388 (t0) REVERT: K 166 ILE cc_start: 0.9409 (mm) cc_final: 0.9207 (mm) REVERT: L 2 LEU cc_start: 0.9489 (mt) cc_final: 0.8682 (mt) REVERT: L 81 MET cc_start: 0.8951 (tpp) cc_final: 0.8241 (tpp) REVERT: L 85 LEU cc_start: 0.9512 (mt) cc_final: 0.9149 (mt) REVERT: L 88 MET cc_start: 0.8252 (mtm) cc_final: 0.7881 (mtp) REVERT: L 89 GLU cc_start: 0.7715 (pp20) cc_final: 0.7358 (tm-30) REVERT: L 120 GLN cc_start: 0.8733 (tm-30) cc_final: 0.8062 (tm-30) REVERT: L 146 ASP cc_start: 0.9451 (t0) cc_final: 0.9133 (t0) REVERT: L 161 GLU cc_start: 0.8813 (tt0) cc_final: 0.7653 (tp30) REVERT: M 33 ARG cc_start: 0.8059 (ttt180) cc_final: 0.7775 (ttt180) REVERT: M 115 LEU cc_start: 0.8897 (tt) cc_final: 0.8373 (tt) REVERT: M 118 ILE cc_start: 0.9694 (tp) cc_final: 0.9201 (tp) REVERT: M 122 PHE cc_start: 0.9233 (m-10) cc_final: 0.8876 (m-10) REVERT: M 129 TYR cc_start: 0.8099 (m-80) cc_final: 0.7621 (m-10) REVERT: N 17 GLU cc_start: 0.7861 (pm20) cc_final: 0.7402 (pm20) REVERT: N 20 THR cc_start: 0.8095 (t) cc_final: 0.7878 (p) REVERT: N 65 GLN cc_start: 0.7665 (pm20) cc_final: 0.7296 (pm20) REVERT: N 67 ILE cc_start: 0.9609 (pt) cc_final: 0.9212 (tp) REVERT: N 87 ASP cc_start: 0.8926 (m-30) cc_final: 0.8698 (m-30) REVERT: N 88 MET cc_start: 0.8543 (ttm) cc_final: 0.7799 (tpp) REVERT: N 89 GLU cc_start: 0.7869 (pp20) cc_final: 0.7351 (pp20) REVERT: N 97 TYR cc_start: 0.8556 (m-10) cc_final: 0.8328 (m-80) REVERT: N 103 ASP cc_start: 0.6969 (t0) cc_final: 0.6617 (t0) REVERT: N 136 MET cc_start: 0.8099 (mtm) cc_final: 0.7770 (mtm) REVERT: O 18 PHE cc_start: 0.8599 (m-80) cc_final: 0.8346 (m-80) REVERT: O 60 TYR cc_start: 0.6341 (m-10) cc_final: 0.6128 (m-10) REVERT: O 61 GLN cc_start: 0.7608 (mt0) cc_final: 0.6924 (tm-30) REVERT: O 94 MET cc_start: 0.9027 (mmp) cc_final: 0.8814 (mmp) REVERT: O 96 THR cc_start: 0.9444 (p) cc_final: 0.9191 (t) REVERT: O 98 CYS cc_start: 0.8325 (m) cc_final: 0.7631 (p) REVERT: O 104 THR cc_start: 0.8915 (p) cc_final: 0.8138 (p) REVERT: P 7 LYS cc_start: 0.9045 (tppt) cc_final: 0.8765 (mmmm) REVERT: P 67 ILE cc_start: 0.8491 (mt) cc_final: 0.8217 (tp) REVERT: P 94 TYR cc_start: 0.8744 (m-80) cc_final: 0.8366 (m-10) REVERT: P 97 TYR cc_start: 0.8758 (m-10) cc_final: 0.7725 (m-80) REVERT: P 122 LEU cc_start: 0.8449 (mm) cc_final: 0.8185 (mm) REVERT: P 134 GLN cc_start: 0.8473 (mm110) cc_final: 0.8182 (mm-40) REVERT: Q 25 GLN cc_start: 0.9031 (mm-40) cc_final: 0.8382 (mm-40) REVERT: Q 39 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6450 (pt0) REVERT: Q 53 ASP cc_start: 0.7331 (m-30) cc_final: 0.6990 (m-30) REVERT: Q 57 GLN cc_start: 0.8487 (mm110) cc_final: 0.7707 (mm-40) REVERT: Q 69 MET cc_start: 0.7597 (ptm) cc_final: 0.7152 (ptm) REVERT: Q 73 GLN cc_start: 0.8223 (pm20) cc_final: 0.7936 (pt0) REVERT: Q 94 MET cc_start: 0.5501 (tpp) cc_final: 0.5078 (tpp) REVERT: Q 108 ASP cc_start: 0.9015 (m-30) cc_final: 0.8323 (m-30) REVERT: R 29 ASN cc_start: 0.7462 (t0) cc_final: 0.7247 (t0) REVERT: R 111 CYS cc_start: 0.8416 (t) cc_final: 0.7940 (t) REVERT: R 113 ASN cc_start: 0.7568 (t0) cc_final: 0.7231 (m-40) REVERT: R 118 THR cc_start: 0.8953 (p) cc_final: 0.7602 (p) REVERT: R 128 SER cc_start: 0.9177 (m) cc_final: 0.8898 (m) REVERT: R 136 MET cc_start: 0.8587 (tmm) cc_final: 0.8083 (tmm) REVERT: R 160 SER cc_start: 0.8621 (t) cc_final: 0.8385 (p) REVERT: S 6 THR cc_start: 0.8582 (p) cc_final: 0.8289 (t) REVERT: S 39 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7812 (mm-30) REVERT: S 49 GLN cc_start: 0.8201 (tp40) cc_final: 0.7677 (pm20) REVERT: S 50 SER cc_start: 0.8455 (p) cc_final: 0.8205 (p) REVERT: S 57 GLN cc_start: 0.8460 (mm-40) cc_final: 0.8041 (mp10) REVERT: S 74 TYR cc_start: 0.8655 (m-80) cc_final: 0.7771 (m-10) REVERT: S 79 GLU cc_start: 0.7954 (mp0) cc_final: 0.7408 (tp30) REVERT: S 90 TYR cc_start: 0.8367 (m-80) cc_final: 0.8049 (m-10) REVERT: S 97 TYR cc_start: 0.8884 (m-10) cc_final: 0.8331 (m-80) REVERT: S 112 ILE cc_start: 0.9504 (mm) cc_final: 0.8899 (tp) REVERT: S 134 LYS cc_start: 0.9464 (mmpt) cc_final: 0.8988 (mmmm) REVERT: S 163 ASN cc_start: 0.8950 (m110) cc_final: 0.8691 (m-40) REVERT: T 1 MET cc_start: 0.7489 (mmp) cc_final: 0.6586 (mmt) REVERT: T 3 ASP cc_start: 0.6842 (p0) cc_final: 0.6604 (p0) REVERT: T 15 ARG cc_start: 0.7742 (mtp85) cc_final: 0.7191 (mmp80) REVERT: T 19 LEU cc_start: 0.7801 (mt) cc_final: 0.7284 (mm) REVERT: T 23 GLN cc_start: 0.8350 (mt0) cc_final: 0.8050 (mp10) REVERT: T 156 SER cc_start: 0.8733 (m) cc_final: 0.8439 (m) REVERT: T 159 MET cc_start: 0.8782 (mpp) cc_final: 0.7949 (mpp) REVERT: U 32 LYS cc_start: 0.9256 (tmmt) cc_final: 0.8991 (tmmt) REVERT: U 63 PHE cc_start: 0.7843 (m-80) cc_final: 0.7424 (m-80) REVERT: U 98 CYS cc_start: 0.7971 (t) cc_final: 0.7380 (t) REVERT: U 109 GLU cc_start: 0.8453 (tm-30) cc_final: 0.7913 (tm-30) REVERT: U 123 ASP cc_start: 0.8177 (t0) cc_final: 0.7705 (t0) REVERT: U 134 LYS cc_start: 0.9096 (tppp) cc_final: 0.8723 (tppt) REVERT: U 161 GLU cc_start: 0.8856 (tp30) cc_final: 0.8579 (tm-30) REVERT: U 171 ASN cc_start: 0.8764 (t0) cc_final: 0.8422 (t0) REVERT: U 174 SER cc_start: 0.7667 (t) cc_final: 0.7242 (t) REVERT: V 94 TYR cc_start: 0.9014 (m-80) cc_final: 0.8766 (m-80) REVERT: V 124 THR cc_start: 0.8810 (m) cc_final: 0.8496 (p) REVERT: V 162 ILE cc_start: 0.8495 (mt) cc_final: 0.8287 (mt) REVERT: W 1 MET cc_start: 0.5453 (pmm) cc_final: 0.4730 (pmm) REVERT: W 42 ARG cc_start: 0.7718 (ttm170) cc_final: 0.6145 (tpt170) REVERT: W 63 PHE cc_start: 0.5853 (m-80) cc_final: 0.5514 (m-80) REVERT: W 69 MET cc_start: 0.5472 (mmm) cc_final: 0.5223 (tpt) REVERT: W 94 MET cc_start: 0.8442 (ptt) cc_final: 0.7951 (ppp) REVERT: W 111 LEU cc_start: 0.8392 (pt) cc_final: 0.7875 (pp) REVERT: W 161 GLU cc_start: 0.8816 (pm20) cc_final: 0.8299 (pm20) REVERT: X 3 ASP cc_start: 0.7719 (p0) cc_final: 0.7320 (p0) REVERT: X 32 LYS cc_start: 0.8099 (mmtp) cc_final: 0.7435 (tptm) REVERT: X 44 ILE cc_start: 0.8034 (mm) cc_final: 0.7828 (tp) REVERT: X 52 VAL cc_start: 0.9242 (t) cc_final: 0.8975 (p) REVERT: X 89 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8063 (tm-30) REVERT: X 93 ARG cc_start: 0.8713 (ttp80) cc_final: 0.8108 (ttt90) REVERT: X 117 GLU cc_start: 0.7960 (pm20) cc_final: 0.7716 (pm20) REVERT: X 119 TYR cc_start: 0.8069 (m-80) cc_final: 0.7794 (m-80) REVERT: X 133 ILE cc_start: 0.8751 (mm) cc_final: 0.8005 (tp) REVERT: X 136 MET cc_start: 0.8013 (mmm) cc_final: 0.7442 (mmm) REVERT: X 166 PHE cc_start: 0.7518 (m-80) cc_final: 0.7092 (m-80) REVERT: Y 64 ARG cc_start: 0.8738 (mtp-110) cc_final: 0.8426 (ttm110) REVERT: Z 42 GLN cc_start: 0.9082 (tp40) cc_final: 0.8767 (tp-100) REVERT: Z 59 GLU cc_start: 0.8475 (pm20) cc_final: 0.8042 (pm20) REVERT: Z 86 PHE cc_start: 0.8764 (m-80) cc_final: 0.8357 (m-80) REVERT: Z 196 THR cc_start: 0.9028 (p) cc_final: 0.8650 (m) REVERT: a 51 ARG cc_start: 0.9009 (ttp80) cc_final: 0.8632 (ptm-80) REVERT: a 65 GLN cc_start: 0.8030 (tt0) cc_final: 0.7790 (tt0) REVERT: a 68 LEU cc_start: 0.8813 (mm) cc_final: 0.8516 (mm) REVERT: a 69 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7614 (mt-10) REVERT: a 74 ASN cc_start: 0.9172 (t0) cc_final: 0.8586 (p0) REVERT: a 84 ARG cc_start: 0.8983 (ttm110) cc_final: 0.8520 (ttm-80) REVERT: a 88 LYS cc_start: 0.8891 (pttm) cc_final: 0.8520 (tptt) REVERT: a 98 GLU cc_start: 0.8211 (pt0) cc_final: 0.7756 (pt0) REVERT: a 114 LEU cc_start: 0.8190 (tp) cc_final: 0.7964 (tp) REVERT: a 151 GLN cc_start: 0.8964 (mm-40) cc_final: 0.8050 (mt0) REVERT: a 156 ASN cc_start: 0.8327 (m-40) cc_final: 0.8070 (m-40) outliers start: 0 outliers final: 0 residues processed: 1562 average time/residue: 0.2046 time to fit residues: 526.1837 Evaluate side-chains 1307 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1307 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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: 4.9990 chunk 430 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 160 optimal weight: 2.9990 chunk 337 optimal weight: 2.9990 chunk 420 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 438 optimal weight: 0.8980 chunk 153 optimal weight: 10.0000 chunk 158 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 GLN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 ASN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 25 GLN G 139 ASN ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 21 ASN ** I 163 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** ** P 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 139 ASN ** R 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 139 ASN ** S 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 47 ASN V 63 GLN X 42 ASN 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.114573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.097156 restraints weight = 112822.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.100794 restraints weight = 56540.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.103133 restraints weight = 32780.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.104694 restraints weight = 21224.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.105759 restraints weight = 15051.918| |-----------------------------------------------------------------------------| 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 | |-----------------------------------------------------------------------------| r_final: 0.3381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.6636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 36155 Z= 0.160 Angle : 0.808 42.936 49243 Z= 0.393 Chirality : 0.042 0.249 5448 Planarity : 0.005 0.059 6402 Dihedral : 10.841 89.243 6599 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.22 % Favored : 96.72 % Rotamer: Outliers : 0.03 % Allowed : 0.32 % Favored : 99.65 % 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 aren not related in a simple way. whole: 0.93 (0.13), residues: 4448 helix: 1.04 (0.09), residues: 3381 sheet: 0.72 (0.86), residues: 28 loop : -0.55 (0.22), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Y 61 TYR 0.053 0.002 TYR M 97 PHE 0.034 0.002 PHE X 24 TRP 0.016 0.001 TRP a 29 HIS 0.005 0.002 HIS M 140 Details of bonding type rmsd covalent geometry : bond 0.00363 (36155) covalent geometry : angle 0.80771 (49243) hydrogen bonds : bond 0.04423 ( 2648) hydrogen bonds : angle 4.44168 ( 7847) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9586.80 seconds wall clock time: 165 minutes 9.58 seconds (9909.58 seconds total)